From dd35823e28a6a989722aff0b15b073dd94ad01e8 Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 18 Jun 2013 16:56:25 +0100 Subject: [PATCH 01/52] - Remove unused DiseaseCard code --- .../coeus/api/plugins/OMIMPlugin.java | 314 ------------------ .../bioinformatics/coeus/common/Builder.java | 5 +- .../coeus/data/connect/PluginFactory.java | 86 ----- .../coeus/ext/COEUSActionBeanContext.java | 62 ---- .../diseasecard/domain/Disease.java | 122 ------- 5 files changed, 1 insertion(+), 588 deletions(-) delete mode 100755 src/main/java/pt/ua/bioinformatics/coeus/api/plugins/OMIMPlugin.java delete mode 100755 src/main/java/pt/ua/bioinformatics/coeus/data/connect/PluginFactory.java delete mode 100755 src/main/java/pt/ua/bioinformatics/coeus/ext/COEUSActionBeanContext.java delete mode 100755 src/main/java/pt/ua/bioinformatics/diseasecard/domain/Disease.java diff --git a/src/main/java/pt/ua/bioinformatics/coeus/api/plugins/OMIMPlugin.java b/src/main/java/pt/ua/bioinformatics/coeus/api/plugins/OMIMPlugin.java deleted file mode 100755 index 4e199b7..0000000 --- a/src/main/java/pt/ua/bioinformatics/coeus/api/plugins/OMIMPlugin.java +++ /dev/null @@ -1,314 +0,0 @@ -package pt.ua.bioinformatics.coeus.api.plugins; - -import au.com.bytecode.opencsv.CSVReader; -import java.io.BufferedReader; -import java.io.InputStreamReader; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.logging.Level; -import java.util.logging.Logger; -import java.util.regex.Matcher; -import java.util.regex.Pattern; -import pt.ua.bioinformatics.coeus.api.API; -import pt.ua.bioinformatics.coeus.api.PrefixFactory; -import pt.ua.bioinformatics.coeus.common.Boot; -import pt.ua.bioinformatics.coeus.common.Config; -import pt.ua.bioinformatics.coeus.data.Predicate; -import pt.ua.bioinformatics.coeus.domain.Resource; -import pt.ua.bioinformatics.diseasecard.domain.Disease; - -/** - * DiseaseCard plugin for OMIM data handling. - *

Generates initial gene and disease dataset based on OMIM's morbid map. - *

- * - * @author pedrolopes - */ -public class OMIMPlugin { - - private Resource res; - private API api; - private HashMap diseases; - private HashMap genotypes; - - public HashMap getGenotypes() { - return genotypes; - } - - public void setGenotypes(HashMap genotypes) { - this.genotypes = genotypes; - } - - public HashMap getDiseases() { - return diseases; - } - - public void setDiseases(HashMap diseases) { - this.diseases = diseases; - } - - public Resource getRes() { - return res; - } - - public void setRes(Resource res) { - this.res = res; - } - - public OMIMPlugin(Resource res) { - this.res = res; - this.diseases = new HashMap(); - this.genotypes = new HashMap(); - this.api = Boot.getAPI(); - } - - /** - * OMIMPlugin controller. - *

Workflow:

    - *
  • Load genotype information from OMIM genemap
    • - *
  • Load phenotype information from OMIM morbidmap
    • - *
  • Import loaded dataset into COEUS SDB
    • - *

- * - */ - public void itemize() { - if (loadGenotype() && loadPhenotype()) { - triplify(); - } - } - - /** - * Loads genotype information from OMIM genemap into internal memory. - * - * @return success of the operation. - */ - private boolean loadGenotype() { - boolean success = true; - try { - //URL u = new URL("ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/genemap"); - URL u = new URL("http://localhost/~pedrolopes/omim/genemap_small"); - BufferedReader in = new BufferedReader(new InputStreamReader(u.openStream())); - CSVReader reader = new CSVReader(in, '|'); - List genemap = reader.readAll(); - for (String[] genes : genemap) { - Disease d = new Disease(genes[7], genes[9]); - d.setLocation(genes[4]); - genotypes.put(d.getOmimId(), d); - String[] genelist = genes[5].split(", "); - d.getGenes().addAll(Arrays.asList(genelist)); - } - success = true; - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][OMIM] Unable to load genotype information from OMIM"); - Logger.getLogger(OMIMPlugin.class.getName()).log(Level.SEVERE, null, ex); - } - } - return success; - - } - - /** - * Loads phenotype information from OMIM morbid into internal memory. - * - * @return success of the operation. - */ - private boolean loadPhenotype() { - boolean success = false; - try { - //URL u = new URL("ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/morbidmap"); - URL u = new URL("http://localhost/~pedrolopes/omim/morbidmap_small"); - BufferedReader in = new BufferedReader(new InputStreamReader(u.openStream())); - CSVReader reader = new CSVReader(in, '|'); - List morbidmap = reader.readAll(); - Pattern p = Pattern.compile("[0-9]{6}"); - - for (String[] disease : morbidmap) { - Disease d; - Matcher m = p.matcher(disease[0]); - String pheno_omim = ""; - String dis_name = ""; - - try { - if (m.find()) { - pheno_omim = m.group(0); - dis_name = disease[0].substring(0, disease[0].length() - 14); - - // check if disease is already on list - if (diseases.containsKey(pheno_omim)) { - d = diseases.get(pheno_omim); - d.getNames().add(dis_name); - Disease genotype = genotypes.get(disease[2]); - if (!d.getGenotypes().contains(genotype)) { - d.getGenotypes().add(genotype); - } - if (!genotype.getPhenotypes().contains(d)) { - genotype.getPhenotypes().add(d); - } - String[] genelist = disease[1].split(", "); - d.getGenes().addAll(Arrays.asList(genelist)); - } else { - d = new Disease(dis_name, pheno_omim); - d.setLocation(disease[3]); - d.getNames().add(dis_name); - diseases.put(pheno_omim, d); - Disease genotype = genotypes.get(disease[2]); - if (!d.getGenotypes().contains(genotype)) { - d.getGenotypes().add(genotype); - } - if (!genotype.getPhenotypes().contains(d)) { - genotype.getPhenotypes().add(d); - } - String[] genelist = disease[1].split(", "); - d.getGenes().addAll(Arrays.asList(genelist)); - } - // not a phenotype, add to only genotypes list - } else { - Disease genotype = genotypes.get(disease[2]); - d = new Disease(disease[0], genotype.getOmimId()); - d.getNames().add(disease[0]); - d.setLocation(disease[3]); - if (!d.getGenotypes().contains(genotype)) { - d.getGenotypes().add(genotype); - } - if (!genotype.getPhenotypes().contains(d)) { - genotype.getPhenotypes().add(d); - } - diseases.put(d.getOmimId(), d); - } - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][OMIM] Unable to load phenotype information from OMIM for " + disease[0]); - Logger.getLogger(OMIMPlugin.class.getName()).log(Level.SEVERE, null, ex); - } - } - } - success = true; - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][OMIM] Unable to load phenotype information from OMIM"); - Logger.getLogger(OMIMPlugin.class.getName()).log(Level.SEVERE, null, ex); - } - } - return success; - } - - /** - * Loads the in-memory data into COEUS SDB. - *

Workflow

    - *
  • Loads genotypes
    • - *
  • Loads genes for each genotype
    • - *
  • Loads genotypes for each genotype
    • - *
  • Loads genes for each phenotype
    • - *

- * - */ - public void triplify() { - for (Disease genotype : genotypes.values()) { - if (!genotype.getOmimId().equals("")) { - try { - String[] itemTmp = res.getIsResourceOf().getLabel().split("_"); - com.hp.hpl.jena.rdf.model.Resource geno_item = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + itemTmp[1] + "_" + genotype.getOmimId()); - com.hp.hpl.jena.rdf.model.Resource geno_obj = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + "Item"); - api.addStatement(geno_item, Predicate.get("rdf:type"), geno_obj); - - // set Item label - api.addStatement(geno_item, Predicate.get("rdfs:label"), "omim_" + genotype.getOmimId()); - - // associate Item with Concept - com.hp.hpl.jena.rdf.model.Resource con = api.getResource(res.getIsResourceOf().getUri()); - api.addStatement(geno_item, Predicate.get("coeus:hasConcept"), con); - api.addStatement(con, Predicate.get("coeus:isConceptOf"), geno_item); - - // add name/comment - api.addStatement(geno_item, Predicate.get("rdfs:comment"), genotype.getName()); - api.addStatement(geno_item, Predicate.get("dc:description"), genotype.getName()); - for (String name : genotype.getNames()) { - api.addStatement(geno_item, Predicate.get("diseasecard:name"), name); - } - - api.addStatement(geno_item, Predicate.get("diseasecard:omim"), genotype.getOmimId()); - api.addStatement(geno_item, Predicate.get("diseasecard:chromosomalLocation"), genotype.getLocation()); - - triplifyGenes(genotype.getGenes(), geno_item); - - for (Disease phenotype : genotype.getPhenotypes()) { - com.hp.hpl.jena.rdf.model.Resource pheno_item = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + itemTmp[1] + "_" + phenotype.getOmimId()); - com.hp.hpl.jena.rdf.model.Resource pheno_obj = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + "Item"); - api.addStatement(pheno_item, Predicate.get("rdf:type"), pheno_obj); - - // set Item label - api.addStatement(pheno_item, Predicate.get("rdfs:label"), "hgnc_" + phenotype.getOmimId()); - - // associate Item with Concept - com.hp.hpl.jena.rdf.model.Resource pheno_concept = api.getResource(res.getIsResourceOf().getUri()); - api.addStatement(pheno_item, Predicate.get("coeus:hasConcept"), pheno_concept); - api.addStatement(pheno_concept, Predicate.get("coeus:isConceptOf"), pheno_item); - - // add name/comment - api.addStatement(pheno_item, Predicate.get("rdfs:comment"), phenotype.getName()); - api.addStatement(pheno_item, Predicate.get("dc:description"), phenotype.getName()); - for (String name : phenotype.getNames()) { - api.addStatement(pheno_item, Predicate.get("diseasecard:name"), name); - } - api.addStatement(pheno_item, Predicate.get("diseasecard:omim"), phenotype.getOmimId()); - api.addStatement(pheno_item, Predicate.get("diseasecard:chromosomalLocation"), phenotype.getLocation()); - - //add diseasecard-specific info - api.addStatement(pheno_item, Predicate.get("diseasecard:phenotype"), "true"); - api.addStatement(pheno_item, Predicate.get("diseasecard:hasGenotype"), geno_item); - api.addStatement(geno_item, Predicate.get("diseasecard:hasPhenotype"), pheno_item); - - triplifyGenes(phenotype.getGenes(), pheno_item); - } - - api.addStatement(geno_item, Predicate.get("diseasecard:genotype"), "true"); - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][OMIM] Unable to triplify inmemory data"); - Logger.getLogger(OMIMPlugin.class.getName()).log(Level.SEVERE, null, ex); - } - } - } - } - } - - /** - * Handles gene writing into COEUS SDB. - * - * @param genes the list of genes to insert. - * @param item the item where the genes will be associated - * (coeus:isAssociatedTo). - */ - private void triplifyGenes(ArrayList genes, com.hp.hpl.jena.rdf.model.Resource item) { - for (String gene : genes) { - try { - com.hp.hpl.jena.rdf.model.Resource gene_item = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + "hgnc_" + gene); - com.hp.hpl.jena.rdf.model.Resource gene_obj = api.createResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + "Item"); - api.addStatement(gene_item, Predicate.get("rdf:type"), gene_obj); - - // set Item label - api.addStatement(gene_item, Predicate.get("rdfs:label"), api.createResource("item_" + gene)); - - // set Item title - api.addStatement(gene_item, Predicate.get("dc:title"), gene.toUpperCase()); - - // associate Item with Concept - com.hp.hpl.jena.rdf.model.Resource gene_concept = api.getResource(PrefixFactory.getURIForPrefix(Config.getKeyPrefix()) + "concept_HGNC"); - api.addStatement(gene_item, Predicate.get("coeus:hasConcept"), gene_concept); - api.addStatement(gene_concept, Predicate.get("coeus:isConceptOf"), gene_item); - api.addStatement(gene_item, Predicate.get("coeus:isAssociatedTo"), item); - api.addStatement(item, Predicate.get("coeus:isAssociatedTo"), gene_item); - - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][OMIM] Unable to triplify gene information"); - Logger.getLogger(OMIMPlugin.class.getName()).log(Level.SEVERE, null, ex); - } - } - } - } -} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Builder.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Builder.java index 0d53f1b..31d1816 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Builder.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Builder.java @@ -10,7 +10,6 @@ import org.json.simple.parser.JSONParser; import pt.ua.bioinformatics.coeus.data.connect.CSVFactory; import pt.ua.bioinformatics.coeus.data.connect.LinkedDataFactory; -import pt.ua.bioinformatics.coeus.data.connect.PluginFactory; import pt.ua.bioinformatics.coeus.data.connect.RDFFactory; import pt.ua.bioinformatics.coeus.data.connect.ResourceFactory; import pt.ua.bioinformatics.coeus.data.connect.SPARQLFactory; @@ -158,9 +157,7 @@ public static boolean readData(Resource r) { ResourceFactory factory; try { if (!r.isBuilt()) { - if (r.getPublisher().equalsIgnoreCase("plugin")) { - factory = new PluginFactory(r); - } else if (r.getPublisher().equalsIgnoreCase("csv")) { + if (r.getPublisher().equalsIgnoreCase("csv")) { factory = new CSVFactory(r); } else if (r.getPublisher().equalsIgnoreCase("xml")) { factory = new XMLFactory(r); diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/PluginFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/PluginFactory.java deleted file mode 100755 index 2a68860..0000000 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/PluginFactory.java +++ /dev/null @@ -1,86 +0,0 @@ -package pt.ua.bioinformatics.coeus.data.connect; - -import java.util.logging.Level; -import java.util.logging.Logger; -import pt.ua.bioinformatics.coeus.api.API; -import pt.ua.bioinformatics.coeus.api.plugins.OMIMPlugin; -import pt.ua.bioinformatics.coeus.common.Boot; -import pt.ua.bioinformatics.coeus.common.Config; -import pt.ua.bioinformatics.coeus.data.Predicate; -import pt.ua.bioinformatics.coeus.domain.Resource; - -/** - * Data factory for transforming SPARQL data into RDF items using generic - * Triplify. - * - * @author pedrolopes - */ -public class PluginFactory implements ResourceFactory { - - private Resource res; - - public Resource getRes() { - return res; - } - - public void setRes(Resource res) { - this.res = res; - } - - public PluginFactory(Resource r) { - this.res = r; - } - - /** - * Reads SPARQL data according to Resource information. - *

Workflow

    - *
  1. Check if resource is starter/extends
    2. - *
  2. Load SPARQL resource into ResultSet
    3. - *
  3. Start Triplify with factory Resource
    4. - *
  4. Get data for Item key into Triplify
    5. - *
  5. Load data for each InheritedResource property into Triplify hashmap - * based on SPARQL elements
    6. - *
  6. Itemize single item
    7. - *

- */ - public void read() { - String[] divide = res.getEndpoint().split("://"); - String type = divide[0]; - try { - if (type.equals("omim")) { - OMIMPlugin omim = new OMIMPlugin(res); - omim.itemize(); - } - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][SPARQLFactory] unable to load data for " + res.getUri()); - Logger.getLogger(PluginFactory.class.getName()).log(Level.SEVERE, null, ex); - } - } - } - - /** - * Updates the resource coeus:built property once the resource finished - * building. - * - * @return success of the operation - */ - public boolean save() { - boolean success = false; - try { - API api = Boot.getAPI(); - com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); - api.addStatement(resource, Predicate.get("coeus:built"), true); - success = true; - if (Config.isDebug()) { - System.out.println("[COEUS][API] Saved resource " + res.getUri()); - } - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][API] Unable to save resource " + res.getUri()); - Logger.getLogger(PluginFactory.class.getName()).log(Level.SEVERE, null, ex); - } - } - return success; - } -} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/ext/COEUSActionBeanContext.java b/src/main/java/pt/ua/bioinformatics/coeus/ext/COEUSActionBeanContext.java deleted file mode 100755 index 9ba40d1..0000000 --- a/src/main/java/pt/ua/bioinformatics/coeus/ext/COEUSActionBeanContext.java +++ /dev/null @@ -1,62 +0,0 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ -package pt.ua.bioinformatics.coeus.ext; - -import java.util.ArrayList; -import net.sourceforge.stripes.action.ActionBeanContext; -import pt.ua.bioinformatics.diseasecard.domain.Disease; - -/** - * Context Extender for COEUS Default Actions. - *

Enables the creation of custom context actions in ActionBeans, check - * Stripes Docs for further information.

- * - * @author pedrolopes - */ -public class COEUSActionBeanContext extends ActionBeanContext { - - private static final String DISEASE = "disease"; - - public void setDisease(String key, Object value) { - getRequest().getSession().setAttribute(key, value); - } - - public void setDisease(Object value) { - getRequest().getSession().setAttribute(DISEASE, value); - } - - public T getDisease() { - return (T) getRequest().getSession().getAttribute(DISEASE); - } - - public T getDisease(String key) { - return (T) getRequest().getSession().getAttribute(key); - } - - public T getDiseases() { - return (T) getRequest().getSession().getAttribute(DISEASE); - } - - public T getDiseases(String key) { - return (T) getRequest().getSession().getAttribute(key); - } - - public void setSearchResults(String key, ArrayList value) { - getRequest().getSession().setAttribute(key, value); - } - - public ArrayList getSearchResults(String key) { - return (ArrayList) getRequest().getSession().getAttribute(key); - } - - public void setCurrent(String key, Object value) { - getRequest().getSession().setAttribute(key, value); - } - - @SuppressWarnings("unchecked") - public T getCurrent(String key) { - return (T) getRequest().getSession().getAttribute(key); - } -} diff --git a/src/main/java/pt/ua/bioinformatics/diseasecard/domain/Disease.java b/src/main/java/pt/ua/bioinformatics/diseasecard/domain/Disease.java deleted file mode 100755 index 4045d22..0000000 --- a/src/main/java/pt/ua/bioinformatics/diseasecard/domain/Disease.java +++ /dev/null @@ -1,122 +0,0 @@ -package pt.ua.bioinformatics.diseasecard.domain; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.logging.Level; -import java.util.logging.Logger; -import pt.ua.bioinformatics.coeus.domain.Item; - -/** - * - * @author pedrolopes - */ -public class Disease { - - private int id; - private String name; - private String omimId; - private String location; - private ArrayList genes = new ArrayList(); - private ArrayList names = new ArrayList(); - private ArrayList genotypes = new ArrayList(); - private ArrayList phenotypes = new ArrayList(); - - public ArrayList getGenes() { - return genes; - } - - public String getOmimId() { - return omimId; - } - - public void setOmimId(String omim_id) { - this.omimId = omim_id; - } - - public void setGenes(ArrayList genes) { - this.genes = genes; - } - - public String getLocation() { - return location; - } - - public void setLocation(String location) { - this.location = location; - } - - public int getId() { - return id; - } - - public void setId(int id) { - this.id = id; - } - - public ArrayList getPhenotypes() { - return phenotypes; - } - - public void setPhenotypes(ArrayList phenotypes) { - this.phenotypes = phenotypes; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public ArrayList getNames() { - return names; - } - - public void setNames(ArrayList names) { - this.names = names; - } - - /** - * Loads Disease information from SDB based on its key - OMIM code. - * - * @param key - */ - public Disease(int key) { - this.id = key; - this.omimId = String.valueOf(key); - // this.omim = String.valueOf(key); - try { - } catch (Exception ex) { - Logger.getLogger(Item.class.getName()).log(Level.SEVERE, null, ex); - } - } - - public Disease(String name, String omim) { - this.name = name; - this.genotypes = new ArrayList(); - this.phenotypes = new ArrayList(); - this.names = new ArrayList(); - } - - public ArrayList getGenotypes() { - return genotypes; - } - - public void setGenotypes(ArrayList genotypes) { - this.genotypes = genotypes; - } - - @Override - public String toString() { - String response = ""; - - response += this.omimId + "\t" + this.name; - for (Disease s : genotypes) { - response += "\n\t" + s.getName() + " > " + s.getOmimId(); - } - response += "\n\tGenes"; - - return response; - } -} From f0f1f58baa742cfed7ecb999c91084645bb0cbce Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 20 Jun 2013 15:05:09 +0100 Subject: [PATCH 02/52] - Add security login to the manager setup --- .../coeus/actions/SeedActionBean.java | 2 +- src/main/resources/config.js | 14 ++-- src/main/resources/joseki.ttl | 2 +- src/main/webapp/WEB-INF/web.xml | 42 +++++++++-- src/main/webapp/login.jsp | 72 +++++++++++++++++++ src/main/webapp/setup/html.jsp | 6 +- src/main/webapp/setup/index.jsp | 1 - 7 files changed, 121 insertions(+), 18 deletions(-) create mode 100644 src/main/webapp/login.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java index 61d2aaa..0f1d77b 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java @@ -17,7 +17,7 @@ * * @author sernadela */ -@UrlBinding("/seed/") +@UrlBinding("/manager/") public class SeedActionBean implements ActionBean{ private static final String VIEW="/setup/index.jsp"; private String name; diff --git a/src/main/resources/config.js b/src/main/resources/config.js index 481bca1..07f0d06 100644 --- a/src/main/resources/config.js +++ b/src/main/resources/config.js @@ -1,14 +1,14 @@ { "config": { -"name": "proteinator", - "description": "COEUS Protein Data Aggregator (Proteinator)", +"name": "coeus.NA", + "description": "COEUS News Aggregator", "keyprefix":"coeus", "version": "1.0a", - "ontology": "http://bioinformatics.ua.pt/diseasecard/diseasecard.owl", - "setup": "proteinator/setup.rdf", - "sdb":"proteinator/sdb.ttl", - "predicates":"proteinator/predicates.csv", - "built": false, + "ontology": "http://bioinformatics.ua.pt/coeus/ontology/", + "setup": "newsaggregator/setup.rdf", + "sdb":"newsaggregator/sdb.ttl", + "predicates":"newsaggregator/predicates.csv", + "built": true, "debug": true, "apikey":"coeus|uavr", "environment": "production" diff --git a/src/main/resources/joseki.ttl b/src/main/resources/joseki.ttl index 8f1b04f..c40d69c 100644 --- a/src/main/resources/joseki.ttl +++ b/src/main/resources/joseki.ttl @@ -43,7 +43,7 @@ sdb:Model rdfs:subClassOf ja:Model . <#sdb> rdf:type sdb:DatasetStore ; ## Number of concurrent connections allowed to this dataset. - joseki:poolSize 200; + joseki:poolSize 2; sdb:store <#store> . <#store> rdf:type sdb:Store ; diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml index a12d0c5..1008314 100755 --- a/src/main/webapp/WEB-INF/web.xml +++ b/src/main/webapp/WEB-INF/web.xml @@ -34,7 +34,8 @@ org.joseki.http.Servlet org.joseki.rdfserver.config - joseki.ttl + + joseki.ttl @@ -49,7 +50,8 @@ config-file - classes/pubby.ttl + + classes/pubby.ttl @@ -64,13 +66,13 @@ de.fuberlin.wiwiss.pubby.servlets.PageURLServlet 1 - + WebURLServlet de.fuberlin.wiwiss.pubby.servlets.PageURLServlet 1 - + WebURLServlet /resource/* @@ -120,9 +122,39 @@ - pt.ua.bioinformatics.coeus.common.HttpListener + pt.ua.bioinformatics.coeus.common.HttpListener + + + + + Secured Setup + + /setup/* + /manager/* + GET + POST + + + + Only managers use this app + + manager-gui + + + + manager-gui + + + FORM + + /login.jsp + /login.jsp?f=error + + + + index.jsp diff --git a/src/main/webapp/login.jsp b/src/main/webapp/login.jsp new file mode 100644 index 0000000..456304f --- /dev/null +++ b/src/main/webapp/login.jsp @@ -0,0 +1,72 @@ + +<%@include file="/layout/style.jsp" %> + + +<% + String err = request.getParameter("f"); +%> + + + + + Setup Login + + + + +
+
+

COEUS Setup

+
+ + +
+ + \ No newline at end of file diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 5e2b6ca..b2cb90a 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -25,9 +25,9 @@
-
  • ">Management
    • +
  • ">Management
  • ">Documentation
    • diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 0a0cc85..1515728 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -20,7 +20,6 @@

    ${actionBean.name} Production

    - refresh
    From 747b2aeca749fe557089fe186f211327788d13fc Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 26 Jun 2013 17:10:49 +0100 Subject: [PATCH 03/52] - Setup: add entity support --- .../coeus/actions/EntityActionBean.java | 68 ++++ ...ActionBean.java => ManagerActionBean.java} | 25 +- .../webapp/assets/js/bootstrap-tooltip.js | 361 ++++++++++++++++++ src/main/webapp/layout/script.jsp | 2 +- src/main/webapp/setup/addentity.jsp | 204 ++++++++++ src/main/webapp/setup/html.jsp | 4 +- src/main/webapp/setup/index.jsp | 139 ++++++- src/main/webapp/setup/listentities.jsp | 109 ++++++ 8 files changed, 891 insertions(+), 21 deletions(-) create mode 100644 src/main/java/pt/ua/bioinformatics/coeus/actions/EntityActionBean.java rename src/main/java/pt/ua/bioinformatics/coeus/actions/{SeedActionBean.java => ManagerActionBean.java} (61%) create mode 100644 src/main/webapp/assets/js/bootstrap-tooltip.js create mode 100644 src/main/webapp/setup/addentity.jsp create mode 100644 src/main/webapp/setup/listentities.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/EntityActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/EntityActionBean.java new file mode 100644 index 0000000..8f2c4ab --- /dev/null +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/EntityActionBean.java @@ -0,0 +1,68 @@ +package pt.ua.bioinformatics.coeus.actions; + +import net.sourceforge.stripes.action.ActionBean; +import net.sourceforge.stripes.action.ActionBeanContext; +import net.sourceforge.stripes.action.DefaultHandler; +import net.sourceforge.stripes.action.ForwardResolution; +import net.sourceforge.stripes.action.Resolution; +import net.sourceforge.stripes.action.StreamingResolution; +import net.sourceforge.stripes.action.UrlBinding; +import pt.ua.bioinformatics.coeus.common.Config; + +/** + * + * @author pedrolopes + */ +@UrlBinding("/manager/entity/{query}") +public class EntityActionBean implements ActionBean { + private static final String VIEW="/setup/listentities.jsp"; + private static final String VIEWADD="/setup/addentity.jsp"; + private ActionBeanContext context; + private String sub; + private String pred; + private String query; + + public String getQuery() { + return query; + } + + public void setQuery(String query) { + this.query = query; + } + + + public String getPred() { + return pred; + } + + public void setPred(String pred) { + this.pred = pred; + } + + public String getSub() { + return sub; + } + + public void setSub(String sub) { + this.sub = sub; + } + + public void setContext(ActionBeanContext context) { + this.context = context; + } + + public ActionBeanContext getContext() { + return context; + } + + @DefaultHandler + public Resolution handle() { + + if(query==null) + return new ForwardResolution(VIEW); + else if(query.equals("add")) return new ForwardResolution(VIEWADD); + else { + return new StreamingResolution("application/json", Config.getFile().toJSONString()); + } + } +} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java similarity index 61% rename from src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java rename to src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java index 0f1d77b..b8b99bc 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/SeedActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java @@ -9,7 +9,12 @@ import net.sourceforge.stripes.action.DefaultHandler; import net.sourceforge.stripes.action.ForwardResolution; import net.sourceforge.stripes.action.Resolution; +import net.sourceforge.stripes.action.StreamingResolution; import net.sourceforge.stripes.action.UrlBinding; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import pt.ua.bioinformatics.coeus.common.Boot; import pt.ua.bioinformatics.coeus.common.Config; @@ -17,16 +22,30 @@ * * @author sernadela */ -@UrlBinding("/manager/") -public class SeedActionBean implements ActionBean{ +@UrlBinding("/manager/home/{param}") +public class ManagerActionBean implements ActionBean{ private static final String VIEW="/setup/index.jsp"; private String name; + private String param; private ActionBeanContext context; @DefaultHandler - public Resolution handle(){ + public Resolution handle() throws ParseException{ setName(Config.getName()); + if(param==null) return new ForwardResolution(VIEW); + else { + Boot.start(); + return new StreamingResolution("application/json", Config.getFile().toJSONString()); + } + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; } public String getName() { diff --git a/src/main/webapp/assets/js/bootstrap-tooltip.js b/src/main/webapp/assets/js/bootstrap-tooltip.js new file mode 100644 index 0000000..a3bbd58 --- /dev/null +++ b/src/main/webapp/assets/js/bootstrap-tooltip.js @@ -0,0 +1,361 @@ +/* =========================================================== + * bootstrap-tooltip.js v2.3.2 + * http://twitter.github.com/bootstrap/javascript.html#tooltips + * Inspired by the original jQuery.tipsy by Jason Frame + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TOOLTIP PUBLIC CLASS DEFINITION + * =============================== */ + + var Tooltip = function (element, options) { + this.init('tooltip', element, options) + } + + Tooltip.prototype = { + + constructor: Tooltip + + , init: function (type, element, options) { + var eventIn + , eventOut + , triggers + , trigger + , i + + this.type = type + this.$element = $(element) + this.options = this.getOptions(options) + this.enabled = true + + triggers = this.options.trigger.split(' ') + + for (i = triggers.length; i--;) { + trigger = triggers[i] + if (trigger == 'click') { + this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this)) + } else if (trigger != 'manual') { + eventIn = trigger == 'hover' ? 'mouseenter' : 'focus' + eventOut = trigger == 'hover' ? 'mouseleave' : 'blur' + this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this)) + this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this)) + } + } + + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle() + } + + , getOptions: function (options) { + options = $.extend({}, $.fn[this.type].defaults, this.$element.data(), options) + + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay + , hide: options.delay + } + } + + return options + } + + , enter: function (e) { + var defaults = $.fn[this.type].defaults + , options = {} + , self + + this._options && $.each(this._options, function (key, value) { + if (defaults[key] != value) options[key] = value + }, this) + + self = $(e.currentTarget)[this.type](options).data(this.type) + + if (!self.options.delay || !self.options.delay.show) return self.show() + + clearTimeout(this.timeout) + self.hoverState = 'in' + this.timeout = setTimeout(function() { + if (self.hoverState == 'in') self.show() + }, self.options.delay.show) + } + + , leave: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type) + + if (this.timeout) clearTimeout(this.timeout) + if (!self.options.delay || !self.options.delay.hide) return self.hide() + + self.hoverState = 'out' + this.timeout = setTimeout(function() { + if (self.hoverState == 'out') self.hide() + }, self.options.delay.hide) + } + + , show: function () { + var $tip + , pos + , actualWidth + , actualHeight + , placement + , tp + , e = $.Event('show') + + if (this.hasContent() && this.enabled) { + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + $tip = this.tip() + this.setContent() + + if (this.options.animation) { + $tip.addClass('fade') + } + + placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement + + $tip + .detach() + .css({ top: 0, left: 0, display: 'block' }) + + this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element) + + pos = this.getPosition() + + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + + switch (placement) { + case 'bottom': + tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'top': + tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'left': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} + break + case 'right': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} + break + } + + this.applyPlacement(tp, placement) + this.$element.trigger('shown') + } + } + + , applyPlacement: function(offset, placement){ + var $tip = this.tip() + , width = $tip[0].offsetWidth + , height = $tip[0].offsetHeight + , actualWidth + , actualHeight + , delta + , replace + + $tip + .offset(offset) + .addClass(placement) + .addClass('in') + + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + + if (placement == 'top' && actualHeight != height) { + offset.top = offset.top + height - actualHeight + replace = true + } + + if (placement == 'bottom' || placement == 'top') { + delta = 0 + + if (offset.left < 0){ + delta = offset.left * -2 + offset.left = 0 + $tip.offset(offset) + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + } + + this.replaceArrow(delta - width + actualWidth, actualWidth, 'left') + } else { + this.replaceArrow(actualHeight - height, actualHeight, 'top') + } + + if (replace) $tip.offset(offset) + } + + , replaceArrow: function(delta, dimension, position){ + this + .arrow() + .css(position, delta ? (50 * (1 - delta / dimension) + "%") : '') + } + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle() + + $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title) + $tip.removeClass('fade in top bottom left right') + } + + , hide: function () { + var that = this + , $tip = this.tip() + , e = $.Event('hide') + + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + + $tip.removeClass('in') + + function removeWithAnimation() { + var timeout = setTimeout(function () { + $tip.off($.support.transition.end).detach() + }, 500) + + $tip.one($.support.transition.end, function () { + clearTimeout(timeout) + $tip.detach() + }) + } + + $.support.transition && this.$tip.hasClass('fade') ? + removeWithAnimation() : + $tip.detach() + + this.$element.trigger('hidden') + + return this + } + + , fixTitle: function () { + var $e = this.$element + if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').attr('title', '') + } + } + + , hasContent: function () { + return this.getTitle() + } + + , getPosition: function () { + var el = this.$element[0] + return $.extend({}, (typeof el.getBoundingClientRect == 'function') ? el.getBoundingClientRect() : { + width: el.offsetWidth + , height: el.offsetHeight + }, this.$element.offset()) + } + + , getTitle: function () { + var title + , $e = this.$element + , o = this.options + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) + + return title + } + + , tip: function () { + return this.$tip = this.$tip || $(this.options.template) + } + + , arrow: function(){ + return this.$arrow = this.$arrow || this.tip().find(".tooltip-arrow") + } + + , validate: function () { + if (!this.$element[0].parentNode) { + this.hide() + this.$element = null + this.options = null + } + } + + , enable: function () { + this.enabled = true + } + + , disable: function () { + this.enabled = false + } + + , toggleEnabled: function () { + this.enabled = !this.enabled + } + + , toggle: function (e) { + var self = e ? $(e.currentTarget)[this.type](this._options).data(this.type) : this + self.tip().hasClass('in') ? self.hide() : self.show() + } + + , destroy: function () { + this.hide().$element.off('.' + this.type).removeData(this.type) + } + + } + + + /* TOOLTIP PLUGIN DEFINITION + * ========================= */ + + var old = $.fn.tooltip + + $.fn.tooltip = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tooltip') + , options = typeof option == 'object' && option + if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tooltip.Constructor = Tooltip + + $.fn.tooltip.defaults = { + animation: true + , placement: 'top' + , selector: false + , template: '
    ' + , trigger: 'hover focus' + , title: '' + , delay: 0 + , html: false + , container: false + } + + + /* TOOLTIP NO CONFLICT + * =================== */ + + $.fn.tooltip.noConflict = function () { + $.fn.tooltip = old + return this + } + +}(window.jQuery); diff --git a/src/main/webapp/layout/script.jsp b/src/main/webapp/layout/script.jsp index 1c53370..f47fc58 100644 --- a/src/main/webapp/layout/script.jsp +++ b/src/main/webapp/layout/script.jsp @@ -33,4 +33,4 @@ document.body.appendChild(e); } - \ No newline at end of file + \ No newline at end of file diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp new file mode 100644 index 0000000..1ed576f --- /dev/null +++ b/src/main/webapp/setup/addentity.jsp @@ -0,0 +1,204 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + + +
    +

    +
    + +
    +

    Entity URI - coeus:

    + +
    +

    New Entity:

    +
    + + +
    + + +
    +
    + + +
    + + +
    +
    + +
    +
    + +
    +
    +
    +
    + + +
    + +
    + + + + +
    + + + + + + + +     +     diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index b2cb90a..79dddd8 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -25,14 +25,14 @@
      -
    • ">Home
      • +
    • ">Home
    • ">Seed
    • Setup
        -
      • Entities
        • +
      • Entities
      • Concepts
      • Resources
      • diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 1515728..0336c47 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -8,9 +8,103 @@ COEUS Setup + + @@ -18,14 +112,14 @@


        -
        -

        ${actionBean.name} Production

        +
        +
        -
        -

        Knowledge Base

        -

        Disease

        +
        +

        Knowledge Base (Entity-Concept)

        +

        Actions

        +
        - Environments + Projects
        @@ -68,7 +163,23 @@
        - Add new Entity + Change environment +
        +
        +
        + +
        +
        + Entities +
        +
        + +
        +
        +
        + Add new Entity
        @@ -78,10 +189,8 @@ Concepts
        - +
        diff --git a/src/main/webapp/setup/listentities.jsp b/src/main/webapp/setup/listentities.jsp new file mode 100644 index 0000000..08bbdca --- /dev/null +++ b/src/main/webapp/setup/listentities.jsp @@ -0,0 +1,109 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + +
        +

        +
        + +
        +
        +
        +

        List of Entities

        +
        +
        +
        + Add Entity +
        +
        + + + + + + + + + + + + + + +
        EntityTitleActions
        + + + + + + + +
        + + + From f4b0bfe6b8baf8ff52f76e23b3ea33664c9ef132 Mon Sep 17 00:00:00 2001 From: sernadela Date: Fri, 28 Jun 2013 10:09:31 +0100 Subject: [PATCH 04/52] - Setup: list and remove entity support; - TODO: Review remove method to remove all hang subjects associated. --- src/main/webapp/assets/js/coeus.api.js | 93 +++++++++++++++++++++- src/main/webapp/setup/addentity.jsp | 47 ++++------- src/main/webapp/setup/listentities.jsp | 105 ++++++++++++++++++------- 3 files changed, 184 insertions(+), 61 deletions(-) diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index a048f5d..60d0a17 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -34,7 +34,7 @@ function writeTriple(subject, predicate, object, key) { * @returns {undefined} */ function updateTriple(subject, predicate, old_object, new_object, key) { - $.ajax({url: './api/' + key + '/update/' + subject + '/' + predicate + '/' + old_object+ ','+new_object, dataType: 'json'}).done(function(data) { + $.ajax({url: './api/' + key + '/update/' + subject + '/' + predicate + '/' + old_object + ',' + new_object, dataType: 'json'}).done(function(data) { if (data.status === 100) { console.log('[COEUS] data successfully updated in knowledge base.'); // All OK function handler. @@ -58,7 +58,7 @@ function updateTriple(subject, predicate, old_object, new_object, key) { * @returns {undefined} */ function deleteTriple(subject, predicate, object, key) { - $.ajax({url: './api/' + key + '/delete/' + subject + '/' + predicate + '/' +object, dataType: 'json'}).done(function(data) { + $.ajax({url: './api/' + key + '/delete/' + subject + '/' + predicate + '/' + object, dataType: 'json'}).done(function(data) { if (data.status === 100) { console.log('[COEUS] data successfully deleted in knowledge base.'); // All OK function handler. @@ -70,4 +70,93 @@ function deleteTriple(subject, predicate, object, key) { console.log('[COEUS] unable to complete data delete request. ' + textStatus); // Server communication error function handler. }); +} +/** + * init service prefix + * @returns {query} */ +function initSparqlerQuery() { + var sparqler = new SPARQL.Service("../../sparql"); + + var prefixes = getPrefixURI(); + for (var key in prefixes) { + sparqler.setPrefix(key, prefixes[key]); + } + + var query = sparqler.createQuery(); + return query; +} + +function getPrefixURI() { + var prefixes = { + dc: "http://purl.org/dc/elements/1.1/", + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + rdfs: "http://www.w3.org/2000/01/rdf-schema#", + coeus: "http://bioinformatics.ua.pt/coeus/resource/", + owl: "http://www.w3.org/2002/07/owl#" + }; + return prefixes; +} + +/** + * Get the namespace prefix + * + * @param {type} uri + * @returns {undefined} + */ +function getPrefix(uri) { + var prefixes = getPrefixURI(); + + for (var key in prefixes) { + if (prefixes[key] === uri) return key; + } + return ''; +} + +/** + * Split the URI to give the namespace + * @param {type} uri + * @returns {splitURIPrefix.mapping} + */ +function splitURIPrefix(uri) { + var value; + var uriToSlit = uri; + if (uriToSlit.indexOf("#") !== -1) + value = uriToSlit.split('#').pop(); + else + value = uriToSlit.split('/').pop(); + var namespace = uri.substr(0, uri.length - value.length); + + var mapping = { + "namespace": namespace, + "value": value + }; + + return mapping; +} +/** + * Call api through URL and change the HTML (component id) according to the result. + * @param {type} url + * @param {type} html + * @returns {undefined} + */ +function callAPI(url, html) { + + $.ajax({url: url, async: false, dataType: 'json'}).done(function(data) { + console.log(url + ' ' + data.status); + if (data.status === 100) { + //$(html).append('Call: ' + url + '
        Message: ' + data.message+'

        '); + $(html).addClass('alert alert-success'); + } else { + $(html).append('Call: '+url + '
        Status: ' + data.status + ' Message: ' + data.message+'

        '); + $(html).addClass('alert alert-error'); + } + + }).fail(function(jqXHR, textStatus) { + $(html).addClass('alert alert-error'); + $(html).html('Call: '+url + '
        ' + 'ERROR: ' + textStatus+'

        '); + // Server communication error function handler. + }); +} +function getApiKey() { + return "coeus"; } \ No newline at end of file diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp index 1ed576f..220540a 100644 --- a/src/main/webapp/setup/addentity.jsp +++ b/src/main/webapp/setup/addentity.jsp @@ -10,6 +10,7 @@ + + @@ -106,7 +104,7 @@
        - Add Entity + Add Entity
        diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 79dddd8..5d71cb8 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -10,7 +10,7 @@ <s:layout-component name="title">COEUS Setup</s:layout-component> - +
        - Add + Add
          @@ -63,5 +80,27 @@
        + + + From d9f1d6b2303d517fb1e4d0be38104af1e58e5953 Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 3 Jul 2013 18:20:39 +0100 Subject: [PATCH 08/52] - Setup: recursive delete, crud complete on model (resources lack) --- .../coeus/actions/ManagerActionBean.java | 2 +- src/main/webapp/assets/js/coeus.api.js | 71 +++++- src/main/webapp/setup/addconcept.jsp | 209 ++++++++++++++++++ src/main/webapp/setup/concepts.jsp | 68 +++--- src/main/webapp/setup/entities.jsp | 19 +- src/main/webapp/setup/html.jsp | 4 +- src/main/webapp/setup/index.jsp | 108 ++++----- 7 files changed, 380 insertions(+), 101 deletions(-) create mode 100644 src/main/webapp/setup/addconcept.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java index ae71d7b..5f72c9c 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java @@ -47,7 +47,7 @@ public Resolution handle() { return new ForwardResolution(ENTITIES_VIEW); } } else if (model.equals("concept")) { - if (method.startsWith("add")) { + if (method.startsWith("add") | method.startsWith("edit")) { return new ForwardResolution(CONCEPT_ADD_VIEW); } else { return new ForwardResolution(CONCEPTS_VIEW); diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 4c78a76..a882279 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -186,7 +186,7 @@ function redirect(location) { } /** * - * remove all subjects and predicates associated. + * remove all subjects and predicates associated. The objects are recursively removed too. * * example urlPrefix = "../../api/" + getApiKey() ; * @@ -215,14 +215,65 @@ function removeAllTriplesFromObject(urlPrefix, object) { objectPrefix = 'xsd:string:' + objectPrefix; var url = "/delete/"+ objectPrefix + splitedSubject.value + '/' + predicatePrefix + splitedPredicate.value + '/' + object; + + console.log("Delete call: "+urlPrefix+url); callAPI(urlPrefix + url, "#result"); + if((splitedPredicate.value!== "includes") & (splitedPredicate.value!== "isEntityOf") & (splitedPredicate.value!== "isConceptOf") & (splitedPredicate.value!== "isResourceOff")) + removeRecursive(urlPrefix,objectPrefix + splitedSubject.value); + + + } + + + }} + ); + +} + +function isModel(key){ + var b=false; + + if(key.indexOf("coeus:seed_") !== -1 | key.indexOf("coeus:entity_") !== -1 | key.indexOf("coeus:concept_") !== -1 | key.indexOf("coeus:resource_") !== -1) b=true; + + console.log(key+' '+b); + return b; + +} + +function removeRecursive(urlPrefix,subject){ + var query=initSparqlerQuery(); + var qObject = "SELECT ?predicate ?object {"+subject+" ?predicate ?object . }"; + console.log("Recursive call: "+qObject); + query.query(qObject, + {success: function(json) { + var result = json.results.bindings; + + for (r in result) { + var splitedPredicate = splitURIPrefix(result[r].predicate.value); + var splitedObject = splitURIPrefix(result[r].object.value); + + var predicatePrefix = getPrefix(splitedPredicate.namespace); + if (predicatePrefix !== '') + predicatePrefix = predicatePrefix + ':'; + var objectPrefix = getPrefix(splitedObject.namespace); + if (objectPrefix !== '') + objectPrefix = objectPrefix + ':'; + else + objectPrefix = 'xsd:string:' + objectPrefix; + var url = "/delete/"+ subject + '/' + predicatePrefix + splitedPredicate.value + '/' + objectPrefix + splitedObject.value; + console.log("Recursive Delete call: "+urlPrefix+url); + callAPI(urlPrefix + url, "#result"); + if(isModel(objectPrefix + splitedObject.value)) { + // console.log("Another recursive call: "+url); + removeRecursive(urlPrefix,objectPrefix + splitedObject.value); + } + } }} ); - } function removeAllTriplesFromSubject(urlPrefix, subject) { @@ -247,7 +298,7 @@ function removeAllTriplesFromSubject(urlPrefix, subject) { var url = "/delete/"+ subject + '/' + predicatePrefix + splitedPredicate.value + '/' + objectPrefix + splitedObject.value; - callAPI(urlPrefix + url, "#result"); + callAPI(urlPrefix + url, "#result"); } @@ -255,8 +306,20 @@ function removeAllTriplesFromSubject(urlPrefix, subject) { if (document.getElementById('result').className !== 'alert alert-error') { // window.location="../entity/"+lastPath(); console.log("REDIRECTING..."); - window.location.reload(true); + //window.location.reload(true); } }} ); } +//function test(callback){ +// var query = initSparqlerQuery(); +// var qSubject = "SELECT ?predicate ?object {coeus:seed_xxx ?predicate ?object . }"; +// query.query(qSubject, +// {success: function(json) { +// var result = json.results.bindings; +// //console.log(result); +// callback(result); +// }} +// ); +// console.log('Do others things...'); +//} \ No newline at end of file diff --git a/src/main/webapp/setup/addconcept.jsp b/src/main/webapp/setup/addconcept.jsp new file mode 100644 index 0000000..5e7e641 --- /dev/null +++ b/src/main/webapp/setup/addconcept.jsp @@ -0,0 +1,209 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + + + +
        +

