Harvester / Simple URL

This commit is a squash of geonetwork/core-geonetwork#5942

A simple harvester which takes a URL expecting for now a JSON document
and loop over document identified by a JSONPointer and applying an XSL
to convert to ISO format.

This should allow GeoNetwork to harvest some of the opendata portal
providing all various search API providing JSON response usually.

Harvester / Simple URL / Paging and basic opendatasoft support.

Json harvester: fix merge conflicts

jsonHarvester: handle JSONLD format with @ in tag names

jsonHarvester: add ESRI JSONLD DCAT transformation

hack: to remove, extract uuid from URIs

harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleUrl/Aligner.java

@@ -0,0 +1,286 @@
+//=============================================================================
+//===	Copyright (C) 2001-2007 Food and Agriculture Organization of the
+//===	United Nations (FAO-UN), United Nations World Food Programme (WFP)
+//===	and United Nations Environment Programme (UNEP)
+//===
+//===	This program is free software; you can redistribute it and/or modify
+//===	it under the terms of the GNU General Public License as published by
+//===	the Free Software Foundation; either version 2 of the License, or (at
+//===	your option) any later version.
+//===
+//===	This program is distributed in the hope that it will be useful, but
+//===	WITHOUT ANY WARRANTY; without even the implied warranty of
+//===	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+//===	General Public License for more details.
+//===
+//===	You should have received a copy of the GNU General Public License
+//===	along with this program; if not, write to the Free Software
+//===	Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA
+//===
+//===	Contact: Jeroen Ticheler - FAO - Viale delle Terme di Caracalla 2,
+//===	Rome - Italy. email: [email protected]
+//==============================================================================
+
+package org.fao.geonet.kernel.harvest.harvester.simpleUrl;
+
+import jeeves.server.context.ServiceContext;
+import org.fao.geonet.GeonetContext;
+import org.fao.geonet.Logger;
+import org.fao.geonet.constants.Geonet;
+import org.fao.geonet.domain.AbstractMetadata;
+import org.fao.geonet.domain.ISODate;
+import org.fao.geonet.domain.Metadata;
+import org.fao.geonet.domain.MetadataType;
+import org.fao.geonet.exceptions.OperationAbortedEx;
+import org.fao.geonet.kernel.DataManager;
+import org.fao.geonet.kernel.UpdateDatestamp;
+import org.fao.geonet.kernel.datamanager.IMetadataIndexer;
+import org.fao.geonet.kernel.datamanager.IMetadataManager;
+import org.fao.geonet.kernel.datamanager.IMetadataUtils;
+import org.fao.geonet.kernel.harvest.BaseAligner;
+import org.fao.geonet.kernel.harvest.harvester.CategoryMapper;
+import org.fao.geonet.kernel.harvest.harvester.GroupMapper;
+import org.fao.geonet.kernel.harvest.harvester.HarvestError;
+import org.fao.geonet.kernel.harvest.harvester.HarvestResult;
+import org.fao.geonet.kernel.harvest.harvester.UUIDMapper;
+import org.fao.geonet.repository.OperationAllowedRepository;
+import org.jdom.Element;
+
+import javax.transaction.Transactional;
+import javax.transaction.Transactional.TxType;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+public class Aligner extends BaseAligner<SimpleUrlParams> {
+
+    private ServiceContext context;
+    private DataManager dataMan;
+    private CategoryMapper localCateg;
+    private GroupMapper localGroups;
+    private UUIDMapper localUuids;
+
+    private IMetadataUtils metadataUtils;
+    private IMetadataManager metadataManager;
+    private IMetadataIndexer metadataIndexer;
+
+    private HarvestResult result;
+    private Map<String, Object> processParams = new HashMap<String, Object>();
+    private Logger log;
+
+    public Aligner(AtomicBoolean cancelMonitor, ServiceContext sc, SimpleUrlParams params, Logger log) throws OperationAbortedEx {
+        super(cancelMonitor);
+        this.context = sc;
+        this.params = params;
+        this.log = log;
+
+        GeonetContext gc = (GeonetContext) context.getHandlerContext(Geonet.CONTEXT_NAME);
+        dataMan = gc.getBean(DataManager.class);
+        metadataUtils = gc.getBean(IMetadataUtils.class);
+        metadataManager = gc.getBean(IMetadataManager.class);
+        metadataIndexer = gc.getBean(IMetadataIndexer.class);
+        result = new HarvestResult();
+        result.unretrievable = 0;
+        result.uuidSkipped = 0;
+        result.couldNotInsert = 0;
+    }
+
+    public HarvestResult align(Map<String, Element> records, Collection<HarvestError> errors) throws Exception {
+        if (cancelMonitor.get()) {
+            return result;
+        }
+
+        log.debug("Start of alignment for : " + params.getName());
+
+        localCateg = new CategoryMapper(context);
+        localGroups = new GroupMapper(context);
+        localUuids = new UUIDMapper(context.getBean(IMetadataUtils.class), params.getUuid());
+
+        insertOrUpdate(records, errors);
+        log.debug("End of alignment for : " + params.getName());
+
+        return result;
+    }
+
+    private void insertOrUpdate(Map<String, Element> records, Collection<HarvestError> errors) {
+        records.entrySet().forEach(e -> {
+            if (cancelMonitor.get()) {
+                return;
+            }
+
+            try {
+                String id = metadataUtils.getMetadataId(e.getKey());
+
+                if (id == null) {
+                    //record doesn't exist (so it doesn't belong to this harvester)
+                    log.debug("Adding record with uuid " + e.getKey());
+                    addMetadata(e, null);
+                } else if (localUuids.getID(e.getKey()) == null) {
+                    //Record does not belong to this harvester
+                    result.datasetUuidExist++;
+
+                    switch (params.getOverrideUuid()) {
+                        case OVERRIDE:
+                            updateMetadata(e, Integer.toString(metadataUtils.findOneByUuid(e.getKey()).getId()), true);
