Merge branch '341-filters-conversion' into 'master'

Resolve "Filters conversion"

Closes #341

See merge request genesys-pgr/genesys-server!239

src/main/java/org/genesys2/server/model/genesys/AccessionData.java

@@ -81,6 +81,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	@JsonView({ JsonViews.Minimal.class })
 	@Field(type = FieldType.Object)
 	@JsonIgnoreProperties({"settings"})
+//	@QueryInit({ "country.region.*" })
 	private FaoInstitute institute;
 
 	@Column(name = "acceNumb", nullable = false, length = 128)
@@ -117,6 +118,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	@JoinColumn(name = "orgCtyId", nullable = true)
 	@JsonView({ JsonViews.Public.class })
 	@Field(type = FieldType.Object)
+//	@QueryInit({ "region.*" })
 	private Country countryOfOrigin;
 
 	@Column(name = "sampStat", length = 3)

src/main/java/org/genesys2/server/model/impl/Country.java

@@ -74,7 +74,7 @@ public class Country extends BasicModel {
 	@JoinColumn(name = "regionId")
 	@JsonView({ JsonViews.Public.class })
 	@JsonIgnoreProperties({ "countries", "parentRegion" })
-	@Field(type = FieldType.Nested)
+	@Field(type = FieldType.Object)
 	private GeoRegion region;
 
 	@Column(name = "minLongitude")

src/main/java/org/genesys2/server/model/impl/GeoRegion.java

@@ -21,6 +21,8 @@ import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.model.VersionedModel;
 import org.genesys.custom.elasticsearch.IgnoreField;
 import org.hibernate.annotations.Type;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldIndex;
 
 import com.fasterxml.jackson.annotation.JsonIdentityReference;
 import com.fasterxml.jackson.annotation.JsonIgnore;
@@ -35,10 +37,11 @@ public class GeoRegion extends VersionedModel {
 
 	private static final long serialVersionUID = -1L;
 
-	@Column
+	@Column(length = 3, nullable = false, unique = true)
+	@Field(index = FieldIndex.not_analyzed)
 	private String isoCode;
 
-	@Column
+	@Column(nullable = false, length = 250)
 	private String name;
 
 	@ManyToOne()

src/main/java/org/genesys2/server/persistence/GeoRegionRepository.java

@@ -4,8 +4,9 @@ import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.GeoRegion;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.querydsl.QueryDslPredicateExecutor;
 
-public interface GeoRegionRepository extends JpaRepository<GeoRegion, Long>{
+public interface GeoRegionRepository extends JpaRepository<GeoRegion, Long>, QueryDslPredicateExecutor<GeoRegion> {
 
     @Query("select distinct gr from GeoRegion gr where gr.isoCode = ?1")
     GeoRegion findByIsoCode(String isoCode);

src/main/java/org/genesys2/server/service/GeoRegionService.java

@@ -6,29 +6,39 @@ import org.xml.sax.SAXException;
 
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.IOException;
+import java.util.Collection;
 import java.util.List;
 import java.util.Locale;
+import java.util.Set;
 
 public interface GeoRegionService {
 
-    GeoRegion find(String regionIsoCode);
+	GeoRegion find(String regionIsoCode);
 
-    void save(GeoRegion geoRegion);
+	void save(GeoRegion geoRegion);
 
-    void delete(GeoRegion geoRegion);
+	void delete(GeoRegion geoRegion);
 
-    List<GeoRegion> findAll();
+	List<GeoRegion> findAll();
 
-    List<GeoRegion> findAll(Locale locale);
+	List<GeoRegion> findAll(Locale locale);
 
-    void updateGeoRegionData() throws IOException, ParserConfigurationException, SAXException;
+	void updateGeoRegionData() throws IOException, ParserConfigurationException, SAXException;
 
 	GeoRegion getRegion(Country country);
 
-    List<GeoRegion> getGeoRegionsForFilter();
+	List<GeoRegion> getGeoRegionsForFilter();
 
-    List<GeoRegion> conversionToSubRegionsList(GeoRegion parentGeo);
+	List<GeoRegion> conversionToSubRegionsList(GeoRegion parentGeo);
 
-    List<GeoRegion> getChildren(String regionIsoCode);
+	List<GeoRegion> getChildren(String regionIsoCode);
+
+	/**
+	 * Get all ISO3 country codes for specified region codes
+	 * 
+	 * @param regionCodes set of region codes
+	 * @return a set of ISO3 country codes of countries in all specified regions
+	 */
+	Collection<String> countryCodesFor(Set<String> regionCodes);
 
