Merge branch 'master' of https://github.com/JULIELab/gepi

gepi/README.md

@@ -19,8 +19,8 @@ The `production` stage expects that the complete GePI project has been built in
 Run the following commands to create a `development` container:
 
 ```bash
-DOCKER_BUILDKIT=1 docker build -t gepi:0.11.0 --target development .
-docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> gepi:0.11.0
+DOCKER_BUILDKIT=1 docker build -t gepi:0.11.1 --target development .
+docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> gepi:0.11.1
 ```
 
 The first command builds an image of the `development` stage. This will also build the `dependencies` stage where all the Java dependencies of the GePI application are downloaded and cached. This will take a while on the first execution but should be faster afterwards thanks to caching.
@@ -38,8 +38,8 @@ To run the `production` container, run
 
 ```bash
 mvn clean package --projects gepi-webapp --also-make
-DOCKER_BUILDKIT=1 docker build -t gepi:0.11.0 --target production .
-docker run -dp 8080:8080 --name gepi gepi:0.11.0
+DOCKER_BUILDKIT=1 docker build -t gepi:0.11.1 --target production .
+docker run -dp 8080:8080 --name gepi gepi:0.11.1
 ```
 
 These commands
@@ -68,7 +68,7 @@ gepi.neo4j.bolt.url=bolt://<host>:<port>
 
 A production environment has a few requirements that are of lesser importance during development. This section explains requirements and solutions that may come up during GePI deployment with the Docker container. While detailed explanations come below, the full Docker `run` command we use for deployment looks like the following:
 ```
-docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:0.11.0 jetty.sslContext.keyStorePassword=<changeit>
+docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:0.11.1 jetty.sslContext.keyStorePassword=<changeit>
 ```
 Alternatively, the `docker-compose-webapp.yml` file can be used with a few additions.
 

gepi/docker-compose-webapp.yml

@@ -1,7 +1,7 @@
 version: "3.2"
 services:
   gepi:
-    image: gepi:0.11.0
+    image: gepi:0.11.1
     container_name: gepi
     ports:
       - 0.0.0.0:80:8080

gepi/docker-compose-with-es.yml

@@ -1,6 +1,6 @@
 services:
   gepi:
-    image: gepi:0.11.0
+    image: gepi:0.11.1
     container_name: gepi
     ports:
       - 0.0.0.0:80:8080

gepi/gepi-concept-database/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>gepi</artifactId>
-		<version>1.0.0-SNAPSHOT</version>
+		<version>0.11.1</version>
 	</parent>
 	<artifactId>gepi-concept-database</artifactId>
 	<name>GePi Concept Database</name>

gepi/gepi-concept-database/src/main/resources/gene-database.xml

@@ -5,7 +5,7 @@
                  http://www.julielab.de/conceptdb/facets/default http://www.julielab.de/conceptdb/facets/defaultfacet-1.1.0.xsd
                  http://julielab.de/conceptdb/concepts/bioportal http://www.julielab.de/conceptdb/concepts/bioportalconcepts-1.1.0.xsd">
     <versioning>
-        <version>0.11.0</version>
+        <version>0.11.1</version>
     </versioning>
     <connection>
         <uri>http://localhost:7474</uri>

gepi/gepi-core/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>gepi</artifactId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <dependencies>

gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/data/GepiRequestData.java

@@ -17,13 +17,15 @@ public class GepiRequestData implements Cloneable {
     private String paragraphFilterString;
     private String filterFieldsConnectionOperator = "AND";
     private EnumSet<InputMode> inputMode;
+    private String docId;
     private long dataSessionId;
     private boolean includeUnary;
     private int eventLikelihood;
     private String[] taxId;
     private String sectionNameFilterString;
     private int pageSize = 10;
-    public GepiRequestData(List<String> eventTypes, boolean includeUnary, int eventLikelihood, Future<IdConversionResult> listAGePiIds, Future<IdConversionResult> listBGePiIds, String[] taxId, String sentenceFilterString, String paragraphFilterString, String filterFieldsConnectionOperator, String sectionNameFilterString, EnumSet<InputMode> inputMode, long dataSessionId) {
+
+    public GepiRequestData(List<String> eventTypes, boolean includeUnary, int eventLikelihood, Future<IdConversionResult> listAGePiIds, Future<IdConversionResult> listBGePiIds, String[] taxId, String sentenceFilterString, String paragraphFilterString, String filterFieldsConnectionOperator, String sectionNameFilterString, EnumSet<InputMode> inputMode, String docId, long dataSessionId) {
         this.includeUnary = includeUnary;
         this.eventLikelihood = eventLikelihood;
         this.taxId = taxId;
@@ -35,13 +37,18 @@ public GepiRequestData(List<String> eventTypes, boolean includeUnary, int eventL
         this.paragraphFilterString = paragraphFilterString;
         this.filterFieldsConnectionOperator = filterFieldsConnectionOperator;
         this.inputMode = inputMode;
+        this.docId = docId;
         this.dataSessionId = dataSessionId;
     }
 