        +
        + +
        +

        Concept URI - coeus:

        + +
        +

        New Concept

        +
        + + +
        + + +
        +
        + + +
        + +
        +
        + +
        +
        + +
        +
        +
        + + +
        + + + + +
        + + + + + + + +         +         diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index ca78ee8..f682bd0 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -13,44 +13,56 @@ @@ -71,13 +84,18 @@
        +
          +
        • +
        • +
        • Concepts
          • +
        -

        List of Entities

        +

        List of Concepts

        - Add Entity + Add Concept
        @@ -86,12 +104,12 @@ - Entity + Concept Title Actions - + @@ -103,10 +121,10 @@ From fc95ae76de86b1fe450f2ad0f881d8025126509a Mon Sep 17 00:00:00 2001 From: sernadela Date: Fri, 12 Jul 2013 17:32:21 +0100 Subject: [PATCH 12/52] - Setup: add and remove selectors, TODO: edit selectors --- .../coeus/actions/WriteActionBean.java | 1 + .../resources/newsaggregator/predicates.csv | 3 +- src/main/resources/proteinator/predicates.csv | 3 +- src/main/resources/tester/predicates.csv | 3 +- src/main/webapp/assets/js/coeus.api.js | 14 +- src/main/webapp/setup/addresource.jsp | 356 +++++++++++++----- 6 files changed, 285 insertions(+), 95 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/WriteActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/WriteActionBean.java index b1b4aa1..ee8d052 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/WriteActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/WriteActionBean.java @@ -92,6 +92,7 @@ public Resolution handle() { //verify if is a xsd type if (obj.startsWith("xsd:")) { String[] old = obj.split(":", 3); + System.err.println(obj); Literal l = Boot.getAPI().getModel().createTypedLiteral(old[2], xsd + old[1]); statToAdd = Boot.getAPI().getModel().createLiteralStatement(Boot.getAPI().createResource(PrefixFactory.decode(sub)), Predicate.get(pred), l); } else if (obj.indexOf(":") > 1) { diff --git a/src/main/resources/newsaggregator/predicates.csv b/src/main/resources/newsaggregator/predicates.csv index 6b0b8fd..1c8c267 100644 --- a/src/main/resources/newsaggregator/predicates.csv +++ b/src/main/resources/newsaggregator/predicates.csv @@ -75,4 +75,5 @@ http://bioinformatics.ua.pt/coeus/resource/enabled http://bioinformatics.ua.pt/coeus/resource/isConnectedTo http://bioinformatics.ua.pt/coeus/resource/loadsFrom http://bioinformatics.ua.pt/coeus/resource/hasBridge -http://bioinformatics.ua.pt/coeus/resource/hasConcept \ No newline at end of file +http://bioinformatics.ua.pt/coeus/resource/hasConcept +http://bioinformatics.ua.pt/coeus/resource/regex \ No newline at end of file diff --git a/src/main/resources/proteinator/predicates.csv b/src/main/resources/proteinator/predicates.csv index 6b0b8fd..1c8c267 100644 --- a/src/main/resources/proteinator/predicates.csv +++ b/src/main/resources/proteinator/predicates.csv @@ -75,4 +75,5 @@ http://bioinformatics.ua.pt/coeus/resource/enabled http://bioinformatics.ua.pt/coeus/resource/isConnectedTo http://bioinformatics.ua.pt/coeus/resource/loadsFrom http://bioinformatics.ua.pt/coeus/resource/hasBridge -http://bioinformatics.ua.pt/coeus/resource/hasConcept \ No newline at end of file +http://bioinformatics.ua.pt/coeus/resource/hasConcept +http://bioinformatics.ua.pt/coeus/resource/regex \ No newline at end of file diff --git a/src/main/resources/tester/predicates.csv b/src/main/resources/tester/predicates.csv index 9f5cce3..8c31162 100644 --- a/src/main/resources/tester/predicates.csv +++ b/src/main/resources/tester/predicates.csv @@ -76,4 +76,5 @@ http://bioinformatics.ua.pt/coeus/resource/isConnectedTo http://bioinformatics.ua.pt/coeus/resource/loadsFrom http://bioinformatics.ua.pt/coeus/resource/hasBridge http://bioinformatics.ua.pt/coeus/resource/hasConcept -http://www.w3.org/2000/01/rdf-schema#seeAlso \ No newline at end of file +http://www.w3.org/2000/01/rdf-schema#seeAlso +http://bioinformatics.ua.pt/coeus/resource/regex \ No newline at end of file diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 7f3e0d6..540f835 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -141,7 +141,7 @@ function splitURIPrefix(uri) { * @returns {undefined} */ function callAPI(url, html) { - + url=encodeURI(url); $.ajax({url: url, async: false, dataType: 'json'}).done(function(data) { console.log(url + ' ' + data.status); if (data.status === 100) { @@ -283,7 +283,7 @@ function removeAllTriplesFromSubject(urlPrefix, subject) { {success: function(json) { var result = json.results.bindings; console.log(result); - for (r in result) { + for (var r in result) { var splitedPredicate = splitURIPrefix(result[r].predicate.value); var splitedObject = splitURIPrefix(result[r].object.value); @@ -295,10 +295,12 @@ function removeAllTriplesFromSubject(urlPrefix, subject) { objectPrefix = objectPrefix + ':'; else objectPrefix = 'xsd:string:' + objectPrefix; - - var url = "/delete/"+ subject + '/' + predicatePrefix + splitedPredicate.value + '/' + objectPrefix + splitedObject.value; - - callAPI(urlPrefix + url, "#result"); + + var url = "/delete/"+ subject + '/' + predicatePrefix + splitedPredicate.value + '/' + objectPrefix; + //TO ALLOW '/' in the string + if(splitedPredicate.value==='query') url=url+result[r].object.value.split("/").join("%2F"); else url=url+splitedObject.value; + + callAPI(urlPrefix + url, "#result"); } diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index ce263a2..12b2a3c 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -13,20 +13,6 @@ From e3a440184b876e7c20163e07fcd077af83d8f662 Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 18 Jul 2013 17:31:07 +0100 Subject: [PATCH 17/52] - Setup: Change the remove strategy --- src/main/webapp/assets/js/coeus.api.js | 234 ++++++++++++++----------- src/main/webapp/setup/addresource.jsp | 2 + src/main/webapp/setup/concepts.jsp | 3 + src/main/webapp/setup/entities.jsp | 3 + src/main/webapp/setup/resources.jsp | 4 +- src/main/webapp/setup/seeds.jsp | 4 +- 6 files changed, 143 insertions(+), 107 deletions(-) diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 0a9d8e0..6ffca80 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -141,7 +141,7 @@ function splitURIPrefix(uri) { * @returns {undefined} */ function callAPI(url, html) { - url=encodeURI(url); + url = encodeURI(url); $.ajax({url: url, async: false, dataType: 'json'}).done(function(data) { console.log(url + ' ' + data.status); if (data.status === 100) { @@ -186,7 +186,7 @@ function redirect(location) { } /** * - * remove all subjects and predicates associated. The objects are recursively removed too. + * remove all subjects and predicates associated. * * example urlPrefix = "../../api/" + getApiKey() ; * @@ -195,97 +195,115 @@ function redirect(location) { * @returns {undefined} */ function removeAllTriplesFromObject(urlPrefix, object) { - var query = initSparqlerQuery(); - var qObject = "SELECT ?subject ?predicate {?subject ?predicate " + object + " . }"; - query.query(qObject, - {success: function(json) { - var result = json.results.bindings; - console.log(result); - for (r in result) { - var splitedPredicate = splitURIPrefix(result[r].predicate.value); - var splitedSubject = splitURIPrefix(result[r].subject.value); - - var predicatePrefix = getPrefix(splitedPredicate.namespace); - if (predicatePrefix !== '') - predicatePrefix = predicatePrefix + ':'; - var objectPrefix = getPrefix(splitedSubject.namespace); - if (objectPrefix !== '') - objectPrefix = objectPrefix + ':'; - else - objectPrefix = 'xsd:string:' + objectPrefix; - - var url = "/delete/"+ objectPrefix + splitedSubject.value + '/' + predicatePrefix + splitedPredicate.value + '/' + object; - - console.log("Delete call: "+urlPrefix+url); - callAPI(urlPrefix + url, "#result"); - if((splitedPredicate.value!== "includes") & (splitedPredicate.value!== "isEntityOf") & (splitedPredicate.value!== "isConceptOf") & (splitedPredicate.value!== "isResourceOf")) - removeRecursive(urlPrefix,objectPrefix + splitedSubject.value); - - - } - - }} - ); + var qObject = "SELECT ?subject ?predicate {?subject ?predicate " + object + " . }"; + queryToResult(qObject, function(result) { + console.log(result); + for (var r in result) { + var subject = resultToObject(result[r].subject); + var predicate = resultToPredicate(result[r].predicate); -} + var url = "/delete/" + subject.prefix + subject.value + '/' + predicate.prefix + predicate.value + '/' + object; -function isModel(key){ - var b=false; - - if(key.indexOf("coeus:seed_") !== -1 | key.indexOf("coeus:entity_") !== -1 | key.indexOf("coeus:concept_") !== -1 | key.indexOf("coeus:resource_") !== -1) b=true; + //console.log("Delete call: " + urlPrefix + url); + callAPI(urlPrefix + url, "#result"); + // if ((predicate.value !== "includes") & (predicate.value !== "isEntityOf") & (predicate.value !== "isConceptOf") & (predicate.value !== "isResourceOf")) + //removeRecursive(urlPrefix, subject.prefix + subject.value); + } - console.log(key+' '+b); - return b; - -} -function removeRecursive(urlPrefix,subject){ - var query=initSparqlerQuery(); - var qObject = "SELECT ?predicate ?object {"+subject+" ?predicate ?object . }"; - console.log("Recursive call: "+qObject); - query.query(qObject, - {success: function(json) { - var result = json.results.bindings; - - for (r in result) { - var splitedPredicate = splitURIPrefix(result[r].predicate.value); - var splitedObject = splitURIPrefix(result[r].object.value); - - var predicatePrefix = getPrefix(splitedPredicate.namespace); - if (predicatePrefix !== '') - predicatePrefix = predicatePrefix + ':'; - var objectPrefix = getPrefix(splitedObject.namespace); - if (objectPrefix !== '') - objectPrefix = objectPrefix + ':'; - else - objectPrefix = 'xsd:string:' + objectPrefix; - - var url = "/delete/"+ subject + '/' + predicatePrefix + splitedPredicate.value + '/' + objectPrefix + splitedObject.value; - console.log("Recursive Delete call: "+urlPrefix+url); - callAPI(urlPrefix + url, "#result"); - if(isModel(objectPrefix + splitedObject.value)) { - // console.log("Another recursive call: "+url); - removeRecursive(urlPrefix,objectPrefix + splitedObject.value); - } - - } + } + ); +} - }} - ); +function cleanUnlikedTriples(urlPrefix){ + //Clean unlinked entities + var qEntities="SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; + queryToResult(qEntities,function (result){ + for(var r in result){ + var entity=splitURIPrefix(result[r].entity.value); + var prefix=getPrefix(entity.namespace)+":"; + removeAllTriplesFromSubject(urlPrefix, prefix+entity.value); + } + }); + //Clean unlinked concepts + var qConcepts="SELECT * {{ ?concept a coeus:Concept . FILTER NOT EXISTS{ ?concept coeus:hasEntity ?entity }}UNION {?concept a coeus:Concept . FILTER NOT EXISTS { ?entity coeus:isEntityOf ?concept }} }"; + queryToResult(qConcepts,function (result){ + for(var r in result){ + var concept=splitURIPrefix(result[r].concept.value); + var prefix=getPrefix(concept.namespace)+":"; + removeAllTriplesFromSubject(urlPrefix, prefix+concept.value); + } + }); + //Clean unlinked resources + var qResources="SELECT * {{ ?resource a coeus:Resource . FILTER NOT EXISTS{ ?resource coeus:isResourceOf ?concept} }UNION {?resource a coeus:Resource . FILTER NOT EXISTS { ?concept coeus:hasResource ?resource}} }"; + queryToResult(qResources,function (result){ + for(var r in result){ + var resource=splitURIPrefix(result[r].resource.value); + var prefix=getPrefix(resource.namespace)+":"; + removeAllTriplesFromSubject(urlPrefix, prefix+resource.value); + } + }); + //Clean unlinked selectores + var qSelectores="SELECT * {{ ?selector coeus:property ?property . FILTER NOT EXISTS { ?selector coeus:loadsFor ?resource } }UNION {?selector coeus:property ?property . FILTER NOT EXISTS { ?resource coeus:loadsFrom ?selector}}}"; + queryToResult(qSelectores,function (result){ + for(var r in result){ + var selector=splitURIPrefix(result[r].selector.value); + var prefix=getPrefix(selector.namespace)+":"; + removeAllTriplesFromSubject(urlPrefix, prefix+selector.value); + } + }); } +//function isModel(key) { +// var b = false; +// +// if (key.indexOf("coeus:seed_") !== -1 | key.indexOf("coeus:entity_") !== -1 | key.indexOf("coeus:concept_") !== -1 | key.indexOf("coeus:resource_") !== -1) +// b = true; +// +// console.log(key + ' ' + b); +// return b; +// +//} +// +//function removeRecursive(urlPrefix, subject) { +// var query = initSparqlerQuery(); +// var qObject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; +// console.log("Recursive call: " + qObject); +// query.query(qObject, +// {success: function(json) { +// var result = json.results.bindings; +// +// for (var r in result) { +// var object = resultToObject(result[r].object); +// var predicate = resultToPredicate(result[r].predicate); +// +// var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; +// console.log("Recursive Delete call: " + urlPrefix + url); +// //callAPI(urlPrefix + url, "#result"); +// if (isModel(object.prefix + object.value)) { +// // console.log("Another recursive call: "+url); +// //removeRecursive(urlPrefix, object.prefix + object.value); +// } +// +// } +// +// +// }} +// ); +//} + function removeAllTriplesFromSubject(urlPrefix, subject) { var qSubject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; queryToResult(qSubject, function(result) { console.log(result); for (var r in result) { - var object=resultToObject(result[r].object); - var predicate=resultToPredicate(result[r].predicate); + var object = resultToObject(result[r].object); + var predicate = resultToPredicate(result[r].predicate); - var url = "/delete/"+ subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; - console.log(url); + var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; + //console.log(url); callAPI(urlPrefix + url, "#result"); } @@ -295,18 +313,19 @@ function removeAllTriplesFromSubject(urlPrefix, subject) { console.log("REDIRECTING..."); //window.location.reload(true); } - } + } ); } function removeAllTriplesFromSubjectAndPredicate(urlPrefix, subject, predicate) { - var qSubject = "SELECT ?object {" + subject + " "+predicate+" ?object . }";console.log(qSubject); + var qSubject = "SELECT ?object {" + subject + " " + predicate + " ?object . }"; + console.log(qSubject); queryToResult(qSubject, function(result) { console.log(result); for (var r in result) { - var object=resultToObject(result[r].object); + var object = resultToObject(result[r].object); - var url = "/delete/"+ subject + '/' + predicate + '/' + object.prefix + object.value; + var url = "/delete/" + subject + '/' + predicate + '/' + object.prefix + object.value; console.log(url); callAPI(urlPrefix + url, "#result"); } @@ -317,20 +336,22 @@ function removeAllTriplesFromSubjectAndPredicate(urlPrefix, subject, predicate) console.log("REDIRECTING..."); //window.location.reload(true); } - } + } ); } function removeAllTriplesFromPredicateAndObject(urlPrefix, predicate, object) { - var qSubject = "SELECT ?subject {?subject " +predicate+" "+object+" . }";console.log(qSubject); + var qSubject = "SELECT ?subject {?subject " + predicate + " " + object + " . }"; + console.log(qSubject); queryToResult(qSubject, function(result) { - console.log(result); - for (var r in result) { - var subject=resultToPredicate(result[r].subject); - var url = "/delete/"+ subject.prefix+subject.value + '/' + predicate + '/' + object; - //console.log(url); - callAPI(urlPrefix + url, "#result"); - } + console.log(result); + for (var r in result) { + var subject = resultToPredicate(result[r].subject); + + var url = "/delete/" + subject.prefix + subject.value + '/' + predicate + '/' + object; + //console.log(url); + callAPI(urlPrefix + url, "#result"); } + } ); } @@ -339,18 +360,20 @@ function removeAllTriplesFromPredicateAndObject(urlPrefix, predicate, object) { * @param {type} object * @returns {resultToObject.mapping} */ -function resultToObject(object){ - var val=object.value; - var objectPrefix=''; - - if(object.type==="uri"){ - var splitedObject=splitURIPrefix(val); +function resultToObject(object) { + var val = object.value; + var objectPrefix = ''; + + if (object.type === "uri") { + var splitedObject = splitURIPrefix(val); val = splitedObject.value; objectPrefix = getPrefix(splitedObject.namespace); } - if (objectPrefix !== '') objectPrefix = objectPrefix + ':'; - else objectPrefix = 'xsd:'+splitURIPrefix(object.datatype).value+':' + objectPrefix; + if (objectPrefix !== '') + objectPrefix = objectPrefix + ':'; + else + objectPrefix = 'xsd:' + splitURIPrefix(object.datatype).value + ':' + objectPrefix; //TO ALLOW '/' in the string call encodeBars(string); var mapping = { "prefix": objectPrefix, @@ -363,10 +386,11 @@ function resultToObject(object){ * @param {type} pred * @returns {resultToPredicate.mapping} */ -function resultToPredicate(pred){ +function resultToPredicate(pred) { var splitedPredicate = splitURIPrefix(pred.value); var predicatePrefix = getPrefix(splitedPredicate.namespace); - if (predicatePrefix !== '') predicatePrefix = predicatePrefix + ':'; + if (predicatePrefix !== '') + predicatePrefix = predicatePrefix + ':'; var mapping = { "prefix": predicatePrefix, @@ -374,7 +398,7 @@ function resultToPredicate(pred){ }; return mapping; - + } /** * Do a query to retrive the result in a callback way @@ -385,7 +409,7 @@ function resultToPredicate(pred){ * @param {type} callback * @returns {undefined} */ -function queryToResult(selectQuery, callback){ +function queryToResult(selectQuery, callback) { var query = initSparqlerQuery(); query.query(selectQuery, {success: function(json) { @@ -393,9 +417,9 @@ function queryToResult(selectQuery, callback){ //console.log(result); callback(result); }} - ); + ); } -function encodeBars(value){ +function encodeBars(value) { return value.split('/').join('%2F'); } \ No newline at end of file diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 4b88832..96deefc 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -189,6 +189,7 @@ } function detachSelector(selector){ var urlDelete = "../../../api/" + getApiKey() + "/delete/"; + //callAPI(urlDelete + lastPath() + "/" + "coeus:isKeyOf" + "/coeus:" + selector, '#res'); callAPI(urlDelete + lastPath() + "/" + "coeus:loadsFrom" + "/coeus:" + selector, '#res'); if (document.getElementById('res').className === 'alert alert-success') { window.location = document.referrer; @@ -236,6 +237,7 @@ var urlPrefix = "../../../api/" + getApiKey(); //remove all subjects associated. removeAllTriplesFromPredicateAndObject(urlPrefix,"coeus:loadsFrom", selector); + removeAllTriplesFromPredicateAndObject(urlPrefix,"coeus:isKeyOf", selector); //remove all predicates and objects associated. removeAllTriplesFromSubject(urlPrefix, selector); diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index 67651fb..984f1d1 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -89,6 +89,9 @@ //header name var path = lastPath(); $('#header').append('

        ' + path + ' env..

        '); + + var urlPrefix = "../../api/" + getApiKey(); + cleanUnlikedTriples(urlPrefix); }); diff --git a/src/main/webapp/setup/entities.jsp b/src/main/webapp/setup/entities.jsp index 79b1da6..eff58a5 100644 --- a/src/main/webapp/setup/entities.jsp +++ b/src/main/webapp/setup/entities.jsp @@ -62,6 +62,9 @@ var path = lastPath(); $('#header').append('

        ' + path + ' env..

        '); $('#breadSeed').html('Seed /'); + + var urlPrefix = "../../api/" + getApiKey(); + cleanUnlikedTriples(urlPrefix); }); diff --git a/src/main/webapp/setup/resources.jsp b/src/main/webapp/setup/resources.jsp index a0eafd4..2b45299 100644 --- a/src/main/webapp/setup/resources.jsp +++ b/src/main/webapp/setup/resources.jsp @@ -26,7 +26,6 @@ removeAllTriplesFromObject(urlPrefix, resource); //remove all predicates and objects associated. removeAllTriplesFromSubject(urlPrefix, resource); - } function fillBreadcumb(result) { console.log(result); @@ -71,6 +70,9 @@ //header name var path = lastPath(); $('#header').append('

        ' + path + ' env..

        '); + + var urlPrefix = "../../api/" + getApiKey(); + cleanUnlikedTriples(urlPrefix); }); diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index ebc9b85..1718787 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -41,7 +41,8 @@ }} ); - + var urlPrefix = "../../api/" + getApiKey(); + cleanUnlikedTriples(urlPrefix); }); @@ -58,6 +59,7 @@ removeAllTriplesFromObject(urlPrefix,seed); //remove all predicates and objects associated. removeAllTriplesFromSubject(urlPrefix,seed); + } From ed925f56d4cb092824da5fcb8ea2b1040f051f89 Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 24 Jul 2013 14:54:40 +0100 Subject: [PATCH 18/52] - Setup: Fix endpoint db connection string on sql --- .../coeus/actions/ManagerActionBean.java | 5 ++++ .../coeus/actions/UpdateActionBean.java | 2 +- src/main/webapp/assets/js/coeus.api.js | 4 ++- src/main/webapp/setup/graph.jsp | 30 +++++++++++++++++++ src/main/webapp/setup/seeds.jsp | 2 +- 5 files changed, 40 insertions(+), 3 deletions(-) create mode 100644 src/main/webapp/setup/graph.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java index 3a49ae6..4c89cab 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java @@ -37,6 +37,7 @@ public class ManagerActionBean implements ActionBean { private static final String RESOURCE_ADD_VIEW = "/setup/addresource.jsp"; private static final String RESOURCES_VIEW = "/setup/resources.jsp"; private static final String NOTFOUND_VIEW = "/setup/404.jsp"; + private static final String GRAPH_VIEW = "/setup/graph.jsp"; private String method; private String model; private ActionBeanContext context; @@ -46,6 +47,10 @@ public Resolution handle() { return new ForwardResolution(NOTFOUND_VIEW); } + + public Resolution graph() { + return new ForwardResolution(GRAPH_VIEW); + } public Resolution export() throws FileNotFoundException { StringWriter outs = new StringWriter(); diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java index f68324d..c89a702 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java @@ -108,7 +108,7 @@ public Resolution handle() { if (sub.indexOf(":") > 1) { try { if (pred.indexOf(":") > 1) { - + System.err.println(old_obj+","+new_obj); // test old_obj String xsd = "http://www.w3.org/2001/XMLSchema#"; Statement statToRemove = null; diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 6ffca80..25ab10a 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -421,5 +421,7 @@ function queryToResult(selectQuery, callback) { } function encodeBars(value) { - return value.split('/').join('%2F'); + value=value.split(';').join('%3B'); + value=value.split('/').join('%2F'); + return value; } \ No newline at end of file diff --git a/src/main/webapp/setup/graph.jsp b/src/main/webapp/setup/graph.jsp new file mode 100644 index 0000000..7685f9f --- /dev/null +++ b/src/main/webapp/setup/graph.jsp @@ -0,0 +1,30 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + +
        + + Error 404 + +
        +

        Page Not Found Error 404

        +
        +

        The page you requested could not be found, either contact your webmaster or try again.

        +

        Use your browsers Back button to navigate to the page you have prevously come from

        +

        Or you could just press this button:

        + Take Me Home +
        +
        + + +         +         diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index 1718787..5cd39f6 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -42,7 +42,7 @@ ); var urlPrefix = "../../api/" + getApiKey(); - cleanUnlikedTriples(urlPrefix); + cleanUnlikedTriples(urlPrefix); }); From b3e20b047b70ba487024845610a7b552d47339c0 Mon Sep 17 00:00:00 2001 From: sernadela Date: Fri, 26 Jul 2013 18:04:58 +0100 Subject: [PATCH 19/52] - Setup: Interface for config in config.js. Working on prefixes. --- .../coeus/actions/ConfigActionBean.java | 160 ++++++++++ .../coeus/actions/ManagerActionBean.java | 10 + src/main/webapp/WEB-INF/web.xml | 1 + src/main/webapp/assets/js/coeus.api.js | 1 + src/main/webapp/setup/config.jsp | 273 ++++++++++++++++++ src/main/webapp/setup/html.jsp | 2 +- 6 files changed, 446 insertions(+), 1 deletion(-) create mode 100644 src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java create mode 100644 src/main/webapp/setup/config.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java new file mode 100644 index 0000000..44a1e29 --- /dev/null +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -0,0 +1,160 @@ +/* + * To change this template, choose Tools | Templates + * and open the template in the editor. + */ +package pt.ua.bioinformatics.coeus.actions; + +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.FileWriter; +import java.io.IOException; +import java.io.OutputStream; +import java.io.PrintStream; +import java.io.StringWriter; +import java.io.Writer; +import java.util.logging.Level; +import java.util.logging.Logger; +import net.sourceforge.stripes.action.ActionBean; +import net.sourceforge.stripes.action.ActionBeanContext; +import net.sourceforge.stripes.action.DefaultHandler; +import net.sourceforge.stripes.action.ForwardResolution; +import net.sourceforge.stripes.action.Resolution; +import net.sourceforge.stripes.action.StreamingResolution; +import net.sourceforge.stripes.action.UrlBinding; +import org.json.simple.JSONObject; +import pt.ua.bioinformatics.coeus.common.Boot; +import pt.ua.bioinformatics.coeus.common.Config; + +/** + * + * @author sernadela + */ +@UrlBinding("/config/{$model}/{method}") +public class ConfigActionBean implements ActionBean { + + private static final String INDEX_VIEW = "/setup/index.jsp"; + private static final String SEEDS_VIEW = "/setup/seeds.jsp"; + private static final String SEEDS_ADD_VIEW = "/setup/addseed.jsp"; + private static final String ENTITY_ADD_VIEW = "/setup/addentity.jsp"; + private static final String ENTITIES_VIEW = "/setup/entities.jsp"; + private static final String CONCEPT_ADD_VIEW = "/setup/addconcept.jsp"; + private static final String CONCEPTS_VIEW = "/setup/concepts.jsp"; + private static final String RESOURCE_ADD_VIEW = "/setup/addresource.jsp"; + private static final String RESOURCES_VIEW = "/setup/resources.jsp"; + private static final String NOTFOUND_VIEW = "/setup/404.jsp"; + private static final String GRAPH_VIEW = "/setup/graph.jsp"; + private String method; + private String model; + private ActionBeanContext context; + + @DefaultHandler + public Resolution handle() { + return new ForwardResolution(NOTFOUND_VIEW); + + } + + public Resolution getconfig() { + Boot.start(); + return new StreamingResolution("application/json", Config.getFile().toJSONString()); + } + + public Resolution putconfig() { + + JSONObject result = updateConfigFile(method); + Config.setLoaded(false); + Config.load(); + return new StreamingResolution("text/javascript", result.toString()); + } + + public Resolution export() throws FileNotFoundException { + StringWriter outs = new StringWriter(); + Boot.start(); + if (method.equals("setup.ttl")) { + Boot.getAPI().getModel().write(outs, "TURTLE"); + } else { + Boot.getAPI().getModel().write(outs, "RDF/XML"); + } + return new StreamingResolution("application/rdf+xml", outs.toString()); + } + + public Resolution seed() { + if (method == null) { + return new ForwardResolution(SEEDS_VIEW); + } else if (method.equals("add") | method.startsWith("edit")) { + return new ForwardResolution(SEEDS_ADD_VIEW); + } else { + return new ForwardResolution(INDEX_VIEW); + } + } + + public Resolution entity() { + if (method.startsWith("add") | method.startsWith("edit")) { + return new ForwardResolution(ENTITY_ADD_VIEW); + } else { + return new ForwardResolution(ENTITIES_VIEW); + } + } + + public Resolution concept() { + if (method.startsWith("add") | method.startsWith("edit")) { + return new ForwardResolution(CONCEPT_ADD_VIEW); + } else { + return new ForwardResolution(CONCEPTS_VIEW); + } + } + + public Resolution resource() { + if (method.startsWith("add") | method.startsWith("edit")) { + return new ForwardResolution(RESOURCE_ADD_VIEW); + } else { + return new ForwardResolution(RESOURCES_VIEW); + } + } + + public String getModel() { + return model; + } + + public void setModel(String model) { + this.model = model; + } + + public String getMethod() { + return method; + } + + public void setMethod(String method) { + this.method = method; + } + + @Override + public void setContext(ActionBeanContext actionBeanContext) { + this.context = actionBeanContext; + } + + @Override + public ActionBeanContext getContext() { + return context; + } + + private JSONObject updateConfigFile(String value) { + JSONObject result = new JSONObject(); + + //System.out.println(value); + + try { + FileWriter writer = new FileWriter(Config.getPath() + "config.js"); + writer.write(value); + writer.flush(); + writer.close(); + result.put("status", 100); + result.put("message", "[COEUS][API][Config] config.js updated."); + } catch (IOException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][Config] ERROR: config.js not updated, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + + return result; + } +} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java index 4c89cab..a7358d4 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java @@ -19,6 +19,7 @@ import net.sourceforge.stripes.action.StreamingResolution; import net.sourceforge.stripes.action.UrlBinding; import pt.ua.bioinformatics.coeus.common.Boot; +import pt.ua.bioinformatics.coeus.common.Config; /** * @@ -47,6 +48,15 @@ public Resolution handle() { return new ForwardResolution(NOTFOUND_VIEW); } + public Resolution config() { + return new ForwardResolution("/setup/config.jsp"); + + } + + public Resolution getconfig() { + Boot.start(); + return new StreamingResolution("application/json", Config.getFile().toJSONString()); + } public Resolution graph() { return new ForwardResolution(GRAPH_VIEW); diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml index 1008314..440ea95 100755 --- a/src/main/webapp/WEB-INF/web.xml +++ b/src/main/webapp/WEB-INF/web.xml @@ -131,6 +131,7 @@ Secured Setup + /config/* /setup/* /manager/* GET diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 25ab10a..f069ba8 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -423,5 +423,6 @@ function queryToResult(selectQuery, callback) { function encodeBars(value) { value=value.split(';').join('%3B'); value=value.split('/').join('%2F'); + value=value.split('#').join('%23'); return value; } \ No newline at end of file diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp new file mode 100644 index 0000000..8ac4037 --- /dev/null +++ b/src/main/webapp/setup/config.jsp @@ -0,0 +1,273 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + +

        +
        + +
        +

        Configuration Page

        +
        +
        +
        +
        +
        + +
        +
        +
        +
        + + +
        + +
        + +

        Name of the Model

        +
        +
        + + +
        + +
        + +

        Model Description

        +
        + +
        + + +
        + +
        + +

        The ontology prefix

        +
        +
        + + +
        + +
        + +

        REST Api Key

        +
        +
        + + +
        + +
        + +

        Ontology Version

        +
        +
        + + +
        + +
        + +
        +
        + + +
        + +
        + + +

        Import from the Model

        +
        +
        + + +
        + +
        + +

        Debug Log

        +
        +
        + + +
        + +
        + +

        Ontology Location

        +
        +
        + + +
        + +
        + +

        RDF File Location to Import to the DB

        +
        +
        + + + +
        +
        + +
        +
        + + + + + + + + + + + + +
        + # + + Prefix + + URL + + Actions +
        +
        + +
        + +
        +
        +

        Predicates..

        +
        +
        +
        +
        +
        +
        + +
        +
        + +
        + + + + diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 577e9f6..904da0e 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -40,7 +40,7 @@
      • -
    • ">Management
      • +
    • ">Management
    • ">Documentation
      • From 8794b461318f41dcffa9c2b191c644d5174b8b2d Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 30 Jul 2013 12:53:32 +0100 Subject: [PATCH 20/52] - Setup: Interface for prefixes in config.js. --- src/main/webapp/assets/js/coeus.api.js | 71 +++++++++------ src/main/webapp/setup/config.jsp | 114 +++++++++++++++++++------ 2 files changed, 131 insertions(+), 54 deletions(-) diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index f069ba8..79d2999 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -217,41 +217,41 @@ function removeAllTriplesFromObject(urlPrefix, object) { } -function cleanUnlikedTriples(urlPrefix){ +function cleanUnlikedTriples(urlPrefix) { //Clean unlinked entities - var qEntities="SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; - queryToResult(qEntities,function (result){ - for(var r in result){ - var entity=splitURIPrefix(result[r].entity.value); - var prefix=getPrefix(entity.namespace)+":"; - removeAllTriplesFromSubject(urlPrefix, prefix+entity.value); + var qEntities = "SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; + queryToResult(qEntities, function(result) { + for (var r in result) { + var entity = splitURIPrefix(result[r].entity.value); + var prefix = getPrefix(entity.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + entity.value); } }); //Clean unlinked concepts - var qConcepts="SELECT * {{ ?concept a coeus:Concept . FILTER NOT EXISTS{ ?concept coeus:hasEntity ?entity }}UNION {?concept a coeus:Concept . FILTER NOT EXISTS { ?entity coeus:isEntityOf ?concept }} }"; - queryToResult(qConcepts,function (result){ - for(var r in result){ - var concept=splitURIPrefix(result[r].concept.value); - var prefix=getPrefix(concept.namespace)+":"; - removeAllTriplesFromSubject(urlPrefix, prefix+concept.value); + var qConcepts = "SELECT * {{ ?concept a coeus:Concept . FILTER NOT EXISTS{ ?concept coeus:hasEntity ?entity }}UNION {?concept a coeus:Concept . FILTER NOT EXISTS { ?entity coeus:isEntityOf ?concept }} }"; + queryToResult(qConcepts, function(result) { + for (var r in result) { + var concept = splitURIPrefix(result[r].concept.value); + var prefix = getPrefix(concept.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + concept.value); } }); //Clean unlinked resources - var qResources="SELECT * {{ ?resource a coeus:Resource . FILTER NOT EXISTS{ ?resource coeus:isResourceOf ?concept} }UNION {?resource a coeus:Resource . FILTER NOT EXISTS { ?concept coeus:hasResource ?resource}} }"; - queryToResult(qResources,function (result){ - for(var r in result){ - var resource=splitURIPrefix(result[r].resource.value); - var prefix=getPrefix(resource.namespace)+":"; - removeAllTriplesFromSubject(urlPrefix, prefix+resource.value); + var qResources = "SELECT * {{ ?resource a coeus:Resource . FILTER NOT EXISTS{ ?resource coeus:isResourceOf ?concept} }UNION {?resource a coeus:Resource . FILTER NOT EXISTS { ?concept coeus:hasResource ?resource}} }"; + queryToResult(qResources, function(result) { + for (var r in result) { + var resource = splitURIPrefix(result[r].resource.value); + var prefix = getPrefix(resource.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + resource.value); } }); //Clean unlinked selectores - var qSelectores="SELECT * {{ ?selector coeus:property ?property . FILTER NOT EXISTS { ?selector coeus:loadsFor ?resource } }UNION {?selector coeus:property ?property . FILTER NOT EXISTS { ?resource coeus:loadsFrom ?selector}}}"; - queryToResult(qSelectores,function (result){ - for(var r in result){ - var selector=splitURIPrefix(result[r].selector.value); - var prefix=getPrefix(selector.namespace)+":"; - removeAllTriplesFromSubject(urlPrefix, prefix+selector.value); + var qSelectores = "SELECT * {{ ?selector coeus:property ?property . FILTER NOT EXISTS { ?selector coeus:loadsFor ?resource } }UNION {?selector coeus:property ?property . FILTER NOT EXISTS { ?resource coeus:loadsFrom ?selector}}}"; + queryToResult(qSelectores, function(result) { + for (var r in result) { + var selector = splitURIPrefix(result[r].selector.value); + var prefix = getPrefix(selector.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + selector.value); } }); } @@ -421,8 +421,23 @@ function queryToResult(selectQuery, callback) { } function encodeBars(value) { - value=value.split(';').join('%3B'); - value=value.split('/').join('%2F'); - value=value.split('#').join('%23'); + value = value.split(';').join('%3B'); + value = value.split('/').join('%2F'); + value = value.split('#').join('%23'); return value; +} +function removeById(childDiv, parentDiv) +{ + console.log(childDiv+' '+ parentDiv); + if (childDiv == parentDiv) { + alert("The parent div cannot be removed."); + } + else if (document.getElementById(childDiv)) { + var child = document.getElementById(childDiv); + var parent = document.getElementById(parentDiv); + parent.removeChild(child); + } + else { + alert("Child div has already been removed or does not exist."); + } } \ No newline at end of file diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 8ac4037..034f968 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -27,7 +27,9 @@ } function fillConfig(result) { - //fill the fields + console.log(result); + + //fill the config fields $('#Name').val(result.config.name); $('#Description').val(result.config.description); $('#KeyPrefix').val(result.config.keyprefix); @@ -37,15 +39,6 @@ $('#ApiKey').val(result.config.apikey); $('#Ontology').val(result.config.ontology); $('#Setup').val(result.config.setup); - var json = JSON.parse(JSON.stringify(result.prefixes)); - console.log(json.length); - var i = 0; - for (var r in json) { - var val = json[r]; - i++; - $('#tablePrefixes').append('' + i + '' + r + '' + val + ''); - } - if (result.config.built.toString() === "true") $('#Built').prop('checked', true); @@ -56,14 +49,40 @@ $('#Debug').prop('checked', true); else $('#Debug').prop('checked', false); + + + //fill the prefixes table + var json = (result.prefixes); + var i = 0; + for (var r in json) { + var val = json[r];console.log(r); + i++; + $('#tablePrefixes').append('' + i + '' + r + '' + val + ''); + } + + //progress bar exit document.getElementById('bar').style.width = "100%"; $('#progress').addClass('hide'); document.getElementById('bar').class = "hide"; - console.log(result); + } function save() { var url = "../../config/"; + //Get all prefixes from table + var tableArray = []; + $("#tablePrefixes tr").each(function() { + var arrayOfThisRow = []; + var tableData = $(this).find('td'); + if (tableData.length > 0) { + tableData.each(function() { + arrayOfThisRow.push($(this).text()); + }); + tableArray.push(arrayOfThisRow); + } + }); + + // fill the config field var json = { "config": {"name": $('#Name').val(), @@ -78,20 +97,19 @@ "debug": $('#Debug').is(':checked'), "apikey": $('#ApiKey').val(), "environment": $('#Environment').val() - }, - "prefixes": { - "coeus": "http://bioinformatics.ua.pt/coeus/resource/", - "owl2xml": "http://www.w3.org/2006/12/owl2-xml#", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "owl": "http://www.w3.org/2002/07/owl#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "dc": "http://purl.org/dc/elements/1.1/", - } + } }; + //fill the prefixes field + var jsonObj = JSON.parse(JSON.stringify(json)); + jsonObj.prefixes = {}; - var send = url + "putconfig/" + encodeBars(JSON.stringify(json)); + for (var i in tableArray) { + jsonObj.prefixes[tableArray[i][1]] = tableArray[i][2]; + } + + //send to server + var send = url + "putconfig/" + encodeBars(JSON.stringify(jsonObj)); console.log(send); callAPI(send, "#result"); @@ -100,6 +118,18 @@ } } + function addPrefix() { + $('#res').html(''); + var num = $("#tablePrefixes tr").length+1; + var key = $('#keyPrefixes').val(); + var value = $('#valuePrefixes').val(); + if ($("#prefix_" + key).html() === undefined) { + $('#tablePrefixes').append('' + num + '' + key + '' + value + ''); + } else { + $('#res').append('

      This Key already exists.