+                            log.debug("Overriding record with uuid " + e.getKey());
+                            result.updatedMetadata++;
+                            break;
+                        case RANDOM:
+                            log.debug("Generating random uuid for remote record with uuid " + e.getKey());
+                            addMetadata(e, UUID.randomUUID().toString());
+                            break;
+                        case SKIP:
+                            log.debug("Skipping record with uuid " + e.getKey());
+                            result.uuidSkipped++;
+                        default:
+                            break;
+                    }
+                } else {
+                    //record exists and belongs to this harvester
+                    updateMetadata(e, id, false);
+                    if (params.isIfRecordExistAppendPrivileges()) {
+                        addPrivileges(id, params.getPrivileges(), localGroups, context);
+                        result.privilegesAppendedOnExistingRecord++;
+                    }
+
+                }
+                result.totalMetadata++;
+            } catch (Throwable t) {
+                errors.add(new HarvestError(this.context, t));
+                log.error("Unable to process record from csw (" + this.params.getName() + ")");
+                log.error("   Record failed: " + e.getKey() + ". Error is: " + t.getMessage());
+                log.error(t);
+            } finally {
+                result.originalMetadata++;
+            }
+        });
+    }
+
+    /**
+     * Remove records no longer on the remote CSW server
+     *
+     * @param records
+     * @throws Exception
+     */
+    @Transactional(value = TxType.REQUIRES_NEW)
+    public HarvestResult cleanupRemovedRecords(Set<String> records) throws Exception {
+
+        if (cancelMonitor.get()) {
+            return result;
+        }
+
+        for (String uuid : localUuids.getUUIDs()) {
+            if (!records.contains(uuid)) {
+                String id = localUuids.getID(uuid);
+                log.debug("  - Removing old metadata with local id:" + id);
+                metadataManager.deleteMetadata(context, id);
+                result.locallyRemoved++;
+            }
+        }
+        dataMan.forceIndexChanges();
+
+        return result;
+    }
+
+
+    private void addMetadata(Map.Entry<String, Element> record, String overrideUuidValue) throws Exception {
+        if (cancelMonitor.get()) {
+            return;
+        }
+
+        Element xml = record.getValue();
+        if (xml == null) {
+            result.unretrievable++;
+            return;
+        }
+
+        String schema = dataMan.autodetectSchema(xml, null);
+        if (schema == null) {
+            log.debug("  - Metadata skipped due to unknown schema. uuid:" + record.getKey());
+            result.unknownSchema++;
+            return;
+        }
+
+        String uuid = record.getKey();
+        if (overrideUuidValue != null) {
+            log.debug(String.format("  - Overriding UUID %s by %s", record.getKey(), overrideUuidValue));
+            uuid = overrideUuidValue;
+            xml = dataMan.setUUID(schema, uuid, record.getValue());
+        }
+
+
+        log.debug("  - Adding metadata with uuid:" + uuid + " schema:" + schema);
+
+        final String dateModified = dataMan.extractDateModified(schema, xml);
+
+        AbstractMetadata metadata = new Metadata();
+        metadata.setUuid(uuid);
+        Integer ownerId = getOwner();
+        metadata.getDataInfo().
+            setSchemaId(schema).
+            setRoot(xml.getQualifiedName()).
+            setType(MetadataType.METADATA).
+            setChangeDate(new ISODate(dateModified)).
+            setCreateDate(new ISODate(dateModified));
+        metadata.getSourceInfo().
+            setSourceId(params.getUuid()).
+            setOwner(ownerId).
+            setGroupOwner(getGroupOwner());
+        metadata.getHarvestInfo().
+            setHarvested(true).
+            setUuid(params.getUuid());
+
+        metadata.getSourceInfo().setGroupOwner(getGroupOwner());
+
+        addCategories(metadata, params.getCategories(), localCateg, context, null, false);
+
+        metadata = metadataManager.insertMetadata(context, metadata, xml, false, false, UpdateDatestamp.NO, false, false);
+
+        String id = String.valueOf(metadata.getId());
+
+        addPrivileges(id, params.getPrivileges(), localGroups, context);
+
+        metadataIndexer.indexMetadata(id, true);
+        result.addedMetadata++;
+    }
+
+
+    @Transactional(value = TxType.REQUIRES_NEW)
+    boolean updateMetadata(Map.Entry<String, Element> ri, String id, Boolean force) throws Exception {
+        Element md = ri.getValue();
+        if (md == null) {
+            result.unchangedMetadata++;
+            return false;
+        }
+
+        boolean validate = false;
+        boolean ufo = false;
+        boolean index = false;
+        String language = context.getLanguage();
+        String schema = dataMan.autodetectSchema(md, null);
+        final String dateModified = dataMan.extractDateModified(schema, ri.getValue());
+
+        final AbstractMetadata metadata = metadataManager.updateMetadata(context, id, md, validate, ufo, index, language, dateModified, true);
+
+        if (force) {
+            //change ownership of metadata to new harvester
+            metadata.getHarvestInfo().setUuid(params.getUuid());
+            metadata.getSourceInfo().setSourceId(params.getUuid());
+
+            metadataManager.save((Metadata) metadata);
+        }
+
+        OperationAllowedRepository repository = context.getBean(OperationAllowedRepository.class);
+        repository.deleteAllByMetadataId(Integer.parseInt(id));
+
+        addPrivileges(id, params.getPrivileges(), localGroups, context);
+
+        metadata.getCategories().clear();
+        addCategories(metadata, params.getCategories(), localCateg, context, null, true);
+        result.updatedMetadata++;
+        return true;
+    }
+}