 }

src/main/java/org/genesys2/server/service/filter/AccessionFilter.java

@@ -15,8 +15,6 @@
  */
 package org.genesys2.server.service.filter;
 
-import static org.genesys2.server.model.genesys.QAccession.accession;
-
 import java.util.Set;
 import java.util.UUID;
 
@@ -24,6 +22,7 @@ import org.genesys.blocks.model.filters.NumberFilter;
 import org.genesys.blocks.model.filters.StringFilter;
 import org.genesys.blocks.model.filters.UuidModelFilter;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.QAccession;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 
 import com.hazelcast.util.CollectionUtil;
@@ -87,12 +86,16 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 	/** acce.lists uuid */
 	public Set<UUID> list;
 
+	public Predicate buildQuery() {
+		return buildQuery(QAccession.accession);
+	}
+	
 	/**
 	 * Builds the query.
 	 *
 	 * @return the predicate
 	 */
-	public Predicate buildQuery() {
+	public Predicate buildQuery(QAccession accession) {
 		final BooleanBuilder and = new BooleanBuilder();
 		super.buildQuery(accession, accession._super._super, and);
 
@@ -174,4 +177,40 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 		return this;
 	}
 
+	public InstituteFilter holder() {
+		if (this.holder==null) {
+			return this.holder = new InstituteFilter();
+		} else {
+			return this.holder;
+		}
+	}
+
+	public CountryFilter origin() {
+		if (this.origin == null) {
+			return this.origin = new CountryFilter();
+		}
+		return this.origin;
+	}
+
+	public AccessionGeoFilter geo() {
+		if (this.geo == null) {
+			return this.geo = new AccessionGeoFilter();
+		}
+		return this.geo;
+	}
+
+	public AccessionCollectFilter coll() {
+		if (this.coll == null) {
+			return this.coll = new AccessionCollectFilter();
+		}
+		return this.coll;
+	}
+
+	public TaxonomyFilter taxa() {
+		if (this.taxa == null) {
+			return this.taxa = new TaxonomyFilter();
+		}
+		return this.taxa;
+	}
+
 }

src/main/java/org/genesys2/server/service/filter/AppliedFiltersConverter.java

@@ -118,49 +118,46 @@ public class AppliedFiltersConverter {
 			}
 			LOG.trace("Converting {}", pretty.writeValueAsString(af));
 
+			switch (filterName) {
+				case "regionHoldInst": {
+					filterName = "institute.country.region";
+					break;
+				}
+				case "regionOrigin": {
+					filterName = "orgCty.region";
+					break;
+				}
+				default:
+			}
+
 			if (filterName.contains(".")) {
-				int lastDot = filterName.lastIndexOf('.');
-				String base = filterName.substring(0, lastDot);
-				String newFilterName = filterName.substring(lastDot + 1);
+				int firstDot = filterName.indexOf('.');
+				String base = filterName.substring(0, firstDot);
+				String newFilterName = filterName.substring(firstDot + 1);
 				LOG.debug("Doing accession.{} for {}", base, af.getFilterName());
 				switch (base) {
 				case "institute": {
-					InstituteFilter ff = f.holder;
-					if (ff == null) {
-						ff = f.holder = new InstituteFilter();
-					}
+					InstituteFilter ff = f.holder();
 					apply(ff, newFilterName, af);
 					break;
 				}
 				case "taxonomy": {
-					TaxonomyFilter ff = f.taxa;
-					if (ff == null) {
-						ff = f.taxa = new TaxonomyFilter();
-					}
+					TaxonomyFilter ff = f.taxa();
 					apply(ff, newFilterName, af);
 					break;
 				}
 				case "coll": {
-					AccessionCollectFilter ff = f.coll;
-					if (ff == null) {
-						ff = f.coll = new AccessionCollectFilter();
-					}
+					AccessionCollectFilter ff = f.coll();
 					apply(ff, newFilterName, af);
 					break;
 				}
 				case "geo": {
-					AccessionGeoFilter ff = f.geo;
-					if (ff == null) {
-						ff = f.geo = new AccessionGeoFilter();
-					}
+					AccessionGeoFilter ff = f.geo();
 					apply(ff, newFilterName, af);
 					break;
 				}
 				case "orgCty": {
-					CountryFilter ff = f.origin;
-					if (ff == null) {
-						ff = f.origin = new CountryFilter();
-					}
+					CountryFilter ff = f.origin();
 					apply(ff, newFilterName, af);
 					break;
 				}
@@ -427,16 +424,22 @@ public class AppliedFiltersConverter {
 		return nf;
 	}
 