      '); + } + } + @@ -120,7 +150,7 @@
    • Predicates
    -
    +
    @@ -165,7 +195,7 @@
    - +

    Ontology Version

    @@ -227,7 +257,7 @@
    -
    +
    @@ -250,7 +280,7 @@
    - +
    @@ -269,5 +299,37 @@
    + + + + + + From 18fad60bca0bf004bbdba32e91caea7f97605f6c Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 1 Aug 2013 16:26:45 +0100 Subject: [PATCH 21/52] - Setup: Wizard for config.js and predicates.csv complete - Fix setup.rdf on news aggregator. --- .../coeus/actions/ConfigActionBean.java | 166 ++++--- src/main/resources/config.js | 8 +- src/main/resources/newsaggregator/setup.rdf | 429 +++++++----------- src/main/resources/predicates.csv | 80 ++++ src/main/webapp/assets/js/coeus.api.js | 7 +- src/main/webapp/setup/config.jsp | 77 +++- src/main/webapp/setup/html.jsp | 8 +- 7 files changed, 429 insertions(+), 346 deletions(-) create mode 100644 src/main/resources/predicates.csv diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index 44a1e29..dfc15b0 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -4,14 +4,24 @@ */ package pt.ua.bioinformatics.coeus.actions; +import com.hp.hpl.jena.ontology.OntModel; +import com.hp.hpl.jena.ontology.OntProperty; +import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.util.iterator.ExtendedIterator; +import java.io.BufferedReader; import java.io.FileNotFoundException; -import java.io.FileOutputStream; import java.io.FileWriter; import java.io.IOException; -import java.io.OutputStream; -import java.io.PrintStream; +import java.io.InputStreamReader; import java.io.StringWriter; -import java.io.Writer; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeSet; import java.util.logging.Level; import java.util.logging.Logger; import net.sourceforge.stripes.action.ActionBean; @@ -32,17 +42,7 @@ @UrlBinding("/config/{$model}/{method}") public class ConfigActionBean implements ActionBean { - private static final String INDEX_VIEW = "/setup/index.jsp"; - private static final String SEEDS_VIEW = "/setup/seeds.jsp"; - private static final String SEEDS_ADD_VIEW = "/setup/addseed.jsp"; - private static final String ENTITY_ADD_VIEW = "/setup/addentity.jsp"; - private static final String ENTITIES_VIEW = "/setup/entities.jsp"; - private static final String CONCEPT_ADD_VIEW = "/setup/addconcept.jsp"; - private static final String CONCEPTS_VIEW = "/setup/concepts.jsp"; - private static final String RESOURCE_ADD_VIEW = "/setup/addresource.jsp"; - private static final String RESOURCES_VIEW = "/setup/resources.jsp"; private static final String NOTFOUND_VIEW = "/setup/404.jsp"; - private static final String GRAPH_VIEW = "/setup/graph.jsp"; private String method; private String model; private ActionBeanContext context; @@ -50,7 +50,6 @@ public class ConfigActionBean implements ActionBean { @DefaultHandler public Resolution handle() { return new ForwardResolution(NOTFOUND_VIEW); - } public Resolution getconfig() { @@ -58,11 +57,82 @@ public Resolution getconfig() { return new StreamingResolution("application/json", Config.getFile().toJSONString()); } + public Resolution readrdf() throws MalformedURLException, IOException { + String location = "http://localhost:8080/coeus/resource/"; + //String location ="http://purl.org/dc/elements/1.1/"; + URL url = new URL(location); + HttpURLConnection conn = (HttpURLConnection) url.openConnection(); + //set linked data content to rdf + conn.setRequestProperty("Accept", " application/rdf+xml"); + //conn.setRequestProperty("User-Agent", ""); + conn.setInstanceFollowRedirects(true);HttpURLConnection.setFollowRedirects(true); + //conn.setRequestProperty("Content-Type", "application/rdf+xml"); + //HttpURLConnection conn=conn.getInputStream(); + + + StringBuilder sb = new StringBuilder(); + String line; + BufferedReader br = new BufferedReader(new InputStreamReader(conn.getInputStream())); + while ((line = br.readLine()) != null) { + sb.append(line); + } + br.close(); + + Map> map = conn.getHeaderFields(); + for (Map.Entry> entry : map.entrySet()) { + System.out.println(entry.getKey() + " : " + entry.getValue()); + } + + System.out.println(context.getRequest().getServletPath()); + System.out.println(context.getRequest().getServerName()); + return new StreamingResolution("text/javascript", sb.toString()); + } + + public Resolution getprop() { + + Config.load(); + Set set = new TreeSet(); + StringBuilder sb = new StringBuilder(); + //get all proprieties for each prefix + JSONObject prefixes = (JSONObject) Config.getFile().get("prefixes"); + for (Object o : prefixes.values()) { + System.err.println("Reading: " + o); + set.addAll(getOntologyProperties(o.toString())); + } + + for (String s : set) { + sb.append(s); + } + + return new StreamingResolution("text/javascript", sb.toString()); + } + public Resolution putconfig() { - JSONObject result = updateConfigFile(method); + //update config.js + String jsonString = method; + JSONObject result = updateFile(jsonString, "config.js"); Config.setLoaded(false); Config.load(); + + //update predicates.csv + Set set = new TreeSet(); + JSONObject prefixes = (JSONObject) Config.getFile().get("prefixes"); + for (Object o : prefixes.values()) { + System.err.println("[COEUS][API][ConfigActionBean] Reading: " + o); + set.addAll(getOntologyProperties(o.toString())); + } + //read local ontology TODO: FIX THAT + String localOntology=context.getRequest().getScheme()+"://"+context.getRequest().getServerName()+":"+context.getRequest().getServerPort()+context.getRequest().getContextPath()+"/ontology/"; + set.addAll(getOntologyProperties(localOntology)); + + StringBuilder sb = new StringBuilder(); + for (String s : set) { + sb.append(s); + } + + updateFile(sb.toString(), "predicates.csv"); + return new StreamingResolution("text/javascript", result.toString()); } @@ -77,40 +147,6 @@ public Resolution export() throws FileNotFoundException { return new StreamingResolution("application/rdf+xml", outs.toString()); } - public Resolution seed() { - if (method == null) { - return new ForwardResolution(SEEDS_VIEW); - } else if (method.equals("add") | method.startsWith("edit")) { - return new ForwardResolution(SEEDS_ADD_VIEW); - } else { - return new ForwardResolution(INDEX_VIEW); - } - } - - public Resolution entity() { - if (method.startsWith("add") | method.startsWith("edit")) { - return new ForwardResolution(ENTITY_ADD_VIEW); - } else { - return new ForwardResolution(ENTITIES_VIEW); - } - } - - public Resolution concept() { - if (method.startsWith("add") | method.startsWith("edit")) { - return new ForwardResolution(CONCEPT_ADD_VIEW); - } else { - return new ForwardResolution(CONCEPTS_VIEW); - } - } - - public Resolution resource() { - if (method.startsWith("add") | method.startsWith("edit")) { - return new ForwardResolution(RESOURCE_ADD_VIEW); - } else { - return new ForwardResolution(RESOURCES_VIEW); - } - } - public String getModel() { return model; } @@ -137,24 +173,44 @@ public ActionBeanContext getContext() { return context; } - private JSONObject updateConfigFile(String value) { + private JSONObject updateFile(String value, String filename) { JSONObject result = new JSONObject(); - //System.out.println(value); + System.out.println("[COEUS][API][ConfigActionBean] Saving.. " + filename); try { - FileWriter writer = new FileWriter(Config.getPath() + "config.js"); + FileWriter writer = new FileWriter(Config.getPath() + filename); writer.write(value); writer.flush(); writer.close(); result.put("status", 100); - result.put("message", "[COEUS][API][Config] config.js updated."); + result.put("message", "[COEUS][API][ConfigActionBean] " + filename + " updated."); } catch (IOException ex) { result.put("status", 200); - result.put("message", "[COEUS][API][Config] ERROR: config.js not updated, check exception."); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + filename + " not updated, check exception."); Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); } return result; } + + public Set getOntologyProperties(String location) { + Set set = new HashSet(); + try { + //auxiliar model + OntModel auxModel = ModelFactory.createOntologyModel(); + auxModel.read(location); + ExtendedIterator op = auxModel.listOntProperties(); + + while (op.hasNext()) { + OntProperty prop = op.next(); + //if (prop.toString().startsWith(location)) { + set.add(prop.toString() + "\n"); + //} + } + } catch (Exception e) { + System.err.println("[COEUS][API][ConfigActionBean] ERROR in read model at: " + location); + } + return set; + } } diff --git a/src/main/resources/config.js b/src/main/resources/config.js index 3a4c0b0..37cd45f 100644 --- a/src/main/resources/config.js +++ b/src/main/resources/config.js @@ -1,19 +1,19 @@ { "config": { -"name": "Model Test", + "name": "Model Test", "description": "COEUS Model Test", "keyprefix":"coeus", "version": "1.0a", "ontology": "http://bioinformatics.ua.pt/coeus/ontology/", - "setup": "", + "setup": "newsaggregator/setup.rdf", "sdb":"newsaggregator/sdb.ttl", - "predicates":"newsaggregator/predicates.csv", + "predicates":"predicates.csv", "built": false, "debug": true, "apikey":"coeus|uavr", "environment": "production" }, - "prefixes" : { +"prefixes" : { "coeus": "http://bioinformatics.ua.pt/coeus/resource/", "owl2xml":"http://www.w3.org/2006/12/owl2-xml#", "xsd": "http://www.w3.org/2001/XMLSchema#", diff --git a/src/main/resources/newsaggregator/setup.rdf b/src/main/resources/newsaggregator/setup.rdf index 2a085c2..a518ecb 100644 --- a/src/main/resources/newsaggregator/setup.rdf +++ b/src/main/resources/newsaggregator/setup.rdf @@ -971,333 +971,234 @@ - - - - - - concept_abola - A Bola - - - + + + News Aggregator + + News Aggregator - - - - - + + + News + Entity News + + + + + + News + + + + - concept_bbc - BBC + Reuters + - - + Reuters - - - - concept_marca - Marca - + + Marca + + Marca - - - - - + + - concept_reuters - Reuters + Abola + - - + Abola - - - - - - - entity_news - News - News entity for coeus.NA - + + + + BBC + + + BBC - - - - - + + + + + + + + - resource_abola - //item - 1 - BBC - Resource loader for A Bola XML feeds. - cache - http://www.abola.pt/rss/index.aspx - xml - - - - - - - - + Abola + Resource loader for A Bola XML feeds. + + 1 + cache + http://www.abola.pt/rss/index.aspx + + //item + xml + Abola - - - - - + + + + + + + - resource_bbc - //item - 1 - BBC - Resource loader for BBC XML feeds. - cache - http://feeds.bbci.co.uk/sport/0/rss.xml - xml - - - - - - - - + Reuters + Resource loader for Reuters XML feeds. + + 4 + cache + http://feeds.reuters.com/reuters/sportsNews + + //item + xml + Reuters - - - - + + + + + + - resource_marca - //item - 1 - Marca - Resource loader for Marca XML feeds. - cache - http://estaticos.marca.com/rss/portada.xml - xml - + Marca + Resource loader for Marca XML feeds. - - - - - - + 2 + cache + http://estaticos.marca.com/rss/portada.xml + + //item + xml + Marca - - - - - + + + + + + + - resource_reuters - //item - 1 - Resource loader for Reuters XML feeds. - Reuters - cache - http://feeds.reuters.com/reuters/sportsNews - xml - - - - - - - - - - - - - - - - - seed_coeusna - coeus.NA - + BBC + Resource loader for BBC XML feeds. + + 3 + cache + http://feeds.bbci.co.uk/sport/0/rss.xml + + //item + xml + BBC - - - - - + - xml_abola_id - A Bola identifier - [0-9]{5,} - dc:identifier - guid - - + xml_link + + + + + dc:publisher + link + xml_link - - - - - + - xml_abola_title - A Bola entry title - dc:title - title - + xml_Reuters_id + + dc:identifier + guid + + xml_Reuters_id + [0-9]{5,} - - - - - + - xml_bbc_id - BBC identifier - [0-9]{5,} - dc:identifier - guid + xml_BBC_id + dc:identifier + guid + xml_BBC_id + [0-9]{5,} - - - - - + - xml_bbc_title - BBC entry title - dc:title - title + xml_description + + + + dc:description + description + xml_description - - - - - + - xml_marca_id - Marca identifier - [0-9]{5,} - dc:identifier - guid - + xml_date + + + + dc:date + pubDate + xml_date - - - - - + - xml_marca_title - Marca entry title - dc:title - title + xml_Marca_id + dc:identifier + guid + + xml_Marca_id + [0-9]{5,} - - - - - + - xml_reuters_id - Reuters identifier - [0-9]{5,} - dc:identifier - guid + xml_title - - - - - - - - - - xml_reuters__title - Reuters entry title - dc:title - title - - - - - - - - - xml_date - dc:date - pubDate - entry date - - - + + dc:title + title + xml_title - - - - - + - xml_description - dc:description - description - entry description - - - - + xml_Abola_id + + dc:identifier + guid + + xml_Abola_id + [0-9]{5,} - - - - - - - xml_link - dc:publisher - link - entry link - - - - - diff --git a/src/main/resources/predicates.csv b/src/main/resources/predicates.csv new file mode 100644 index 0000000..8c31162 --- /dev/null +++ b/src/main/resources/predicates.csv @@ -0,0 +1,80 @@ +http://purl.org/dc/elements/1.1/description +http://www.w3.org/2000/01/rdf-schema#comment +http://www.w3.org/2000/01/rdf-schema#label +http://bioinformatics.ua.pt/coeus/resource/isConceptOf +http://bioinformatics.ua.pt/coeus/resource/isAssociatedTo +http://purl.org/dc/elements/1.1/title +http://purl.org/dc/elements/1.1/identifier +http://purl.org/dc/elements/1.1/source +http://bioinformatics.ua.pt/coeus/resource/isEntityOf +http://bioinformatics.ua.pt/coeus/resource/extension +http://purl.org/dc/elements/1.1/subject +http://purl.org/dc/elements/1.1/date +http://www.w3.org/2000/01/rdf-schema#range +http://www.w3.org/1999/02/22-rdf-syntax-ns#type +http://bioinformatics.ua.pt/coeus/resource/hasConcept +http://bioinformatics.ua.pt/coeus/resource/isResourceOf +http://bioinformatics.ua.pt/coeus/resource/extends +http://www.w3.org/2002/07/owl#inverseOf +http://bioinformatics.ua.pt/coeus/resource/loadsFrom +http://bioinformatics.ua.pt/coeus/resource/hasKey +http://www.w3.org/2000/01/rdf-schema#domain +http://www.w3.org/2000/01/rdf-schema#subClassOf +http://www.w3.org/2002/07/owl#versionInfo +http://bioinformatics.ua.pt/coeus/resource/endpoint +http://purl.org/dc/elements/1.1/language +http://bioinformatics.ua.pt/coeus/resource/query +http://bioinformatics.ua.pt/coeus/resource/order +http://bioinformatics.ua.pt/coeus/resource/method +http://bioinformatics.ua.pt/coeus/resource/isKeyOf +http://bioinformatics.ua.pt/coeus/resource/loadsFor +http://bioinformatics.ua.pt/coeus/resource/hasResource +http://www.w3.org/2002/07/owl#imports +http://purl.org/dc/elements/1.1/creator +http://bioinformatics.ua.pt/coeus/resource/built +http://bioinformatics.ua.pt/coeus/resource/property +http://bioinformatics.ua.pt/coeus/resource/hasEntity +http://bioinformatics.ua.pt/coeus/resource/includes +http://purl.org/dc/elements/1.1/publisher +http://bioinformatics.ua.pt/coeus/resource/isIncludedIn +http://purl.org/dc/elements/1.1/rights +http://bioinformatics.ua.pt/coeus/resource/property +http://bioinformatics.ua.pt/coeus/resource/isConceptOf +http://bioinformatics.ua.pt/coeus/resource/includes +http://bioinformatics.ua.pt/coeus/resource/isModuleOf +http://bioinformatics.ua.pt/coeus/resource/host +http://bioinformatics.ua.pt/coeus/resource/mapsTo +http://bioinformatics.ua.pt/coeus/resource/mappedFrom +http://bioinformatics.ua.pt/coeus/resource/isIncludedIn +http://bioinformatics.ua.pt/coeus/resource/built +http://bioinformatics.ua.pt/coeus/resource/isExtendedBy +http://bioinformatics.ua.pt/coeus/resource/isKeyOf +http://bioinformatics.ua.pt/coeus/resource/select +http://bioinformatics.ua.pt/coeus/resource/query +http://bioinformatics.ua.pt/coeus/resource/hasKey +http://bioinformatics.ua.pt/coeus/resource/line +http://bioinformatics.ua.pt/coeus/resource/extension +http://bioinformatics.ua.pt/coeus/resource/delimiter +http://bioinformatics.ua.pt/coeus/resource/replace +http://bioinformatics.ua.pt/coeus/resource/database +http://bioinformatics.ua.pt/coeus/resource/method +http://bioinformatics.ua.pt/coeus/resource/isResourceOf +http://bioinformatics.ua.pt/coeus/resource/isEntityOf +http://bioinformatics.ua.pt/coeus/resource/endpoint +http://bioinformatics.ua.pt/coeus/resource/hasModule +http://bioinformatics.ua.pt/coeus/resource/public +http://bioinformatics.ua.pt/coeus/resource/hasEntity +http://bioinformatics.ua.pt/coeus/resource/order +http://bioinformatics.ua.pt/coeus/resource/isAssociatedTo +http://bioinformatics.ua.pt/coeus/resource/isBridgedTo +http://bioinformatics.ua.pt/coeus/resource/plugin +http://bioinformatics.ua.pt/coeus/resource/loadsFor +http://bioinformatics.ua.pt/coeus/resource/hasResource +http://bioinformatics.ua.pt/coeus/resource/extends +http://bioinformatics.ua.pt/coeus/resource/enabled +http://bioinformatics.ua.pt/coeus/resource/isConnectedTo +http://bioinformatics.ua.pt/coeus/resource/loadsFrom +http://bioinformatics.ua.pt/coeus/resource/hasBridge +http://bioinformatics.ua.pt/coeus/resource/hasConcept +http://www.w3.org/2000/01/rdf-schema#seeAlso +http://bioinformatics.ua.pt/coeus/resource/regex \ No newline at end of file diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 79d2999..d73c954 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -429,7 +429,7 @@ function encodeBars(value) { function removeById(childDiv, parentDiv) { console.log(childDiv+' '+ parentDiv); - if (childDiv == parentDiv) { + if (childDiv === parentDiv) { alert("The parent div cannot be removed."); } else if (document.getElementById(childDiv)) { @@ -440,4 +440,9 @@ function removeById(childDiv, parentDiv) else { alert("Child div has already been removed or does not exist."); } +} + +function callURL(url, success, error) { + url = encodeURI(url); + $.ajax({url: url, dataType: 'json'}).done(success).fail(error); } \ No newline at end of file diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 034f968..d71f051 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -55,7 +55,7 @@ var json = (result.prefixes); var i = 0; for (var r in json) { - var val = json[r];console.log(r); + var val = json[r]; i++; $('#tablePrefixes').append('' + i + '' + r + '' + val + ''); } @@ -92,7 +92,7 @@ "ontology": $('#Ontology').val(), "setup": $('#Setup').val(), "sdb": "newsaggregator/sdb.ttl", - "predicates": "newsaggregator/predicates.csv", + "predicates": "predicates.csv", "built": $('#Built').is(':checked'), "debug": $('#Debug').is(':checked'), "apikey": $('#ApiKey').val(), @@ -111,16 +111,32 @@ //send to server var send = url + "putconfig/" + encodeBars(JSON.stringify(jsonObj)); console.log(send); - callAPI(send, "#result"); + //callAPI(send, "#result"); - if (document.getElementById('result').className === 'alert alert-success') { - window.location.reload(); - } + //progress bar init + document.getElementById('bar').style.width = "10%"; + $('#progress').removeClass('hide'); + $('#btnSave').html("Saving..."); + $('#btnSave').addClass('disabled'); + + callURL(send, saveSuccess, saveError); } + function saveSuccess(data) { + console.log(data); + $('#btnSave').removeClass('disabled'); + $('#btnSave').html("Save it!"); + //progress bar exit + document.getElementById('bar').style.width = "100%"; + $('#progress').addClass('hide'); + document.getElementById('bar').class = "hide"; + } + function saveError(jqXHR, textStatus) { + console.log(textStatus); + } function addPrefix() { $('#res').html(''); - var num = $("#tablePrefixes tr").length+1; + var num = $("#tablePrefixes tr").length + 1; var key = $('#keyPrefixes').val(); var value = $('#valuePrefixes').val(); if ($("#prefix_" + key).html() === undefined) { @@ -129,6 +145,10 @@ $('#res').append('

    This Key already exists.

    '); } } + function changeTab(old_tab, new_tab) { + $(old_tab).removeClass('active'); + $(new_tab).addClass('active'); + } @@ -138,19 +158,28 @@
    -

    Configuration Page

    +

    COEUS Setup

    -
    +
    +
    +

    In this section you will give some information to complete some setup files for COEUS.

    +

    To begin press the Start Wizard button.

    + Start Wizard +
    + +
    +
    @@ -250,7 +279,9 @@

    RDF File Location to Import to the DB

    - +
    + Next > +
    @@ -282,15 +313,25 @@
    +
    + Next > +
    +
    -

    Predicates..

    -
    -
    -
    -
    +
    +

    In order to save your progress press the Save button, please.

    +

    Warning: If you leaves this wizard without save it, all of configurations will be lost.

    + +
    +
    +

    After saving the configurations you can start build the model for your application:

    + Build Model + +
    +
    diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 904da0e..f9e5445 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -28,9 +28,9 @@
  • ">Home
  • ">Seeds
    • - + +
  • ">Setup
  • ">Documentation
    • From a7a9f277917935b5b42e9601256c4b41f45060a3 Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 6 Aug 2013 16:08:47 +0100 Subject: [PATCH 22/52] - Setup: Included Setup Wizard. --- .../coeus/actions/ConfigActionBean.java | 455 ++++++++++++++++-- .../bioinformatics/coeus/common/Config.java | 20 +- src/main/resources/config.js | 6 +- src/main/resources/init/joseki.ttl | 97 ++++ src/main/resources/init/map.js | 15 + src/main/resources/init/pubby.ttl | 91 ++++ src/main/resources/init/sdb.ttl | 19 + src/main/resources/sdb.ttl | 19 + src/main/webapp/WEB-INF/web.xml | 2 +- src/main/webapp/assets/js/coeus.api.js | 18 +- src/main/webapp/setup/config.jsp | 298 ++++++++++-- 11 files changed, 961 insertions(+), 79 deletions(-) create mode 100644 src/main/resources/init/joseki.ttl create mode 100644 src/main/resources/init/map.js create mode 100644 src/main/resources/init/pubby.ttl create mode 100644 src/main/resources/init/sdb.ttl create mode 100644 src/main/resources/sdb.ttl diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index dfc15b0..cf67152 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -9,17 +9,29 @@ import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.util.iterator.ExtendedIterator; import java.io.BufferedReader; +import java.io.File; +import java.io.FileInputStream; import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.FileReader; import java.io.FileWriter; +import java.io.FilenameFilter; import java.io.IOException; +import java.io.InputStream; import java.io.InputStreamReader; +import java.io.OutputStream; import java.io.StringWriter; import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; import java.util.HashSet; +import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.Set; import java.util.TreeSet; import java.util.logging.Level; @@ -32,6 +44,8 @@ import net.sourceforge.stripes.action.StreamingResolution; import net.sourceforge.stripes.action.UrlBinding; import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; import pt.ua.bioinformatics.coeus.common.Boot; import pt.ua.bioinformatics.coeus.common.Config; @@ -47,16 +61,264 @@ public class ConfigActionBean implements ActionBean { private String model; private ActionBeanContext context; + public String getModel() { + return model; + } + + public void setModel(String model) { + this.model = model; + } + + public String getMethod() { + return method; + } + + public void setMethod(String method) { + this.method = method; + } + + @Override + public void setContext(ActionBeanContext actionBeanContext) { + this.context = actionBeanContext; + } + + @Override + public ActionBeanContext getContext() { + return context; + } + @DefaultHandler public Resolution handle() { return new ForwardResolution(NOTFOUND_VIEW); } + /** + * return the config.js file + * + * @return + */ public Resolution getconfig() { Boot.start(); return new StreamingResolution("application/json", Config.getFile().toJSONString()); } + /** + * List all environments (i.e., all folders started by 'env_' string) + * + * @return + */ + public Resolution listenv() { + JSONObject result = new JSONObject(); + File src = new File(ConfigActionBean.class.getResource("/").getPath()); + String env[] = src.list(new FilenameFilter() { + @Override + public boolean accept(File dir, String name) { + if (dir.isDirectory() && name.startsWith("env_")) { + return true; + } else { + return false; + } + } + }); + Map> m = new HashMap>(); + List l = new ArrayList(); + l.addAll(Arrays.asList(env)); + m.put("environments", l); + result.putAll(m); + + return new StreamingResolution("application/json", result.toJSONString()); + } + + /** + * Do the mapping from map.js to the configuration files. + * + * @param path + * @throws ParseException + */ + public void updateFilesFromMap(String path) throws ParseException, IOException { + JSONParser parser = new JSONParser(); + JSONObject map = (JSONObject) parser.parse(readToString(path + "map.js")); + + //ensures that files are clean + copyFolder(new File(Config.getPath() + "init"), new File(path)); + + File src = new File(path); + //list all the directory contents + String files[] = src.list(); + for (String file : files) { + if (!file.endsWith("map.js")) { + String readString = readToString(path + file); + for (Iterator it = map.entrySet().iterator(); it.hasNext();) { + Map.Entry e = (Map.Entry) it.next(); + //System.out.println(e.getKey().toString() + " " + e.getValue().toString()); + readString = readString.replace(e.getKey().toString(), e.getValue().toString()); + } + System.out.println(file); + updateFile(readString, path + file); + } + } + } + + /** + * Update a Environment: + *

    Copy all values from map.js to do the mapping in the configuration + * files.

    + *

    Copy files to the root dir and change the environment key in + * config.js

    + * + * @return + */ + public Resolution upenv() { + JSONObject result = new JSONObject(); + try { + Config.load(); + String path = Config.getPath() + "env_" + method + "/"; + + updateFilesFromMap(path); + changeEnvironment(path, Config.getPath(), "env_" + method); + + //Load new settings + Config.setLoaded(false); + Config.load(); + + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] Environment updated: " + method); + + } catch (Exception ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: Evironment " + method + " not updated, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + + //Boot.start(); + return new StreamingResolution("application/json", result.toJSONString()); + } + + /** + * Change the environment: Copy files to the root dir and change the + * environment key in config.js + * + * @param src + * @param dest + * @param environment + * @throws IOException + */ + public void changeEnvironment(String src, String dest, String environment) throws IOException { + //copy all files from enviroment to root dir + copyFolder(new File(src), new File(dest)); + // update environment in config.js + JSONObject f = Config.getFile(); + JSONObject config = (JSONObject) f.get("config"); + + Map m = new HashMap(); + for (Iterator it = config.entrySet().iterator(); it.hasNext();) { + Entry e = (Entry) it.next(); + m.put(e.getKey(), e.getValue()); + } + m.put("environment", environment); + f.put("config", m); + + updateFile(f.toJSONString(), Config.getPath() + "config.js"); + } + + /** + * Create a new environment according to the init directory (i.e., copy all + * files to the new directory) + * + * @return + */ + public Resolution newenv() { + JSONObject result = new JSONObject(); + try { + String name = "env_" + method; + Config.load(); + String envStr = Config.getPath() + name; + String initStr = Config.getPath() + "init"; + File env = new File(envStr); + if (env.exists()) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + method + " already exists."); + return new StreamingResolution("application/json", result.toJSONString()); + } + File init = new File(initStr); + + copyFolder(init, env); + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] Environment created: " + method); + } catch (IOException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + method + " not created, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + + //Boot.start(); + return new StreamingResolution("application/json", result.toJSONString()); + } + + /** + * Receives a map.js file and update it in according to the environment key + * in config.js. + * + * @return + */ + public Resolution putmap() { + JSONObject result = new JSONObject(); + try { + Config.load(); + + JSONParser parser = new JSONParser(); + System.out.println(method); + JSONObject env = (JSONObject) parser.parse(method); + String environment = "env_" + env.get("$environment").toString(); + String path = Config.getPath() + environment + "/"; + String map = path + "map.js"; + //update map.js file + result = updateFile(method, map); + //update files on the environment + updateFilesFromMap(path); + //change it to use + changeEnvironment(path, Config.getPath(), environment); + //apply values + Config.setLoaded(false); + Config.load(); + + } catch (ParseException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: On parse map.js, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } catch (Exception ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: On update map.js, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + return new StreamingResolution("application/json", result.toJSONString()); + } + + /** + * Delete a environment. + * + * @return + */ + public Resolution delenv() { + JSONObject result = new JSONObject(); + try { + Config.load(); + String envStr = Config.getPath() + "env_" + method; + File env = new File(envStr); + if (env.exists()) { + delete(env); + } + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] Environment deleted: " + method); + } catch (IOException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + method + " not deleted, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + + return new StreamingResolution("application/json", result.toJSONString()); + } + public Resolution readrdf() throws MalformedURLException, IOException { String location = "http://localhost:8080/coeus/resource/"; //String location ="http://purl.org/dc/elements/1.1/"; @@ -65,7 +327,8 @@ public Resolution readrdf() throws MalformedURLException, IOException { //set linked data content to rdf conn.setRequestProperty("Accept", " application/rdf+xml"); //conn.setRequestProperty("User-Agent", ""); - conn.setInstanceFollowRedirects(true);HttpURLConnection.setFollowRedirects(true); + conn.setInstanceFollowRedirects(true); + HttpURLConnection.setFollowRedirects(true); //conn.setRequestProperty("Content-Type", "application/rdf+xml"); //HttpURLConnection conn=conn.getInputStream(); @@ -88,6 +351,11 @@ public Resolution readrdf() throws MalformedURLException, IOException { return new StreamingResolution("text/javascript", sb.toString()); } + /** + * List all Ontology Proprieties. + * + * @return + */ public Resolution getprop() { Config.load(); @@ -107,6 +375,12 @@ public Resolution getprop() { return new StreamingResolution("text/javascript", sb.toString()); } + /** + * Update the config.js file and Load all Object Proprieties to the + * predicates.csv file according to the prefixes section on config.js. + * + * @return + */ public Resolution putconfig() { //update config.js @@ -123,19 +397,25 @@ public Resolution putconfig() { set.addAll(getOntologyProperties(o.toString())); } //read local ontology TODO: FIX THAT - String localOntology=context.getRequest().getScheme()+"://"+context.getRequest().getServerName()+":"+context.getRequest().getServerPort()+context.getRequest().getContextPath()+"/ontology/"; + String localOntology = context.getRequest().getScheme() + "://" + context.getRequest().getServerName() + ":" + context.getRequest().getServerPort() + context.getRequest().getContextPath() + "/ontology/"; set.addAll(getOntologyProperties(localOntology)); - + StringBuilder sb = new StringBuilder(); for (String s : set) { sb.append(s); } - - updateFile(sb.toString(), "predicates.csv"); + + updateFile(sb.toString(), Config.getPath() + "predicates.csv"); return new StreamingResolution("text/javascript", result.toString()); } + /** + * Export model in rdf or ttl. + * + * @return + * @throws FileNotFoundException + */ public Resolution export() throws FileNotFoundException { StringWriter outs = new StringWriter(); Boot.start(); @@ -147,45 +427,26 @@ public Resolution export() throws FileNotFoundException { return new StreamingResolution("application/rdf+xml", outs.toString()); } - public String getModel() { - return model; - } - - public void setModel(String model) { - this.model = model; - } - - public String getMethod() { - return method; - } - - public void setMethod(String method) { - this.method = method; - } - - @Override - public void setContext(ActionBeanContext actionBeanContext) { - this.context = actionBeanContext; - } - - @Override - public ActionBeanContext getContext() { - return context; - } - + /** + * Update a existing file (writing the string value) + * + * @param value + * @param filename + * @return + */ private JSONObject updateFile(String value, String filename) { JSONObject result = new JSONObject(); System.out.println("[COEUS][API][ConfigActionBean] Saving.. " + filename); try { - FileWriter writer = new FileWriter(Config.getPath() + filename); + FileWriter writer = new FileWriter(filename); writer.write(value); writer.flush(); writer.close(); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] " + filename + " updated."); - } catch (IOException ex) { + } catch (Exception ex) { result.put("status", 200); result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + filename + " not updated, check exception."); Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); @@ -194,6 +455,12 @@ private JSONObject updateFile(String value, String filename) { return result; } + /** + * Return all ontology properties from location URL. + * + * @param location + * @return + */ public Set getOntologyProperties(String location) { Set set = new HashSet(); try { @@ -205,7 +472,7 @@ public Set getOntologyProperties(String location) { while (op.hasNext()) { OntProperty prop = op.next(); //if (prop.toString().startsWith(location)) { - set.add(prop.toString() + "\n"); + set.add(prop.toString() + "\n"); //} } } catch (Exception e) { @@ -213,4 +480,124 @@ public Set getOntologyProperties(String location) { } return set; } + + /** + * Copy a directory. + * + * @param src + * @param dest + * @throws IOException + */ + public static void copyFolder(File src, File dest) + throws IOException { + + if (src.isDirectory()) { + + //if directory not exists, create it + if (!dest.exists()) { + dest.mkdir(); + System.out.println("[COEUS][API][ConfigActionBean] Directory copied from " + + src + " to " + dest); + } + + //list all the directory contents + String files[] = src.list(); + + for (String file : files) { + //construct the src and dest file structure + File srcFile = new File(src, file); + File destFile = new File(dest, file); + //recursive copy + copyFolder(srcFile, destFile); + } + + } else { + //if file, then copy it + //Use bytes stream to support all file types + InputStream in = new FileInputStream(src); + OutputStream out = new FileOutputStream(dest); + + byte[] buffer = new byte[1024]; + + int length; + //copy the file content in bytes + while ((length = in.read(buffer)) > 0) { + out.write(buffer, 0, length); + } + + in.close(); + out.close(); + //System.out.println("File copied from " + src + " to " + dest); + } + } + + /** + * Delete a File or Directory. + * + * @param file + * @throws IOException + */ + public static void delete(File file) + throws IOException { + + if (file.isDirectory()) { + + //directory is empty, then delete it + if (file.list().length == 0) { + + file.delete(); + System.out.println("[COEUS][API][ConfigActionBean] Directory is deleted : " + + file.getAbsolutePath()); + + } else { + + //list all the directory contents + String files[] = file.list(); + + for (String temp : files) { + //construct the file structure + File fileDelete = new File(file, temp); + + //recursive delete + delete(fileDelete); + } + + //check the directory again, if empty then delete it + if (file.list().length == 0) { + file.delete(); + System.out.println("[COEUS][API][ConfigActionBean] Directory is deleted : " + + file.getAbsolutePath()); + } + } + + } else { + //if file, then delete it + file.delete(); + System.out.println("[COEUS][API][ConfigActionBean] File is deleted : " + file.getAbsolutePath()); + } + } + + /** + * Read and Convert a File to a String + * + * @param filename + * @return + */ + public String readToString(String filename) { + StringBuilder sb = new StringBuilder(); + try { + BufferedReader br = new BufferedReader(new FileReader(filename)); + String line = br.readLine(); + + while (line != null) { + sb.append(line); + sb.append('\n'); + line = br.readLine(); + } + br.close(); + } catch (IOException ex) { + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + return sb.toString(); + } } diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java index bbe6183..1862736 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java @@ -33,7 +33,7 @@ public class Config { private static boolean debug = false; private static boolean built = false; private static String path = ""; - private static String environment = "development"; + //private static String environment = "development"; private static ArrayList apikeys = new ArrayList(); public static ArrayList getApikeys() { @@ -44,13 +44,13 @@ public static void setApikeys(ArrayList apikeys) { Config.apikeys = apikeys; } - public static String getEnvironment() { - return environment; - } - - public static void setEnvironment(String environment) { - Config.environment = environment; - } +// public static String getEnvironment() { +// return environment; +// } +// +// public static void setEnvironment(String environment) { +// Config.environment = environment; +// } public static String getPath() { return path; @@ -190,9 +190,9 @@ public static boolean load() { debug = (Boolean) config.get("debug"); built = (Boolean) config.get("built"); predicates = (String) config.get("predicates"); - environment = (String) config.get("environment"); +// environment = (String) config.get("environment"); apikeys.addAll(Arrays.asList(((String) config.get("apikey")).split("\\|"))); - sdb = ((String) config.get("sdb")).replace(".ttl", "_" + environment + ".ttl"); + sdb = ((String) config.get("sdb"));//.replace(".ttl", "_" + environment + ".ttl"); keyPrefix = (String) config.get("keyprefix"); JSONObject prefixes = (JSONObject) file.get("prefixes"); for (Object o : prefixes.keySet()) { diff --git a/src/main/resources/config.js b/src/main/resources/config.js index 37cd45f..99677a4 100644 --- a/src/main/resources/config.js +++ b/src/main/resources/config.js @@ -5,13 +5,13 @@ "keyprefix":"coeus", "version": "1.0a", "ontology": "http://bioinformatics.ua.pt/coeus/ontology/", - "setup": "newsaggregator/setup.rdf", - "sdb":"newsaggregator/sdb.ttl", + "setup": "setup.rdf", + "sdb":"sdb.ttl", "predicates":"predicates.csv", "built": false, "debug": true, "apikey":"coeus|uavr", - "environment": "production" + "environment":"" }, "prefixes" : { "coeus": "http://bioinformatics.ua.pt/coeus/resource/", diff --git a/src/main/resources/init/joseki.ttl b/src/main/resources/init/joseki.ttl new file mode 100644 index 0000000..19b8e38 --- /dev/null +++ b/src/main/resources/init/joseki.ttl @@ -0,0 +1,97 @@ +@prefix rdfs: . +@prefix rdf: . +@prefix xsd: . +@prefix coeus: . +@prefix module: . +@prefix joseki: . +@prefix ja: . +@prefix sdb: . + +<> rdfs:label "Joseki Configuration File - SDB example" . +# Stripped down to support one service that exposes an +# SDB store as a SPARQL endpoint for query and one for +# one of the graphs in an SDB store. + +[] rdf:type joseki:Server . + +## -------------------------------------------------------------- +## Services + +# Service publishes the whole of the SDB store - this is the usual way to use SDB. +<#service1> + rdf:type joseki:Service ; + rdfs:label "SPARQL-SDB" ; + joseki:serviceRef "sparql" ; # web.xml must route this name to Joseki + joseki:dataset <#sdb> ; + joseki:processor joseki:ProcessorSPARQL_FixedDS ; + . + + +## -------------------------------------------------------------- +## Datasets + +## See also SDB documentation -- http://jena.hpl.hp.com/wiki/SDB +## Special declarations to cause SDB to be used. + +## Initialize SDB. +## Tell the system that sdb:DatasetStore is an implementation of ja:RDFDataset . +## Tell the system that sdb:Model is an implementation of ja:RDFDataset . + +[] ja:loadClass "com.hp.hpl.jena.sdb.SDB" . +sdb:DatasetStore rdfs:subClassOf ja:RDFDataset . +sdb:Model rdfs:subClassOf ja:Model . + +<#sdb> rdf:type sdb:DatasetStore ; + ## Number of concurrent connections allowed to this dataset. + joseki:poolSize 2; + sdb:store <#store> . + +<#store> rdf:type sdb:Store ; + rdfs:label "SDB" ; + sdb:layout "layout2" ; + sdb:connection + [ rdf:type sdb:SDBConnection ; + sdb:sdbType "mysql" ; + #sdb:sdbHost "localhost:3306" ; + #sdb:sdbName "coeus" ; + sdb:jdbcURL "$sdb:jdbcURL" ; + sdb:sdbUser "$sdb:sdbUser" ; + sdb:sdbPassword "$sdb:sdbPassword" ; + ] + . + +# Pick one graph out of the SDB store. +# Do not assemble the whole of the store this way - it is less efficient for that. +<#sdb-part> rdf:type ja:RDFDataset ; + # If ja:namedGraph is used here, there is no correspondence + # with the name in the SDB store. + ja:defaultGraph <#sdb-one-graph> ; + . + +<#sdb-one-graph> a sdb:Model ; + sdb:dataset <#sdb> ; + # Uncomment to pick out a named graph from the store. + # If no "sdb:namedGraph" appearsm the store's default graph is used. + # is used as default graph of the dataset publically visible. + #sdb:graphName ; + # Or even the merge of all named graphs + #sdb:graphName ; + . + +## -------------------------------------------------------------- +## Processors + +joseki:ProcessorSPARQL_FixedDS + rdfs:label "SPARQL processor for fixed datasets" ; + rdf:type joseki:Processor ; + module:implementation + [ rdf:type joseki:ServiceImpl ; + module:className + ] ; + + # This processor does not accept queries with FROM/FROM NAMED + joseki:allowExplicitDataset "false"^^xsd:boolean ; + joseki:allowWebLoading "false"^^xsd:boolean ; + # The database is safe for MRSW (multiple-reader, single-writer). + joseki:lockingPolicy joseki:lockingPolicyMRSW ; + . \ No newline at end of file diff --git a/src/main/resources/init/map.js b/src/main/resources/init/map.js new file mode 100644 index 0000000..43e9dee --- /dev/null +++ b/src/main/resources/init/map.js @@ -0,0 +1,15 @@ +{ + "$sdb:jdbcURL" : "jdbc:mysql://localhost:3306/coeus?autoReconnect=true", + "$sdb:sdbUser" : "demo", + "$sdb:sdbPassword" :"demo", + + "$conf:projectName" :"coeus.demo", + "$conf:projectHomepage" :"http://bioinformatics.ua.pt/coeus/", + "$conf:webBase" :"http://localhost:8080/coeus/", + "$conf:sparqlEndpoint" :"http://localhost:8080/coeus/sparql", + "$conf:datasetBase" :"http://bioinformatics.ua.pt/coeus/resource/", + "$conf:webResourcePrefix" :"resource/", + + "$environment" :"", + +} \ No newline at end of file diff --git a/src/main/resources/init/pubby.ttl b/src/main/resources/init/pubby.ttl new file mode 100644 index 0000000..1a5d679 --- /dev/null +++ b/src/main/resources/init/pubby.ttl @@ -0,0 +1,91 @@ +# Pubby Example Configuration +# +# This configuration connects to the DBpedia SPARQL endpoint and +# re-publishes on your local machine, with dereferenceable +# localhost URIs. +# +# This assumes you already have a servlet container running +# on your machine at http://localhost:8080/ . +# +# Install Pubby as the root webapp of your servlet container, +# and make sure the config-file parameter in Pubby's web.xml +# points to this configuration file. +# +# Then browse to http://localhost:8080/ . + +# Prefix declarations to be used in RDF output +@prefix conf: . +@prefix meta: . +@prefix rdf: . +@prefix rdfs: . +@prefix xsd: . +@prefix owl: . +@prefix dc: . +@prefix dcterms: . +@prefix foaf: . +@prefix skos: . +@prefix geo: . +@prefix dbpedia: . +@prefix p: . +@prefix yago: . +@prefix units: . +@prefix geonames: . +@prefix prv: . +@prefix prvTypes: . +@prefix doap: . +@prefix void: . +@prefix ir: . +@prefix coeus: . + +# Server configuration section +<> a conf:Configuration; + # Project name for display in page titles + conf:projectName "$conf:projectName"; + # Homepage with description of the project for the link in the page header + conf:projectHomepage <$conf:projectHomepage>; + # The Pubby root, where the webapp is running inside the servlet container. + conf:webBase <$conf:webBase>; + # URL of an RDF file whose prefix mapping is to be used by the + # server; defaults to <>, which is *this* file. + conf:usePrefixesFrom <>; + # If labels and descriptions are available in multiple languages, + # prefer this one. + conf:defaultLanguage "en"; + # When the homepage of the server is accessed, this resource will + # be shown. + #conf:indexResource ; + +# Dataset configuration section #1 (for DBpedia resources) +# +# URIs in the SPARQL endpoint: http://dbpedia.org/resource/* +# URIs on the Web: http://localhost:8080/resource/* + conf:dataset [ + # SPARQL endpoint URL of the dataset + conf:sparqlEndpoint <$conf:sparqlEndpoint>; + #conf:sparqlEndpoint ; + # Default graph name to query (not necessary for most endpoints) + # conf:sparqlDefaultGraph <>; + # Common URI prefix of all resource URIs in the SPARQL dataset + conf:datasetBase <$conf:datasetBase>; + # Will be appended to the conf:webBase to form the public + # resource URIs; if not present, defaults to "" + conf:webResourcePrefix "$conf:webResourcePrefix"; + # Fixes an issue with the server running behind an Apache proxy; + # can be ignored otherwise + conf:fixUnescapedCharacters "(),'!$&*+;=@"; + + # include metadata + #conf:metadataTemplate "metadata.ttl"; + + # configure your metadata here + # Use properties with the meta: prefix where the property name + # corresponds to the placeholder URIs in metadata.ttl that begin + # with about:metadata:metadata: + # Examples for such properties are: +# meta:pubbyUser ; +# meta:pubbyOperator ; +# meta:endpointUser ; +# meta:endpointOperator ; +# meta:endpointDataset ; + ]; + . diff --git a/src/main/resources/init/sdb.ttl b/src/main/resources/init/sdb.ttl new file mode 100644 index 0000000..ac180fd --- /dev/null +++ b/src/main/resources/init/sdb.ttl @@ -0,0 +1,19 @@ +@prefix sdb: . +@prefix rdfs: . +@prefix rdf: . +@prefix ja: . +@prefix coeus: . + +<#store> rdf:type sdb:Store ; + sdb:layout "layout2" ; + sdb:connection <#conn> ; + sdb:engine "InnoDB" ; +. + +<#conn> rdf:type sdb:SDBConnection ; + sdb:sdbType "MySQL" ; + sdb:jdbcURL "$sdb:jdbcURL" ; + sdb:sdbUser "$sdb:sdbUser" ; + sdb:sdbPassword "$sdb:sdbPassword" ; + sdb:driver "com.mysql.jdbc.Driver" ; + . \ No newline at end of file diff --git a/src/main/resources/sdb.ttl b/src/main/resources/sdb.ttl new file mode 100644 index 0000000..b8d5d4e --- /dev/null +++ b/src/main/resources/sdb.ttl @@ -0,0 +1,19 @@ +@prefix sdb: . +@prefix rdfs: . +@prefix rdf: . +@prefix ja: . +@prefix coeus: . + +<#store> rdf:type sdb:Store ; + sdb:layout "layout2" ; + sdb:connection <#conn> ; + sdb:engine "InnoDB" ; +. + +<#conn> rdf:type sdb:SDBConnection ; + sdb:sdbType "MySQL" ; + sdb:jdbcURL "jdbc:mysql://localhost:3306/coeus?autoReconnect=true" ; + sdb:sdbUser "demo" ; + sdb:sdbPassword "demo" ; + sdb:driver "com.mysql.jdbc.Driver" ; + . \ No newline at end of file diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml index 440ea95..21452de 100755 --- a/src/main/webapp/WEB-INF/web.xml +++ b/src/main/webapp/WEB-INF/web.xml @@ -131,7 +131,7 @@ Secured Setup - /config/* + /setup/* /manager/* GET diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index d73c954..c992104 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -428,7 +428,7 @@ function encodeBars(value) { } function removeById(childDiv, parentDiv) { - console.log(childDiv+' '+ parentDiv); + console.log(childDiv + ' ' + parentDiv); if (childDiv === parentDiv) { alert("The parent div cannot be removed."); } @@ -445,4 +445,18 @@ function removeById(childDiv, parentDiv) function callURL(url, success, error) { url = encodeURI(url); $.ajax({url: url, dataType: 'json'}).done(success).fail(error); -} \ No newline at end of file +} + +/** + * Generate a html code message + * Ex: var htmlMessage=generateHtmlMessage("Error!", "It already exists!","alert-error"); + * + * @param {type} strong + * @param {type} message + * @param {type} type + * @returns {String} + */ +function generateHtmlMessage(strong, message, type) { + var error = '
    ' + strong + ' ' + message + '
    '; + return error; +} diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index d71f051..ea174a2 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -14,10 +14,66 @@ @@ -160,15 +270,19 @@

    COEUS Setup

    +
    +
    +
    @@ -180,9 +294,147 @@
    - +
    + 1.Environment + + +
    + +
    + +

    Name of the Environment

    +
    +
    + + +
    + +
    + Create +
    +
    + +
    + +
    + +
    + +
    +
    + 2.Database + + +
    + +
    + jdbc:mysql:// + + : + / + +

    Database connection URL

    +
    +
    + + +
    + +
    + + +
    +
    + +
    + +
    + + +
    +
    + + 3.Pubby + + +
    + +
    + +

    The name of the project, for display in page titles.