     public GepiRequestData() {
 
     }
 
+    public String getDocId() {
+        return docId;
+    }
+
     public boolean isIncludeUnary() {
         return includeUnary;
     }
@@ -114,6 +121,7 @@ public GepiRequestData withIncludeUnary(boolean includeUnary) {
         this.includeUnary = includeUnary;
         return this;
     }
+
     public GepiRequestData withEventTypes(List<String> eventTypes) {
         this.eventTypes = eventTypes;
         return this;
@@ -177,6 +185,11 @@ public GepiRequestData withSectionNameFilterString(String sectionNameFilterStrin
         return this;
     }
 
+    public GepiRequestData withDocId(String docid) {
+        this.docId = docid;
+        return this;
+    }
+
     @Override
     public String toString() {
         return "GepiRequestData{" +

gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/services/EventQueries.java

@@ -90,6 +90,15 @@ public static BoolQuery getClosedQuery(GepiRequestData requestData, Set<String>
             taxIdFilterClause.addQuery(taxQuery);
             eventQuery.addClause(taxIdFilterClause);
         }
+        if (requestData.getDocId() != null && !requestData.getDocId().isBlank()) {
+            final MultiMatchQuery docIdQuery = new MultiMatchQuery();
+            docIdQuery.query = requestData.getDocId();
+            docIdQuery.fields = List.of(FIELD_PMID, FIELD_PMCID);
+            final BoolClause docIdFilterClause = new BoolClause();
+            docIdFilterClause.addQuery(docIdQuery);
+            docIdFilterClause.occur = FILTER;
+            eventQuery.addClause(docIdFilterClause);
+        }
         return eventQuery;
     }
 
@@ -155,6 +164,15 @@ public static BoolQuery getOpenQuery(GepiRequestData requestData) throws Interru
             taxIdFilterClause.addQuery(taxQuery);
             eventQuery.addClause(taxIdFilterClause);
         }
+        if (requestData.getDocId() != null && !requestData.getDocId().isBlank()) {
+            final MultiMatchQuery docIdQuery = new MultiMatchQuery();
+            docIdQuery.query = requestData.getDocId();
+            docIdQuery.fields = List.of(FIELD_PMID, FIELD_PMCID);
+            final BoolClause docIdFilterClause = new BoolClause();
+            docIdFilterClause.addQuery(docIdQuery);
+            docIdFilterClause.occur = FILTER;
+            eventQuery.addClause(docIdFilterClause);
+        }
 
         return eventQuery;
     }
@@ -169,9 +187,19 @@ private static void addEventLikelihoodFilter(BoolQuery eventQuery, int likelihoo
         eventQuery.addClause(likelihoodFilterClause);
     }
 
-    public static BoolQuery getFulltextQuery(List<String> eventTypes, int eventLikelihood, String sentenceFilter, String paragraphFilter, String sectionNameFilter, String filterFieldsConnectionOperator, String[] taxIds, boolean includeUnary) {
+    public static BoolQuery getFulltextQuery(GepiRequestData requestData) {
         BoolQuery eventQuery = new BoolQuery();
 
+        final List<String> eventTypes = requestData.getEventTypes();
+        final boolean includeUnary = requestData.isIncludeUnary();
+        final String filterFieldsConnectionOperator = requestData.getFilterFieldsConnectionOperator();
+        final String sentenceFilter = requestData.getSentenceFilterString();
+        final String paragraphFilter = requestData.getParagraphFilterString();
+        final String sectionNameFilter = requestData.getSectionNameFilterString();
+        final int eventLikelihood = requestData.getEventLikelihood();
+        final String[] taxIds = requestData.getTaxId();
+        final String docId = requestData.getDocId();
+
         if (eventTypes != null && !eventTypes.isEmpty()) {
             TermsQuery eventTypesQuery = new TermsQuery(new ArrayList<>(eventTypes));
             eventTypesQuery.field = FIELD_EVENT_ALL_EVENTTYPES;
@@ -216,6 +244,15 @@ public static BoolQuery getFulltextQuery(List<String> eventTypes, int eventLikel
             taxIdFilterClause.addQuery(taxQuery);
             eventQuery.addClause(taxIdFilterClause);
         }
+        if (docId != null && docId.isBlank()) {
+            final MultiMatchQuery docIdQuery = new MultiMatchQuery();
+            docIdQuery.query = docId;
+            docIdQuery.fields = List.of(FIELD_PMID, FIELD_PMCID);
+            final BoolClause docIdFilterClause = new BoolClause();
+            docIdFilterClause.addQuery(docIdQuery);
+            docIdFilterClause.occur = FILTER;
+            eventQuery.addClause(docIdFilterClause);
+        }
         return eventQuery;
     }
 

gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/services/EventRetrievalService.java