-	private static void apply(CountryFilter ff, String filterName, AppliedFilter af) {
+	private static void apply(CountryFilter countryFilter, String filterName, AppliedFilter af) {
 		switch (filterName) {
 		case "iso3": {
-			Set<String> iso3 = ff.iso3;
+			Set<String> iso3 = countryFilter.iso3;
 			if (iso3 == null) {
-				iso3 = ff.iso3 = new HashSet<>();
+				iso3 = countryFilter.iso3 = new HashSet<>();
 			}
 			iso3.addAll(toStringSet(af));
 			break;
 		}
+		case "region": {
+			Set<String> codes = toStringSet(af);
+			LOG.debug("Got country region codes {}", codes);
+			countryFilter.region = codes;
+			break;
+		}
 		default:
 			throw new RuntimeException("Unhandled Institute filter property=" + filterName);
 		}
@@ -450,22 +453,37 @@ public class AppliedFiltersConverter {
 		return af.getValues().stream().map(fv -> (UUID) ((LiteralValueFilter) fv).getValue()).collect(Collectors.toSet());
 	}
 
-	private static void apply(InstituteFilter ff, String filterName, AppliedFilter af) {
+	private static void apply(InstituteFilter instituteFilter, String filterName, AppliedFilter af) {
 		switch (filterName) {
 		case "code": {
-			Set<String> code = ff.code;
+			Set<String> code = instituteFilter.code;
 			if (code == null) {
-				code = ff.code = new HashSet<>();
+				code = instituteFilter.code = new HashSet<>();
 			}
 			Set<String> codes = toStringSet(af);
 			LOG.debug("Got Institute codes {}", codes);
 			code.addAll(codes);
 			break;
 		}
+		case "country.iso3": {
+			CountryFilter countryFilter = instituteFilter.country();
+			Set<String> codes = toStringSet(af);
+			LOG.debug("Got countries codes {}", codes);
+			countryFilter.iso3 = new HashSet<>();
+			countryFilter.iso3.addAll(codes);
+			break;
+		}
+		case "country.region": {
+			Set<String> codes = toStringSet(af);
+			LOG.debug("Got country region codes {}", codes);
+			CountryFilter countryFilter = instituteFilter.country();
+			countryFilter.region = codes;
+			break;
+		}
 		case "networks": {
-			Set<String> networks = ff.networks;
+			Set<String> networks = instituteFilter.networks;
 			if (networks == null) {
-				networks = ff.networks = new HashSet<>();
+				networks = instituteFilter.networks = new HashSet<>();
 			}
 			Set<String> codes = toStringSet(af);
 			LOG.debug("Got Institute networks {}", codes);
@@ -477,24 +495,4 @@ public class AppliedFiltersConverter {
 		}
 	}
 
-	// private static void apply(CountryFilter country, AppliedFilter af) {
-	// String filterName = af.getFilterName();
-	// switch (filterName) {
-	// case "code": {
-	// Set<String> code = country.iso3;
-	// if (code == null) {
-	// code = country.iso3 = new HashSet<>();
-	// }
-	// Set<String> codes = af.getValues().stream().map(fv -> (String)
-	// ((LiteralValueFilter) fv).getValue()).collect(Collectors.toSet());
-	// LOG.debug("Got origin iso3 codes {}", codes);
-	// code.addAll(codes);
-	// break;
-	// }
-	// default:
-	// throw new RuntimeException("Unhandled country filter property=" +
-	// filterName);
-	// }
-	// }
-
 }

src/main/java/org/genesys2/server/service/filter/CountryFilter.java

@@ -17,24 +17,29 @@ package org.genesys2.server.service.filter;
 
 import static org.genesys2.server.model.impl.QCountry.country;
 
+import java.util.Collection;
 import java.util.Set;
 
 import org.genesys.blocks.model.filters.BasicModelFilter;
+import org.genesys.blocks.util.CurrentApplicationContext;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.QCountry;
+import org.genesys2.server.service.GeoRegionService;
 
 import com.querydsl.core.BooleanBuilder;
 import com.querydsl.core.types.Predicate;
 