    +
    +
    + + +
    + +
    + +

    A project homepage or similar URL, for linking in page titles.

    +
    +
    + +
    + +
    + +

    The root URL where the Pubby web application is installed.

    +
    +
    + +
    + +
    + +

    The URL of the SPARQL endpoint whose data we want to expose.

    +
    +
    + +
    + +
    + +

    The common URI prefix of the resource identifiers in the SPARQL dataset. Only resources with this prefix will be mapped and made available by Pubby.

    +
    +
    + +
    + +
    + +

    Prefix to the mapped web URIs.

    +
    +

    For more information please visit the Pubby Homepage.

    + +
    +
    + + +
    + +
    + Save Configuration +
    +
    + +
    + +
    + + +
    +
    + +
    + Next > +
    +
    +
    +
    +
    + 4.Model Configurations
    @@ -229,16 +481,6 @@
    - -
    - -
    - -
    -
    -
    @@ -280,7 +522,7 @@
    - Next > + Next >
    @@ -288,7 +530,8 @@
    -
    +
    + 5.Prefix Configurations @@ -314,16 +557,19 @@
    - Next > + Next >
    -
    +

    In order to save your progress press the Save button, please.

    -

    Warning: If you leaves this wizard without save it, all of configurations will be lost.

    +

    Warning: If you leaves this wizard without save it, some configurations will be lost.

    +

    +
    +

    After saving the configurations you can start build the model for your application:

    @@ -334,8 +580,7 @@
    -
    -
    +
    @@ -357,11 +602,6 @@
    - -
    - -
    -
    From 2f7cdc7c59d06a4e67f9624e4abb55176ba4879d Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 7 Aug 2013 17:38:20 +0100 Subject: [PATCH 23/52] - Setup: Included Environment Setup. --- .../coeus/actions/ConfigActionBean.java | 2 +- .../coeus/actions/ManagerActionBean.java | 15 +- src/main/webapp/setup/editenvironment.jsp | 197 +++++++++++++++++ src/main/webapp/setup/environments.jsp | 208 ++++++++++++++++++ src/main/webapp/setup/html.jsp | 17 +- src/main/webapp/setup/index.jsp | 38 +++- 6 files changed, 455 insertions(+), 22 deletions(-) create mode 100644 src/main/webapp/setup/editenvironment.jsp create mode 100644 src/main/webapp/setup/environments.jsp diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index cf67152..422ddb6 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -215,7 +215,7 @@ public void changeEnvironment(String src, String dest, String environment) throw Entry e = (Entry) it.next(); m.put(e.getKey(), e.getValue()); } - m.put("environment", environment); + m.put("environment", environment.split("env_", 2)[1]); f.put("config", m); updateFile(f.toJSONString(), Config.getPath() + "config.js"); diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java index a7358d4..f15dd40 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java @@ -5,12 +5,7 @@ package pt.ua.bioinformatics.coeus.actions; import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.FileWriter; -import java.io.OutputStream; -import java.io.PrintStream; import java.io.StringWriter; -import java.io.Writer; import net.sourceforge.stripes.action.ActionBean; import net.sourceforge.stripes.action.ActionBeanContext; import net.sourceforge.stripes.action.DefaultHandler; @@ -37,6 +32,8 @@ public class ManagerActionBean implements ActionBean { private static final String CONCEPTS_VIEW = "/setup/concepts.jsp"; private static final String RESOURCE_ADD_VIEW = "/setup/addresource.jsp"; private static final String RESOURCES_VIEW = "/setup/resources.jsp"; + private static final String ENVIRONMENTS_VIEW = "/setup/environments.jsp"; + private static final String ENVIRONMENTS_EDIT_VIEW = "/setup/editenvironment.jsp"; private static final String NOTFOUND_VIEW = "/setup/404.jsp"; private static final String GRAPH_VIEW = "/setup/graph.jsp"; private String method; @@ -72,6 +69,14 @@ public Resolution export() throws FileNotFoundException { } return new StreamingResolution("application/rdf+xml", outs.toString()); } + + public Resolution environments() { + if (method!=null && method.startsWith("edit")) { + return new ForwardResolution(ENVIRONMENTS_EDIT_VIEW); + } else { + return new ForwardResolution(ENVIRONMENTS_VIEW); + } + } public Resolution seed() { if (method == null) { diff --git a/src/main/webapp/setup/editenvironment.jsp b/src/main/webapp/setup/editenvironment.jsp new file mode 100644 index 0000000..017f3d0 --- /dev/null +++ b/src/main/webapp/setup/editenvironment.jsp @@ -0,0 +1,197 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + + + +
    +

    +
    + +
    + +
    + + +
    +
    +

    Database Configuration:

    + + +
    + +
    + jdbc:mysql:// + + : + / + +

    Database connection URL

    +
    +
    + + +
    + +
    + + +
    + +
    + +
    + +
    + + +
    +
    + +

    Pubby Configuration:

    + + +
    + +
    + +

    The name of the project, for display in page titles.

    +
    +
    + + +
    + +
    + +

    A project homepage or similar URL, for linking in page titles.

    +
    +
    + +
    + +
    + +

    The root URL where the Pubby web application is installed.

    +
    +
    + +
    + +
    + +

    The URL of the SPARQL endpoint whose data we want to expose.

    +
    +
    + +
    + +
    + +

    The common URI prefix of the resource identifiers in the SPARQL dataset. Only resources with this prefix will be mapped and made available by Pubby.

    +
    +
    + +
    + +
    + +

    Prefix to the mapped web URIs.

    +
    +

    For more information please visit the Pubby Homepage.

    + +
    +
    + + +
    + +
    + Save Configuration + or + +
    +
    + +
    + +
    + + +
    + +
    + + +
    + + + + + + + +     +     diff --git a/src/main/webapp/setup/environments.jsp b/src/main/webapp/setup/environments.jsp new file mode 100644 index 0000000..979e445 --- /dev/null +++ b/src/main/webapp/setup/environments.jsp @@ -0,0 +1,208 @@ +<%-- + Document : index + Created on : May 28, 2013, 11:20:32 AM + Author : sernadela +--%> + +<%@include file="/layout/taglib.jsp" %> + + COEUS Setup + + + + + + + + +
    +

    +
    +

    Environments Setup

    +
    + +
    +
    + +
    + + + +
    +

    List of Environments

    +
    + + +
    +
    + Create Environment +
    +
    + + +
    + + + + + + + + + + + + +
    #NameStatusActions
    + + + + + + + + + + +
    + + + diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index f9e5445..ca458ad 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -28,19 +28,18 @@
  • ">Home
  • ">Seeds
    • - ---> -
  • ">Setup
    • + +
  • ">Documentation
    • diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 6cef0fb..a8d553c 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -73,10 +73,23 @@ window.location = "../entity/" + path; } + function fillHeader(result) { + $('#header').html('

    ' + lastPath() + ' ' + result.config.environment + '

    '); + } + function fillEnvironments(result) { + console.log(result); + var array = result.environments; + for (var r in array) { + var value = array[r].replace('env_', ''); + $('#environments').append(''); + } + } + $(document).ready(function() { //get seed from url var seed = lastPath(); - $('#header').append('

    ' + seed + ' enviroment

    '); + callURL("../../config/getconfig/", fillHeader); + callURL("../../config/listenv/", fillEnvironments); var query = initSparqlerQuery(); // passes standard JSON results object to success callback @@ -127,6 +140,20 @@ redirect("../seed/" + "coeus:" + title); } + function changeEnv() { + var env = $('#environments').val(); + callURL("../../config/upenv/" + env, changeEnvResult, changeEnvResult, changeEnvError); + } + function changeEnvResult(result) { + if (result.status === 100) + callURL("../../config/getconfig/", fillHeader); + else + $('#info').html(generateHtmlMessage("Warning!", result.message)); + } + function changeEnvError(result, text) { + $('#info').html(generateHtmlMessage("ERROR!", text, "alert-error")); + } + @@ -136,7 +163,7 @@
    - +

    Knowledge Base (Entity-Concept)

    @@ -174,15 +201,12 @@ Environments
    -
    - Change environment + Change environment
    From a9772d22ee00b380af92f65dfa143131079d355c Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 8 Aug 2013 17:46:06 +0100 Subject: [PATCH 24/52] - Setup: Included Environment Configuration. --- .../coeus/actions/ConfigActionBean.java | 88 +++-- src/main/webapp/setup/editenvironment.jsp | 310 +++++++++++------- 2 files changed, 243 insertions(+), 155 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index 422ddb6..bd3a1ff 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -139,8 +139,8 @@ public void updateFilesFromMap(String path) throws ParseException, IOException { JSONParser parser = new JSONParser(); JSONObject map = (JSONObject) parser.parse(readToString(path + "map.js")); - //ensures that files are clean - copyFolder(new File(Config.getPath() + "init"), new File(path)); + //ensures that files (pubby, sdb and joseki) are clean + copyFolder(new File(Config.getPath() + "init"), new File(path),new File(path + "map.js")); File src = new File(path); //list all the directory contents @@ -205,7 +205,7 @@ public Resolution upenv() { */ public void changeEnvironment(String src, String dest, String environment) throws IOException { //copy all files from enviroment to root dir - copyFolder(new File(src), new File(dest)); + copyFolder(new File(src), new File(dest),null); // update environment in config.js JSONObject f = Config.getFile(); JSONObject config = (JSONObject) f.get("config"); @@ -242,7 +242,7 @@ public Resolution newenv() { } File init = new File(initStr); - copyFolder(init, env); + copyFolder(init, env,null); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] Environment created: " + method); } catch (IOException ex) { @@ -255,6 +255,27 @@ public Resolution newenv() { return new StreamingResolution("application/json", result.toJSONString()); } + /** + * Returns a map.js file in the environment (method) + * + * @return + */ + public Resolution getmap() { + JSONObject result = new JSONObject(); + try { + Config.load(); + String environment = "env_" + method; + String path = Config.getPath() + environment + "/"; + String map = path + "map.js"; + JSONParser parser = new JSONParser(); + String json = readToString(map); + result = (JSONObject) parser.parse(json); + } catch (Exception ex) { + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + return new StreamingResolution("application/json", result.toJSONString()); + } + /** * Receives a map.js file and update it in according to the environment key * in config.js. @@ -437,8 +458,6 @@ public Resolution export() throws FileNotFoundException { private JSONObject updateFile(String value, String filename) { JSONObject result = new JSONObject(); - System.out.println("[COEUS][API][ConfigActionBean] Saving.. " + filename); - try { FileWriter writer = new FileWriter(filename); writer.write(value); @@ -446,6 +465,8 @@ private JSONObject updateFile(String value, String filename) { writer.close(); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] " + filename + " updated."); + + System.out.println("[COEUS][API][ConfigActionBean] Saved: " + filename); } catch (Exception ex) { result.put("status", 200); result.put("message", "[COEUS][API][ConfigActionBean] ERROR: " + filename + " not updated, check exception."); @@ -488,7 +509,7 @@ public Set getOntologyProperties(String location) { * @param dest * @throws IOException */ - public static void copyFolder(File src, File dest) + public static void copyFolder(File src, File dest, File skipFile) throws IOException { if (src.isDirectory()) { @@ -508,26 +529,28 @@ public static void copyFolder(File src, File dest) File srcFile = new File(src, file); File destFile = new File(dest, file); //recursive copy - copyFolder(srcFile, destFile); + copyFolder(srcFile, destFile, skipFile); } } else { - //if file, then copy it - //Use bytes stream to support all file types - InputStream in = new FileInputStream(src); - OutputStream out = new FileOutputStream(dest); - - byte[] buffer = new byte[1024]; + if (skipFile==null || !(skipFile.getName().equals(src.getName()))) { + //if file, then copy it + //Use bytes stream to support all file types + InputStream in = new FileInputStream(src); + OutputStream out = new FileOutputStream(dest); + + byte[] buffer = new byte[1024]; + + int length; + //copy the file content in bytes + while ((length = in.read(buffer)) > 0) { + out.write(buffer, 0, length); + } - int length; - //copy the file content in bytes - while ((length = in.read(buffer)) > 0) { - out.write(buffer, 0, length); + in.close(); + out.close(); + System.out.println("[COEUS][API][ConfigActionBean] File copied from " + src + " to " + dest); } - - in.close(); - out.close(); - //System.out.println("File copied from " + src + " to " + dest); } } @@ -583,21 +606,18 @@ public static void delete(File file) * @param filename * @return */ - public String readToString(String filename) { + public String readToString(String filename) throws IOException { StringBuilder sb = new StringBuilder(); - try { - BufferedReader br = new BufferedReader(new FileReader(filename)); - String line = br.readLine(); - while (line != null) { - sb.append(line); - sb.append('\n'); - line = br.readLine(); - } - br.close(); - } catch (IOException ex) { - Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + BufferedReader br = new BufferedReader(new FileReader(filename)); + String line = br.readLine(); + + while (line != null) { + sb.append(line); + sb.append('\n'); + line = br.readLine(); } + br.close(); return sb.toString(); } } diff --git a/src/main/webapp/setup/editenvironment.jsp b/src/main/webapp/setup/editenvironment.jsp index 017f3d0..72a0b3a 100644 --- a/src/main/webapp/setup/editenvironment.jsp +++ b/src/main/webapp/setup/editenvironment.jsp @@ -20,18 +20,86 @@ var path = lastPath(); $('#header').html('

    Environment ' + path + '

    '); + callURL("../../../config/getmap/" + path, getMapSuccess, getMapError); + }); + function getMapSuccess(result) { + + //fill boxs with values + var jdbcURL = result["$sdb:jdbcURL"].replace("jdbc:mysql://", "").replace("?autoReconnect=true", ""); + $('#host').val(jdbcURL.split(":", 2)[0]); + $('#port').val(jdbcURL.split(":", 2)[1].split("/", 2)[0]); + $('#path').val(jdbcURL.split("/", 2)[1]); + + $('#username').val(result["$sdb:sdbUser"]); + $('#password').val(result["$sdb:sdbPassword"]); + + $('#projectName').val(result["$conf:projectName"]); + $('#projectHomepage').val(result["$conf:projectHomepage"]); + $('#WebBase').val(result["$conf:webBase"]); + $('#Endpoint').val(result["$conf:sparqlEndpoint"]); + $('#DatasetBase').val(result["$conf:datasetBase"]); + $('#WebResourcePrefix').val(result["$conf:webResourcePrefix"]); + + } + + function generateMap() { + + var host = $('#host').val(); + var port = $('#port').val(); + var path = $('#path').val(); + var jdbcURL = "jdbc:mysql://" + host + ":" + port + "/" + path + "%3FautoReconnect=true"; + + var username = $('#username').val(); + var password = $('#password').val(); + + var projectName = $('#projectName').val(); + var projectHomepage = $('#projectHomepage').val(); + var webBase = $('#WebBase').val(); + var endpoint = $('#Endpoint').val(); + var datasetBase = $('#DatasetBase').val(); + var webResourcePrefix = $('#WebResourcePrefix').val(); + + var environment=lastPath(); + + var json = { + "$sdb:jdbcURL": jdbcURL, + "$sdb:sdbUser": username, + "$sdb:sdbPassword": password, + "$conf:projectName": projectName, + "$conf:projectHomepage": projectHomepage, + "$conf:webBase": webBase, + "$conf:sparqlEndpoint": endpoint, + "$conf:datasetBase": datasetBase, + "$conf:webResourcePrefix": webResourcePrefix, + "$environment": environment + }; + + return JSON.stringify(json); + } + + function getMapError(result, text) { + console.log(text); + } + + function updateFilesOnEnv(){ + callURL("../../../config/putmap/" + encodeBars(generateMap()), upEnvResult, upEnvFail); + } + function upEnvResult(result) { + console.log(result); + if (result.status === 100) { + window.location = document.referrer; + //$('#resultUpEnv').html(generateHtmlMessage("Success!", "Configurations saved on environment "+env+". Please, press the next button.", "alert-success")); + } else { + $('#resultUpEnv').html(generateHtmlMessage("Warning!", result.message)); + } + + } + + function upEnvFail(jqXHR, textStatus) { + $('#resultUpEnv').html(generateHtmlMessage("Error!", textStatus, "alert-error")); + } -// $('#submit').click(function() { -// -// //if one fail the others fails too -// if (document.getElementById('result').className === 'alert alert-error') { -// $('#callModal').click(); -// } -// if (document.getElementById('result').className === 'alert alert-success') { -// window.location = document.referrer; -// } -// });     @@ -42,120 +110,120 @@
    - +
    - - + +
    -
    -

    Database Configuration:

    - - -
    - -
    - jdbc:mysql:// - - : - / - -

    Database connection URL

    -
    -
    - - -
    - -
    - - -
    - -
    - -
    - -
    - - -
    -
    - -

    Pubby Configuration:

    - - -
    - -
    - -

    The name of the project, for display in page titles.

    -
    -
    - - -
    - -
    - -

    A project homepage or similar URL, for linking in page titles.

    -
    -
    - -
    - -
    - -

    The root URL where the Pubby web application is installed.

    -
    -
    - -
    - -
    - -

    The URL of the SPARQL endpoint whose data we want to expose.

    -
    -
    - -
    - -
    - -

    The common URI prefix of the resource identifiers in the SPARQL dataset. Only resources with this prefix will be mapped and made available by Pubby.

    -
    -
    - -
    - -
    - -

    Prefix to the mapped web URIs.

    -
    -

    For more information please visit the Pubby Homepage.

    - -
    -
    - - -
    - -
    - Save Configuration - or - -
    -
    - -
    - -
    - - -
    -
    +
    +

    Database Configuration:

    + + +
    + +
    + jdbc:mysql:// + + : + / + +

    Database connection URL

    +
    +
    + + +
    + +
    + + +
    + +
    + +
    + +
    + + +
    +
    + +

    Pubby Configuration:

    + + +
    + +
    + +

    The name of the project, for display in page titles.

    +
    +
    + + +
    + +
    + +

    A project homepage or similar URL, for linking in page titles.

    +
    +
    + +
    + +
    + +

    The root URL where the Pubby web application is installed.

    +
    +
    + +
    + +
    + +

    The URL of the SPARQL endpoint whose data we want to expose.

    +
    +
    + +
    + +
    + +

    The common URI prefix of the resource identifiers in the SPARQL dataset. Only resources with this prefix will be mapped and made available by Pubby.

    +
    +
    + +
    + +
    + +

    Prefix to the mapped web URIs.

    +
    +

    For more information please visit the Pubby Homepage.

    + +
    +
    + + +
    + +
    + Save Configuration + or + +
    +
    + +
    + +
    + + +
    +
    - - + +
    From 684dafb6f34d9cd43ad0f485e877d32ce15c5ef2 Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 8 Aug 2013 17:50:14 +0100 Subject: [PATCH 25/52] - Setup: Include top navigator for Setup. --- src/main/webapp/layout/html.jsp | 2 ++ src/main/webapp/setup/html.jsp | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/main/webapp/layout/html.jsp b/src/main/webapp/layout/html.jsp index 0bf0509..667d9d5 100644 --- a/src/main/webapp/layout/html.jsp +++ b/src/main/webapp/layout/html.jsp @@ -32,6 +32,8 @@
  • ">Science
  • ">SPARQL
    • + +
  • ">Setup
  • Contact
    • diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index ca458ad..0ce55a6 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -25,7 +25,7 @@
      -
    • ">Home
      • +
    • ">Home
    • ">Seeds
      • From 6beada92782ad6994117779bb7532ec07b47522a Mon Sep 17 00:00:00 2001 From: sernadela Date: Mon, 26 Aug 2013 11:17:59 +0100 Subject: [PATCH 26/52] - Setup: Include option to clean sdb. --- .../coeus/actions/ConfigActionBean.java | 56 +++++++++++++++++-- .../bioinformatics/coeus/common/Tester.java | 9 ++- src/main/webapp/setup/config.jsp | 3 + 3 files changed, 61 insertions(+), 7 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index bd3a1ff..96bdc1c 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -46,8 +46,10 @@ import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; +import pt.ua.bioinformatics.coeus.api.DB; import pt.ua.bioinformatics.coeus.common.Boot; import pt.ua.bioinformatics.coeus.common.Config; +import pt.ua.bioinformatics.coeus.common.Tester; /** * @@ -102,6 +104,52 @@ public Resolution getconfig() { return new StreamingResolution("application/json", Config.getFile().toJSONString()); } + /** + * Cleans the DB of one environment (method) + * + * @return + */ + public Resolution cleandb() { + JSONObject result = new JSONObject(); + try { + //get map.js file + String environment = "env_" + method; + String path = Config.getPath() + environment + "/"; + String map = path + "map.js"; + JSONParser parser = new JSONParser(); + String json = readToString(map); + result = (JSONObject) parser.parse(json); + int index=result.get("$sdb:jdbcURL").toString().lastIndexOf("/"); + String dbName=result.get("$sdb:jdbcURL").toString().substring(index); + DB db = new DB(dbName, result.get("$sdb:jdbcURL") + "&user=" + result.get("$sdb:sdbUser").toString() + "&password=" + result.get("$sdb:sdbPassword").toString()); + // test db connection + boolean success = db.connectX(); + + if (success) { + db.update("Truncate table Node", "TRUNCATE TABLE Nodes;"); + db.update("Truncate table Prefixes", "TRUNCATE TABLE Prefixes;"); + db.update("Truncate table Quads", "TRUNCATE TABLE Quads;"); + db.update("Truncate table Triples", "TRUNCATE TABLE Triples;"); + System.out.println("[COEUS][API][ConfigActionBean] Sdb clean OK\n"); + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] DB Cleaned in environment: " + method); + } else { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: Clean DB, check exception."); + } + + } catch (IOException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: Clean DB, check exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } catch (ParseException ex) { + result.put("status", 200); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: Clean DB, check parse exception."); + Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); + } + return new StreamingResolution("application/json", result.toJSONString()); + } + /** * List all environments (i.e., all folders started by 'env_' string) * @@ -140,7 +188,7 @@ public void updateFilesFromMap(String path) throws ParseException, IOException { JSONObject map = (JSONObject) parser.parse(readToString(path + "map.js")); //ensures that files (pubby, sdb and joseki) are clean - copyFolder(new File(Config.getPath() + "init"), new File(path),new File(path + "map.js")); + copyFolder(new File(Config.getPath() + "init"), new File(path), new File(path + "map.js")); File src = new File(path); //list all the directory contents @@ -205,7 +253,7 @@ public Resolution upenv() { */ public void changeEnvironment(String src, String dest, String environment) throws IOException { //copy all files from enviroment to root dir - copyFolder(new File(src), new File(dest),null); + copyFolder(new File(src), new File(dest), null); // update environment in config.js JSONObject f = Config.getFile(); JSONObject config = (JSONObject) f.get("config"); @@ -242,7 +290,7 @@ public Resolution newenv() { } File init = new File(initStr); - copyFolder(init, env,null); + copyFolder(init, env, null); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] Environment created: " + method); } catch (IOException ex) { @@ -533,7 +581,7 @@ public static void copyFolder(File src, File dest, File skipFile) } } else { - if (skipFile==null || !(skipFile.getName().equals(src.getName()))) { + if (skipFile == null || !(skipFile.getName().equals(src.getName()))) { //if file, then copy it //Use bytes stream to support all file types InputStream in = new FileInputStream(src); diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Tester.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Tester.java index 67c29b5..fe19ad8 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Tester.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Tester.java @@ -40,7 +40,7 @@ public static void main(String[] args) { try { // clean sdb - cleanSDB("localhost","coeus", "demo", "demo"); + cleanSDB("localhost","3306","coeus", "demo", "demo"); // Start import process Boot.start(); @@ -81,9 +81,10 @@ public static void main(String[] args) { * @param dbUserName * @param dbPassword */ - public static void cleanSDB(String host, String dbname, String dbUserName, String dbPassword) { + public static boolean cleanSDB(String host,String port, String dbname, String dbUserName, String dbPassword) { - DB db = new DB(dbname, "jdbc:mysql://"+host+":3306/" + dbname + "?autoReconnect=true&user=" + dbUserName + "&password=" + dbPassword); + boolean result=false; + DB db = new DB(dbname, "jdbc:mysql://"+host+":"+port+"/" + dbname + "?autoReconnect=true&user=" + dbUserName + "&password=" + dbPassword); // test db connection boolean success = db.connectX(); @@ -94,9 +95,11 @@ public static void cleanSDB(String host, String dbname, String dbUserName, Strin db.update("Truncate table Quads", "TRUNCATE TABLE Quads;"); db.update("Truncate table Triples", "TRUNCATE TABLE Triples;"); System.out.println("Sdb clean OK\n"); + result=true; } else { System.err.println("FAIL: Sdb not clean!!"); } + return result; } /** diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index ea174a2..f3887b1 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -290,6 +290,9 @@

      In this section you will give some information to complete some setup files for COEUS.

      To begin press the Start Wizard button.

      Start Wizard +

      +

      If you do not want to change the configurations files, please skip this wizard.

      + Skip
    From 9883109b565ad4d5e5d9cedddb49a315f90fedbf Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 27 Aug 2013 18:41:34 +0100 Subject: [PATCH 27/52] - Setup: Fix breadcrumbs on all pages - Setup: Add UI icons - Setup: Minor Fixes --- .../coeus/actions/ConfigActionBean.java | 9 ++- src/main/webapp/setup/addconcept.jsp | 21 +++++- src/main/webapp/setup/addentity.jsp | 14 +++- src/main/webapp/setup/addresource.jsp | 65 +++++++++++++++---- src/main/webapp/setup/addseed.jsp | 9 ++- src/main/webapp/setup/concepts.jsp | 17 +++-- src/main/webapp/setup/config.jsp | 22 +++---- src/main/webapp/setup/entities.jsp | 12 ++-- src/main/webapp/setup/environments.jsp | 49 +++++++++++--- src/main/webapp/setup/index.jsp | 10 ++- src/main/webapp/setup/resources.jsp | 18 ++--- src/main/webapp/setup/seeds.jsp | 10 ++- 12 files changed, 192 insertions(+), 64 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index 96bdc1c..afb72fe 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -32,8 +32,10 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; +import java.util.Random; import java.util.Set; import java.util.TreeSet; +import java.util.UUID; import java.util.logging.Level; import java.util.logging.Logger; import net.sourceforge.stripes.action.ActionBean; @@ -50,6 +52,7 @@ import pt.ua.bioinformatics.coeus.common.Boot; import pt.ua.bioinformatics.coeus.common.Config; import pt.ua.bioinformatics.coeus.common.Tester; +import pt.ua.bioinformatics.coeus.data.Storage; /** * @@ -227,7 +230,11 @@ public Resolution upenv() { //Load new settings Config.setLoaded(false); + Boot.setStarted(false); Config.load(); + //TODO: FIX THAT - NEEDS SERVERS RESTART TO APPLY NEW CONFIGS + Storage.connect(); + Boot.start(); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] Environment updated: " + method); @@ -454,7 +461,7 @@ public Resolution putconfig() { //update config.js String jsonString = method; - JSONObject result = updateFile(jsonString, "config.js"); + JSONObject result = updateFile(jsonString, Config.getPath()+"config.js"); Config.setLoaded(false); Config.load(); diff --git a/src/main/webapp/setup/addconcept.jsp b/src/main/webapp/setup/addconcept.jsp index 89db9ac..5dad22f 100644 --- a/src/main/webapp/setup/addconcept.jsp +++ b/src/main/webapp/setup/addconcept.jsp @@ -19,11 +19,13 @@ //header name var path = lastPath(); $('#header').html('

    ' + path + ' env..

    '); + var qconcept = "SELECT DISTINCT ?seed {" + path + " coeus:isIncludedIn ?seed }"; + queryToResult(qconcept, fillBreadcumb); //if the type mode is EDIT if (penulPath() === 'edit') { $('#type').html("Edit Concept"); - $('#submit').html('Edit '); + $('#submit').html('Save '); var query = initSparqlerQuery(); var q = "SELECT ?title ?label {" + path + " dc:title ?title . " + path + " rdfs:label ?label . }"; @@ -122,6 +124,13 @@ //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; document.getElementById('uri').innerHTML = 'coeus:concept_' + value.split(' ').join('_'); } + function fillBreadcumb(result) { + var seed = result[0].seed.value; + seed = "coeus:" + splitURIPrefix(seed).value; + $('#breadSeed').html('Seed /'); + $('#breadEntities').html('Entities /'); + $('#breadConcepts').html('Concepts /'); + } @@ -131,6 +140,14 @@
    +
      +
    • /
      • +
    • Seeds /
      • +
    • +
    • +
    • +
    • Concept
      • +

    Concept URI - coeus:

    @@ -152,7 +169,7 @@
    - +
    diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp index ca2f78d..765c3c3 100644 --- a/src/main/webapp/setup/addentity.jsp +++ b/src/main/webapp/setup/addentity.jsp @@ -19,11 +19,14 @@ //header name var path = lastPath(); $('#header').html('

    ' + path + ' env..

    '); + $('#breadSeed').html('Seed / '); + $('#breadEntities').html('Entities / '); + //if the type mode is EDIT if (penulPath() === 'edit') { $('#type').html("Edit Entity:"); - $('#submit').html('Edit '); + $('#submit').html('Save '); var query = initSparqlerQuery(); var q = "SELECT ?seed ?title ?label ?comment {" + path + " coeus:isIncludedIn ?seed . " + path + " dc:title ?title . " + path + " rdfs:label ?label . " + path + " rdfs:comment ?comment . }"; @@ -139,6 +142,13 @@
    +
      +
    • /
      • +
    • Seeds /
      • +
    • +
    • +
    • Entity
      • +

    Entity URI - coeus:

    @@ -160,7 +170,7 @@
    - +
    diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 96deefc..93d5c1a 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -18,6 +18,7 @@ //header name var path = lastPath(); $('#header').html('

    ' + path + ' env..

    '); + //fill the concepts extensions var q = "SELECT ?concept ?c {?concept a coeus:Concept . ?concept dc:title ?c}"; @@ -26,9 +27,7 @@ //if the type mode is EDIT if (penulPath() === 'edit') { $('#type').html("Edit Resource"); - $('#submit').html('Edit '); - - + $('#submit').html('Save '); var query = initSparqlerQuery(); var q = "SELECT ?title ?label ?comment ?method ?publisher ?endpoint ?query ?order ?extends ?built {" + path + " dc:title ?title . " + path + " rdfs:label ?label . " + path + " rdfs:comment ?comment . " + path + " coeus:method ?method . " + path + " dc:publisher ?publisher . " + path + " coeus:endpoint ?endpoint . " + path + " coeus:query ?query . " + path + " coeus:order ?order . " + path + " coeus:extends ?extends . OPTIONAL{" + path + " coeus:built ?built } }"; @@ -72,12 +71,19 @@ var qselectors = "SELECT * {" + path + " coeus:loadsFrom ?selector . ?selector dc:title ?title . ?selector rdfs:label ?label . ?selector coeus:property ?property . ?selector coeus:query ?query . OPTIONAL { ?selector coeus:isKeyOf ?key } . OPTIONAL { ?selector coeus:regex ?regex }}"; queryToResult(qselectors, fillSelectors); - + //path is a resource + var qresourceEdit = "SELECT DISTINCT ?seed ?entity ?concept {" + path + " coeus:isResourceOf ?concept . ?concept coeus:hasEntity ?entity . ?entity coeus:isIncludedIn ?seed }"; + console.log(qresourceEdit); + queryToResult(qresourceEdit, fillBreadcumbEdit); //end of EDIT } else { //not showing selectores and built option if one resource is been add $('#selectorsForm').addClass('hide'); $('#builtForm').addClass('hide'); + + //path is a concept + var qresourceAdd = "SELECT DISTINCT ?seed ?entity {" + path + " coeus:hasEntity ?entity . ?entity coeus:isIncludedIn ?seed }"; + queryToResult(qresourceAdd, fillBreadcumbAdd); } @@ -162,8 +168,8 @@ + result[r].property.value + '' + regex + '' + '
    ' - + '' - + '' + + '' + + '' + '
    ' + ''; @@ -198,7 +204,7 @@ function editSelector(selector) { //document.getElementById('myModalLabel').value="Edit Selector"; $('#selectorsModalLabel').html("Edit Selector"); - $('#addSelectorButton').html("Edit"); + $('#addSelectorButton').html('Save '); console.log($('#selectorsModalLabel').html()); $('#selectorUri').html("coeus:" + selector); var q = "SELECT * {coeus:" + selector + " dc:title ?title . coeus:" + selector + " rdfs:label ?label . coeus:" + selector + " coeus:property ?property . coeus:" + selector + " coeus:query ?query . OPTIONAL { coeus:" + selector + " coeus:isKeyOf ?key } . OPTIONAL { coeus:" + selector + " coeus:regex ?regex }}"; @@ -235,12 +241,13 @@ //var query = initSparqlerQuery(); console.log('Remove: ' + selector); var urlPrefix = "../../../api/" + getApiKey(); + //remove all subjects associated. removeAllTriplesFromPredicateAndObject(urlPrefix,"coeus:loadsFrom", selector); removeAllTriplesFromPredicateAndObject(urlPrefix,"coeus:isKeyOf", selector); //remove all predicates and objects associated. removeAllTriplesFromSubject(urlPrefix, selector); - + } function updatePublisherOnSelectores(urlUpdate, res, oldPublisher, newPublisher) { var q = "SELECT * {" + res + " coeus:loadsFrom ?selector}"; @@ -482,6 +489,31 @@ //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; document.getElementById('selectorUri').innerHTML = 'coeus:selector_' + value.split(' ').join('_'); } + function fillBreadcumbAdd(result) { + console.log(result); + var seed = result[0].seed.value; + var entity = result[0].entity.value; + seed = "coeus:" + splitURIPrefix(seed).value; + entity = "coeus:" + splitURIPrefix(entity).value; + $('#breadSeed').html('Seed /'); + $('#breadEntities').html('Entities /'); + $('#breadConcepts').html('Concepts /'); + $('#breadResources').html('Resources /'); + } + function fillBreadcumbEdit(result) { + console.log("ERROR:"); + console.log(result); + var seed = result[0].seed.value; + var entity = result[0].entity.value; + var concept = result[0].concept.value; + seed = "coeus:" + splitURIPrefix(seed).value; + entity = "coeus:" + splitURIPrefix(entity).value; + concept = "coeus:" + splitURIPrefix(concept).value; + $('#breadSeed').html('Seed /'); + $('#breadEntities').html('Entities /'); + $('#breadConcepts').html('Concepts /'); + $('#breadResources').html('Resources /'); + } @@ -491,6 +523,15 @@
    +
      +
    • /
      • +
    • Seeds /
      • +
    • +
    • +
    • +
    • +
    • Resource
      • +

    Resource URI - coeus:

    @@ -513,7 +554,7 @@
    - +
    @@ -573,7 +614,7 @@
    - +



    @@ -677,7 +718,7 @@
    - +
    @@ -701,7 +742,7 @@ diff --git a/src/main/webapp/setup/addseed.jsp b/src/main/webapp/setup/addseed.jsp index db064f6..b6c9a4d 100644 --- a/src/main/webapp/setup/addseed.jsp +++ b/src/main/webapp/setup/addseed.jsp @@ -23,7 +23,7 @@ //if the type mode is EDIT if (penulPath() === 'edit') { $('#type').html("Edit Seed"); - $('#submit').html('Edit '); + $('#submit').html('Save '); var query = initSparqlerQuery(); var q = "SELECT ?label ?title {" + path + " dc:title ?title . " + path + " rdfs:label ?label . }"; @@ -126,6 +126,11 @@
    +

    Seed URI - coeus:

    @@ -147,7 +152,7 @@
    - +
    diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index 984f1d1..7fbef9e 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -32,7 +32,8 @@ var seed = result[0].seed.value; seed = "coeus:" + splitURIPrefix(seed).value; $('#breadSeed').html('Seed /'); - $('#breadEntity').html('Entities /'); + $('#breadEntities').html('Entities /'); + } function fillListOfConcepts(result) { for (var key in result) { @@ -41,10 +42,10 @@ + result[key].concept.value + '' + result[key].c.value + '' + '
    ' - + 'Edit' - + '' + + 'Edit ' + + '' + '
    ' - + ' Resources' + + ' Show Resources ' +' ' +' - + diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index f3887b1..7a841d3 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -147,7 +147,7 @@ "version": $('#Version').val(), "ontology": $('#Ontology').val(), "setup": $('#Setup').val(), - "sdb": "newsaggregator/sdb.ttl", + "sdb": "sdb.ttl", "predicates": "predicates.csv", "built": $('#Built').is(':checked'), "debug": $('#Debug').is(':checked'), @@ -289,10 +289,10 @@

    In this section you will give some information to complete some setup files for COEUS.

    To begin press the Start Wizard button.

    - Start Wizard + Start Wizard

    If you do not want to change the configurations files, please skip this wizard.

    - Skip + Skip
    @@ -314,7 +314,7 @@
    - Create + Create
    @@ -431,7 +431,7 @@
    - Next > + Next
    @@ -525,7 +525,7 @@
    - Next > + Next
    @@ -557,10 +557,10 @@
    - +
    - Next > + Next
    @@ -569,14 +569,14 @@

    In order to save your progress press the Save button, please.

    Warning: If you leaves this wizard without save it, some configurations will be lost.

    - +

    After saving the configurations you can start build the model for your application:

    - Build Model + Build Model
    @@ -608,7 +608,7 @@
    - +
    diff --git a/src/main/webapp/setup/entities.jsp b/src/main/webapp/setup/entities.jsp index eff58a5..3e165eb 100644 --- a/src/main/webapp/setup/entities.jsp +++ b/src/main/webapp/setup/entities.jsp @@ -44,10 +44,10 @@ + json.results.bindings[key].entity.value + '' + json.results.bindings[key].e.value + '' + '
    ' - + 'Edit' - + '' + + 'Edit ' + + '' + '
    ' - + ' View Concepts' + + ' Show Concepts ' //+ 'Remove' + ''; $('#entities').append(a); @@ -77,6 +77,8 @@ @@ -89,7 +91,7 @@
    - Add Entity + Add Entity
    @@ -129,7 +131,7 @@
    - +
    diff --git a/src/main/webapp/setup/environments.jsp b/src/main/webapp/setup/environments.jsp index 979e445..d6d47e4 100644 --- a/src/main/webapp/setup/environments.jsp +++ b/src/main/webapp/setup/environments.jsp @@ -27,10 +27,11 @@ var n = parseInt(r) + 1; $('#environments').append('' + (n) + '' + value + 'DISABLED' + '
    ' - + '' + + '' + '
    ' - + 'Configuration ' - + 'Enable' + + 'Configuration ' + + 'Clean DB ' + + 'Enable ' + ''); } callURL("../../config/getconfig/", changeStatus); @@ -78,9 +79,8 @@ } function selectEnv(env) { - + $('#cleanModalLabel').html(env); $('#removeModalLabel').html(env); - console.log($('#removeModalLabel').html()); } function removeEnv() { callURL("../../config/delenv/" + $('#removeModalLabel').html(), removeEnvResult); @@ -88,6 +88,16 @@ function removeEnvResult(result) { callURL("../../config/listenv/", fillEnvironments); } + function cleanDB() { + callURL("../../config/cleandb/" + $('#cleanModalLabel').html(), cleanDBResult); + } + function cleanDBResult(result) { + if (result.status === 100) { + $('#info').html(generateHtmlMessage("Success!", result.message, "alert-success")); + } else { + $('#info').html(generateHtmlMessage("Warning!", result.message)); + } + } @@ -105,16 +115,17 @@
    - +
    +

    ATTENTION: Every change in this page needs a server restart.

    List of Environments

    - Create Environment + Create Environment
    @@ -158,6 +169,28 @@
    + + +
    - Change environment + Change environment
    @@ -220,7 +224,7 @@
    - Manage Entities + Show Entities
    diff --git a/src/main/webapp/setup/resources.jsp b/src/main/webapp/setup/resources.jsp index 2b45299..dac5f8a 100644 --- a/src/main/webapp/setup/resources.jsp +++ b/src/main/webapp/setup/resources.jsp @@ -34,8 +34,8 @@ seed = "coeus:" + splitURIPrefix(seed).value; entity = "coeus:" + splitURIPrefix(entity).value; $('#breadSeed').html('Seed /'); - $('#breadEntity').html('Entities /'); - $('#breadConcept').html('Concepts /'); + $('#breadEntities').html('Entities /'); + $('#breadConcepts').html('Concepts /'); } function fillListOfResources(result) { for (var key = 0, size = result.length; key < size; key++) { @@ -47,8 +47,8 @@ + result[key].c.value + '' + result[key].order.value + '' //+ '
    ' - + ' ' - + 'Configuration ' + + ' ' + + 'Configuration ' //+ '
    ' //+ ' Selectors' //+ 'Remove' @@ -85,9 +85,11 @@
      +
    • /
      • +
    • Seeds /
    • -
    • -
    • +
    • +
    • Resources
    @@ -96,7 +98,7 @@
    - Add Resource + Add Resource
    @@ -137,7 +139,7 @@
    - +
    diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index 5cd39f6..8418f14 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -28,7 +28,7 @@ var seed=getPrefix(splitedURI.namespace)+':'+splitedURI.value; var a = '
  • ' - +'Select' + +'Choose ' +'

    '+result[key].s.value+'

    ' +'URI: '+seed+'' +'' @@ -72,12 +72,16 @@

    Please, choose the seed:

    +
      +
    • /
      • +
    • Seeds
      • +
    - Add + Add Seed
      @@ -104,7 +108,7 @@
      - +
    From d1ffbeda7905811b89da9088d47851fed4a29634 Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 29 Aug 2013 17:56:52 +0100 Subject: [PATCH 28/52] - Setup: Add Enter keyboard key when add or edit - Setup: Fix Resource extensions to only allow concepts from same seed - Setup: Fix LinkedData links to local instance - Setup: Show the selected environment on all pages --- src/main/webapp/setup/addconcept.jsp | 41 +++++-- src/main/webapp/setup/addentity.jsp | 31 ++++-- src/main/webapp/setup/addresource.jsp | 53 +++++---- src/main/webapp/setup/addseed.jsp | 26 +++-- src/main/webapp/setup/concepts.jsp | 13 +-- src/main/webapp/setup/entities.jsp | 15 ++- src/main/webapp/setup/index.jsp | 11 +- src/main/webapp/setup/resources.jsp | 12 ++- src/main/webapp/setup/seeds.jsp | 150 +++++++++++++------------- 9 files changed, 214 insertions(+), 138 deletions(-) diff --git a/src/main/webapp/setup/addconcept.jsp b/src/main/webapp/setup/addconcept.jsp index 5dad22f..047585d 100644 --- a/src/main/webapp/setup/addconcept.jsp +++ b/src/main/webapp/setup/addconcept.jsp @@ -18,14 +18,17 @@ //header name var path = lastPath(); - $('#header').html('

    ' + path + ' env..