@@ -415,7 +415,7 @@ private HighlightCommand getHighlightCommand(String hlTerm, String hlClass, Stri
     public CompletableFuture<EventRetrievalResult> getFulltextFilteredEvents(GepiRequestData requestData, int from, int numRows, boolean forCharts) {
         log.debug("Returning async result");
         return CompletableFuture.supplyAsync(() -> {
-            BoolQuery eventQuery = EventQueries.getFulltextQuery(requestData.getEventTypes(), requestData.getEventLikelihood(), requestData.getSentenceFilterString(), requestData.getParagraphFilterString(), requestData.getSectionNameFilterString(), requestData.getFilterFieldsConnectionOperator(), requestData.getTaxId(), requestData.isIncludeUnary());
+            BoolQuery eventQuery = EventQueries.getFulltextQuery(requestData);
 
             boolean downloadAll = forCharts || numRows == Integer.MAX_VALUE;
 

gepi/gepi-indexing/gepi-indexing-base/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

gepi/gepi-indexing/gepi-indexing-debug/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>gepi-indexing-base</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
+            <version>0.11.1</version>
         </dependency>
     </dependencies>
 </project>

gepi/gepi-indexing/gepi-indexing-pmc/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>gepi-indexing-base</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
+            <version>0.11.1</version>
         </dependency>
     </dependencies>
 </project>

gepi/gepi-indexing/gepi-indexing-pubmed/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <artifactId>gepi-indexing</artifactId>
     <groupId>de.julielab</groupId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>0.11.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
     <dependency>
       <groupId>de.julielab</groupId>
       <artifactId>gepi-indexing-base</artifactId>
-      <version>1.0.0-SNAPSHOT</version>
+      <version>0.11.1</version>
     </dependency>
   </dependencies>
 </project>

gepi/gepi-indexing/gepi-indexing-testdata/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <artifactId>gepi-indexing</artifactId>
     <groupId>de.julielab</groupId>
-    <version>1.0.0-SNAPSHOT</version>
+    <version>0.11.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
     <dependency>
       <groupId>de.julielab</groupId>
       <artifactId>gepi-indexing-base</artifactId>
-      <version>1.0.0-SNAPSHOT</version>
+      <version>0.11.1</version>
     </dependency>
   </dependencies>
 </project>

gepi/gepi-indexing/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <packaging>pom</packaging>

gepi/gepi-test-data/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

gepi/gepi-webapp/pom.xml

@@ -224,7 +224,7 @@ of testing facilities designed for use with TestNG (http://testng.org/), so it's
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>gepi</artifactId>
-        <version>1.0.0-SNAPSHOT</version>
+        <version>0.11.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 </project>

gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/EventPagesDataSource.java

@@ -3,10 +3,10 @@
 import de.julielab.gepi.core.retrieval.data.Argument;
 import de.julielab.gepi.core.retrieval.data.Event;
 import de.julielab.gepi.core.retrieval.data.EventRetrievalResult;
+import de.julielab.gepi.core.retrieval.data.GepiRequestData;
 import de.julielab.gepi.core.retrieval.services.EventRetrievalService;
 import de.julielab.gepi.core.retrieval.services.IEventRetrievalService;
 import de.julielab.gepi.core.services.IGeneIdService;
-import de.julielab.gepi.webapp.data.FilteredGepiRequestData;
 import org.apache.tapestry5.grid.GridDataSource;
 import org.apache.tapestry5.grid.SortConstraint;
 import org.slf4j.Logger;
@@ -22,13 +22,13 @@
 
 public class EventPagesDataSource implements GridDataSource {
     private final IEventRetrievalService eventRetrievalService;
-    private final FilteredGepiRequestData requestData;
+    private final GepiRequestData requestData;
     private IGeneIdService geneIdService;
     private Logger log;
     private Future<EventRetrievalResult> events;
     private int start;
 
-    public EventPagesDataSource(Logger log, Future<EventRetrievalResult> events, IEventRetrievalService eventRetrievalService, IGeneIdService geneIdService, FilteredGepiRequestData requestData) {
+    public EventPagesDataSource(Logger log, Future<EventRetrievalResult> events, IEventRetrievalService eventRetrievalService, IGeneIdService geneIdService, GepiRequestData requestData) {
         this.log = log;
         this.events = events;
         this.eventRetrievalService = eventRetrievalService;