    '); - var qconcept = "SELECT DISTINCT ?seed {" + path + " coeus:isIncludedIn ?seed }"; - queryToResult(qconcept, fillBreadcumb); + callURL("../../../config/getconfig/", fillHeader); + //Associate Enter key: + document.onkeypress = keyboard; //if the type mode is EDIT if (penulPath() === 'edit') { $('#type').html("Edit Concept"); $('#submit').html('Save '); + + var qconcept = "SELECT DISTINCT ?seed ?entity {" + path + " coeus:hasEntity ?entity . ?entity coeus:isIncludedIn ?seed }"; + queryToResult(qconcept, fillBreadcumbEdit); var query = initSparqlerQuery(); var q = "SELECT ?title ?label {" + path + " dc:title ?title . " + path + " rdfs:label ?label . }"; @@ -33,7 +36,6 @@ {success: function(json) { //var resultTitle = json.results.bindings[0].title; console.log(json); - $('#header').html('

    ' + path + ' env..

    '); //PUT VALUES IN THE INPUT FIELD $('#title').val(json.results.bindings[0].title.value); changeURI(json.results.bindings[0].title.value); @@ -46,14 +48,23 @@ //$('#commentForm').append(''); }} ); + }else{ + var qconcept = "SELECT DISTINCT ?seed {" + path + " coeus:isIncludedIn ?seed }"; + queryToResult(qconcept, fillBreadcumbAdd); } //end of EDIT //activate tooltip (bootstrap-tooltip.js is need) $('.icon-question-sign').tooltip(); }); + + // Callback to generate the pages header + function fillHeader(result) { + $('#header').html('

    ' + lastPath() + ' ' + result.config.environment + '

    '); + } - $('#submit').click(function() { + $('#submit').click(testMode); + function testMode() { //EDIT if (penulPath() === 'edit') { update(); @@ -69,7 +80,7 @@ window.location = document.referrer; } - }); + } function submit() { @@ -124,13 +135,27 @@ //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; document.getElementById('uri').innerHTML = 'coeus:concept_' + value.split(' ').join('_'); } - function fillBreadcumb(result) { + function fillBreadcumbAdd(result) { var seed = result[0].seed.value; seed = "coeus:" + splitURIPrefix(seed).value; $('#breadSeed').html('Seed /'); $('#breadEntities').html('Entities /'); $('#breadConcepts').html('Concepts /'); } + function fillBreadcumbEdit(result) { + var seed = result[0].seed.value; + seed = "coeus:" + splitURIPrefix(seed).value; + var entity = result[0].entity.value; + entity = "coeus:" + splitURIPrefix(entity).value; + $('#breadSeed').html('Dashboard /'); + $('#breadEntities').html('Entities /'); + $('#breadConcepts').html('Concepts /'); + } + function keyboard(event) { + //Enter key pressed + if (event.charCode === 13) + testMode(); + } @@ -148,7 +173,7 @@
  • Concept
    • -

    Concept URI - coeus:

    +

    Concept URI - coeus:

    New Concept

    diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp index 765c3c3..9f60152 100644 --- a/src/main/webapp/setup/addentity.jsp +++ b/src/main/webapp/setup/addentity.jsp @@ -18,10 +18,12 @@ //header name var path = lastPath(); - $('#header').html('

    ' + path + ' env..

    '); - $('#breadSeed').html('Seed / '); - $('#breadEntities').html('Entities / '); - + callURL("../../../config/getconfig/", fillHeader); + $('#breadSeed').html('Dashboard / '); + $('#breadEntities').html('Entities / '); + + //Associate Enter key: + document.onkeypress = keyboard; //if the type mode is EDIT if (penulPath() === 'edit') { @@ -34,7 +36,6 @@ {success: function(json) { //var resultTitle = json.results.bindings[0].title; console.log(json); - $('#header').html('

    ' + path + ' env..

    '); //PUT VALUES IN THE INPUT FIELD $('#title').val(json.results.bindings[0].title.value); changeURI(json.results.bindings[0].title.value); @@ -54,7 +55,13 @@ $('.icon-question-sign').tooltip(); }); - $('#submit').click(function() { + // Callback to generate the pages header + function fillHeader(result) { + $('#header').html('

    ' + lastPath() + ' ' + result.config.environment + '

    '); + } + + $('#submit').click(testMode); + function testMode() { //EDIT if (penulPath() === 'edit') { update(); @@ -70,8 +77,7 @@ window.location = document.referrer; } - }); - + } function submit() { var type = 'Entity'; @@ -133,6 +139,11 @@ //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; document.getElementById('uri').innerHTML = 'coeus:entity_' + value.split(' ').join('_'); } + function keyboard(event) { + //Enter key pressed + if (event.charCode === 13) + testMode(); + } @@ -142,14 +153,14 @@
    -
      + -

      Entity URI - coeus:

      +

      Entity URI - coeus:

      New Entity:

      diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 93d5c1a..a631749 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -17,16 +17,13 @@ //header name var path = lastPath(); - $('#header').html('

      ' + path + ' env..

      '); - - - //fill the concepts extensions - var q = "SELECT ?concept ?c {?concept a coeus:Concept . ?concept dc:title ?c}"; - queryToResult(q, fillConceptsExtension); + callURL("../../../config/getconfig/", fillHeader); + //Associate Enter key: + document.onkeypress = keyboard; //if the type mode is EDIT if (penulPath() === 'edit') { - $('#type').html("Edit Resource"); + $('#type').html("Resource"); $('#submit').html('Save '); var query = initSparqlerQuery(); @@ -35,7 +32,6 @@ {success: function(json) { //var resultTitle = json.results.bindings[0].title; console.log(json); - $('#header').html('

      ' + path + ' env..

      '); //PUT VALUES IN THE INPUT FIELD $('#title').val(json.results.bindings[0].title.value); changeURI(json.results.bindings[0].title.value); @@ -71,6 +67,9 @@ var qselectors = "SELECT * {" + path + " coeus:loadsFrom ?selector . ?selector dc:title ?title . ?selector rdfs:label ?label . ?selector coeus:property ?property . ?selector coeus:query ?query . OPTIONAL { ?selector coeus:isKeyOf ?key } . OPTIONAL { ?selector coeus:regex ?regex }}"; queryToResult(qselectors, fillSelectors); + var q="SELECT ?concept ?c {?concept_aux coeus:hasResource "+path+" . ?entity coeus:isEntityOf ?concept_aux . ?seed coeus:includes ?entity . ?concept coeus:hasEntity ?ent . ?ent coeus:isIncludedIn ?seed . ?concept dc:title ?c}"; + queryToResult(q, fillConceptsExtension); + //path is a resource var qresourceEdit = "SELECT DISTINCT ?seed ?entity ?concept {" + path + " coeus:isResourceOf ?concept . ?concept coeus:hasEntity ?entity . ?entity coeus:isIncludedIn ?seed }"; console.log(qresourceEdit); @@ -81,9 +80,13 @@ $('#selectorsForm').addClass('hide'); $('#builtForm').addClass('hide'); + //path is a concept var qresourceAdd = "SELECT DISTINCT ?seed ?entity {" + path + " coeus:hasEntity ?entity . ?entity coeus:isIncludedIn ?seed }"; queryToResult(qresourceAdd, fillBreadcumbAdd); + + var q="SELECT ?concept ?c {?entity coeus:isEntityOf "+path+" . ?seed coeus:includes ?entity . ?concept coeus:hasEntity ?ent . ?ent coeus:isIncludedIn ?seed . ?concept dc:title ?c}"; + queryToResult(q, fillConceptsExtension); } @@ -101,7 +104,9 @@ }); - $('#submit').click(function() { + $('#submit').click(testMode); + + function testMode() { //EDIT if (penulPath() === 'edit') { update(); @@ -111,7 +116,7 @@ } - }); + } function fillExitingSelectors(result){console.log(result); @@ -490,7 +495,6 @@ document.getElementById('selectorUri').innerHTML = 'coeus:selector_' + value.split(' ').join('_'); } function fillBreadcumbAdd(result) { - console.log(result); var seed = result[0].seed.value; var entity = result[0].entity.value; seed = "coeus:" + splitURIPrefix(seed).value; @@ -501,19 +505,30 @@ $('#breadResources').html('Resources /'); } function fillBreadcumbEdit(result) { - console.log("ERROR:"); - console.log(result); var seed = result[0].seed.value; var entity = result[0].entity.value; var concept = result[0].concept.value; seed = "coeus:" + splitURIPrefix(seed).value; entity = "coeus:" + splitURIPrefix(entity).value; concept = "coeus:" + splitURIPrefix(concept).value; - $('#breadSeed').html('Seed /'); + $('#breadSeed').html('Dashboard /'); $('#breadEntities').html('Entities /'); $('#breadConcepts').html('Concepts /'); $('#breadResources').html('Resources /'); } + function keyboard(event) { + //Enter key pressed + if (event.charCode === 13) + testMode(); + } + + function publisherChange(){ + console.log($('#publisher').val()); + } + // Callback to generate the pages header + function fillHeader(result) { + $('#header').html('

      ' + lastPath() + ' ' + result.config.environment + '

      '); + } @@ -532,7 +547,7 @@
    • Resource
    -

    Resource URI - coeus:

    +

    Resource URI - coeus:

    @@ -600,12 +615,12 @@
    - - + + +
    diff --git a/src/main/webapp/setup/addseed.jsp b/src/main/webapp/setup/addseed.jsp index b6c9a4d..eb1e642 100644 --- a/src/main/webapp/setup/addseed.jsp +++ b/src/main/webapp/setup/addseed.jsp @@ -16,6 +16,9 @@ $(document).ready(function() { + //Associate Enter key: + document.onkeypress = keyboard; + //header name var path = lastPath(); $('#header').html('

    COEUS env..

    '); @@ -51,7 +54,9 @@ $('.icon-question-sign').tooltip(); }); - $('#submit').click(function() { + $('#submit').click(testMode); + + function testMode() { //EDIT if (penulPath() === 'edit') { update(); @@ -67,7 +72,7 @@ window.location = document.referrer; } - }); + } function submit() { @@ -110,13 +115,18 @@ var urlUpdate = "../../../api/" + getApiKey() + "/update/"; if ($('#oldLabel').val() !== $('#label').val()) callAPI(urlUpdate + lastPath() + "/" + "rdfs:label" + "/xsd:string:" + $('#oldLabel').val() + ",xsd:string:" + $('#label').val(), '#result'); - + } function changeURI(value) { //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; document.getElementById('uri').innerHTML = 'coeus:seed_' + value.split(' ').join('_'); } + function keyboard(event) { + //Enter key pressed + if (event.charCode === 13) + testMode(); + } @@ -131,7 +141,7 @@
  • Seeds /
  • Seed
    • -

    Seed URI - coeus:

    +

    Seed URI - coeus:

    New Seed:

    @@ -156,10 +166,10 @@
    - +
    diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index 7fbef9e..de5bcbe 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -12,7 +12,10 @@ @@ -79,55 +79,55 @@
    -
    +
    Add Seed
      - +
    - - - - - -
    - +
    +
    + + + Driver: + +
    + Host: + +
    + DB Name: + + Port: + +
    + Login: + + + +
    +
    + + + + +
    From 893741cc6000fe75e8738f38bdf57108eac09f02 Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 4 Sep 2013 10:04:58 +0100 Subject: [PATCH 30/52] - Setup: Fix footer --- src/main/webapp/layout/html.jsp | 9 ++--- src/main/webapp/setup/addresource.jsp | 50 +++++++++++++++------------ src/main/webapp/setup/concepts.jsp | 2 +- src/main/webapp/setup/config.jsp | 2 +- src/main/webapp/setup/entities.jsp | 2 +- src/main/webapp/setup/html.jsp | 41 +++++++++++----------- src/main/webapp/setup/resources.jsp | 2 +- 7 files changed, 57 insertions(+), 51 deletions(-) diff --git a/src/main/webapp/layout/html.jsp b/src/main/webapp/layout/html.jsp index 667d9d5..fe267aa 100644 --- a/src/main/webapp/layout/html.jsp +++ b/src/main/webapp/layout/html.jsp @@ -51,7 +51,7 @@
    - COEUS, A/C Pedro Lopes
    + COEUS, A/C Pedro Lopes & Pedro Sernadela
    DETI/IEETA, University of Aveiro
    Campus Universitario de Santiago
    3810 - 193 Aveiro
    @@ -65,7 +65,9 @@ -
    + + + - diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 0534d76..88e5cdc 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -381,7 +381,7 @@ $('#endpointForm').addClass('controls control-group error'); empty = true; } - if (query === '' && publisher!== ("csv")) { + if (query === '' && publisher !== ("csv")) { $('#queryForm').addClass('controls control-group error'); empty = true; } @@ -533,15 +533,19 @@ //Endpoint example: jdbc:mysql://host:3306;database=name;user=user;password=pass if (endpoint !== "") { - var url = endpoint.split("://"); - var driver = url[0].split("jdbc:")[1]; - var cut = url[1].split(":"); - var host = cut[0]; - var cut2 = cut[1].split(";"); - var port = cut2[0]; - var db = cut2[1].split("database=")[1]; - var user = cut2[2].split("user=")[1]; - var password = cut2[3].split("password=")[1]; + try { + var url = endpoint.split("://"); + var driver = url[0].split("jdbc:")[1]; + var cut = url[1].split(":"); + var host = cut[0]; + var cut2 = cut[1].split(";"); + var port = cut2[0]; + var db = cut2[1].split("database=")[1]; + var user = cut2[2].split("user=")[1]; + var password = cut2[3].split("password=")[1]; + } catch (e) { + //ignore errors + } $('#driverEndpoint').val(driver); $('#hostEndpoint').val(host); @@ -555,20 +559,20 @@ $('#sqlEndpointForm').addClass('hide'); $('#endpointForm').removeClass('hide'); } - - if(publisher === "csv"){ + + if (publisher === "csv") { $('#queryForm').addClass('hide'); $('#csvQueryForm').removeClass('hide'); var query = $('#query').val(); - - if (query !== "") { - var q=query.split("|"); + + if (query !== "") { + var q = query.split("|"); $('#csvQueryColumn').val(q[0]); $('#csvQueryDelimiter').val(q[1]); $('#csvQueryHeaderSkip').val(q[2]); } - + } else { $('#csvQueryForm').addClass('hide'); @@ -589,12 +593,12 @@ var endpoint = "jdbc:" + $('#driverEndpoint').val() + "://" + $('#hostEndpoint').val() + port + ";database=" + $('#dbEndpoint').val() + user + password; $('#endpoint').val(endpoint); } - - function refreshQuery(){ - var tab=$('#csvQueryColumn').val().slice(-1); - var delimiter=$('#csvQueryDelimiter').val().slice(-1); - var header=$('#csvQueryHeaderSkip').val().slice(-1); - $('#query').val(tab+"|"+delimiter+"|"+header); + + function refreshQuery() { + var tab = $('#csvQueryColumn').val().slice(-1); + var delimiter = $('#csvQueryDelimiter').val().slice(-1); + var header = $('#csvQueryHeaderSkip').val().slice(-1); + $('#query').val(tab + "|" + delimiter + "|" + header); } // Callback to generate the pages header @@ -729,7 +733,7 @@ DB Name: Port: - +
    Login: diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index de5bcbe..edb19ac 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -163,6 +163,6 @@
    - + diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 7a841d3..78938a1 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -613,7 +613,7 @@ - + diff --git a/src/main/webapp/setup/entities.jsp b/src/main/webapp/setup/entities.jsp index aaa439a..8c6c7a8 100644 --- a/src/main/webapp/setup/entities.jsp +++ b/src/main/webapp/setup/entities.jsp @@ -143,6 +143,6 @@ - + diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 0ce55a6..8a7f20a 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -6,7 +6,7 @@ " /> "> - + <s:layout-component name="title">COEUS Setup</s:layout-component> @@ -34,7 +34,7 @@ @@ -59,8 +59,7 @@
    - Pedro Lopes
    - @pedrolopes
    + COEUS, A/C Pedro Lopes & Pedro Sernadela
    DETI/IEETA, University of Aveiro
    Campus Universitario de Santiago
    3810 - 193 Aveiro
    @@ -69,32 +68,34 @@
    - Send Mail + Send Mail
    - - + + + + \ No newline at end of file diff --git a/src/main/webapp/setup/resources.jsp b/src/main/webapp/setup/resources.jsp index 66d879a..b1df7c2 100644 --- a/src/main/webapp/setup/resources.jsp +++ b/src/main/webapp/setup/resources.jsp @@ -148,6 +148,6 @@ - +     From cb6881a4f21050bb2502f7c43a341510dcce1eba Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 4 Sep 2013 16:00:29 +0100 Subject: [PATCH 31/52] - Setup: Fix resource duplication (done by built property) --- .../pt/ua/bioinformatics/coeus/data/connect/SQLFactory.java | 3 +++ src/main/webapp/setup/config.jsp | 6 +++--- src/main/webapp/setup/html.jsp | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SQLFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SQLFactory.java index 3cbb8fa..6450b48 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SQLFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SQLFactory.java @@ -1,5 +1,6 @@ package pt.ua.bioinformatics.coeus.data.connect; +import com.hp.hpl.jena.rdf.model.Statement; import java.sql.ResultSet; import java.util.ArrayList; import java.util.HashMap; @@ -212,6 +213,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 78938a1..e129bfd 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -284,9 +284,9 @@
  • Prefixes
  • Finish
    • -
    -
    -
    +
    +
    +

    In this section you will give some information to complete some setup files for COEUS.

    To begin press the Start Wizard button.

    Start Wizard diff --git a/src/main/webapp/setup/html.jsp b/src/main/webapp/setup/html.jsp index 8a7f20a..0f5e95b 100644 --- a/src/main/webapp/setup/html.jsp +++ b/src/main/webapp/setup/html.jsp @@ -83,7 +83,7 @@
    -
    +
    Back to top

     

    COEUS Setup Beta From 4eb8a7947998ddedaa5ac933ce5c02ea15e01eb3 Mon Sep 17 00:00:00 2001 From: sernadela Date: Thu, 5 Sep 2013 15:03:28 +0100 Subject: [PATCH 32/52] - Setup: Added Rebuild and Unbuild options - Setup: Changed apikey to work correctly from the config.js file - Setup: Fix the resource build duplication in all Factories. - Setup: Changed CSVFactory to use always the guessDelimiter function. --- .../coeus/actions/ConfigActionBean.java | 20 +++++++- .../coeus/actions/UpdateActionBean.java | 2 +- .../coeus/data/connect/CSVFactory.java | 51 ++++--------------- .../coeus/data/connect/JSONFactory.java | 3 ++ .../coeus/data/connect/LinkedDataFactory.java | 3 ++ .../coeus/data/connect/RDFFactory.java | 3 ++ .../coeus/data/connect/SPARQLFactory.java | 3 ++ .../coeus/data/connect/XMLFactory.java | 3 ++ src/main/webapp/assets/js/coeus.api.js | 8 ++- src/main/webapp/setup/addconcept.jsp | 2 + src/main/webapp/setup/addentity.jsp | 2 + src/main/webapp/setup/addresource.jsp | 44 ++++++++-------- src/main/webapp/setup/addseed.jsp | 9 +++- src/main/webapp/setup/concepts.jsp | 2 + src/main/webapp/setup/entities.jsp | 3 +- src/main/webapp/setup/index.jsp | 37 ++++++++++++-- src/main/webapp/setup/resources.jsp | 2 + src/main/webapp/setup/seeds.jsp | 7 ++- 18 files changed, 132 insertions(+), 72 deletions(-) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index afb72fe..0dcc9ab 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -103,9 +103,27 @@ public Resolution handle() { * @return */ public Resolution getconfig() { - Boot.start(); + Config.load(); return new StreamingResolution("application/json", Config.getFile().toJSONString()); } + + /** + * Build (Boot.start() call) + * + * @return + */ + public Resolution build() { + JSONObject result = new JSONObject(); + try { + Boot.start(); + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] Build done. "); + } catch (Exception e) { + result.put("status", 201); + result.put("message", "[COEUS][API][ConfigActionBean] Exception: "+e); + } + return new StreamingResolution("application/json", result.toJSONString()); + } /** * Cleans the DB of one environment (method) diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java index c89a702..7174ecb 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java @@ -108,7 +108,7 @@ public Resolution handle() { if (sub.indexOf(":") > 1) { try { if (pred.indexOf(":") > 1) { - System.err.println(old_obj+","+new_obj); + System.err.println(old_obj+" , "+new_obj); // test old_obj String xsd = "http://www.w3.org/2001/XMLSchema#"; Statement statToRemove = null; diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java index 961f554..b21a0fb 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java @@ -1,6 +1,7 @@ package pt.ua.bioinformatics.coeus.data.connect; import au.com.bytecode.opencsv.CSVReader; +import com.hp.hpl.jena.rdf.model.Statement; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; @@ -91,17 +92,9 @@ public void read() { reader = new CSVReader(in, csvDelimiter, defaultCsvQuotes, defaultCsvHeader); } else { String[] csvKeys = res.getQuery().split("\\|"); - char querySeparator = csvKeys[0].charAt(0); char queryQuotes = csvKeys[1].charAt(0); - char queryLinesSkip = csvKeys[2].charAt(0); - - //Fix that - if (querySeparator == 't') { - querySeparator = '\t'; - } - if (querySeparator == 'n') { - querySeparator = '\n'; - } + char queryLinesSkip = csvKeys[0].charAt(0); + char querySeparator = guessDelimiter(u, queryQuotes, queryLinesSkip); //System.out.println(res.getQuery() + " - " +querySeparator+ queryQuotes + queryLinesSkip); reader = new CSVReader(in, querySeparator, queryQuotes, queryLinesSkip); @@ -147,17 +140,9 @@ public void read() { reader = new CSVReader(in, csvDelimiter, defaultCsvQuotes, defaultCsvHeader); } else { String[] csvKeys = res.getQuery().split("\\|"); - char querySeparator = csvKeys[0].charAt(0); char queryQuotes = csvKeys[1].charAt(0); - char queryLinesSkip = csvKeys[2].charAt(0); - - //Fix that - if (querySeparator == 't') { - querySeparator = '\t'; - } - if (querySeparator == 'n') { - querySeparator = '\n'; - } + char queryLinesSkip = csvKeys[0].charAt(0); + char querySeparator = guessDelimiter(u, queryQuotes, queryLinesSkip); //System.out.println(res.getQuery() + " - " +querySeparator+ queryQuotes + queryLinesSkip); reader = new CSVReader(in, querySeparator, queryQuotes, queryLinesSkip); @@ -195,17 +180,9 @@ public void read() { reader = new CSVReader(in, csvDelimiter, defaultCsvQuotes, defaultCsvHeader); } else { String[] csvKeys = res.getQuery().split("\\|"); - char querySeparator = csvKeys[0].charAt(0); char queryQuotes = csvKeys[1].charAt(0); - char queryLinesSkip = csvKeys[2].charAt(0); - - //Fix that - if (querySeparator == 't') { - querySeparator = '\t'; - } - if (querySeparator == 'n') { - querySeparator = '\n'; - } + char queryLinesSkip = csvKeys[0].charAt(0); + char querySeparator = guessDelimiter(u, queryQuotes, queryLinesSkip); //System.out.println(res.getQuery() + " - " +querySeparator+ queryQuotes + queryLinesSkip); reader = new CSVReader(in, querySeparator, queryQuotes, queryLinesSkip); @@ -258,17 +235,9 @@ public void read() { reader = new CSVReader(in, csvDelimiter, defaultCsvQuotes, defaultCsvHeader); } else { String[] csvKeys = res.getQuery().split("\\|"); - char querySeparator = csvKeys[0].charAt(0); char queryQuotes = csvKeys[1].charAt(0); - char queryLinesSkip = csvKeys[2].charAt(0); - - //Fix that - if (querySeparator == 't') { - querySeparator = '\t'; - } - if (querySeparator == 'n') { - querySeparator = '\n'; - } + char queryLinesSkip = csvKeys[0].charAt(0); + char querySeparator = guessDelimiter(u, queryQuotes, queryLinesSkip); //System.out.println(res.getQuery() + " - " + querySeparator + queryQuotes + queryLinesSkip); reader = new CSVReader(in, querySeparator, queryQuotes, queryLinesSkip); @@ -325,6 +294,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/JSONFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/JSONFactory.java index 04b15e5..4d4ee47 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/JSONFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/JSONFactory.java @@ -4,6 +4,7 @@ */ package pt.ua.bioinformatics.coeus.data.connect; +import com.hp.hpl.jena.rdf.model.Statement; import com.jayway.jsonpath.JsonPath; import java.io.InputStreamReader; import java.net.URL; @@ -270,6 +271,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/LinkedDataFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/LinkedDataFactory.java index 9293483..7663441 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/LinkedDataFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/LinkedDataFactory.java @@ -4,6 +4,7 @@ */ package pt.ua.bioinformatics.coeus.data.connect; +import com.hp.hpl.jena.rdf.model.Statement; import java.net.URL; import java.net.URLConnection; import java.util.HashMap; @@ -115,6 +116,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/RDFFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/RDFFactory.java index fb55b8c..c1e6ab2 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/RDFFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/RDFFactory.java @@ -8,6 +8,7 @@ import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.util.iterator.ExtendedIterator; import java.net.URL; import java.net.URLConnection; @@ -158,6 +159,8 @@ public boolean save() { boolean success = false; try { com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SPARQLFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SPARQLFactory.java index 4b814ae..d178ab2 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SPARQLFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/SPARQLFactory.java @@ -6,6 +6,7 @@ import com.hp.hpl.jena.query.QuerySolution; import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.query.Syntax; +import com.hp.hpl.jena.rdf.model.Statement; import java.util.ArrayList; import java.util.HashMap; import java.util.logging.Level; @@ -159,6 +160,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/XMLFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/XMLFactory.java index ac18057..918921e 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/XMLFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/XMLFactory.java @@ -1,5 +1,6 @@ package pt.ua.bioinformatics.coeus.data.connect; +import com.hp.hpl.jena.rdf.model.Statement; import java.net.URL; import java.net.URLEncoder; import java.util.HashMap; @@ -277,6 +278,8 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); + Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; if (Config.isDebug()) { diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index c992104..189cebc 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -158,8 +158,12 @@ function callAPI(url, html) { // Server communication error function handler. }); } +/** +* Return the first apikey +* + * @returns {unresolved} */ function getApiKey() { - return "coeus"; + return document.getElementById('apikey').innerHTML.split('|')[0]; } /** * Return last element divided by / of url @@ -443,7 +447,7 @@ function removeById(childDiv, parentDiv) } function callURL(url, success, error) { - url = encodeURI(url); + url = encodeURI(url);console.log(url); $.ajax({url: url, dataType: 'json'}).done(success).fail(error); } diff --git a/src/main/webapp/setup/addconcept.jsp b/src/main/webapp/setup/addconcept.jsp index 047585d..00b01be 100644 --- a/src/main/webapp/setup/addconcept.jsp +++ b/src/main/webapp/setup/addconcept.jsp @@ -61,6 +61,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

    ' + lastPath() + ' ' + result.config.environment + '

    '); + $('#apikey').html(result.config.apikey); } $('#submit').click(testMode); @@ -165,6 +166,7 @@
    +
    • /
    • Seeds /
      • diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp index 9f60152..2f7e39c 100644 --- a/src/main/webapp/setup/addentity.jsp +++ b/src/main/webapp/setup/addentity.jsp @@ -58,6 +58,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

      ' + lastPath() + ' ' + result.config.environment + '

      '); + $('#apikey').html(result.config.apikey); } $('#submit').click(testMode); @@ -153,6 +154,7 @@
      +
      • /
      • Seeds /
        • diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 88e5cdc..6b1d772 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -494,7 +494,7 @@ } function changeSelectorURI(value) { //var specialChars = "!@#$^&%*()+=-[]\/{}|:<>?,. "; - document.getElementById('selectorUri').innerHTML = 'coeus:selector_' + value.split(' ').join('_'); + document.getElementById('selectorUri').innerHTML = 'coeus:selector_' + $('#concept').html().replace('coeus:concept_','')+'_' + value.split(' ').join('_'); } function fillBreadcumbAdd(result) { var seed = result[0].seed.value; @@ -517,6 +517,7 @@ $('#breadEntities').html('Entities /'); $('#breadConcepts').html('Concepts /'); $('#breadResources').html('Resources /'); + $('#concept').html(splitURIPrefix(concept).value); } function keyboard(event) { //Enter key pressed @@ -568,9 +569,11 @@ if (query !== "") { var q = query.split("|"); - $('#csvQueryColumn').val(q[0]); $('#csvQueryDelimiter').val(q[1]); - $('#csvQueryHeaderSkip').val(q[2]); + $('#csvQueryHeaderSkip').val(q[0]); + } else { + $('#csvQueryHeaderSkip').val("1"); + refreshQuery(); } } @@ -595,15 +598,16 @@ } function refreshQuery() { - var tab = $('#csvQueryColumn').val().slice(-1); - var delimiter = $('#csvQueryDelimiter').val().slice(-1); - var header = $('#csvQueryHeaderSkip').val().slice(-1); - $('#query').val(tab + "|" + delimiter + "|" + header); + + var delimiter = $('#csvQueryDelimiter').val(); + var header = $('#csvQueryHeaderSkip').val(); + $('#query').val(header + "|" + delimiter); } // Callback to generate the pages header function fillHeader(result) { $('#header').html('

        ' + lastPath() + ' ' + result.config.environment + '

        '); + $('#apikey').html(result.config.apikey); } @@ -614,6 +618,8 @@
        +
        +
        • /
        • Seeds /
          • @@ -721,22 +727,21 @@
          - Driver: + jdbc: -
          - Host: + :// -
          - DB Name: - - Port: + : + / + +
          Login: - +
          @@ -745,15 +750,12 @@
    - - + +
    @@ -811,7 +813,7 @@

    Add Selector

    -

    Selector URI - coeus:

    +

    Selector URI - coeus:

    diff --git a/src/main/webapp/setup/addseed.jsp b/src/main/webapp/setup/addseed.jsp index eb1e642..1ae4eb5 100644 --- a/src/main/webapp/setup/addseed.jsp +++ b/src/main/webapp/setup/addseed.jsp @@ -21,7 +21,7 @@ //header name var path = lastPath(); - $('#header').html('

    COEUS env..

    '); + callURL("../../../config/getconfig/", fillHeader); //if the type mode is EDIT if (penulPath() === 'edit') { @@ -34,7 +34,6 @@ {success: function(json) { //var resultTitle = json.results.bindings[0].title; console.log(json); - $('#header').html('

    ' + path + ' env..

    '); //PUT VALUES IN THE INPUT FIELD $('#title').val(json.results.bindings[0].title.value); changeURI(json.results.bindings[0].title.value); @@ -53,6 +52,11 @@ //activate tooltip (bootstrap-tooltip.js is need) $('.icon-question-sign').tooltip(); }); + + function fillHeader(result){ + $('#header').html('

    Seed ' + result.config.environment + '

    '); + $('#apikey').html(result.config.apikey); + } $('#submit').click(testMode); @@ -136,6 +140,7 @@
    +
    • /
    • Seeds /
      • diff --git a/src/main/webapp/setup/concepts.jsp b/src/main/webapp/setup/concepts.jsp index edb19ac..3079992 100644 --- a/src/main/webapp/setup/concepts.jsp +++ b/src/main/webapp/setup/concepts.jsp @@ -15,6 +15,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

      ' + lastPath() + ' ' + result.config.environment + '

      '); + $('#apikey').html(result.config.apikey); } function selectConcept(concept) { $('#removeModalLabel').html('coeus:concept_' + concept.split(' ').join('_')); @@ -105,6 +106,7 @@
      +
      • /
      • Seeds /
        • diff --git a/src/main/webapp/setup/entities.jsp b/src/main/webapp/setup/entities.jsp index 8c6c7a8..b51a7ba 100644 --- a/src/main/webapp/setup/entities.jsp +++ b/src/main/webapp/setup/entities.jsp @@ -32,6 +32,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

        ' + lastPath() + ' ' + result.config.environment + '

        '); + $('#apikey').html(result.config.apikey); } $(document).ready(function() { @@ -82,7 +83,7 @@
        - +
        • /
        • Seeds /
          • diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index b2d8479..44372dd 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -86,6 +86,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

          ' + lastPath() + ' ' + result.config.environment + '

          '); + $('#apikey').html(result.config.apikey); } $(document).ready(function() { @@ -156,6 +157,32 @@ function changeEnvError(result, text) { $('#info').html(generateHtmlMessage("ERROR!", text, "alert-error")); } + function build(){ + callURL("../../config/build/", buildResult); + } + function buildResult(result){ + console.log(result); + } + function unbuild(){ + var qresource = "SELECT DISTINCT ?resource {" + lastPath() + " coeus:includes ?entity . ?entity coeus:isEntityOf ?concept . ?concept coeus:hasResource ?resource }"; + queryToResult(qresource, unbuildResult); + } + function unbuildResult(result){ + var urlPrefix = "../../api/" + getApiKey(); + console.log(result); + for(var r in result){ + var res=splitURIPrefix(result[r].resource.value); + var resource=getPrefix(res.namespace)+":"+res.value; + callURL(urlPrefix+"/update/"+resource+"/coeus:built/xsd:boolean:true,xsd:boolean:false",unbuiltResource.bind(this,resource)); + } + + } + function unbuiltResource(resource,result){ + if(result.status===100) + console.log("The "+resource+" has been changed. "); + else console.log("The "+resource+" has already unbuild. "); + } + @@ -166,6 +193,7 @@
          +
    diff --git a/src/main/webapp/setup/resources.jsp b/src/main/webapp/setup/resources.jsp index b1df7c2..aa5af25 100644 --- a/src/main/webapp/setup/resources.jsp +++ b/src/main/webapp/setup/resources.jsp @@ -60,6 +60,7 @@ // Callback to generate the pages header function fillHeader(result) { $('#header').html('

    ' + lastPath() + ' ' + result.config.environment + '

    '); + $('#apikey').html(result.config.apikey); } $(document).ready(function() { @@ -88,6 +89,7 @@
    +
    • /
    • Seeds /
      • diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index e793e4d..f98a787 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -14,11 +14,16 @@ + @@ -825,9 +855,19 @@
    -
    +
    - + +
    + + + +
    +
    diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 44372dd..6b802fa 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -157,32 +157,33 @@ function changeEnvError(result, text) { $('#info').html(generateHtmlMessage("ERROR!", text, "alert-error")); } - function build(){ + function build() { callURL("../../config/build/", buildResult); } - function buildResult(result){ + function buildResult(result) { console.log(result); } - function unbuild(){ + function unbuild() { var qresource = "SELECT DISTINCT ?resource {" + lastPath() + " coeus:includes ?entity . ?entity coeus:isEntityOf ?concept . ?concept coeus:hasResource ?resource }"; queryToResult(qresource, unbuildResult); } - function unbuildResult(result){ + function unbuildResult(result) { var urlPrefix = "../../api/" + getApiKey(); console.log(result); - for(var r in result){ - var res=splitURIPrefix(result[r].resource.value); - var resource=getPrefix(res.namespace)+":"+res.value; - callURL(urlPrefix+"/update/"+resource+"/coeus:built/xsd:boolean:true,xsd:boolean:false",unbuiltResource.bind(this,resource)); + for (var r in result) { + var res = splitURIPrefix(result[r].resource.value); + var resource = getPrefix(res.namespace) + ":" + res.value; + callURL(urlPrefix + "/update/" + resource + "/coeus:built/xsd:boolean:true,xsd:boolean:false", unbuiltResource.bind(this, resource)); } - + + } + function unbuiltResource(resource, result) { + if (result.status === 100) + console.log("The " + resource + " has been changed. "); + else + console.log("The " + resource + " has already unbuild. "); } - function unbuiltResource(resource,result){ - if(result.status===100) - console.log("The "+resource+" has been changed. "); - else console.log("The "+resource+" has already unbuild. "); - } - + @@ -193,7 +194,7 @@
    -
    +
    Show Entities - +
    - +
    +
    +
    +
    +
    + +
    +
    +
    + + Export + + + +
    +
    +
    + + +
    From 27eae335f117afef3d7abf3cb90ec0d8df0a0cf1 Mon Sep 17 00:00:00 2001 From: sernadela Date: Mon, 9 Sep 2013 18:43:08 +0100 Subject: [PATCH 34/52] - Setup: Fix autocomplete for property (selectors) when edit. --- src/main/webapp/setup/addresource.jsp | 33 +++++++++++++++++++-------- 1 file changed, 23 insertions(+), 10 deletions(-) diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 13b7b59..7973f84 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -249,7 +249,8 @@ $('#querySelectorsForm').append(''); $('#regexSelectorsForm').append(''); $('#titleSelectorsForm').append(''); - + //fill the properties + buildSelectoresProperties(); }); //$('#callSelectorsModal').click(); @@ -623,20 +624,32 @@ function updateSelectorProperties() { var typeahead = $('#typeahead').val(); var prop = $('#propertySelectors').val(); - if (typeahead !== "") { + + if (typeahead !== "" && prop.indexOf(typeahead) === -1) { if (prop !== "") prop = prop + "|"; $('#propertySelectors').val(prop + typeahead); $('#typeahead').val(""); - var array = $('#propertySelectors').val().split("|"); - console.log(array); - $('#dropdownprop').html('
  • Properties Added
  • '); - for (var i in array) { - $('#dropdownprop').append('
  • ' + array[i] + '
    • '); - } - } + buildSelectoresProperties(); + } + } + function buildSelectoresProperties() { + var array = $('#propertySelectors').val().split("|"); + console.log(array); + $('#dropdownprop').html('
  • Properties Added
  • '); + for (var i in array) { + $('#dropdownprop').append('
  • ' + array[i] + '
    • '); + } + } + function removeSelectorProperty(value) { + removeById(value, "dropdownprop"); + var q = $('#propertySelectors').val(); + q = q.replace("|" + value, ""); + q = q.replace(value + "|", ""); + q = q.replace(value, ""); + $('#propertySelectors').val(q); } @@ -864,7 +877,7 @@
    From c01c2d30566103a8d74f0150c4e24652949c4e8a Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 10 Sep 2013 10:53:43 +0100 Subject: [PATCH 35/52] - Setup: Fix when change from edit to add in selectors. --- src/main/webapp/setup/addresource.jsp | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 7973f84..d840038 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -255,6 +255,19 @@ //$('#callSelectorsModal').click(); } + function resetSelectorModal(){ + $('#selectorUri').html("coeus:" ); + $('#selectorsModalLabel').html("Add Selector"); + $('#addSelectorButton').html('Add '); + $('#titleSelectors').val(""); + document.getElementById('titleSelectors').removeAttribute("disabled"); + $('#labelSelectors').val(""); + $('#propertySelectors').val(""); + $('#querySelectors').val(""); + $('#regexSelectors').val(""); + $('#keySelectorsForm').prop('checked', false); + buildSelectoresProperties(); + } function removeSelector() { var selector = $('#removeModalLabel').html(); //var query = initSparqlerQuery(); @@ -692,7 +705,7 @@
    - +
    From e8890350c60939c3a4f8151703ff9233e220d52a Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 11 Sep 2013 09:42:59 +0100 Subject: [PATCH 36/52] - Setup: Completed tree with shortcut actions. --- src/main/webapp/setup/addresource.jsp | 2 +- src/main/webapp/setup/index.jsp | 143 +++++++++++++++++--------- 2 files changed, 93 insertions(+), 52 deletions(-) diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index d840038..5e7d375 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -526,7 +526,7 @@ var entity = result[0].entity.value; seed = "coeus:" + splitURIPrefix(seed).value; entity = "coeus:" + splitURIPrefix(entity).value; - $('#breadSeed').html('Seed /'); + $('#breadSeed').html('Dashboard /'); $('#breadEntities').html('Entities /'); $('#breadConcepts').html('Concepts /'); $('#breadResources').html('Resources /'); diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 6b802fa..0716402 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -55,17 +55,55 @@ }); }*/ - function queryConcepts(entity, query) { - var qConcepts = "SELECT DISTINCT ?c ?concept {?concept coeus:hasEntity coeus:entity_" + entity + " . ?concept dc:title ?c }"; + function queryConcepts(entity) { + var qConcepts = "SELECT DISTINCT ?concept {?concept coeus:hasEntity coeus:" + entity + " }"; + queryToResult(qConcepts, fillConcepts.bind(this, entity)); + } + function queryResources(concept) { + var qResources = "SELECT DISTINCT ?resource {?resource coeus:isResourceOf coeus:" + concept + " }"; + queryToResult(qResources, fillResources.bind(this, concept)); + } + + function fillResources(concept, result) { + var arrayOfConcepts = new Array(); + var c = ''; + for (var i in result) { + var auxResource = splitURIPrefix(result[i].resource.value); + var resource = auxResource.value; + var prefix = getPrefix(auxResource.namespace); + arrayOfConcepts[i] = resource; + c += '

    ' + + prefix + ":" + resource + '

    '; + } + //console.log(entity); + $('#' + concept).append(c); + //console.log('Append on #' + entity + ': ' + c); + + } + + function fillConcepts(entity, result) { + var arrayOfConcepts = new Array(); var c = ''; - query.query(qConcepts, {success: function(json) { - for (var i = 0, s = json.results.bindings.length; i < s; i++) { - c += '

    ' + json.results.bindings[i].c.value + '

    '; - - } - $('#entity_' + entity).append(c); - console.log('Append on #' + entity + ': ' + c); - }}); + for (var i in result) { + var auxConcept = splitURIPrefix(result[i].concept.value); + var concept = auxConcept.value; + var prefix = getPrefix(auxConcept.namespace); + arrayOfConcepts[i] = concept; + c += '

    ' + +' ' + + prefix + ":" + concept + + ' ' + + ' ' + +'

      '; + } + //console.log(entity); + $('#' + entity).append(c); + //console.log('Append on #' + entity + ': ' + c); + + for (i in arrayOfConcepts) { + queryResources(arrayOfConcepts[i]); + } } function selectEntity() { @@ -89,54 +127,57 @@ $('#apikey').html(result.config.apikey); } + function fillEntities(result) { + // fill Entities + console.log(result); + var arrayOfEntities = new Array(); + var e = ''; + for (var key in result) { + var auxEntity = splitURIPrefix(result[key].entity.value); + var entity = auxEntity.value; + var prefix = getPrefix(auxEntity.namespace); + arrayOfEntities[key] = entity; + + e += '

      ' + +' ' + + prefix + ":" + entity + +' ' + +' ' + +'

        '; + + } + $('#kb').append(e); + + // fill Concepts + for (var k = 0, s = arrayOfEntities.length; k < s; k++) { + //$('#addentity').append(''); + queryConcepts(arrayOfEntities[k]); + } + } + $(document).ready(function() { //get seed from url var seed = lastPath(); callURL("../../config/getconfig/", fillHeader); callURL("../../config/listenv/", fillEnvironments); - var query = initSparqlerQuery(); - // passes standard JSON results object to success callback - var qEntities = "SELECT DISTINCT ?entity ?e ?s {" + seed + " coeus:includes ?entity . ?concept coeus:hasEntity ?entity . ?entity dc:title ?e . }"; - - query.query(qEntities, - {success: function(json) { - // fill Entities - var arrayOfEntities = new Array(); - var e = ''; - for (var key = 0, size = json.results.bindings.length; key < size; key++) { - arrayOfEntities[key] = json.results.bindings[key].e.value; - - e += '

        ' - + arrayOfEntities[key] + '

          '; - - } - $('#concepts').append(e); - - // fill Concepts - for (var k = 0, s = arrayOfEntities.length; k < s; k++) { - //$('#addentity').append(''); - queryConcepts(arrayOfEntities[k], query); - } - }} - ); - //header name - //$.get('../home/config', function(config, status) { - // console.log(config); - - // }, 'json'); + var qEntities = "SELECT DISTINCT ?entity {" + seed + " coeus:includes ?entity }"; + queryToResult(qEntities, fillEntities); var qseeds = "SELECT DISTINCT ?seed ?s {?seed a coeus:Seed . ?seed dc:title ?s . }"; - - query.query(qseeds, - {success: function(json) { - // fill Concepts - for (var k = 0, s = json.results.bindings.length; k < s; k++) { - $('#seeds').append(''); - } - $('#seeds option:contains(' + lastPath().split('coeus:')[1] + ')').prop({selected: true}); - }} + queryToResult(qseeds, function(result) { + for (var k in result) { + $('#seeds').append(''); + } + $('#seeds option:contains(' + lastPath().split('coeus:')[1] + ')').prop({selected: true}); + } ); + + var qEntities = "SELECT (COUNT(*) AS ?triples) {?s ?p ?o}"; + queryToResult(qEntities, function(result) { + $('#triples').html(result[0].triples.value); + }); + }); function changeSeed() { @@ -201,8 +242,8 @@
          -
          -

          Knowledge Base (Entity-Concept)

          +
          +

          Knowledge Base (Entity-Concept) 0

          -
          +

          Actions

          -
          -
          - Seeds -
          -
          - -
          -
          -
          - Change seed -
          -
          +
          + Add Entity + Explorer
          - -
          -
          - Environments -
          -
          - -
          -
          -
          - Change environment -
          -
          -
          - -
          -
          -
          - Rebuild - Unbuild -
          -
          - -
          -
          -
          - Show Entities - -
          - -
          -
          - -
          -
          -
          -
          - -
          -
          -
          - - Export - - - -
          +
          + Rebuild + Unbuild +
          + + Export + + +
          + From 8169e742ba3af3c74d3aa00b482979baf6181df7 Mon Sep 17 00:00:00 2001 From: sernadela Date: Fri, 4 Oct 2013 14:53:31 +0100 Subject: [PATCH 40/52] - Add Executor Thread to run integration process in different thread - Fix Storage running threads. - Fix csv guessDelimiter function - Add a default environment - Setup: Change build and unbuild options. --- .../coeus/actions/ConfigActionBean.java | 129 +- .../ua/bioinformatics/coeus/common/Boot.java | 97 +- .../bioinformatics/coeus/common/Config.java | 47 +- .../coeus/common/ExecutorContextListener.java | 47 + .../coeus/common/HttpListener.java | 1 - .../ua/bioinformatics/coeus/common/Run.java | 1 + .../bioinformatics/coeus/common/Worker.java | 29 + .../ua/bioinformatics/coeus/data/Storage.java | 25 +- .../coeus/data/connect/CSVFactory.java | 24 +- src/main/resources/config.js | 2 +- src/main/resources/env_default/joseki.ttl | 97 ++ src/main/resources/env_default/map.js | 15 + src/main/resources/env_default/pubby.ttl | 91 ++ src/main/resources/env_default/sdb.ttl | 19 + src/main/resources/setup.rdf | 1207 +++++++++++++++++ src/main/webapp/WEB-INF/web.xml | 9 +- src/main/webapp/docs/ontology.jsp | 2 +- src/main/webapp/setup/addentity.jsp | 4 + src/main/webapp/setup/config.jsp | 4 +- src/main/webapp/setup/index.jsp | 54 +- 20 files changed, 1802 insertions(+), 102 deletions(-) create mode 100644 src/main/java/pt/ua/bioinformatics/coeus/common/ExecutorContextListener.java create mode 100644 src/main/java/pt/ua/bioinformatics/coeus/common/Worker.java create mode 100644 src/main/resources/env_default/joseki.ttl create mode 100644 src/main/resources/env_default/map.js create mode 100644 src/main/resources/env_default/pubby.ttl create mode 100644 src/main/resources/env_default/sdb.ttl create mode 100644 src/main/resources/setup.rdf diff --git a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java index 205faed..dfa5c6e 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/actions/ConfigActionBean.java @@ -36,6 +36,7 @@ import java.util.Map.Entry; import java.util.Set; import java.util.TreeSet; +import java.util.concurrent.ExecutorService; import java.util.logging.Level; import java.util.logging.Logger; import net.sourceforge.stripes.action.ActionBean; @@ -52,8 +53,8 @@ import pt.ua.bioinformatics.coeus.api.DB; import pt.ua.bioinformatics.coeus.common.Boot; import pt.ua.bioinformatics.coeus.common.Config; +import pt.ua.bioinformatics.coeus.common.Worker; import pt.ua.bioinformatics.coeus.data.Predicate; -import pt.ua.bioinformatics.coeus.data.Storage; /** * @@ -104,26 +105,28 @@ public Resolution handle() { * @return */ public Resolution getconfig() { - Config.load(); + Boot.start(); return new StreamingResolution("application/json", Config.getFile().toJSONString()); } - - /** + + /** * return existent properties that matches with $method * * @return */ public Resolution properties() { - JSONArray array=new JSONArray(); - String matchingStr=method; + JSONArray array = new JSONArray(); + String matchingStr = method; //HashMap map= PrefixFactory.getPrefixes(); - HashMap map= Predicate.getPredicates(); - + HashMap map = Predicate.getPredicates(); + for (Entry e : map.entrySet()) { - String key=e.getKey(); - if(matchingStr!=null){ - if(key.contains(matchingStr)) array.add(key); - }else{ + String key = e.getKey(); + if (matchingStr != null) { + if (key.contains(matchingStr)) { + array.add(key); + } + } else { array.add(key); } } @@ -131,11 +134,12 @@ public Resolution properties() { //System.out.println(array.toJSONString()); return new StreamingResolution("application/json", array.toJSONString()); } - + /** - * Export the database content + * Export the database content + * * @return - * @throws FileNotFoundException + * @throws FileNotFoundException */ public Resolution export() throws FileNotFoundException { StringWriter outs = new StringWriter(); @@ -147,25 +151,65 @@ public Resolution export() throws FileNotFoundException { } return new StreamingResolution("application/rdf+xml", outs.toString()); } - - /** - * Build (Boot.start() call) + + /** + * Build (Boot.build() call in a different thread) * * @return */ public Resolution build() { JSONObject result = new JSONObject(); + String value = method; try { - Boot.start(); + + ExecutorService executor = (ExecutorService) context.getServletContext().getAttribute("INTEGRATION_EXECUTOR"); + Runnable worker = new Worker("worker" + System.currentTimeMillis()); + executor.execute(worker); + + result.put("status", 100); + result.put("message", "[COEUS][API][ConfigActionBean] Build done."); + } catch (Exception e) { + result.put("status", 201); + result.put("message", "[COEUS][API][ConfigActionBean] Build fail. Exception: " + e); + } + return new StreamingResolution("application/json", result.toJSONString()); + } + + /** + * Change built property in config.js file. The method value only can be true or false. + * + * @return + */ + public Resolution changebuilt() { + JSONObject result = new JSONObject(); + try { + JSONObject f = Config.getFile(); + JSONObject config = (JSONObject) f.get("config"); + + config.put("built", Boolean.parseBoolean(method)); + f.put("config", config); + + updateFile(f.toJSONString(), Config.getPath() + "config.js"); + //apply values + Boot.resetConfig(); + result.put("status", 100); - result.put("message", "[COEUS][API][ConfigActionBean] Build done. "); + result.put("message", "[COEUS][API][ConfigActionBean] Built property changed."); } catch (Exception e) { result.put("status", 201); - result.put("message", "[COEUS][API][ConfigActionBean] Exception: "+e); + result.put("message", "[COEUS][API][ConfigActionBean] Built not property changed. Exception: " + e); } return new StreamingResolution("application/json", result.toJSONString()); } +// public Resolution executor(){ +// JSONObject result = new JSONObject(); +// ExecutorService executor = (ExecutorService )context.getServletContext().getAttribute("INTEGRATION_EXECUTOR"); +// +// result.put("executor.isShutdown()", executor.isShutdown()); +// result.put("executor.isTerminated()", executor.isTerminated()); +// return new StreamingResolution("application/json", result.toJSONString()); +// } /** * Cleans the DB of one environment (method) * @@ -181,8 +225,8 @@ public Resolution cleandb() { JSONParser parser = new JSONParser(); String json = readToString(map); result = (JSONObject) parser.parse(json); - int index=result.get("$sdb:jdbcURL").toString().lastIndexOf("/"); - String dbName=result.get("$sdb:jdbcURL").toString().substring(index); + int index = result.get("$sdb:jdbcURL").toString().lastIndexOf("/"); + String dbName = result.get("$sdb:jdbcURL").toString().substring(index); DB db = new DB(dbName, result.get("$sdb:jdbcURL") + "&user=" + result.get("$sdb:sdbUser").toString() + "&password=" + result.get("$sdb:sdbPassword").toString()); // test db connection boolean success = db.connectX(); @@ -281,19 +325,16 @@ public void updateFilesFromMap(String path) throws ParseException, IOException { public Resolution upenv() { JSONObject result = new JSONObject(); try { - Config.load(); + Boot.start(); String path = Config.getPath() + "env_" + method + "/"; updateFilesFromMap(path); changeEnvironment(path, Config.getPath(), "env_" + method); //Load new settings - Config.setLoaded(false); - Boot.setStarted(false); - Config.load(); + Boot.resetConfig(); + Boot.resetStorage(); //TODO: FIX THAT - NEEDS SERVERS RESTART TO APPLY NEW CONFIGS - Storage.connect(); - Boot.start(); result.put("status", 100); result.put("message", "[COEUS][API][ConfigActionBean] Environment updated: " + method); @@ -344,8 +385,8 @@ public void changeEnvironment(String src, String dest, String environment) throw public Resolution newenv() { JSONObject result = new JSONObject(); try { + Boot.start(); String name = "env_" + method; - Config.load(); String envStr = Config.getPath() + name; String initStr = Config.getPath() + "init"; File env = new File(envStr); @@ -377,7 +418,7 @@ public Resolution newenv() { public Resolution getmap() { JSONObject result = new JSONObject(); try { - Config.load(); + Boot.start(); String environment = "env_" + method; String path = Config.getPath() + environment + "/"; String map = path + "map.js"; @@ -389,7 +430,7 @@ public Resolution getmap() { } return new StreamingResolution("application/json", result.toJSONString()); } - + /** * Receives a map.js file and update it in according to the environment key * in config.js. @@ -399,15 +440,15 @@ public Resolution getmap() { public Resolution putmap() { JSONObject result = new JSONObject(); try { - Config.load(); + Boot.start(); JSONParser parser = new JSONParser(); System.out.println(method); JSONObject env = (JSONObject) parser.parse(method); //create the DB if not exists - DB creator=new DB(); + DB creator = new DB(); creator.createDB(env.get("$sdb:jdbcURL").toString(), env.get("$sdb:sdbUser").toString(), env.get("$sdb:sdbPassword").toString()); - + String environment = "env_" + env.get("$environment").toString(); String path = Config.getPath() + environment + "/"; String map = path + "map.js"; @@ -416,18 +457,17 @@ public Resolution putmap() { //update files on the environment updateFilesFromMap(path); //change it to use - changeEnvironment(path, Config.getPath(), environment); + //changeEnvironment(path, Config.getPath(), environment); //apply values - Config.setLoaded(false); - Config.load(); + Boot.resetConfig(); } catch (ParseException ex) { result.put("status", 200); result.put("message", "[COEUS][API][ConfigActionBean] ERROR: On parse map.js, check exception."); Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); - } catch(SQLException ex){ + } catch (SQLException ex) { result.put("status", 200); - result.put("message", "[COEUS][API][ConfigActionBean] ERROR: On creating database, check exception: "+ex); + result.put("message", "[COEUS][API][ConfigActionBean] ERROR: On creating database, check exception: " + ex); Logger.getLogger(ConfigActionBean.class.getName()).log(Level.SEVERE, null, ex); } catch (Exception ex) { result.put("status", 200); @@ -445,7 +485,7 @@ public Resolution putmap() { public Resolution delenv() { JSONObject result = new JSONObject(); try { - Config.load(); + Boot.start(); String envStr = Config.getPath() + "env_" + method; File env = new File(envStr); if (env.exists()) { @@ -501,7 +541,7 @@ public Resolution readrdf() throws MalformedURLException, IOException { */ public Resolution getprop() { - Config.load(); + Boot.start(); Set set = new TreeSet(); StringBuilder sb = new StringBuilder(); //get all proprieties for each prefix @@ -528,9 +568,8 @@ public Resolution putconfig() { //update config.js String jsonString = method; - JSONObject result = updateFile(jsonString, Config.getPath()+"config.js"); - Config.setLoaded(false); - Config.load(); + JSONObject result = updateFile(jsonString, Config.getPath() + "config.js"); + Boot.resetConfig(); //update predicates.csv Set set = new TreeSet(); diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Boot.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Boot.java index cf38f7b..17960dd 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Boot.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Boot.java @@ -31,6 +31,74 @@ public static void setAPI(API api) { Boot.api = api; } + /** + * Reset and load COEUS config.js. + */ + public static void resetConfig() { + try { + Config.setLoaded(false); + Config.load(); + } catch (Exception e) { + if (Config.isDebug()) { + System.out.println("[COEUS][Boot] Unable to reset COEUS instance"); + } + Logger.getLogger(Boot.class.getName()).log(Level.SEVERE, null, e); + } + + } + + /** + * Reset and load COEUS Storage information (connect, ontology, setup, + * predicates). + *

            + *
          1. Reset and load
            2. + *
          2. Reset and load config.js
            3. + *

          + */ + public static void resetStorage() { + try { + Storage.setLoaded(false); + Storage.load(); + Storage.loadPredicates(); + } catch (Exception e) { + if (Config.isDebug()) { + System.out.println("[COEUS][Boot] Unable to reset COEUS instance"); + } + Logger.getLogger(Boot.class.getName()).log(Level.SEVERE, null, e); + } + + } + + /** + * Build COEUS instance. + *

            + *
          1. Load Storage information (connect, ontology, setup, predicates)
            2. + *
          2. Build instance
            3. + *
          3. Save and restart
            4. + *

          + */ + public synchronized static void build() { + try { + Boot.start(); + if (!Config.isBuilt()) { + long i = System.currentTimeMillis(); + Builder.build(); + Builder.save(); + long f = System.currentTimeMillis(); + System.out.println("\n\t[COEUS] " + Config.getName() + " Integration done in " + ((f - i) / 1000) + " seconds.\n"); + Config.setBuiltOnFile(true); + } else { + System.out.println("\n\t[COEUS] " + Config.getName() + " Integration Already done.\n"); + } + } catch (Exception e) { + if (Config.isDebug()) { + System.out.println("[COEUS][Boot] Unable to build COEUS instance"); + } + Logger.getLogger(Boot.class.getName()).log(Level.SEVERE, null, e); + } + + } + /** * Starts the configured COEUS instance. *

          Built workflow

            @@ -46,30 +114,11 @@ public static void setAPI(API api) { public static void start() { if (!started) { try { - try { - Config.load(); - } catch (Exception ex) { - if (Config.isDebug()) { - System.out.println("[COEUS][Boot] Unable to load configuration"); - } - Logger.getLogger(Boot.class.getName()).log(Level.SEVERE, null, ex); - } - if (!Config.isBuilt()) { - Storage.load(); - api = new API(); - Storage.loadPredicates(); - Builder.build(); - Builder.save(); - //remove - Config.setBuilt(true); - start(); - } else { - Storage.connect(); - api = new API(); - Storage.loadPredicates(); - System.out.println("\n\t[COEUS] " + Config.getName() + " Online\n"); - } - + Config.load(); + Storage.load(); + api = new API(); + Storage.loadPredicates(); + System.out.println("\n\t[COEUS] " + Config.getName() + " Online\n"); started = true; } catch (Exception ex) { if (Config.isDebug()) { diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java index 1862736..d7fbf28 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Config.java @@ -3,6 +3,7 @@ import java.io.BufferedInputStream; import java.io.File; import java.io.FileInputStream; +import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; @@ -11,6 +12,7 @@ import org.json.simple.JSONArray; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; +import pt.ua.bioinformatics.coeus.actions.ConfigActionBean; import pt.ua.bioinformatics.coeus.api.PrefixFactory; /** @@ -51,7 +53,6 @@ public static void setApikeys(ArrayList apikeys) { // public static void setEnvironment(String environment) { // Config.environment = environment; // } - public static String getPath() { return path; } @@ -238,4 +239,48 @@ private static String readFile() { } return new String(buffer); } + + /** + * Write new config.js file + * + * @param file + */ + static void writeFile(JSONObject file) { + try { + FileWriter writer = new FileWriter(path + "config.js"); + writer.write(file.toJSONString()); + writer.flush(); + writer.close(); + + if (Config.isDebug()) { + System.out.println("[COEUS][Config] config.js file updated."); + } + } catch (Exception ex) { + if (Config.isDebug()) { + System.out.println("[COEUS][Config] ERROR: updating config.js."); + } + Logger.getLogger(Config.class.getName()).log(Level.SEVERE, null, ex); + } + } + + /** + * Change built property on config file + * + * @param builder + */ + static void setBuiltOnFile(boolean builder) { + try { + JSONObject f = Config.getFile(); + JSONObject config = (JSONObject) f.get("config"); + config.put("built", builder); + f.put("config", config); + writeFile(f); + Config.setBuilt(builder); + } catch (Exception ex) { + if (Config.isDebug()) { + System.out.println("[COEUS][Config] ERROR: setBuiltOnFile."); + } + Logger.getLogger(Config.class.getName()).log(Level.SEVERE, null, ex); + } + } } \ No newline at end of file diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/ExecutorContextListener.java b/src/main/java/pt/ua/bioinformatics/coeus/common/ExecutorContextListener.java new file mode 100644 index 0000000..62a13a9 --- /dev/null +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/ExecutorContextListener.java @@ -0,0 +1,47 @@ +/* + * To change this template, choose Tools | Templates + * and open the template in the editor. + */ +package pt.ua.bioinformatics.coeus.common; + +import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import javax.servlet.ServletContext; +import javax.servlet.ServletContextEvent; +import javax.servlet.ServletContextListener; + +/** + * + * @author sernadela + */ +public class ExecutorContextListener implements ServletContextListener{ + private ExecutorService executor; + + @Override + public void contextInitialized(ServletContextEvent sce) { + ServletContext context = sce.getServletContext(); + executor = Executors.newFixedThreadPool(4); + context.setAttribute("INTEGRATION_EXECUTOR", executor); + Boot.start(); + System.out.println("ServletContextListener started"); + } + + @Override + public void contextDestroyed(ServletContextEvent sce) { + ServletContext context = sce.getServletContext(); + System.out.println("ServletContextListener destroyed"); + List list=executor.shutdownNow(); + //System.err.println("\n\n\nList of runnables:\n\n"); + //for(Runnable r : list){ + // System.err.println(r.toString()); + //} +// System.err.println("\n\n\nList of Threads:\n\n"); +// Set threadSet = Thread.getAllStackTraces().keySet(); +// Thread[] threadArray = threadSet.toArray(new Thread[threadSet.size()]); +// for(Thread t:threadArray) { +// System.err.println(t.getName()); +// } + } + +} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/HttpListener.java b/src/main/java/pt/ua/bioinformatics/coeus/common/HttpListener.java index ef30aa3..04c9f59 100644 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/HttpListener.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/HttpListener.java @@ -20,7 +20,6 @@ public void sessionCreated(HttpSessionEvent se) { @Override public void sessionDestroyed(HttpSessionEvent se) { - } } diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Run.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Run.java index ec79b1c..25be558 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/common/Run.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Run.java @@ -2,6 +2,7 @@ import java.util.logging.Level; import java.util.logging.Logger; +import org.json.simple.JSONObject; /** * diff --git a/src/main/java/pt/ua/bioinformatics/coeus/common/Worker.java b/src/main/java/pt/ua/bioinformatics/coeus/common/Worker.java new file mode 100644 index 0000000..b9d77e9 --- /dev/null +++ b/src/main/java/pt/ua/bioinformatics/coeus/common/Worker.java @@ -0,0 +1,29 @@ +/* + * To change this template, choose Tools | Templates + * and open the template in the editor. + */ +package pt.ua.bioinformatics.coeus.common; + +/** + * + * @author sernadela + */ +public class Worker implements Runnable{ + String name; + + public Worker(String name){ + this.name=name; + } + + @Override + public void run() { + System.out.println("worker run call"); + Boot.build(); + } + + @Override + public String toString(){ + return name; + } + +} diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/Storage.java b/src/main/java/pt/ua/bioinformatics/coeus/data/Storage.java index 06123d2..2cc2241 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/Storage.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/Storage.java @@ -98,6 +98,7 @@ public static void setStore(Store store) { */ public static boolean connect() { try { + Storage.close(); store = (Store) SDBFactory.connectStore(Config.getPath() + Config.getSdb()); model = SDBFactory.connectDefaultModel(store); infmodel = ModelFactory.createInfModel(reasoner, model); @@ -125,6 +126,7 @@ public static boolean connect() { */ public static boolean connectX() { try { + Storage.close(); store = (Store) SDBFactory.connectStore(Config.getPath() + Config.getSdb()); model = SDBFactory.connectDefaultModel(store); connected = true; @@ -189,7 +191,7 @@ private static boolean loadSetup() { } catch (Exception ex) { if (Config.isDebug()) { System.out.println("[COEUS][Storage] Unable to load " + Config.getName() + " setup"); - //Logger.getLogger(Storage.class.getName()).log(Level.SEVERE, null, ex); + Logger.getLogger(Storage.class.getName()).log(Level.SEVERE, null, ex); } } return success; @@ -388,4 +390,25 @@ private static boolean reset() { } return success; } + + /** + * Close COEUS Store connection if is not closed: + * + * Prevent the launch of new threads if already exists. + * + * @return + */ + private static boolean close() { + boolean success = true; + try { + if(store!=null && !store.isClosed()) store.close(); + success = true; + } catch (Exception ex) { + if (Config.isDebug()) { + System.out.println("[COEUS][Storage] unable to close COEUS SDB"); + } + Logger.getLogger(Storage.class.getName()).log(Level.SEVERE, null, ex); + } + return success; + } } diff --git a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java index b21a0fb..57cc34b 100755 --- a/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java +++ b/src/main/java/pt/ua/bioinformatics/coeus/data/connect/CSVFactory.java @@ -294,7 +294,7 @@ public boolean save() { try { API api = Boot.getAPI(); com.hp.hpl.jena.rdf.model.Resource resource = api.getResource(this.res.getUri()); - Statement statementToRemove=api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); + Statement statementToRemove = api.getModel().createLiteralStatement(resource, Predicate.get("coeus:built"), false); api.removeStatement(statementToRemove); api.addStatement(resource, Predicate.get("coeus:built"), true); success = true; @@ -327,10 +327,9 @@ public char guessDelimiter(URL urlLocation, char quotes, int headerSkip) { int minColums = 1; int linesToCheck = 4; - try { - - for (int a = 0; a < delimiters.length; a++) { - boolean b = true; + for (int a = 0; a < delimiters.length; a++) { + boolean b = true; + try { BufferedReader br = new BufferedReader(new InputStreamReader(urlLocation.openStream())); CSVReader testReader = new CSVReader(br, delimiters[a], quotes, headerSkip); @@ -352,17 +351,16 @@ public char guessDelimiter(URL urlLocation, char quotes, int headerSkip) { } } - if (b) { - //System.out.println("Find:" + delimiters[a]); - return delimiters[a]; - } + } catch (Exception e) { + b = false; } - } catch (IOException ex) { - Logger.getLogger(CSVFactory.class.getName()).log(Level.SEVERE, null, ex); - } catch (NullPointerException ex) { - Logger.getLogger(CSVFactory.class.getName()).log(Level.SEVERE, null, ex); + if (b) { + //System.out.println("Find:" + delimiters[a]); + return delimiters[a]; + } } + return failReturn; } } diff --git a/src/main/resources/config.js b/src/main/resources/config.js index 99677a4..d700950 100644 --- a/src/main/resources/config.js +++ b/src/main/resources/config.js @@ -11,7 +11,7 @@ "built": false, "debug": true, "apikey":"coeus|uavr", - "environment":"" + "environment":"default" }, "prefixes" : { "coeus": "http://bioinformatics.ua.pt/coeus/resource/", diff --git a/src/main/resources/env_default/joseki.ttl b/src/main/resources/env_default/joseki.ttl new file mode 100644 index 0000000..19b8e38 --- /dev/null +++ b/src/main/resources/env_default/joseki.ttl @@ -0,0 +1,97 @@ +@prefix rdfs: . +@prefix rdf: . +@prefix xsd: . +@prefix coeus: . +@prefix module: . +@prefix joseki: . +@prefix ja: . +@prefix sdb: . + +<> rdfs:label "Joseki Configuration File - SDB example" . +# Stripped down to support one service that exposes an +# SDB store as a SPARQL endpoint for query and one for +# one of the graphs in an SDB store. + +[] rdf:type joseki:Server . + +## -------------------------------------------------------------- +## Services + +# Service publishes the whole of the SDB store - this is the usual way to use SDB. +<#service1> + rdf:type joseki:Service ; + rdfs:label "SPARQL-SDB" ; + joseki:serviceRef "sparql" ; # web.xml must route this name to Joseki + joseki:dataset <#sdb> ; + joseki:processor joseki:ProcessorSPARQL_FixedDS ; + . + + +## -------------------------------------------------------------- +## Datasets + +## See also SDB documentation -- http://jena.hpl.hp.com/wiki/SDB +## Special declarations to cause SDB to be used. + +## Initialize SDB. +## Tell the system that sdb:DatasetStore is an implementation of ja:RDFDataset . +## Tell the system that sdb:Model is an implementation of ja:RDFDataset . + +[] ja:loadClass "com.hp.hpl.jena.sdb.SDB" . +sdb:DatasetStore rdfs:subClassOf ja:RDFDataset . +sdb:Model rdfs:subClassOf ja:Model . + +<#sdb> rdf:type sdb:DatasetStore ; + ## Number of concurrent connections allowed to this dataset. + joseki:poolSize 2; + sdb:store <#store> . + +<#store> rdf:type sdb:Store ; + rdfs:label "SDB" ; + sdb:layout "layout2" ; + sdb:connection + [ rdf:type sdb:SDBConnection ; + sdb:sdbType "mysql" ; + #sdb:sdbHost "localhost:3306" ; + #sdb:sdbName "coeus" ; + sdb:jdbcURL "$sdb:jdbcURL" ; + sdb:sdbUser "$sdb:sdbUser" ; + sdb:sdbPassword "$sdb:sdbPassword" ; + ] + . + +# Pick one graph out of the SDB store. +# Do not assemble the whole of the store this way - it is less efficient for that. +<#sdb-part> rdf:type ja:RDFDataset ; + # If ja:namedGraph is used here, there is no correspondence + # with the name in the SDB store. + ja:defaultGraph <#sdb-one-graph> ; + . + +<#sdb-one-graph> a sdb:Model ; + sdb:dataset <#sdb> ; + # Uncomment to pick out a named graph from the store. + # If no "sdb:namedGraph" appearsm the store's default graph is used. + # is used as default graph of the dataset publically visible. + #sdb:graphName ; + # Or even the merge of all named graphs + #sdb:graphName ; + . + +## -------------------------------------------------------------- +## Processors + +joseki:ProcessorSPARQL_FixedDS + rdfs:label "SPARQL processor for fixed datasets" ; + rdf:type joseki:Processor ; + module:implementation + [ rdf:type joseki:ServiceImpl ; + module:className + ] ; + + # This processor does not accept queries with FROM/FROM NAMED + joseki:allowExplicitDataset "false"^^xsd:boolean ; + joseki:allowWebLoading "false"^^xsd:boolean ; + # The database is safe for MRSW (multiple-reader, single-writer). + joseki:lockingPolicy joseki:lockingPolicyMRSW ; + . \ No newline at end of file diff --git a/src/main/resources/env_default/map.js b/src/main/resources/env_default/map.js new file mode 100644 index 0000000..43e9dee --- /dev/null +++ b/src/main/resources/env_default/map.js @@ -0,0 +1,15 @@ +{ + "$sdb:jdbcURL" : "jdbc:mysql://localhost:3306/coeus?autoReconnect=true", + "$sdb:sdbUser" : "demo", + "$sdb:sdbPassword" :"demo", + + "$conf:projectName" :"coeus.demo", + "$conf:projectHomepage" :"http://bioinformatics.ua.pt/coeus/", + "$conf:webBase" :"http://localhost:8080/coeus/", + "$conf:sparqlEndpoint" :"http://localhost:8080/coeus/sparql", + "$conf:datasetBase" :"http://bioinformatics.ua.pt/coeus/resource/", + "$conf:webResourcePrefix" :"resource/", + + "$environment" :"", + +} \ No newline at end of file diff --git a/src/main/resources/env_default/pubby.ttl b/src/main/resources/env_default/pubby.ttl new file mode 100644 index 0000000..1a5d679 --- /dev/null +++ b/src/main/resources/env_default/pubby.ttl @@ -0,0 +1,91 @@ +# Pubby Example Configuration +# +# This configuration connects to the DBpedia SPARQL endpoint and +# re-publishes on your local machine, with dereferenceable +# localhost URIs. +# +# This assumes you already have a servlet container running +# on your machine at http://localhost:8080/ . +# +# Install Pubby as the root webapp of your servlet container, +# and make sure the config-file parameter in Pubby's web.xml +# points to this configuration file. +# +# Then browse to http://localhost:8080/ . + +# Prefix declarations to be used in RDF output +@prefix conf: . +@prefix meta: . +@prefix rdf: . +@prefix rdfs: . +@prefix xsd: . +@prefix owl: . +@prefix dc: . +@prefix dcterms: . +@prefix foaf: . +@prefix skos: . +@prefix geo: . +@prefix dbpedia: . +@prefix p: . +@prefix yago: . +@prefix units: . +@prefix geonames: . +@prefix prv: . +@prefix prvTypes: . +@prefix doap: . +@prefix void: . +@prefix ir: . +@prefix coeus: . + +# Server configuration section +<> a conf:Configuration; + # Project name for display in page titles + conf:projectName "$conf:projectName"; + # Homepage with description of the project for the link in the page header + conf:projectHomepage <$conf:projectHomepage>; + # The Pubby root, where the webapp is running inside the servlet container. + conf:webBase <$conf:webBase>; + # URL of an RDF file whose prefix mapping is to be used by the + # server; defaults to <>, which is *this* file. + conf:usePrefixesFrom <>; + # If labels and descriptions are available in multiple languages, + # prefer this one. + conf:defaultLanguage "en"; + # When the homepage of the server is accessed, this resource will + # be shown. + #conf:indexResource ; + +# Dataset configuration section #1 (for DBpedia resources) +# +# URIs in the SPARQL endpoint: http://dbpedia.org/resource/* +# URIs on the Web: http://localhost:8080/resource/* + conf:dataset [ + # SPARQL endpoint URL of the dataset + conf:sparqlEndpoint <$conf:sparqlEndpoint>; + #conf:sparqlEndpoint ; + # Default graph name to query (not necessary for most endpoints) + # conf:sparqlDefaultGraph <>; + # Common URI prefix of all resource URIs in the SPARQL dataset + conf:datasetBase <$conf:datasetBase>; + # Will be appended to the conf:webBase to form the public + # resource URIs; if not present, defaults to "" + conf:webResourcePrefix "$conf:webResourcePrefix"; + # Fixes an issue with the server running behind an Apache proxy; + # can be ignored otherwise + conf:fixUnescapedCharacters "(),'!$&*+;=@"; + + # include metadata + #conf:metadataTemplate "metadata.ttl"; + + # configure your metadata here + # Use properties with the meta: prefix where the property name + # corresponds to the placeholder URIs in metadata.ttl that begin + # with about:metadata:metadata: + # Examples for such properties are: +# meta:pubbyUser ; +# meta:pubbyOperator ; +# meta:endpointUser ; +# meta:endpointOperator ; +# meta:endpointDataset ; + ]; + . diff --git a/src/main/resources/env_default/sdb.ttl b/src/main/resources/env_default/sdb.ttl new file mode 100644 index 0000000..ac180fd --- /dev/null +++ b/src/main/resources/env_default/sdb.ttl @@ -0,0 +1,19 @@ +@prefix sdb: . +@prefix rdfs: . +@prefix rdf: . +@prefix ja: . +@prefix coeus: . + +<#store> rdf:type sdb:Store ; + sdb:layout "layout2" ; + sdb:connection <#conn> ; + sdb:engine "InnoDB" ; +. + +<#conn> rdf:type sdb:SDBConnection ; + sdb:sdbType "MySQL" ; + sdb:jdbcURL "$sdb:jdbcURL" ; + sdb:sdbUser "$sdb:sdbUser" ; + sdb:sdbPassword "$sdb:sdbPassword" ; + sdb:driver "com.mysql.jdbc.Driver" ; + . \ No newline at end of file diff --git a/src/main/resources/setup.rdf b/src/main/resources/setup.rdf new file mode 100644 index 0000000..a518ecb --- /dev/null +++ b/src/main/resources/setup.rdf @@ -0,0 +1,1207 @@ + + + + + + + + + +]> + + + + + coeusna + 1.0b + 2013-03-15 + COEUS and COEUS Ontology are licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. + Pedro Lopes pedrolopes@ua.pt + coeus.NA + coeus.NA + coeus.NA + en + http://bioinformatics.ua.pt + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + objectproperty_extends + 1.0a + 2011-01-20 + A Resource extends a Concept - items are source for data loading + A Resource extends a Concept - items are source for data loading + Pedro Lopes pedrolopes@ua.pt + extends + + + + + + + + + + objectproperty_hasbridge + 1.0a + 2011-01-19 + A Concept has a Bridge + A Concept has a Bridge + Pedro Lopes pedrolopes@ua.pt + hasBridge + + + + + + + + + + objectproperty_hasconcept + 1.0a + 2011-01-14 + Item individuals belong to Concept individuals + Item individuals belong to Concept individuals + Pedro Lopes pedrolopes@ua.pt + hasConcept + + + + + + + + + + objectproperty_hasentity + 1.0a + 2011-01-14 + Concept individuals has Entity individuals + Concept individuals has Entity individuals + Pedro Lopes pedrolopes@ua.pt + hasEntity + + + + + + + + + + objectproperty_haskey + 1.0a + 2011-01-27 + Defines the key for a given Resource + Defines the key for a given Resource + Pedro Lopes pedrolopes@ua.pt + hasKey + + + + + + + + + + + + + objectproperty_hasmodule + 1.0a + 2011-01-19 + A Seed has a Module + A Seed has a Module + Pedro Lopes pedrolopes@ua.pt + hasModule + + + + + + + + + + objectproperty_hasresource + 1.0a + 2011-01-19 + A Concept has a Resource + A Concept has a Resource + Pedro Lopes pedrolopes@ua.pt + hasResource + + + + + + + + + + objectproperty_includes + 1.0a + 2011-01-14 + Defines which Entity individuals are included in Seed individuals + Defines which Entity individuals are included in Seed individuals + Pedro Lopes pedrolopes@ua.pt + includes + + + + + + + + + + + + + objectproperty_isassociatedto + 1.0a + 2011-01-19 + Pedro Lopes pedrolopes@ua.pt + Relationship between two "Item" individuals + Relationship between two "Item" individuals + isAssociatedTo + + + + + + + + + + + iobjectproperty_sbridgedto + 1.0a + 2011-01-19 + A Briged is bridged to a Concept + A Briged is bridged to a Concept + Pedro Lopes pedrolopes@ua.pt + isBridgedTo + + + + + + + + + + + objectproperty_isconceptof + 1.0a + 2011-01-19 + A Concept has an Item + A Concept has an Item + Pedro Lopes pedrolopes@ua.pt + isConceptOf + + + + + + + + + + + + + objectproperty_isconnectedto + 1.0a + 2011-01-14 + Defines connection between two Concept individuals + Defines connection between two Concept individuals + Pedro Lopes pedrolopes@ua.pt + isConnectedTo + + + + + + + + + + + objectproperty_isentityof + 1.0a + 2011-01-19 + An Entity is of a Concept + An Entity is of a Concept + Pedro Lopes pedrolopes@ua.pt + isEntityOf + + + + + + + + + + + objectproperty_isextendedby + 1.0a + 2011-01-27 + A Resource extends a Concept - items are source for data loading + A Resource extends a Concept - items are source for data loading + Pedro Lopes pedrolopes@ua.pt + isExtendedBy + + + + + + + + + + + objectproperty_isincludedin + 1.0a + 2011-01-14 + Defines which Entity individuals are included in Seed individuals + Defines which Entity individuals are included in Seed individuals + Pedro Lopes pedrolopes@ua.pt + isIncludedIn + + + + + + + + + + objectproperty_iskeyof + 1.0a + 2011-01-27 + Defines the key for a given Resource + Defines the key for a given Resource + Pedro Lopes pedrolopes@ua.pt + isKeyOf + + + + + + + + + + + + + + objectproperty_ismoduleof + 1.0a + 2011-01-19 + A Module is of a Seed + A Module is of a Seed + Pedro Lopes pedrolopes@ua.pt + isModuleOf + + + + + + + + + + + objectproperty_isresourceof + 1.0a + 2011-01-19 + A Resource is of a Concept + A Resource is of a Concept + Pedro Lopes pedrolopes@ua.pt + isResourceOf + + + + + + + + + + + objectproperty_loadsfor + 1.0a + 2011-01-20 + A CSV,XML,SQL loads data for a Resource + A CSV,XML,SQL loads data for a Resource + Pedro Lopes pedrolopes@ua.pt + loadsFor + + + + + + + + + + + + + + objectproperty_loadsfrom + 1.0a + 2011-01-20 + A Resource loads data from a CSV, XML, SQL, SPARQL + A Resource loads data from a CSV, XML, SQL, SPARQL + Pedro Lopes pedrolopes@ua.pt + loadsFrom + + + + + + + + + + + + + objectproperty_mappedfrom + 1.0b + 2011-03-24 + Defines a mapping destination (Concept) for a given Resource + Defines a mapping destination (Concept) for a given Resource + Pedro Lopes pedrolopes@ua.pt + mappedFrom + + + + + + + + + + + objectproperty_mapsto + 1.0b + 2011-03-24 + Defines a mapping destination (Concept) for a given Resource + Defines a mapping destination (Concept) for a given Resource + Pedro Lopes pedrolopes@ua.pt + mapsTo + + + + + + + + + + + + + + + dataproperty_loaded + 1.0b + 2011-03-31 + Defines that a Seed, Entity, Concept is or is not built. + Defines that a Seed, Entity, Concept is or is not built. + Pedro Lopes pedrolopes@ua.pt + loaded + + + + + + + + + + + + + + + + + + + + dataproperty_database + 1.0b + 2011-03-24 + Database identifier for connectionn info in .js config file + Database identifier for connectionn info in .js config file + Pedro Lopes pedrolopes@ua.pt + database + + + + + + + + + + dataproperty_delimiter + 1.0a + 2011-01-19 + Column separator in CSV file + Column separator in CSV file + Pedro Lopes pedrolopes@ua.pt + delimiter + + + + + + + + + + dataproperty_enabled + 1.0a + 2011-01-14 + Defines if an individual is enabled or not + Defines if an individual is enabled or not + Pedro Lopes pedrolopes@ua.pt + enabled + + + + + + + + + dataproperty_endpoint + 1.0b + 2011-04-04 + Endpoint for a given Resource. + Endpoint for a given Resource. + Pedro Lopes pedrolopes@ua.pt + endpoint + + + + + + + + dataproperty_extension + 1.0b + 2011-03-24 + Defines the source for a Resource extension + Defines the source for a Resource extension + Pedro Lopes pedrolopes@ua.pt + extension + + + + + + + + + + dataproperty_host + 1.0a + 2011-01-14 + Defines a Seed individual host + Defines a Seed individual host + Pedro Lopes pedrolopes@ua.pt + host + + + + + + + + + + dataproperty_line + 1.0a + 2011-01-19 + Pedro Lopes pedrolopes@ua.pt + The line where the CSV reader will start + The line where the CSV reader will start + line + + + + + + + + + + dataproperty_method + 1.0a + 2011-01-19 + A Resource access method or Bridge method + A Resource access method or Bridge method + Pedro Lopes pedrolopes@ua.pt + method + + + + + + + + + + + dataproperty_order + 1.0a + 2011-02-21 + Defines resource load order, useful for data-dependencies. + Defines resource load order, useful for data-dependencies. + Pedro Lopes pedrolopes@ua.pt + order + + + + + + + + + + dataproperty_plugin + 1.0a + 2011-01-20 + Defines if a module is a plugin or not + Defines if a module is a plugin or not + Pedro Lopes pedrolopes@ua.pt + plugin + + + + + + + + + + dataproperty_property + 1.0a + 2011-01-19 + An Item predicate where Resource will be loaded into + An Item predicate where Resource will be loaded into + Pedro Lopes pedrolopes@ua.pt + property + + + + + + + + + + + + + dataproperty_public + 1.0a + 2011-01-14 + Defines if a Seed data is publishable or not + Defines if a Seed data is publishable or not + Pedro Lopes pedrolopes@ua.pt + public + + + + + + + + + dataproperty_query + 1.0a + 2011-01-27 + A Column selector for the associated Resource + A Column selector for the associated Resource + Pedro Lopes pedrolopes@ua.pt + query + + + + + + + + + + + + + dataproperty_regex + 1.0b + 2011-05-03 + Description for used regular expressions. + Description for used regular expressions. + Pedro Lopes pedrolopes@ua.pt + regex + + + + + + + + + dataproperty_replace + 1.0a + 2011-01-19 + Pedro Lopes pedrolopes@ua.pt + The replaceable token in a Resource + The replaceable token in a Resource + replace + + + + + + + + + + + + + dataproperty_select + 1.0a + 2011-01-27 + Pedro Lopes pedrolopes@ua.pt + The select statement to get data from a Resource + The select statement to get data from a Resource + select + + + + + + + + + + + + + + + class_bridge + + 1.0a + 2011-01-19 + Bridge individuals are connections to external resources. They are used to interact with these resources. A Bridge can be a composeable URL or simple text to be replaced with data from the 3SDB. + Bridge individuals are connections to external resources. They are used to interact with these resources. A Bridge can be a composeable URL or simple text to be replaced with data from the 3SDB. + Pedro Lopes pedrolopes@ua.pt + Title + + + + + + + + class_csv + + 1.0a + 2011-01-18 + CSV + Class for CSV resource individuals and definitions + Class for CSV resource individuals and definitions + Pedro Lopes pedrolopes@ua.pt + + + + + + + + class_concept + + 1.0a + 2011-01-14 + Concept + Concept element are used to organize distinct resources. + + Examples: + - HGNC + - UniProt + Concept element are used to organize distinct resources. + + Examples: + - HGNC + - UniProt + Pedro Lopes pedrolopes@ua.pt + + + + + + + + class_entity + + 1.0a + 2011-01-14 + Entity + Entity elements are the main data organizational class inside COEUS. Entities act as upper classes to all other elements in the Seed. + + Everything is an Entity. + + Example: + - Gene + - Protein + Entity elements are the main data organizational class inside COEUS. Entities act as upper classes to all other elements in the Seed. + + Everything is an Entity. + + Example: + - Gene + - Protein + Pedro Lopes pedrolopes@ua.pt + + + + + + + + class_item + + 1.0a + 2011-01-14 + Item + Item elements are the most atomic information units in COEUS. + Item elements are the most atomic information units in COEUS. + Pedro Lopes pedrolopes@ua.pt + + + + + + + + class_module + + 1.0a + 2011-01-19 + Class for platform modules: "Module" individual + Class for platform modules: "Module" individual + Module + Pedro Lopes pedrolopes@ua.pt + + + + + + + + class_resource + + 1.0a + 2011-01-18 + Pedro Lopes pedrolopes@ua.pt + Resource + Resource individuals reflect the data, information or knowledge sources for each Seed Concept + Resource individuals reflect the data, information or knowledge sources for each Seed Concept + + + + + + + + class_sparql + + 1.0a + 2011-01-26 + Class for SPARQL resource individuals and definitions + Class for SPARQL resource individuals and definitions + Pedro Lopes pedrolopes@ua.pt + SPARQL + + + + + + + + class_sql + + 1.0a + 2011-01-18 + Class for SQL resource individuals and definitions + Class for SQL resource individuals and definitions + Pedro Lopes pedrolopes@ua.pt + SQL + + + + + + + + class_seed + 1.0a + 2011-01-14 + Pedro Lopes pedrolopes@ua.pt + Seed + This class is used to store Seed information such has host features or availability. + This class is used to store Seed information such has host features or availability. + + + + + + + + class_xml + + 1.0a + 2011-01-18 + Class for XML resource individuals and definitions + Class for XML resource individuals and definitions + Pedro Lopes pedrolopes@ua.pt + XML + + + + + + + + + + + + + + + + + News Aggregator + + News Aggregator + + + + + News + Entity News + + + + + + News + + + + + + Reuters + + + Reuters + + + + + + Marca + + + Marca + + + + + + Abola + + + Abola + + + + + + BBC + + + BBC + + + + + + + + + + + + Abola + Resource loader for A Bola XML feeds. + + 1 + cache + http://www.abola.pt/rss/index.aspx + + //item + xml + Abola + + + + + + + + + + + Reuters + Resource loader for Reuters XML feeds. + + 4 + cache + http://feeds.reuters.com/reuters/sportsNews + + //item + xml + Reuters + + + + + + + + + + + Marca + Resource loader for Marca XML feeds. + + 2 + cache + http://estaticos.marca.com/rss/portada.xml + + //item + xml + Marca + + + + + + + + + + + BBC + Resource loader for BBC XML feeds. + + 3 + cache + http://feeds.bbci.co.uk/sport/0/rss.xml + + //item + xml + BBC + + + + + xml_link + + + + + dc:publisher + link + xml_link + + + + + xml_Reuters_id + + dc:identifier + guid + + xml_Reuters_id + [0-9]{5,} + + + + + xml_BBC_id + + dc:identifier + guid + + xml_BBC_id + [0-9]{5,} + + + + + xml_description + + + + + dc:description + description + xml_description + + + + + xml_date + + + + + dc:date + pubDate + xml_date + + + + + xml_Marca_id + + dc:identifier + guid + + xml_Marca_id + [0-9]{5,} + + + + + xml_title + + + + + dc:title + title + xml_title + + + + + xml_Abola_id + + dc:identifier + guid + + xml_Abola_id + [0-9]{5,} + + + + + + + + diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml index 21452de..a08d544 100755 --- a/src/main/webapp/WEB-INF/web.xml +++ b/src/main/webapp/WEB-INF/web.xml @@ -124,14 +124,17 @@ pt.ua.bioinformatics.coeus.common.HttpListener + + pt.ua.bioinformatics.coeus.common.ExecutorContextListener + - + + /config/* /setup/* /manager/* GET @@ -153,7 +156,7 @@ /login.jsp /login.jsp?f=error - + --> diff --git a/src/main/webapp/docs/ontology.jsp b/src/main/webapp/docs/ontology.jsp index 3200b96..976a167 100644 --- a/src/main/webapp/docs/ontology.jsp +++ b/src/main/webapp/docs/ontology.jsp @@ -328,7 +328,7 @@
          1. For resources, this means the global object query. For each individual answer to this query, new Item individuals will be created.
              -
            • For CSV resources, query is the combination of the column delimiter with the quotes delimiter and with the headers skip number (Ex: t|"|1) [1].
              • +
            • For CSV resources, query is the combination of the headers skip number with the quotes delimiter (Ex: 1|") [1].
            • For XML resources, query is the global XPath query (//entry).
              • diff --git a/src/main/webapp/setup/addentity.jsp b/src/main/webapp/setup/addentity.jsp index 275b7a4..7d0aca4 100644 --- a/src/main/webapp/setup/addentity.jsp +++ b/src/main/webapp/setup/addentity.jsp @@ -44,6 +44,10 @@ $('#titleForm').append(''); $('#labelForm').append(''); $('#commentForm').append(''); + + $('#breadSeed').html('Dashboard / '); + $('#breadEntities').html('Entities / '); + } ); } diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 87d9861..57d7396 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -94,7 +94,7 @@ //$('#Environment').val(result.config.environment); $('#ApiKey').val(result.config.apikey); $('#Ontology').val(result.config.ontology); - $('#Setup').val(result.config.setup); + $('#SetupFile').val(result.config.setup); if (result.config.built.toString() === "true") $('#Built').prop('checked', true); @@ -146,7 +146,7 @@ "keyprefix": $('#KeyPrefix').val(), "version": $('#Version').val(), "ontology": $('#Ontology').val(), - "setup": $('#Setup').val(), + "setup": $('#SetupFile').val(), "sdb": "sdb.ttl", "predicates": "predicates.csv", "built": $('#Built').is(':checked'), diff --git a/src/main/webapp/setup/index.jsp b/src/main/webapp/setup/index.jsp index 7b080fd..48d9d8b 100644 --- a/src/main/webapp/setup/index.jsp +++ b/src/main/webapp/setup/index.jsp @@ -125,6 +125,14 @@ function fillHeader(result) { $('#header').html('

              ' + lastPath() + ' ' + result.config.environment + '

              '); $('#apikey').html(result.config.apikey); + var built = result.config.built; + if (built == false) { + $('#btnUnbuild').removeClass("active"); + $('#btnBuild').addClass("active"); + } else { + $('#btnUnbuild').addClass("active"); + $('#btnBuild').removeClass("active"); + } } function fillEntities(result) { @@ -142,7 +150,7 @@ + ' ' + prefix + ":" + entity + ' ' - + ' ' + + ' ' + '

                '; } @@ -173,7 +181,7 @@ } ); - var qEntities = "SELECT (COUNT(*) AS ?triples) {?s a coeus:Item}"; + var qEntities = "SELECT (COUNT(*) AS ?triples) {?s a coeus:Item . ?s coeus:hasConcept ?concept . ?concept coeus:hasEntity ?entity . ?entity coeus:isIncludedIn " + seed + "}"; queryToResult(qEntities, function(result) { $('#triples').html(result[0].triples.value); }); @@ -187,7 +195,7 @@ function changeEnv() { var env = $('#environments').val(); - callURL("../../config/upenv/" + env, changeEnvResult, changeEnvResult, changeEnvError); + callURL("../../config/upenv/" + env, changeEnvResult, changeEnvResult, showError); } function changeEnvResult(result) { if (result.status === 100) @@ -195,7 +203,7 @@ else $('#info').html(generateHtmlMessage("Warning!", result.message)); } - function changeEnvError(result, text) { + function showError(result, text) { $('#info').html(generateHtmlMessage("ERROR!", text, "alert-error")); } function build() { @@ -211,6 +219,7 @@ function unbuildResult(result) { var urlPrefix = "../../api/" + getApiKey(); console.log(result); + $('#info').html(''); for (var r in result) { var res = splitURIPrefix(result[r].resource.value); var resource = getPrefix(res.namespace) + ":" + res.value; @@ -219,13 +228,32 @@ } function unbuiltResource(resource, result) { - if (result.status === 100) - console.log("The " + resource + " has been changed. "); - else - console.log("The " + resource + " has already unbuild. "); + if (result.status === 100) { + var text = "The " + resource + " has been changed. "; + console.log(text); + $('#info').append(generateHtmlMessage("Success!", text, "alert-success")); + } + else { + var text = "The " + resource + " has already unbuild. "; + console.log(text); + $('#info').append(generateHtmlMessage("Alert!", text, "alert-warning")); + } + } + function changeBuiltResult(bool, result) { + if (result.status === 100) { + var text = "The property built has been changed to " + bool + "."; + console.log(text); + $('#info').html(generateHtmlMessage("Success!", text, "alert-success")); + } + else { + var text = "The property built has not been changed to " + bool + "."; + console.log(text); + $('#info').html(generateHtmlMessage("Alert!", text, "alert-warning")); + } } + @@ -262,8 +290,14 @@ Explorer
            - Rebuild - Unbuild + (Re)Build +
            + KB not Built + KB is Built + +
            + + Change all Resources to unbuild
            Export From 66ddd32be3991d7dfa062b6ece9b438775560e58 Mon Sep 17 00:00:00 2001 From: sernadela Date: Tue, 8 Oct 2013 14:04:59 +0100 Subject: [PATCH 41/52] - Setup: Fix remove seed. - Setup: Add SWAT4LS workshop. - Change Add/Edit Seeds to modals. --- src/main/webapp/assets/js/coeus.api.js | 95 +++++----- src/main/webapp/index.jsp | 7 +- src/main/webapp/science.jsp | 27 ++- src/main/webapp/setup/addseed.jsp | 36 ++-- src/main/webapp/setup/seeds.jsp | 246 ++++++++++++++++++++++--- 5 files changed, 323 insertions(+), 88 deletions(-) diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 007601d..3807af8 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -159,8 +159,8 @@ function callAPI(url, html) { }); } /** -* Return the first apikey -* + * Return the first apikey + * * @returns {unresolved} */ function getApiKey() { return document.getElementById('apikey').innerHTML.split('|')[0]; @@ -198,37 +198,34 @@ function redirect(location) { * @param {type} object * @returns {undefined} */ -function removeAllTriplesFromObject(urlPrefix, object) { +function removeAllTriplesFromObject(urlPrefix, object, showResult, showError) { var qObject = "SELECT ?subject ?predicate {?subject ?predicate " + object + " . }"; - queryToResult(qObject, function(result) { - console.log(result); - for (var r in result) { - var subject = resultToObject(result[r].subject); - var predicate = resultToPredicate(result[r].predicate); - - var url = "/delete/" + subject.prefix + subject.value + '/' + predicate.prefix + predicate.value + '/' + object; - - //console.log("Delete call: " + urlPrefix + url); - callAPI(urlPrefix + url, "#result"); - // if ((predicate.value !== "includes") & (predicate.value !== "isEntityOf") & (predicate.value !== "isConceptOf") & (predicate.value !== "isResourceOf")) - //removeRecursive(urlPrefix, subject.prefix + subject.value); - } + queryToResult(qObject, foreachRemoveObjects.bind(this, urlPrefix, object, showResult, showError)); +} +function foreachRemoveObjects(urlPrefix, object, showResult, showError, result) { + console.log(result); + for (var r in result) { + var subject = resultToObject(result[r].subject); + var predicate = resultToPredicate(result[r].predicate); + var url = "/delete/" + subject.prefix + subject.value + '/' + predicate.prefix + predicate.value + '/' + object; + console.log("Delete call: " + urlPrefix + url); + callURL(urlPrefix + url, showResult, showError); } - ); - } -function cleanUnlikedTriples(urlPrefix) { + +function cleanUnlikedTriples(urlPrefix, showResult, showError) { + console.log("cleanUnlikedTriples call"); //Clean unlinked entities var qEntities = "SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; queryToResult(qEntities, function(result) { for (var r in result) { var entity = splitURIPrefix(result[r].entity.value); var prefix = getPrefix(entity.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + entity.value); + removeAllTriplesFromSubject(urlPrefix, prefix + entity.value, showResult, showError); } }); //Clean unlinked concepts @@ -237,7 +234,7 @@ function cleanUnlikedTriples(urlPrefix) { for (var r in result) { var concept = splitURIPrefix(result[r].concept.value); var prefix = getPrefix(concept.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + concept.value); + removeAllTriplesFromSubject(urlPrefix, prefix + concept.value, showResult, showError); } }); //Clean unlinked resources @@ -246,7 +243,7 @@ function cleanUnlikedTriples(urlPrefix) { for (var r in result) { var resource = splitURIPrefix(result[r].resource.value); var prefix = getPrefix(resource.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + resource.value); + removeAllTriplesFromSubject(urlPrefix, prefix + resource.value, showResult, showError); } }); //Clean unlinked selectores @@ -255,7 +252,7 @@ function cleanUnlikedTriples(urlPrefix) { for (var r in result) { var selector = splitURIPrefix(result[r].selector.value); var prefix = getPrefix(selector.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + selector.value); + removeAllTriplesFromSubject(urlPrefix, prefix + selector.value, showResult, showError); } }); } @@ -298,27 +295,30 @@ function cleanUnlikedTriples(urlPrefix) { // ); //} -function removeAllTriplesFromSubject(urlPrefix, subject) { +/** + * Remove all triples associated with the subject + * + * @param {type} urlPrefix + * @param {type} subject + * @param {type} showResult + * @param {type} showError + * @returns {undefined} + */ +function removeAllTriplesFromSubject(urlPrefix, subject, showResult, showError) { var qSubject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; - queryToResult(qSubject, function(result) { - console.log(result); - for (var r in result) { - var object = resultToObject(result[r].object); - var predicate = resultToPredicate(result[r].predicate); - - var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; - //console.log(url); - callAPI(urlPrefix + url, "#result"); - } - - //if success refresh page - if (document.getElementById('result').className !== 'alert alert-error') { - // window.location="../entity/"+lastPath(); - console.log("REDIRECTING..."); - //window.location.reload(true); - } + queryToResult(qSubject, foreachRemoveSubjects.bind(this, urlPrefix, subject, showResult, showError) + ); +} +function foreachRemoveSubjects(urlPrefix, subject, showResult, showError, result) { + console.log(result); + for (var r in result) { + var object = resultToObject(result[r].object); + var predicate = resultToPredicate(result[r].predicate); + + var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; + console.log("Deleting: " + url); + callURL(urlPrefix + url, showResult, showError); } - ); } function removeAllTriplesFromSubjectAndPredicate(urlPrefix, subject, predicate) { @@ -447,8 +447,17 @@ function removeById(childDiv, parentDiv) } } +/** + * Call a url with 2 callbacks functions (success or error) + * + * @param {type} url + * @param {type} success + * @param {type} error + * @returns {undefined} + */ function callURL(url, success, error) { - url = encodeURI(url);console.log(url); + url = encodeURI(url); + console.log(url); $.ajax({url: url, dataType: 'json'}).done(success).fail(error); } diff --git a/src/main/webapp/index.jsp b/src/main/webapp/index.jsp index 20e6f68..ab1e907 100644 --- a/src/main/webapp/index.jsp +++ b/src/main/webapp/index.jsp @@ -23,7 +23,12 @@
            - +
            +

            SWAT4LS Workshop New!!

            +

            A COEUS Workshop/Tutorial will be presented in the next edition of SWAT4LS.

            +

            This workshop will be helded in Edinburgh, UK, December 9-12, 2013.

            +

            View more »

            +

            Hello, Semantic Web!

            diff --git a/src/main/webapp/science.jsp b/src/main/webapp/science.jsp index 35b7382..f2237ab 100644 --- a/src/main/webapp/science.jsp +++ b/src/main/webapp/science.jsp @@ -17,7 +17,8 @@ @@ -46,6 +47,30 @@

            ">Get Whitepaper

            +
            +
            +

            SWAT4LS 2013 Workshop

            +
            +

            Visit website
            + December 9-12, 2013 Edinburgh, United Kingdom

            +

            Intro

            +

            Since 2008, the SWAT4LS Workshop (http://www.swat4ls.org) has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in the domains of health care and life sciences. The next edition of SWAT4LS will be held in Edinburgh, UK, December 9-12, 2013, preceded by tutorials and followed by hackathon / model-a-thin. All information can be found at http://www.swat4ls.org/workshops/edinburgh2013/.

            +

            The COEUS Platform

            +

            On the tutorial day, the COEUS - Semantic Web Application Framework will be presented. This platform targets the quick creation of new biomedical applications. The framework combines the latest Semantic Web technologies with Rapid Application Development ideals to provide, in a single package, the required tools and algorithms to build a new semantic web information system from scratch. +

            In this tutorial/hands-on session, we will guide you through the process of creating your own custom COEUS knowledge base. You will learn how to:

            +
              +
            1. Create a new COEUS instance
              2. +
            2. From GitHub download to web deployment
              3. +
            3. Integrate data from heterogeneous *omics sources into your COEUS knowledge base
              4. +
            4. Create your mashup merging multiple datasets
              5. +
            5. Explore COEUS API to access aggregated data
              6. +
            6. Build new rich web information systems using the API
              7. +
            7. Access knowledge federation through the SPARQL and LinkedData interfaces +
              8. +
            + Further information regarding this tutorial is available online at http://www.swat4ls.org/workshops/edinburgh2013/scientific-programme/. 

            +
            +

            SWAT4LS 2011

            diff --git a/src/main/webapp/setup/addseed.jsp b/src/main/webapp/setup/addseed.jsp index 6311b18..5e6528d 100644 --- a/src/main/webapp/setup/addseed.jsp +++ b/src/main/webapp/setup/addseed.jsp @@ -28,7 +28,7 @@ $('#type').html("Edit Seed"); $('#submit').html('Save '); - var q = "SELECT ?label ?title {" + path + " dc:title ?title . " + path + " rdfs:label ?label . }"; + var q = "SELECT ?label ?title ?comment {" + path + " dc:title ?title . " + path + " rdfs:label ?label . " + path + " rdfs:comment ?comment }"; queryToResult(q,function(result) { //var resultTitle = json.results.bindings[0].title; console.log(result); @@ -37,11 +37,11 @@ changeURI(result[0].title.value); //document.getElementById('title').setAttribute("disabled"); $('#label').val(result[0].label.value); - //$('#comment').val(json.results.bindings[0].comment.value); + $('#comment').val(result[0].comment.value); //PUT OLD VALUES IN THE STATIC FIELD $('#titleForm').append(''); $('#labelForm').append(''); - //$('#commentForm').append(''); + $('#commentForm').append(''); } ); } @@ -82,10 +82,12 @@ var individual = $('#uri').html(); var title = $('#title').val(); var label = $('#label').val(); + var comment = $('#comment').val(); var predType = "rdf:type"; var predTitle = "dc:title"; var predLabel = "rdfs:label"; + var predComment = "rdfs:comment"; var urlWrite = "../../../api/" + getApiKey() + "/write/"; @@ -99,6 +101,10 @@ $('#labelForm').addClass('controls control-group error'); empty = true; } + if (comment === '') { + $('#commentForm').addClass('controls control-group error'); + empty = true; + } if (!empty) { callAPI(urlWrite + individual + "/" + predType + "/owl:NamedIndividual", '#result'); @@ -107,7 +113,7 @@ //callAPI(urlWrite + individual + "/" + predSeed + "/" + lastPath(), '#result'); //callAPI(urlWrite + lastPath() + "/" + seedIncludes + "/" + individual, '#result'); callAPI(urlWrite + individual + "/" + predLabel + "/xsd:string:" + label, '#result'); - //callAPI(urlWrite + individual + "/" + predComment + "/xsd:string:" + comment, '#result'); + callAPI(urlWrite + individual + "/" + predComment + "/xsd:string:" + comment, '#result'); } @@ -119,6 +125,8 @@ callAPI(urlUpdate + lastPath() + "/" + "rdfs:label" + "/xsd:string:" + $('#oldLabel').val() + ",xsd:string:" + $('#label').val(), '#result'); if ($('#oldTitle').val() !== $('#title').val()) callAPI(urlUpdate + lastPath() + "/" + "dc:title" + "/xsd:string:" + $('#oldTitle').val() + ",xsd:string:" + $('#title').val(), '#result'); + if ($('#oldComment').val() !== $('#comment').val()) + callAPI(urlUpdate + lastPath() + "/" + "rdfs:comment" + "/xsd:string:" + $('#oldComment').val() + ",xsd:string:" + $('#comment').val(), '#result'); } @@ -173,10 +181,10 @@
            - +
            @@ -197,21 +205,7 @@
            - +
            diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index f98a787..2b13a8a 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -11,18 +11,35 @@ + @@ -76,18 +228,19 @@

            Please, choose the seed:

            -
            +
            • /
            • Seeds
            +
            - + Add Seed
            -
            +
              @@ -105,34 +258,83 @@

              Are you sure do you want to remove the seed?

              Warning: All dependents triples are removed too.

              -
              +
              + +
              + +
              + + +
              +
            + + - -
            - Add Concept + Add Concept
            @@ -139,9 +295,6 @@ - - - -
            + + diff --git a/src/main/webapp/setup/entities.jsp b/src/main/webapp/setup/entities.jsp index b51a7ba..dba1030 100644 --- a/src/main/webapp/setup/entities.jsp +++ b/src/main/webapp/setup/entities.jsp @@ -1,4 +1,4 @@ -<%-- +<%-- Document : index Created on : May 28, 2013, 11:20:32 AM Author : sernadela @@ -11,9 +11,58 @@ + @@ -83,7 +253,7 @@
            -
            +
            • /
            • Seeds /
              • @@ -96,10 +266,9 @@

              List of Entities

            -
            - Add Entity + Add Entity
            @@ -118,9 +287,6 @@ - - - -
            - - + + + + diff --git a/src/main/webapp/setup/seeds.jsp b/src/main/webapp/setup/seeds.jsp index 2b13a8a..866091c 100644 --- a/src/main/webapp/setup/seeds.jsp +++ b/src/main/webapp/setup/seeds.jsp @@ -16,7 +16,7 @@ $(document).ready(function() { callURL("../../config/getconfig/", fillHeader); - refreshSeeds(); + refresh(); //activate tooltip (bootstrap-tooltip.js is need) $('.icon-question-sign').tooltip(); @@ -26,8 +26,8 @@ if (event.charCode === 13) if (document.getElementById('addModal').style.display === "block" && document.activeElement.getAttribute('id') === "addModal") add(); - if (document.getElementById('editModal').style.display === "block" && document.activeElement.getAttribute('id') === "editModal") - edit(); + if (document.getElementById('editModal').style.display === "block" && document.activeElement.getAttribute('id') === "editModal") + edit(); }; }); @@ -41,7 +41,7 @@ var urlPrefix = "../../api/" + getApiKey(); cleanUnlikedTriples(urlPrefix); } - function refreshSeeds() { + function refresh() { var qSeeds = "SELECT DISTINCT ?seed ?s {?seed a coeus:Seed . ?seed dc:title ?s . }"; console.log(qSeeds); queryToResult(qSeeds, fillSeeds); @@ -59,7 +59,7 @@ + '

            ' + result[key].s.value + '

            ' + 'URI: ' + seed + '' + '' - + ' ' + + ' ' + '
            '; $('#seeds').append(a); @@ -67,51 +67,58 @@ } //Edit functions - function prepareEditSeed(seed) { + function prepareEdit(individual) { //reset values $('#editResult').html(""); - document.getElementById('editURI').innerHTML = seed; + document.getElementById('editURI').innerHTML = individual; $('#editTitle').val(""); $('#editLabel').val(""); $('#editComment').val(""); - - var q = "SELECT ?label ?title ?comment {" + seed + " dc:title ?title . " + seed + " rdfs:label ?label . " + seed + " rdfs:comment ?comment }"; - queryToResult(q, fillEditSeed); + + var q = "SELECT ?label ?title ?comment {" + individual + " dc:title ?title . " + individual + " rdfs:label ?label . " + individual + " rdfs:comment ?comment }"; + queryToResult(q, fillEdit); } - function fillEditSeed(result) { + function fillEdit(result) { //var resultTitle = json.results.bindings[0].title; console.log(result); - //PUT VALUES IN THE INPUT FIELD - $('#editTitle').val(result[0].title.value); - //document.getElementById('title').setAttribute("disabled"); - $('#editLabel').val(result[0].label.value); - $('#editComment').val(result[0].comment.value); + try + { + //PUT VALUES IN THE INPUT FIELD + $('#editTitle').val(result[0].title.value); + //document.getElementById('title').setAttribute("disabled"); + $('#editLabel').val(result[0].label.value); + $('#editComment').val(result[0].comment.value); + } + catch (err) + { + $('#editResult').append(generateHtmlMessage("Error!", "Some fields do not exist." + err, "alert-error")); + } //PUT OLD VALUES IN THE STATIC FIELD $('#oldTitle').val($('#editTitle').val()); $('#oldLabel').val($('#editLabel').val()); $('#oldComment').val($('#editComment').val()); } - function edit(){ - var individual=$('#editURI').html(); + function edit() { + var individual = $('#editURI').html(); var urlUpdate = "../../api/" + getApiKey() + "/update/"; var url; timer = setTimeout(function() { - $('#closeEditModal').click(); - refreshSeeds(); - }, delay); - - if ($('#oldLabel').val() !== $('#editLabel').val()){ - url=urlUpdate + individual + "/" + "rdfs:label" + "/xsd:string:" + $('#oldLabel').val() + ",xsd:string:" + $('#editLabel').val(); - callURL(url, showResult.bind(this,"#editResult",url),(this,"#editResult",url)); + $('#closeEditModal').click(); + refresh(); + }, delay); + + if ($('#oldLabel').val() !== $('#editLabel').val()) { + url = urlUpdate + individual + "/" + "rdfs:label" + "/xsd:string:" + $('#oldLabel').val() + ",xsd:string:" + $('#editLabel').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); } - if ($('#oldTitle').val() !== $('#editTitle').val()){ - url=urlUpdate + individual + "/" + "dc:title" + "/xsd:string:" + $('#oldTitle').val() + ",xsd:string:" + $('#editTitle').val(); - callURL(url, showResult.bind(this,"#editResult",url),(this,"#editResult",url)); + if ($('#oldTitle').val() !== $('#editTitle').val()) { + url = urlUpdate + individual + "/" + "dc:title" + "/xsd:string:" + $('#oldTitle').val() + ",xsd:string:" + $('#editTitle').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); } - if ($('#oldComment').val() !== $('#editComment').val()){ - url=urlUpdate + individual + "/" + "rdfs:comment" + "/xsd:string:" + $('#oldComment').val() + ",xsd:string:" + $('#editComment').val(); - callURL(url, showResult.bind(this,"#editResult",url),(this,"#editResult",url)); + if ($('#oldComment').val() !== $('#editComment').val()) { + url = urlUpdate + individual + "/" + "rdfs:comment" + "/xsd:string:" + $('#oldComment').val() + ",xsd:string:" + $('#editComment').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); } } //End of Edit functions @@ -120,25 +127,25 @@ $('#removeResult').html(""); $('#removeModalLabel').html(seed); } - function removeSeed() { + function remove() { var seed = $('#removeModalLabel').html(); //var query = initSparqlerQuery(); console.log('Remove: ' + seed); var urlPrefix = "../../api/" + getApiKey(); //remove all subjects and predicates associated. - removeAllTriplesFromObject(urlPrefix, seed, showResult.bind(this,"#removeResult",""), showError.bind(this,"#removeResult","")); + removeAllTriplesFromObject(urlPrefix, seed, showResult.bind(this, "#removeResult", ""), showError.bind(this, "#removeResult", "")); //remove all predicates and objects associated. - removeAllTriplesFromSubject(urlPrefix, seed, showResult.bind(this,"#removeResult",""), showError.bind(this,"#removeResult","")); + removeAllTriplesFromSubject(urlPrefix, seed, showResult.bind(this, "#removeResult", ""), showError.bind(this, "#removeResult", "")); timer = setTimeout(function() { $('#closeRemoveModal').click(); - refreshSeeds(); + refresh(); }, delay); } //End of Remove functions - function changeURI(id,value) { + function changeURI(id, value) { document.getElementById(id).innerHTML = 'coeus:seed_' + value.split(' ').join('_'); } function add() { @@ -184,15 +191,15 @@ console.log(result[0].total.value); if (result[0].total.value == 0) { array.forEach(function(url) { - callURL(url, showResult.bind(this,"#addResult", url), showError.bind(this,"#addResult", url)); + callURL(url, showResult.bind(this, "#addResult", url), showError.bind(this, "#addResult", url)); }); timer = setTimeout(function() { $('#closeAddModal').click(); - refreshSeeds(); + refresh(); }, delay); } else { $('#addResult').append(generateHtmlMessage("Warning!", "This individual already exists.", "alert-warning")); - refreshSeeds(); + refresh(); } }); } @@ -264,7 +271,7 @@
            - +
            @@ -281,7 +288,7 @@
            - +
            From 8fc857b55cad7789170edfd8e21be40a771e8f8c Mon Sep 17 00:00:00 2001 From: sernadela Date: Wed, 16 Oct 2013 11:58:41 +0100 Subject: [PATCH 43/52] - Setup: Change Edit/Add/Remove Resources to modals. - Setup: Code improvements. --- src/main/webapp/assets/js/coeus.api.js | 405 +----- src/main/webapp/assets/js/coeus.setup.js | 1162 +++++++++++++++++ src/main/webapp/setup/addresource.jsp | 140 +- src/main/webapp/setup/concepts.jsp | 344 +---- src/main/webapp/setup/config.jsp | 2 +- src/main/webapp/setup/editenvironment.jsp | 2 +- src/main/webapp/setup/entities.jsp | 284 +--- src/main/webapp/setup/environments.jsp | 2 +- src/main/webapp/setup/index.jsp | 180 +-- src/main/webapp/setup/management.jsp | 78 -- src/main/webapp/setup/modals/add.jsp | 34 + src/main/webapp/setup/modals/addResource.jsp | 113 ++ src/main/webapp/setup/modals/edit.jsp | 35 + src/main/webapp/setup/modals/editResource.jsp | 131 ++ src/main/webapp/setup/modals/remove.jsp | 21 + src/main/webapp/setup/resources.jsp | 122 +- src/main/webapp/setup/seeds.jsp | 271 +--- 17 files changed, 1713 insertions(+), 1613 deletions(-) create mode 100644 src/main/webapp/assets/js/coeus.setup.js delete mode 100644 src/main/webapp/setup/management.jsp create mode 100644 src/main/webapp/setup/modals/add.jsp create mode 100644 src/main/webapp/setup/modals/addResource.jsp create mode 100644 src/main/webapp/setup/modals/edit.jsp create mode 100644 src/main/webapp/setup/modals/editResource.jsp create mode 100644 src/main/webapp/setup/modals/remove.jsp diff --git a/src/main/webapp/assets/js/coeus.api.js b/src/main/webapp/assets/js/coeus.api.js index 3807af8..1380531 100644 --- a/src/main/webapp/assets/js/coeus.api.js +++ b/src/main/webapp/assets/js/coeus.api.js @@ -70,407 +70,4 @@ function deleteTriple(subject, predicate, object, key) { console.log('[COEUS] unable to complete data delete request. ' + textStatus); // Server communication error function handler. }); -} -/** - * init service prefix - * @returns {query} */ -function initSparqlerQuery() { - var sparqler = new SPARQL.Service("/coeus/sparql"); - - var prefixes = getPrefixURI(); - for (var key in prefixes) { - sparqler.setPrefix(key, prefixes[key]); - } - - var query = sparqler.createQuery(); - return query; -} - -function getPrefixURI() { - var prefixes = { - dc: "http://purl.org/dc/elements/1.1/", - rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - rdfs: "http://www.w3.org/2000/01/rdf-schema#", - coeus: "http://bioinformatics.ua.pt/coeus/resource/", - owl: "http://www.w3.org/2002/07/owl#" - }; - return prefixes; -} - -/** - * Get the namespace prefix - * - * @param {type} uri - * @returns {undefined} - */ -function getPrefix(uri) { - var prefixes = getPrefixURI(); - - for (var key in prefixes) { - if (prefixes[key] === uri) - return key; - } - return ''; -} - -/** - * Split the URI to give the namespace - * @param {type} uri - * @returns {splitURIPrefix.mapping} - */ -function splitURIPrefix(uri) { - var value; - var uriToSlit = uri; - if (uriToSlit.indexOf("#") !== -1) - value = uriToSlit.split('#').pop(); - else - value = uriToSlit.split('/').pop(); - var namespace = uri.substr(0, uri.length - value.length); - - var mapping = { - "namespace": namespace, - "value": value - }; - - return mapping; -} -/** - * Call api through URL and change the HTML (component id) according to the result. - * @param {type} url - * @param {type} html - * @returns {undefined} - */ -function callAPI(url, html) { - url = encodeURI(url); - $.ajax({url: url, async: false, dataType: 'json'}).done(function(data) { - console.log(url + ' ' + data.status); - if (data.status === 100) { - //$(html).append('Call: ' + url + '
            Message: ' + data.message+'

            '); - $(html).addClass('alert alert-success'); - } else { - $(html).addClass('alert alert-error'); - $(html).append('Call: ' + url + '
            Status: ' + data.status + ' Message: ' + data.message + '

            '); - } - - }).fail(function(jqXHR, textStatus) { - $(html).addClass('alert alert-error'); - $(html).append('Call: ' + url + '
            ' + 'ERROR: ' + textStatus + '

            '); - // Server communication error function handler. - }); -} -/** - * Return the first apikey - * - * @returns {unresolved} */ -function getApiKey() { - return document.getElementById('apikey').innerHTML.split('|')[0]; -} -/** - * Return last element divided by / of url - * @returns {unresolved} - */ -function lastPath() { - var pathArray = window.location.pathname.split('/'); - var path = pathArray[pathArray.length - 1]; - return path; -} - -/** - * Return penultimate element divided by / of url - * @returns {unresolved} - */ -function penulPath() { - var pathArray = window.location.pathname.split('/'); - var path = pathArray[pathArray.length - 2]; - return path; -} - -function redirect(location) { - window.location = location; -} -/** - * - * remove all subjects and predicates associated. - * - * example urlPrefix = "../../api/" + getApiKey() ; - * - * @param {type} urlPrefix - * @param {type} object - * @returns {undefined} - */ -function removeAllTriplesFromObject(urlPrefix, object, showResult, showError) { - - var qObject = "SELECT ?subject ?predicate {?subject ?predicate " + object + " . }"; - queryToResult(qObject, foreachRemoveObjects.bind(this, urlPrefix, object, showResult, showError)); -} -function foreachRemoveObjects(urlPrefix, object, showResult, showError, result) { - console.log(result); - for (var r in result) { - var subject = resultToObject(result[r].subject); - var predicate = resultToPredicate(result[r].predicate); - - var url = "/delete/" + subject.prefix + subject.value + '/' + predicate.prefix + predicate.value + '/' + object; - - console.log("Delete call: " + urlPrefix + url); - callURL(urlPrefix + url, showResult, showError); - } -} - - -function cleanUnlikedTriples(urlPrefix, showResult, showError) { - console.log("cleanUnlikedTriples call"); - //Clean unlinked entities - var qEntities = "SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; - queryToResult(qEntities, function(result) { - for (var r in result) { - var entity = splitURIPrefix(result[r].entity.value); - var prefix = getPrefix(entity.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + entity.value, showResult, showError); - } - }); - //Clean unlinked concepts - var qConcepts = "SELECT * {{ ?concept a coeus:Concept . FILTER NOT EXISTS{ ?concept coeus:hasEntity ?entity }}UNION {?concept a coeus:Concept . FILTER NOT EXISTS { ?entity coeus:isEntityOf ?concept }} }"; - queryToResult(qConcepts, function(result) { - for (var r in result) { - var concept = splitURIPrefix(result[r].concept.value); - var prefix = getPrefix(concept.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + concept.value, showResult, showError); - } - }); - //Clean unlinked resources - var qResources = "SELECT * {{ ?resource a coeus:Resource . FILTER NOT EXISTS{ ?resource coeus:isResourceOf ?concept} }UNION {?resource a coeus:Resource . FILTER NOT EXISTS { ?concept coeus:hasResource ?resource}} }"; - queryToResult(qResources, function(result) { - for (var r in result) { - var resource = splitURIPrefix(result[r].resource.value); - var prefix = getPrefix(resource.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + resource.value, showResult, showError); - } - }); - //Clean unlinked selectores - var qSelectores = "SELECT * {{ ?selector coeus:property ?property . FILTER NOT EXISTS { ?selector coeus:loadsFor ?resource } }UNION {?selector coeus:property ?property . FILTER NOT EXISTS { ?resource coeus:loadsFrom ?selector}}}"; - queryToResult(qSelectores, function(result) { - for (var r in result) { - var selector = splitURIPrefix(result[r].selector.value); - var prefix = getPrefix(selector.namespace) + ":"; - removeAllTriplesFromSubject(urlPrefix, prefix + selector.value, showResult, showError); - } - }); -} - -//function isModel(key) { -// var b = false; -// -// if (key.indexOf("coeus:seed_") !== -1 | key.indexOf("coeus:entity_") !== -1 | key.indexOf("coeus:concept_") !== -1 | key.indexOf("coeus:resource_") !== -1) -// b = true; -// -// console.log(key + ' ' + b); -// return b; -// -//} -// -//function removeRecursive(urlPrefix, subject) { -// var query = initSparqlerQuery(); -// var qObject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; -// console.log("Recursive call: " + qObject); -// query.query(qObject, -// {success: function(json) { -// var result = json.results.bindings; -// -// for (var r in result) { -// var object = resultToObject(result[r].object); -// var predicate = resultToPredicate(result[r].predicate); -// -// var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; -// console.log("Recursive Delete call: " + urlPrefix + url); -// //callAPI(urlPrefix + url, "#result"); -// if (isModel(object.prefix + object.value)) { -// // console.log("Another recursive call: "+url); -// //removeRecursive(urlPrefix, object.prefix + object.value); -// } -// -// } -// -// -// }} -// ); -//} - -/** - * Remove all triples associated with the subject - * - * @param {type} urlPrefix - * @param {type} subject - * @param {type} showResult - * @param {type} showError - * @returns {undefined} - */ -function removeAllTriplesFromSubject(urlPrefix, subject, showResult, showError) { - var qSubject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; - queryToResult(qSubject, foreachRemoveSubjects.bind(this, urlPrefix, subject, showResult, showError) - ); -} -function foreachRemoveSubjects(urlPrefix, subject, showResult, showError, result) { - console.log(result); - for (var r in result) { - var object = resultToObject(result[r].object); - var predicate = resultToPredicate(result[r].predicate); - - var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; - console.log("Deleting: " + url); - callURL(urlPrefix + url, showResult, showError); - } -} - -function removeAllTriplesFromSubjectAndPredicate(urlPrefix, subject, predicate) { - var qSubject = "SELECT ?object {" + subject + " " + predicate + " ?object . }"; - console.log(qSubject); - queryToResult(qSubject, function(result) { - console.log(result); - for (var r in result) { - var object = resultToObject(result[r].object); - - var url = "/delete/" + subject + '/' + predicate + '/' + object.prefix + object.value; - console.log(url); - callAPI(urlPrefix + url, "#result"); - } - - //if success refresh page - if (document.getElementById('result').className !== 'alert alert-error') { - // window.location="../entity/"+lastPath(); - console.log("REDIRECTING..."); - //window.location.reload(true); - } - } - ); -} -function removeAllTriplesFromPredicateAndObject(urlPrefix, predicate, object) { - var qSubject = "SELECT ?subject {?subject " + predicate + " " + object + " . }"; - console.log(qSubject); - queryToResult(qSubject, function(result) { - console.log(result); - for (var r in result) { - var subject = resultToPredicate(result[r].subject); - - var url = "/delete/" + subject.prefix + subject.value + '/' + predicate + '/' + object; - //console.log(url); - callAPI(urlPrefix + url, "#result"); - } - } - ); -} - -/** - * Converts a object from the json result to a url usage - * @param {type} object - * @returns {resultToObject.mapping} - */ -function resultToObject(object) { - var val = object.value; - var objectPrefix = ''; - - if (object.type === "uri") { - var splitedObject = splitURIPrefix(val); - val = splitedObject.value; - objectPrefix = getPrefix(splitedObject.namespace); - } - - if (objectPrefix !== '') - objectPrefix = objectPrefix + ':'; - else - objectPrefix = 'xsd:' + splitURIPrefix(object.datatype).value + ':' + objectPrefix; - //TO ALLOW '/' in the string call encodeBars(string); - var mapping = { - "prefix": objectPrefix, - "value": encodeBars(val) - }; - return mapping; -} -/** - * Converts a predicate from the json result to a url usage - * @param {type} pred - * @returns {resultToPredicate.mapping} - */ -function resultToPredicate(pred) { - var splitedPredicate = splitURIPrefix(pred.value); - var predicatePrefix = getPrefix(splitedPredicate.namespace); - if (predicatePrefix !== '') - predicatePrefix = predicatePrefix + ':'; - - var mapping = { - "prefix": predicatePrefix, - "value": splitedPredicate.value - }; - - return mapping; - -} -/** - * Do a query to retrive the result in a callback way - * - * return callback(result); - * - * @param {type} selectQuery - * @param {type} callback - * @returns {undefined} - */ -function queryToResult(selectQuery, callback) { - var query = initSparqlerQuery(); - query.query(selectQuery, - {success: function(json) { - var result = json.results.bindings; - //console.log(result); - callback(result); - }} - ); -} - -function encodeBars(value) { - value = value.split(';').join('%3B'); - value = value.split('/').join('%2F'); - value = value.split('#').join('%23'); - value = value.split('?').join('%3F'); - return value; -} -function removeById(childDiv, parentDiv) -{ - console.log(childDiv + ' ' + parentDiv); - if (childDiv === parentDiv) { - alert("The parent div cannot be removed."); - } - else if (document.getElementById(childDiv)) { - var child = document.getElementById(childDiv); - var parent = document.getElementById(parentDiv); - parent.removeChild(child); - } - else { - alert("Child div has already been removed or does not exist."); - } -} - -/** - * Call a url with 2 callbacks functions (success or error) - * - * @param {type} url - * @param {type} success - * @param {type} error - * @returns {undefined} - */ -function callURL(url, success, error) { - url = encodeURI(url); - console.log(url); - $.ajax({url: url, dataType: 'json'}).done(success).fail(error); -} - -/** - * Generate a html code message - * Ex: var htmlMessage=generateHtmlMessage("Error!", "It already exists!","alert-error"); - * - * @param {type} strong - * @param {type} message - * @param {type} type - * @returns {String} - */ -function generateHtmlMessage(strong, message, type) { - var error = '
            ' + strong + ' ' + message + '
            '; - return error; -} +} \ No newline at end of file diff --git a/src/main/webapp/assets/js/coeus.setup.js b/src/main/webapp/assets/js/coeus.setup.js new file mode 100644 index 0000000..c58631e --- /dev/null +++ b/src/main/webapp/assets/js/coeus.setup.js @@ -0,0 +1,1162 @@ +/** + * COEUS Setup JS functions (included in most pages..) + */ + +/** + * init service prefix + * @returns {query} */ +function initSparqlerQuery() { + var sparqler = new SPARQL.Service("/coeus/sparql"); + + var prefixes = getPrefixURI(); + for (var key in prefixes) { + sparqler.setPrefix(key, prefixes[key]); + } + + var query = sparqler.createQuery(); + return query; +} + +function getPrefixURI() { + var prefixes = { + dc: "http://purl.org/dc/elements/1.1/", + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + rdfs: "http://www.w3.org/2000/01/rdf-schema#", + coeus: "http://bioinformatics.ua.pt/coeus/resource/", + owl: "http://www.w3.org/2002/07/owl#" + }; + return prefixes; +} + +/** + * Get the namespace prefix + * + * @param {type} uri + * @returns {undefined} + */ +function getPrefix(uri) { + var prefixes = getPrefixURI(); + + for (var key in prefixes) { + if (prefixes[key] === uri) + return key; + } + return ''; +} + +/** + * Split the URI to give the namespace + * @param {type} uri + * @returns {splitURIPrefix.mapping} + */ +function splitURIPrefix(uri) { + var value; + var uriToSlit = uri; + if (uriToSlit.indexOf("#") !== -1) + value = uriToSlit.split('#').pop(); + else + value = uriToSlit.split('/').pop(); + var namespace = uri.substr(0, uri.length - value.length); + + var mapping = { + "namespace": namespace, + "value": value + }; + + return mapping; +} +/** + * Call api through URL and change the HTML (component id) according to the result. + * @param {type} url + * @param {type} html + * @returns {undefined} + */ +//function callAPI(url, html) { +// url = encodeURI(url); +// $.ajax({url: url, async: false, dataType: 'json'}).done(function(data) { +// console.log(url + ' ' + data.status); +// if (data.status === 100) { +// //$(html).append('Call: ' + url + '
            Message: ' + data.message+'

            '); +// $(html).addClass('alert alert-success'); +// } else { +// $(html).addClass('alert alert-error'); +// $(html).append('Call: ' + url + '
            Status: ' + data.status + ' Message: ' + data.message + '

            '); +// } +// +// }).fail(function(jqXHR, textStatus) { +// $(html).addClass('alert alert-error'); +// $(html).append('Call: ' + url + '
            ' + 'ERROR: ' + textStatus + '

            '); +// // Server communication error function handler. +// }); +//} +/** + * Return the first apikey + * + * @returns {unresolved} */ +function getApiKey() { + return document.getElementById('apikey').innerHTML.split('|')[0]; +} +/** + * Return last element divided by / of url + * @returns {unresolved} + */ +function lastPath() { + var pathArray = window.location.pathname.split('/'); + var path = pathArray[pathArray.length - 1]; + return path; +} + +/** + * Return penultimate element divided by / of url + * @returns {unresolved} + */ +function penulPath() { + var pathArray = window.location.pathname.split('/'); + var path = pathArray[pathArray.length - 2]; + return path; +} + +function redirect(location) { + window.location = location; +} +/** + * + * remove all subjects and predicates associated. + * + * example urlPrefix = "../../api/" + getApiKey() ; + * + * @param {type} urlPrefix + * @param {type} object + * @returns {undefined} + */ +function removeAllTriplesFromObject(urlPrefix, object, showResult, showError) { + + var qObject = "SELECT ?subject ?predicate {?subject ?predicate " + object + " . }"; + queryToResult(qObject, foreachRemoveObjects.bind(this, urlPrefix, object, showResult, showError)); +} +function foreachRemoveObjects(urlPrefix, object, showResult, showError, result) { + console.log(result); + for (var r in result) { + var subject = resultToObject(result[r].subject); + var predicate = resultToPredicate(result[r].predicate); + + var url = "/delete/" + subject.prefix + subject.value + '/' + predicate.prefix + predicate.value + '/' + object; + + console.log("Delete call: " + urlPrefix + url); + callURL(urlPrefix + url, showResult, showError); + } +} + +/** + * Clears all unlinked triples in the DB + * @param {type} urlPrefix + * @param {type} showResult + * @param {type} showError + * @returns {undefined} + */ +function cleanUnlikedTriples(urlPrefix, showResult, showError) { + console.log("cleanUnlikedTriples call"); + //Clean unlinked entities + var qEntities = "SELECT * {{ ?entity a coeus:Entity . FILTER NOT EXISTS{ ?entity coeus:isIncludedIn ?seed }}UNION {?entity a coeus:Entity . FILTER NOT EXISTS { ?seed coeus:includes ?entity }} }"; + queryToResult(qEntities, function(result) { + for (var r in result) { + var entity = splitURIPrefix(result[r].entity.value); + var prefix = getPrefix(entity.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + entity.value, showResult, showError); + } + }); + //Clean unlinked concepts + var qConcepts = "SELECT * {{ ?concept a coeus:Concept . FILTER NOT EXISTS{ ?concept coeus:hasEntity ?entity }}UNION {?concept a coeus:Concept . FILTER NOT EXISTS { ?entity coeus:isEntityOf ?concept }} }"; + queryToResult(qConcepts, function(result) { + for (var r in result) { + var concept = splitURIPrefix(result[r].concept.value); + var prefix = getPrefix(concept.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + concept.value, showResult, showError); + } + }); + //Clean unlinked resources + var qResources = "SELECT * {{ ?resource a coeus:Resource . FILTER NOT EXISTS{ ?resource coeus:isResourceOf ?concept} }UNION {?resource a coeus:Resource . FILTER NOT EXISTS { ?concept coeus:hasResource ?resource}} }"; + queryToResult(qResources, function(result) { + for (var r in result) { + var resource = splitURIPrefix(result[r].resource.value); + var prefix = getPrefix(resource.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + resource.value, showResult, showError); + } + }); + //Clean unlinked selectores + var qSelectores = "SELECT * {{ ?selector coeus:property ?property . FILTER NOT EXISTS { ?selector coeus:loadsFor ?resource } }UNION {?selector coeus:property ?property . FILTER NOT EXISTS { ?resource coeus:loadsFrom ?selector}}}"; + queryToResult(qSelectores, function(result) { + for (var r in result) { + var selector = splitURIPrefix(result[r].selector.value); + var prefix = getPrefix(selector.namespace) + ":"; + removeAllTriplesFromSubject(urlPrefix, prefix + selector.value, showResult, showError); + } + }); +} + +//function isModel(key) { +// var b = false; +// +// if (key.indexOf("coeus:seed_") !== -1 | key.indexOf("coeus:entity_") !== -1 | key.indexOf("coeus:concept_") !== -1 | key.indexOf("coeus:resource_") !== -1) +// b = true; +// +// console.log(key + ' ' + b); +// return b; +// +//} +// +//function removeRecursive(urlPrefix, subject) { +// var query = initSparqlerQuery(); +// var qObject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; +// console.log("Recursive call: " + qObject); +// query.query(qObject, +// {success: function(json) { +// var result = json.results.bindings; +// +// for (var r in result) { +// var object = resultToObject(result[r].object); +// var predicate = resultToPredicate(result[r].predicate); +// +// var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; +// console.log("Recursive Delete call: " + urlPrefix + url); +// //callAPI(urlPrefix + url, "#result"); +// if (isModel(object.prefix + object.value)) { +// // console.log("Another recursive call: "+url); +// //removeRecursive(urlPrefix, object.prefix + object.value); +// } +// +// } +// +// +// }} +// ); +//} + +/** + * Remove all triples associated with the subject + * + * @param {type} urlPrefix + * @param {type} subject + * @param {type} showResult + * @param {type} showError + * @returns {undefined} + */ +function removeAllTriplesFromSubject(urlPrefix, subject, showResult, showError) { + var qSubject = "SELECT ?predicate ?object {" + subject + " ?predicate ?object . }"; + queryToResult(qSubject, foreachRemoveSubjects.bind(this, urlPrefix, subject, showResult, showError) + ); +} +function foreachRemoveSubjects(urlPrefix, subject, showResult, showError, result) { + console.log(result); + for (var r in result) { + var object = resultToObject(result[r].object); + var predicate = resultToPredicate(result[r].predicate); + + var url = "/delete/" + subject + '/' + predicate.prefix + predicate.value + '/' + object.prefix + object.value; + console.log("Deleting: " + url); + callURL(urlPrefix + url, showResult, showError); + } +} + +//function removeAllTriplesFromSubjectAndPredicate(urlPrefix, subject, predicate) { +// var qSubject = "SELECT ?object {" + subject + " " + predicate + " ?object . }"; +// console.log(qSubject); +// queryToResult(qSubject, function(result) { +// console.log(result); +// for (var r in result) { +// var object = resultToObject(result[r].object); +// +// var url = "/delete/" + subject + '/' + predicate + '/' + object.prefix + object.value; +// console.log(url); +// callAPI(urlPrefix + url, "#result"); +// } +// +// //if success refresh page +// if (document.getElementById('result').className !== 'alert alert-error') { +// // window.location="../entity/"+lastPath(); +// console.log("REDIRECTING..."); +// //window.location.reload(true); +// } +// } +// ); +//} +//function removeAllTriplesFromPredicateAndObject(urlPrefix, predicate, object) { +// var qSubject = "SELECT ?subject {?subject " + predicate + " " + object + " . }"; +// console.log(qSubject); +// queryToResult(qSubject, function(result) { +// console.log(result); +// for (var r in result) { +// var subject = resultToPredicate(result[r].subject); +// +// var url = "/delete/" + subject.prefix + subject.value + '/' + predicate + '/' + object; +// //console.log(url); +// callAPI(urlPrefix + url, "#result"); +// } +// } +// ); +//} + +/** + * Converts a object from the json result to a url usage + * @param {type} object + * @returns {resultToObject.mapping} + */ +function resultToObject(object) { + var val = object.value; + var objectPrefix = ''; + + if (object.type === "uri") { + var splitedObject = splitURIPrefix(val); + val = splitedObject.value; + objectPrefix = getPrefix(splitedObject.namespace); + } + + if (objectPrefix !== '') + objectPrefix = objectPrefix + ':'; + else + objectPrefix = 'xsd:' + splitURIPrefix(object.datatype).value + ':' + objectPrefix; + //TO ALLOW '/' in the string call encodeBars(string); + var mapping = { + "prefix": objectPrefix, + "value": encodeBars(val) + }; + return mapping; +} +/** + * Converts a predicate from the json result to a url usage + * @param {type} pred + * @returns {resultToPredicate.mapping} + */ +function resultToPredicate(pred) { + var splitedPredicate = splitURIPrefix(pred.value); + var predicatePrefix = getPrefix(splitedPredicate.namespace); + if (predicatePrefix !== '') + predicatePrefix = predicatePrefix + ':'; + + var mapping = { + "prefix": predicatePrefix, + "value": splitedPredicate.value + }; + + return mapping; + +} +/** + * Do a query to retrive the result in a callback way + * + * return callback(result); + * + * @param {type} selectQuery + * @param {type} callback + * @returns {undefined} + */ +function queryToResult(selectQuery, callback) { + var query = initSparqlerQuery(); + query.query(selectQuery, + {success: function(json) { + var result = json.results.bindings; + //console.log(result); + callback(result); + }} + ); +} + +/** + * Manually encode of some chars (;/#?) + * @param {type} value + * @returns {unresolved} + */ +function encodeBars(value) { + value = value.split(';').join('%3B'); + value = value.split('/').join('%2F'); + value = value.split('#').join('%23'); + value = value.split('?').join('%3F'); + return value; +} +/** + * Remove an component by id + * @param {type} childDiv + * @param {type} parentDiv + * @returns {undefined} + */ +function removeById(childDiv, parentDiv) +{ + console.log(childDiv + ' ' + parentDiv); + if (childDiv === parentDiv) { + alert("The parent div cannot be removed."); + } + else if (document.getElementById(childDiv)) { + var child = document.getElementById(childDiv); + var parent = document.getElementById(parentDiv); + parent.removeChild(child); + } + else { + alert("Child div has already been removed or does not exist."); + } +} + +/** + * Call a url with 2 callbacks functions (success or error) + * + * @param {type} url + * @param {type} success + * @param {type} error + * @returns {undefined} + */ +function callURL(url, success, error) { + url = encodeURI(url); + console.log(url); + $.ajax({url: url, dataType: 'json'}).done(success).fail(error); +} + +/** + * Generate a html code message + * Ex: var htmlMessage=generateHtmlMessage("Error!", "It already exists!","alert-error"); + * + * @param {type} strong + * @param {type} message + * @param {type} type + * @returns {String} + */ +function generateHtmlMessage(strong, message, type) { + var error = '
            ' + strong + ' ' + message + '
            '; + return error; +} + +/** + * Begin of the code used to manage the modals (Seed,Entity,Concept) + */ + +/** + * Associate click event to loading btn's. + */ +$('.loading').click(function() { + var text = $(this).html(); + $(this).html('Waiting...'); + $(this).addClass('disabled'); + setTimeout(btnInit.bind(this, text), 1500); + + function btnInit(text) { + $(this).html(text); + $(this).removeClass('disabled'); + } +}); +//timer for manage success or errors on modals +var timer; +var delay = 1000; + +/** + * Remove the link between the triples and the triples + * @returns {undefined} + */ +function remove() { + var individual = $('#removeModalLabel').html(); + //var query = initSparqlerQuery(); + console.log('Remove: ' + individual); + + var urlPrefix = "../../api/" + getApiKey(); + //remove all subjects and predicates associated. + removeAllTriplesFromObject(urlPrefix, individual, showResult.bind(this, "#removeResult", ""), showError.bind(this, "#removeResult", "")); + //remove all predicates and objects associated. + removeAllTriplesFromSubject(urlPrefix, individual, showResult.bind(this, "#removeResult", ""), showError.bind(this, "#removeResult", "")); + + timer = setTimeout(function() { + $('#closeRemoveModal').click(); + refresh(); + }, delay); + +} +/** + * remove preview - called before remove + * @param {type} individual + * @returns {undefined} + */ +function selectToRemove(individual) { + $('#removeResult').html(""); + $('#removeModalLabel').html(individual); + if (individual.indexOf('coeus:entity') === 0) { + $('#removeType').html("Entity"); + } else if (individual.indexOf('coeus:concept') === 0) { + $('#removeType').html("Concept"); + } else if (individual.indexOf('coeus:seed') === 0) { + $('#removeType').html("Seed"); + } else if (individual.indexOf('coeus:resource') === 0) { + $('#removeType').html("Resource"); + } else { + } +} +//End of Remove functions +//Edit functions +/** + * Edit preview for Seed,Entity or Concept + * @param {type} individual + * @returns {undefined} + */ +function prepareEdit(individual) { + //reset values + $('#editResult').html(""); + document.getElementById('editURI').innerHTML = individual; + if (individual.indexOf('coeus:entity') === 0) { + $('#editType').html("Entity"); + $('#helpEdit').html("Entity individuals match the general data terms. These elements grouping concepts with a common set of properties."); + } else if (individual.indexOf('coeus:concept') === 0) { + $('#editType').html("Concept"); + $('#helpEdit').html("Concept individuals are area-specific terms, aggregating any number of items and belonging to a unique entity. Concept individuals are also connected to Resources."); + } else if (individual.indexOf('coeus:seed') === 0) { + $('#editType').html("Seed"); + $('#helpEdit').html("A Seed defines a single framework instance that permits access to all data available in the seed, providing an over-arching entry point to the system information. Seed individuals are also connected to included entities. "); + } else { + } + + $('#editTitle').val(""); + $('#editLabel').val(""); + $('#editComment').val(""); + + var q = "SELECT ?label ?title ?comment {" + individual + " dc:title ?title . " + individual + " rdfs:label ?label . " + individual + " rdfs:comment ?comment }"; + queryToResult(q, fillEdit); +} +function fillEdit(result) { + //var resultTitle = json.results.bindings[0].title; + console.log(result); + try + { + //PUT VALUES IN THE INPUT FIELD + $('#editTitle').val(result[0].title.value); + //document.getElementById('title').setAttribute("disabled"); + $('#editLabel').val(result[0].label.value); + $('#editComment').val(result[0].comment.value); + } + catch (err) + { + $('#editResult').append(generateHtmlMessage("Error!", "Some fields do not exist." + err, "alert-error")); + } + //PUT OLD VALUES IN THE STATIC FIELD + $('#oldTitle').val($('#editTitle').val()); + $('#oldLabel').val($('#editLabel').val()); + $('#oldComment').val($('#editComment').val()); + +} +/** + * Function to edit a Seed, Entity or Concept + * @returns {undefined} + */ +function edit() { + var individual = $('#editURI').html(); + var urlUpdate = "../../api/" + getApiKey() + "/update/"; + var url; + timer = setTimeout(function() { + $('#closeEditModal').click(); + refresh(); + }, delay); + + if ($('#oldLabel').val() !== $('#editLabel').val()) { + url = urlUpdate + individual + "/" + "rdfs:label" + "/xsd:string:" + $('#oldLabel').val() + ",xsd:string:" + $('#editLabel').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); + } + if ($('#oldTitle').val() !== $('#editTitle').val()) { + url = urlUpdate + individual + "/" + "dc:title" + "/xsd:string:" + $('#oldTitle').val() + ",xsd:string:" + $('#editTitle').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); + } + if ($('#oldComment').val() !== $('#editComment').val()) { + url = urlUpdate + individual + "/" + "rdfs:comment" + "/xsd:string:" + $('#oldComment').val() + ",xsd:string:" + $('#editComment').val(); + callURL(url, showResult.bind(this, "#editResult", url), (this, "#editResult", url)); + } +} +//End of Edit functions + +/** + * change the uri when the user fill the title box. + * @param {type} type + * @param {type} link + * @returns {undefined} + */ +function changeURI(id, type, value) { + document.getElementById(id).innerHTML = 'coeus:' + type.toLowerCase() + '_' + value.split(' ').join('_'); +} +/** + * Function to be called before add a Seed, Entity or Concept + * @param {type} type + * @param {type} link + * @returns {undefined} + */ +function prepareAdd(type, link) { + $('#addResult').html(""); + $('#title').val(""); + $('#label').val(""); + $('#comment').val(""); + $('#linkedWith').val(link); + //$('#addType').html(type); + var individual = 'coeus:' + type.toLowerCase(); + document.getElementById('uri').innerHTML = individual; + + if (individual.indexOf('coeus:entity') === 0) { + $('#addType').html("Entity"); + $('#helpAdd').html("Entity individuals match the general data terms. These elements grouping concepts with a common set of properties."); + } else if (individual.indexOf('coeus:concept') === 0) { + $('#addType').html("Concept"); + $('#helpAdd').html("Concept individuals are area-specific terms, aggregating any number of items and belonging to a unique entity. Concept individuals are also connected to Resources."); + } else if (individual.indexOf('coeus:seed') === 0) { + $('#addType').html("Seed"); + $('#helpAdd').html("A Seed defines a single framework instance that permits access to all data available in the seed, providing an over-arching entry point to the system information. Seed individuals are also connected to included entities. "); + } else { + } + +} +/** + * Function to add a Seed, Entity or Concept + * @param {type} id + * @param {type} url + * @param {type} result + * @returns {undefined} + */ +function add() { + + var individual = $('#uri').html(); + var type = $('#addType').html(); + console.log("Adding type: " + type); + var title = $('#title').val(); + var label = $('#label').val(); + var comment = $('#comment').val(); + var urlWrite = "../../api/" + getApiKey() + "/write/"; + var link = $('#linkedWith').val(); + + // verify all fields: + var empty = false; + if (title === '') { + $('#titleForm').addClass('controls control-group error'); + empty = true; + } else + $('#titleForm').removeClass('controls control-group error'); + if (label === '') { + $('#labelForm').addClass('controls control-group error'); + empty = true; + } else + $('#labelForm').removeClass('controls control-group error'); + if (comment === '') { + $('#commentForm').addClass('controls control-group error'); + empty = true; + } else + $('#commentForm').removeClass('controls control-group error'); + if (!empty) { + var array = new Array(); + var urlIndividual = urlWrite + individual + "/rdf:type/owl:NamedIndividual"; + var urlType = urlWrite + individual + "/rdf:type/coeus:" + type; + var urlTitle = urlWrite + individual + "/dc:title/xsd:string:" + title; + var urlLabel = urlWrite + individual + "/rdfs:label/xsd:string:" + label; + var urlComment = urlWrite + individual + "/rdfs:comment/xsd:string:" + comment; + if (type === 'Entity') { + var urlIsIncludedIn = urlWrite + individual + "/coeus:isIncludedIn/" + link; + var urlIncludes = urlWrite + link + "/coeus:includes/" + individual; + array.push(urlIndividual, urlType, urlTitle, urlLabel, urlComment, urlIsIncludedIn, urlIncludes); + } else if (type === 'Concept') { + var urlHasEntity = urlWrite + individual + "/coeus:hasEntity/" + link; + var urlIsEntityOf = urlWrite + link + "/coeus:isEntityOf/" + individual; + array.push(urlIndividual, urlType, urlTitle, urlLabel, urlComment, urlHasEntity, urlIsEntityOf); + } else { + array.push(urlIndividual, urlType, urlTitle, urlLabel, urlComment); + } + submitIfNotExists(array, individual); + } +} +function submitIfNotExists(array, individual) { + var qSeeds = "SELECT (COUNT(*) AS ?total) {" + individual + " ?p ?o }"; + queryToResult(qSeeds, function(result) { + if (result[0].total.value == 0) { + + timer = setTimeout(function() { + if (individual.indexOf('coeus:resource') === 0) { + $('#closeAddResourceModal').click(); + refresh(); + } + else { + $('#closeAddModal').click(); + refresh(); + } + }, delay); + + if (individual.indexOf('coeus:resource') !== 0) { + var idResult = "#addResult"; + } else { + var idResult = "#addResourceResult"; + } + //call the service + array.forEach(function(url) { + callURL(url, showResult.bind(this, idResult, url), showError.bind(this, idResult, url)); + + }); + } else { + console.log('This individual ' + individual + ' already exists.'); + if (individual.indexOf('coeus:resource') !== 0) { + $('#addResult').append(generateHtmlMessage("Warning!", "This individual already exists. Try another title.", "alert-warning")); + } else { + $('#addResourceResult').append(generateHtmlMessage("Warning!", "This individual already exists. Try another title.", "alert-warning")); + } + } + }); +} +/** + * show the retrived result in the div (id) + * + * @param {type} id + * @param {type} url + * @param {type} result + * @returns {undefined} + */ +function showResult(id, url, result) { + if (result.status === 100) { + $(id).append(generateHtmlMessage("Success!", url + "
            " + result.message, "alert-success")); + } + else { + clearTimeout(timer); + $(id).append(generateHtmlMessage("Warning!", url + "
            Status Code:" + result.status + " " + result.message, "alert-warning")); + } +} +/** + * show the error result in the div (id) + * @param {type} id + * @param {type} url + * @param {type} jqXHR + * @param {type} result + * @returns {undefined} + */ +function showError(id, url, jqXHR, result) { + clearTimeout(timer); + $(id).append(generateHtmlMessage("Server error!", url + "
            Status Code:" + result.status + " " + result.message, "alert-error")); +} + +/** + * End of the code used to manage the modals (Seed,Entity,Concept) + */ + +/** + * Begin of the code used to manage the modals (Resource) + */ + +/** + * called before add resource to clean input fields + * @param {type} link + * @returns {undefined} + */ +function prepareAddResourceModal(link) { + $('#addResourceResult').html(""); + $('#titleResource').val(""); + $('#labelResource').val(""); + $('#commentResource').val(""); + document.getElementById('resourceURI').innerHTML = 'coeus:resource'; + $('#method').val(""); + $('#publisher').val(""); + $('#endpoint').val(""); + $('#query').val(""); + $('#order').val(""); + $('#extends').val(""); + $('#resourceLink').val(link); + var q = "SELECT ?concept ?c {?entity coeus:isEntityOf " + link + " . ?seed coeus:includes ?entity . ?concept coeus:hasEntity ?ent . ?ent coeus:isIncludedIn ?seed . ?concept dc:title ?c}"; + queryToResult(q, fillConceptsExtension); +} +function fillConceptsExtension(result) { + $('#extends').html(""); + $('#editExtends').html(""); + for (var r in result) { + var concept = splitURIPrefix(result[r].concept.value); + $('#extends').append(''); + $('#editExtends').append(''); + } +} +/** + * Add a Resource + * @returns {undefined} + */ +function addResource() { + + var type = 'Resource'; + var individual = $('#resourceURI').html(); + var title = $('#titleResource').val(); + var label = $('#labelResource').val(); + var comment = $('#commentResource').val(); + var method = $('#method').val(); + var publisher = $('#publisher').val(); + var endpoint = $('#endpoint').val(); + var query = $('#query').val(); + var order = $('#order').val(); + var concept_ext = $('#extends').val(); + var link = $('#resourceLink').val(); + var urlWrite = "../../api/" + getApiKey() + "/write/"; + + // verify all fields: + var empty = false; + if (title === '') { + $('#resourceTitleForm').addClass('controls control-group error'); + empty = true; + } else + $('#resourceTitleForm').removeClass('controls control-group error'); + if (label === '') { + $('#resourceLabelForm').addClass('controls control-group error'); + empty = true; + } else + $('#resourceLabelForm').removeClass('controls control-group error'); + if (comment === '') { + $('#resourceCommentForm').addClass('controls control-group error'); + empty = true; + } else + $('#resourceCommentForm').removeClass('controls control-group error'); + if (endpoint === '') { + $('#endpointForm').addClass('controls control-group error'); + empty = true; + } else + $('#endpointForm').removeClass('controls control-group error'); + if (query === '' && publisher !== ("csv")) { + $('#queryForm').addClass('controls control-group error'); + empty = true; + } else + $('#queryForm').removeClass('controls control-group error'); + if (order === '') { + $('#orderForm').addClass('controls control-group error'); + empty = true; + } else + $('#orderForm').removeClass('controls control-group error'); + if (!empty) { + var array = new Array(); + var urlIndividual = urlWrite + individual + "/rdf:type/owl:NamedIndividual"; + var urlType = urlWrite + individual + "/rdf:type/coeus:" + type; + var urlTitle = urlWrite + individual + "/dc:title/xsd:string:" + title; + var urlLabel = urlWrite + individual + "/rdfs:label/xsd:string:" + label; + var urlComment = urlWrite + individual + "/rdfs:comment/xsd:string:" + comment; + var urlIsResourceOf = urlWrite + individual + "/" + "coeus:isResourceOf" + "/" + link; + var urlHasResource = urlWrite + link + "/" + "coeus:hasResource" + "/" + individual; + var urlMethod = urlWrite + individual + "/" + "coeus:method" + "/xsd:string:" + method; + var urlPublisher = urlWrite + individual + "/" + "dc:publisher" + "/xsd:string:" + publisher; + var urlEndpoint = urlWrite + individual + "/" + "coeus:endpoint" + "/xsd:string:" + encodeBars(endpoint); + var urlQuery = urlWrite + individual + "/" + "coeus:query" + "/xsd:string:" + encodeBars(query); + var urlOrder = urlWrite + individual + "/" + "coeus:order" + "/xsd:string:" + order; + var urlExtends = urlWrite + individual + "/" + "coeus:extends" + "/coeus:" + concept_ext; + var urlIsExtendedBy = urlWrite + "coeus:" + concept_ext + "/" + "coeus:isExtendedBy" + "/" + individual; + var urlBuilt = urlWrite + individual + "/" + "coeus:built" + "/xsd:boolean:false"; + + array.push(urlIndividual, urlType, urlTitle, urlLabel, urlComment, urlIsResourceOf, urlHasResource, urlMethod, urlPublisher, urlEndpoint, urlQuery, urlOrder, urlExtends, urlIsExtendedBy, urlBuilt); + submitIfNotExists(array, individual); + } +} +/** + * Called when user change publisher in the modal Resource + * @param {type} mode + * @returns {undefined} + */ +function publisherChange(mode) { + + if (mode === 'edit') { + //sql + var publisher = $('#editPublisher').val(); + var sqlEnpointForm = '#editSqlEndpointForm'; + var enpointForm = '#editEndpointForm'; + var endpoint = '#editEndpoint'; + var driverEndpoint = '#editDriverEndpoint'; + var hostEndpoint = '#editHostEndpoint'; + var dbEndpoint = '#editBbEndpoint'; + var portEndpoint = '#editPortEndpoint'; + var userEndpoint = '#editUserEndpoint'; + var passwordEndpoint = '#editPasswordEndpoint'; + //csv + var query = '#editQuery'; + var queryForm = '#editQueryForm'; + var csvQueryForm = '#editCsvQueryForm'; + var csvQueryDelimiter = '#editCsvQueryDelimiter'; + var csvQueryHeaderSkip = '#editCsvQueryHeaderSkip'; + } else { + //sql + var publisher = $('#publisher').val(); + var sqlEnpointForm = '#sqlEndpointForm'; + var enpointForm = '#endpointForm'; + var endpoint = '#endpoint'; + var driverEndpoint = '#driverEndpoint'; + var hostEndpoint = '#hostEndpoint'; + var dbEndpoint = '#dbEndpoint'; + var portEndpoint = '#portEndpoint'; + var userEndpoint = '#userEndpoint'; + var passwordEndpoint = '#passwordEndpoint'; + //csv + var query = '#query'; + var queryForm = '#queryForm'; + var csvQueryForm = '#csvQueryForm'; + var csvQueryDelimiter = '#csvQueryDelimiter'; + var csvQueryHeaderSkip = '#csvQueryHeaderSkip'; + } + + if (publisher === "sql") { + $(sqlEnpointForm).removeClass('hide'); + $(enpointForm).addClass('hide'); + var endpoint = $(endpoint).val(); + //Endpoint example: jdbc:mysql://host:3306;database=name;user=user;password=pass + + if (endpoint !== "") { + try { + var url = endpoint.split("://"); + var driver = url[0].split("jdbc:")[1]; + var cut = url[1].split(":"); + var host = cut[0]; + var cut2 = cut[1].split(";"); + var port = cut2[0]; + var db = cut2[1].split("database=")[1]; + var user = cut2[2].split("user=")[1]; + var password = cut2[3].split("password=")[1]; + } catch (e) { + //ignore errors + } + + $(driverEndpoint).val(driver); + $(hostEndpoint).val(host); + $(dbEndpoint).val(db); + $(portEndpoint).val(port); + $(userEndpoint).val(user); + $(passwordEndpoint).val(password); + } + + } else { + $(sqlEnpointForm).addClass('hide'); + $(enpointForm).removeClass('hide'); + } + + if (publisher === "csv") { + $(queryForm).addClass('hide'); + $(csvQueryForm).removeClass('hide'); + + query = $(query).val(); + + if (query !== "") { + var q = query.split("|"); + + $(csvQueryDelimiter).val(q[1]); + $(csvQueryHeaderSkip).val(q[0]); + } else { + $(csvQueryHeaderSkip).val("1"); + refreshQuery(); + } + + } + else { + $(csvQueryForm).addClass('hide'); + $(queryForm).removeClass('hide'); + } +} + +/** + * Called when user change endpoint in the modal Resource + * @param {type} mode + * @returns {undefined} + */ +function refreshEnpoint(mode) { + + if (mode === 'edit') { + var portEndpoint = '#editPortEndpoint'; + var userEndpoint = '#editUserEndpoint'; + var passwordEndpoint = '#editPasswordEndpoint'; + var driverEndpoint = '#editDriverEndpoint'; + var hostEndpoint = '#editHostEndpoint'; + var dbEndpoint = '#editDbEndpoint'; + var endpoint = '#editEndpoint'; + } else { + var portEndpoint = '#portEndpoint'; + var userEndpoint = '#userEndpoint'; + var passwordEndpoint = '#passwordEndpoint'; + var driverEndpoint = '#driverEndpoint'; + var hostEndpoint = '#hostEndpoint'; + var dbEndpoint = '#dbEndpoint'; + var endpoint = '#endpoint'; + } + + var port = $(portEndpoint).val(); + if (port !== "") + port = ":" + port; + var user = $(userEndpoint).val(); + if (user !== "") + user = ";user=" + user; + var password = $(passwordEndpoint).val(); + if (password !== "") + password = ";password=" + password; + var endpointFinal = "jdbc:" + $(driverEndpoint).val() + "://" + $(hostEndpoint).val() + port + ";database=" + $(dbEndpoint).val() + user + password; + $(endpoint).val(endpointFinal); +} + +/** + * Called when user change query in the modal Resource + * @param {type} mode + * @returns {undefined} + */ +function refreshQuery(mode) { + if (mode === 'edit') { + var delimiter = $('#editCsvQueryDelimiter').val(); + var header = $('#editCsvQueryHeaderSkip').val(); + $('#editQuery').val(header + "|" + delimiter); + } else { + var delimiter = $('#csvQueryDelimiter').val(); + var header = $('#csvQueryHeaderSkip').val(); + $('#query').val(header + "|" + delimiter); + + } +} +/** + * Called before the edit of a Resource + * @param {type} individual + * @returns {undefined} + */ +function prepareResourceEdit(individual) { + //reset values + $('#editResourceResult').html(""); + document.getElementById('editResourceURI').innerHTML = individual; + //CLEAN THE INPUT FIELDS + $('#editResourceTitle').val(""); + $('#editResourceLabel').val(""); + $('#editResourceComment').val(""); + $('#editMethod').val(""); + $('#editPublisher').val(""); + $('#editEndpoint').val(""); + $('#editQuery').val(""); + $('#editOrder').val(""); + $('#editExtends').val(""); + $('#built').prop('checked', false); + + //CLEAN ALSO OLD VALUES IN THE STATIC FIELD + $('#oldTitle').val(""); + $('#oldLabel').val(""); + $('#oldComment').val(""); + $('#oldMethod').val(""); + $('#oldPublisher').val(""); + $('#oldEndpoint').val(""); + $('#oldQuery').val(""); + $('#oldOrder').val(""); + $('#oldExtends').val(""); + $('#oldBuilt').val("false"); + + var q = "SELECT ?concept ?c {?concep coeus:hasResource " + individual + " . ?entity coeus:isEntityOf ?concep . ?seed coeus:includes ?entity . ?concept coeus:hasEntity ?ent . ?ent coeus:isIncludedIn ?seed . ?concept dc:title ?c}"; + queryToResult(q, fillConceptsExtension); + var q = "SELECT ?title ?label ?comment ?method ?publisher ?endpoint ?query ?order ?extends ?built {" + individual + " dc:title ?title . " + individual + " rdfs:label ?label . " + individual + " rdfs:comment ?comment . " + individual + " coeus:method ?method . " + individual + " dc:publisher ?publisher . " + individual + " coeus:endpoint ?endpoint . " + individual + " coeus:query ?query . " + individual + " coeus:order ?order . " + individual + " coeus:extends ?extends . OPTIONAL{" + individual + " coeus:built ?built } }"; + queryToResult(q, fillResourceEdit); + +} +function fillResourceEdit(result) { + console.log(result); + try + { + //PUT VALUES IN THE INPUT FIELD + $('#editResourceTitle').val(result[0].title.value); + $('#editResourceLabel').val(result[0].label.value); + $('#editResourceComment').val(result[0].comment.value); + $('#editMethod').val(result[0].method.value); + $('#editPublisher option:contains(' + result[0].publisher.value + ')').prop({selected: true}); + $('#editEndpoint').val(result[0].endpoint.value); + $('#editQuery').val(result[0].query.value); + $('#editOrder').val(result[0].order.value); + $('#editExtends option:contains(' + splitURIPrefix(result[0].extends.value).value + ')').prop({selected: true}); + if (result[0].built !== undefined && result[0].built.value === "true") + $('#built').prop('checked', true); + else + $('#built').prop('checked', false); + } + catch (err) + { + $('#editResourceResult').append(generateHtmlMessage("Error!", "Some fields do not exist." + err, "alert-error")); + } + //PUT OLD VALUES IN THE STATIC FIELD + $('#oldResourceTitle').val($('#editResourceTitle').val()); + $('#oldResourceLabel').val($('#editResourceLabel').val()); + $('#oldResourceComment').val($('#editResourceComment').val()); + $('#oldMethod').val($('#editMethod').val()); + $('#oldPublisher').val($('#editPublisher').val()); + $('#oldEndpoint').val($('#editEndpoint').val()); + $('#oldQuery').val($('#editQuery').val()); + $('#oldOrder').val($('#editOrder').val()); + $('#oldExtends').val(splitURIPrefix(result[0].extends.value).value); + $('#oldBuilt').val($('#built').is(':checked')); + //change publisher according to the result + publisherChange('edit'); + +} + +/** + * Called when a Resource is edited / updated + * @returns {undefined} + */ +function editResource() { + var individual = $('#editResourceURI').html(); + var urlUpdate = "../../api/" + getApiKey() + "/update/"; + var urlDelete = "../../api/" + getApiKey() + "/delete/"; + var urlWrite = "../../api/" + getApiKey() + "/write/"; + var url; + var array = new Array(); + + if ($('#oldResourceLabel').val() !== $('#editResourceLabel').val()) { + url = urlUpdate + individual + "/" + "rdfs:label" + "/xsd:string:" + $('#oldResourceLabel').val() + ",xsd:string:" + $('#editResourceLabel').val(); + array.push(url); + } + if ($('#oldResourceTitle').val() !== $('#editResourceTitle').val()) { + url = urlUpdate + individual + "/" + "dc:title" + "/xsd:string:" + $('#oldResourceTitle').val() + ",xsd:string:" + $('#editResourceTitle').val(); + array.push(url); + } + if ($('#oldResourceComment').val() !== $('#editResourceComment').val()) { + url = urlUpdate + individual + "/" + "rdfs:comment" + "/xsd:string:" + $('#oldResourceComment').val() + ",xsd:string:" + $('#editResourceComment').val(); + array.push(url); + } + if ($('#oldMethod').val() !== $('#editMethod').val()) { + url = urlUpdate + individual + "/" + "coeus:method" + "/xsd:string:" + $('#oldMethod').val() + ",xsd:string:" + $('#editMethod').val(); + array.push(url); + } + if ($('#oldEndpoint').val() !== $('#editEndpoint').val()) { + url = urlUpdate + individual + "/" + "coeus:endpoint" + "/xsd:string:" + encodeBars($('#oldEndpoint').val()) + ",xsd:string:" + encodeBars($('#editEndpoint').val()); + array.push(url); + } + if ($('#oldQuery').val() !== $('#editQuery').val()) { + url = urlUpdate + individual + "/" + "coeus:query" + "/xsd:string:" + encodeBars($('#oldQuery').val()) + ",xsd:string:" + encodeBars($('#editQuery').val()); + array.push(url); + } + if ($('#oldOrder').val() !== $('#editOrder').val()) { + url = urlUpdate + individual + "/" + "coeus:order" + "/xsd:string:" + $('#oldOrder').val() + ",xsd:string:" + $('#editOrder').val(); + array.push(url); + } + if ($('#oldExtends').val() !== $('#editExtends').val()) { + url = urlUpdate + individual + "/" + "coeus:extends" + "/coeus:" + $('#oldExtends').val() + ",coeus:" + $('#editExtends').val(); + array.push(url); + url = urlDelete + "coeus:" + $('#oldExtends').val() + "/" + "coeus:isExtendedBy" + "/" + individual; + array.push(url); + url = urlWrite + "coeus:" + $('#editExtends').val() + "/" + "coeus:isExtendedBy" + "/" + individual; + array.push(url); + } + if ($('#oldPublisher').val() !== $('#editPublisher').val()) { + url = urlUpdate + individual + "/" + "dc:publisher" + "/xsd:string:" + $('#oldPublisher').val() + ",xsd:string:" + $('#editPublisher').val(); + updatePublisherOnSelectores(urlUpdate, individual, $('#oldPublisher').val(), $('#editPublisher').val()); + array.push(url); + } + if ($('#oldBuilt').val().toString() !== $('#built').is(':checked').toString()) { + url = urlUpdate + individual + "/" + "coeus:built" + "/xsd:boolean:" + $('#oldBuilt').val() + ",xsd:boolean:" + $('#built').is(':checked'); + array.push(url); + } + + timer = setTimeout(function() { + $('#closeEditResourceModal').click(); + refresh(); + }, delay); + + array.forEach(function(url) { + callURL(url, showResult.bind(this, "#editResourceResult", url), showError.bind(this, "#editResourceResult", url)); + }); +} +/** + * Update all selectors type (csv,xml,sql,..) of the resource when the resource publisher change. + * @param {type} urlUpdate + * @param {type} res + * @param {type} oldPublisher + * @param {type} newPublisher + * @returns {undefined} + */ +function updatePublisherOnSelectores(urlUpdate, res, oldPublisher, newPublisher) { + var q = "SELECT * {" + res + " coeus:loadsFrom ?selector}"; + queryToResult(q, function(result) { + for (var r in result) { + var res = splitURIPrefix(result[r].selector.value); + var url = urlUpdate + "coeus:" + res.value + "/rdf:type/coeus:" + oldPublisher.toUpperCase() + ",coeus:" + newPublisher.toUpperCase(); + callURL(url, showResult.bind(this, "#editResourceResult", url), showError.bind(this, "#editResourceResult", url)); + } + }); +} + +/** + * End of the code used to manage the modals (Resource) + */ \ No newline at end of file diff --git a/src/main/webapp/setup/addresource.jsp b/src/main/webapp/setup/addresource.jsp index 96dea78..a5da2a4 100644 --- a/src/main/webapp/setup/addresource.jsp +++ b/src/main/webapp/setup/addresource.jsp @@ -715,121 +715,7 @@
            - -
            -

            New Resource

            -
            - -
            - -
            -
            - - -
            -
            - - -
            - -
            - - -
            -
            - - -
            -
            - - -
            -
            -
            - -
            -
            - -
            -


            -
            - -
            - - -
            -
            - - -
            -
            - - - jdbc: - - :// - - : - - / - - -
            - Login: - - - -
            -
            - - -
            -
            - - - - -
            -
            - - -
            - -
            - - - - - - -
            - + @@ -917,29 +803,7 @@ - - +
            - Add Concept + Add Concept
            @@ -294,92 +146,12 @@ - - - - - - - - - - - + + + + <%@include file="/setup/modals/add.jsp" %> + <%@include file="/setup/modals/addResource.jsp" %> + <%@include file="/setup/modals/edit.jsp" %> + <%@include file="/setup/modals/remove.jsp" %> + + diff --git a/src/main/webapp/setup/config.jsp b/src/main/webapp/setup/config.jsp index 57d7396..ed5e2a0 100644 --- a/src/main/webapp/setup/config.jsp +++ b/src/main/webapp/setup/config.jsp @@ -10,7 +10,7 @@ - + - + - + @@ -268,7 +100,7 @@
            - Add Entity + Add Entity
            @@ -286,92 +118,10 @@ - - - - - - - - - + + + <%@include file="/setup/modals/add.jsp" %> + <%@include file="/setup/modals/edit.jsp" %> + <%@include file="/setup/modals/remove.jsp" %> diff --git a/src/main/webapp/setup/environments.jsp b/src/main/webapp/setup/environments.jsp index d6d47e4..14637d1 100644 --- a/src/main/webapp/setup/environments.jsp +++ b/src/main/webapp/setup/environments.jsp @@ -10,7 +10,7 @@ - + - + - - -
            -

            -
            -

            Management

            -
            - -

            Knowledge Base

            -
            -
            -

            Triples

            -
            -
            - 0 -
            -
            -

            Environment

            -
            -
            -
            - - Production - - - -
            -
            - -
            - -

            Actions

            -
            -
            -
            - Cleanup -
            -
            -
            - -
            -
            -
            - - Export - - - -
            -
            -
            - - - -
            -             - diff --git a/src/main/webapp/setup/modals/add.jsp b/src/main/webapp/setup/modals/add.jsp new file mode 100644 index 0000000..6956574 --- /dev/null +++ b/src/main/webapp/setup/modals/add.jsp @@ -0,0 +1,34 @@ + + \ No newline at end of file diff --git a/src/main/webapp/setup/modals/addResource.jsp b/src/main/webapp/setup/modals/addResource.jsp new file mode 100644 index 0000000..9bbbd29 --- /dev/null +++ b/src/main/webapp/setup/modals/addResource.jsp @@ -0,0 +1,113 @@ +<%-- + Document : addResource + Created on : Oct 14, 2013, 3:41:38 PM + Author : sernadela +--%> + + + \ No newline at end of file diff --git a/src/main/webapp/setup/modals/edit.jsp b/src/main/webapp/setup/modals/edit.jsp new file mode 100644 index 0000000..72d534d --- /dev/null +++ b/src/main/webapp/setup/modals/edit.jsp @@ -0,0 +1,35 @@ + + \ No newline at end of file diff --git a/src/main/webapp/setup/modals/editResource.jsp b/src/main/webapp/setup/modals/editResource.jsp new file mode 100644 index 0000000..ea90697 --- /dev/null +++ b/src/main/webapp/setup/modals/editResource.jsp @@ -0,0 +1,131 @@ +<%-- + Document : addResource + Created on : Oct 14, 2013, 3:41:38 PM + Author : sernadela +--%> + + \ No newline at end of file diff --git a/src/main/webapp/setup/modals/remove.jsp b/src/main/webapp/setup/modals/remove.jsp new file mode 100644 index 0000000..34da719 --- /dev/null +++ b/src/main/webapp/setup/modals/remove.jsp @@ -0,0 +1,21 @@ + + \ No newline at end of file diff --git a/src/main/webapp/setup/resources.jsp b/src/main/webapp/setup/resources.jsp index aa5af25..f6ba02b 100644 --- a/src/main/webapp/setup/resources.jsp +++ b/src/main/webapp/setup/resources.jsp @@ -10,23 +10,35 @@ - + + @@ -91,7 +101,7 @@