-// TODO: Auto-generated Javadoc
 /**
- * The Class CountryFilter.
+ * The filter for {@link Country}
  */
 public class CountryFilter extends BasicModelFilter<CountryFilter, Country> {
 
 	/** The iso 3. */
 	public Set<String> iso3;
 
+	/** The region codes. */
+	public Set<String> region;
+
 	/**
 	 * Builds the query.
 	 *
@@ -57,8 +62,16 @@ public class CountryFilter extends BasicModelFilter<CountryFilter, Country> {
 		if (iso3 != null && !iso3.isEmpty()) {
 			and.and(country.code3.in(iso3));
 		}
+		if (region != null && ! region.isEmpty()) {
+			and.and(country.code3.in(getCountriesInRegions(region)));
+		}
 
 		return and;
 	}
 
+	private Collection<String> getCountriesInRegions(Set<String> regionCodes) {
+		GeoRegionService geoRegionService = CurrentApplicationContext.getContext().getBean(GeoRegionService.class);
+		return geoRegionService.countryCodesFor(regionCodes);
+	}
+
 }

src/main/java/org/genesys2/server/service/filter/GeoRegionFilter.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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.
+ */
+package org.genesys2.server.service.filter;
+
+import java.util.Set;
+
+import org.genesys.blocks.model.filters.BasicModelFilter;
+import org.genesys2.server.model.impl.GeoRegion;
+import org.genesys2.server.model.impl.QGeoRegion;
+
+import com.querydsl.core.BooleanBuilder;
+import com.querydsl.core.types.Predicate;
+
+/**
+ * The filter for {@link GeoRegion}
+ */
+public class GeoRegionFilter extends BasicModelFilter<GeoRegionFilter, GeoRegion> {
+
+	/** The region code. */
+	public Set<String> code;
+
+	/**
+	 * Builds the query.
+	 *
+	 * @return the predicate
+	 */
+	public Predicate buildQuery() {
+		return buildQuery(QGeoRegion.geoRegion);
+	}
+
+	/**
+	 * Builds the query.
+	 *
+	 * @param georegion the georegion
+	 * @return the predicate
+	 */
+	public Predicate buildQuery(QGeoRegion georegion) {
+		final BooleanBuilder and = new BooleanBuilder();
+		super.buildQuery(georegion, georegion._super._super, and);
+
+		if (code != null && !code.isEmpty()) {
+			and.and(georegion.isoCode.in(code));
+		}
+
+		return and;
+	}
+
+}

src/main/java/org/genesys2/server/service/filter/InstituteFilter.java

@@ -91,5 +91,12 @@ public class InstituteFilter extends BasicModelFilter<InstituteFilter, FaoInstit
 
 		return and;
 	}
-	
+
+	public CountryFilter country() {
+		if (this.country == null) {
+			return this.country = new CountryFilter();
+		} else {
+			return this.country;
+		}
+	}
 }

src/main/java/org/genesys2/server/service/impl/ElasticsearchServiceImpl.java

@@ -395,8 +395,10 @@ public class ElasticsearchServiceImpl implements ElasticsearchService, Initializ
 			} catch (org.springframework.data.elasticsearch.ElasticsearchException e) {
 				LOG.error(e.getMessage());
 				Map<String, String> failedDocs = e.getFailedDocuments();
-				for (String key : failedDocs.keySet()) {
-					LOG.error("{} {}", key, failedDocs.get(key));
+				if (failedDocs != null) {
+					for (String key : failedDocs.keySet()) {
+						LOG.error("{} {}", key, failedDocs.get(key));
+					}
 				}
 			} catch (ElasticsearchException e) {
 				LOG.error("Could not index document", e);

src/main/java/org/genesys2/server/service/impl/GeoRegionServiceImpl.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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.
+ */
 package org.genesys2.server.service.impl;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Optional;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.GeoRegion;
+import org.genesys2.server.model.impl.QGeoRegion;
 import org.genesys2.server.persistence.CountryRepository;
 import org.genesys2.server.persistence.GeoRegionRepository;
 import org.genesys2.server.service.GeoRegionService;
@@ -25,21 +43,38 @@ import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 import org.xml.sax.SAXException;
 
+import com.querydsl.jpa.impl.JPAQuery;
+import com.querydsl.jpa.impl.JPAQueryFactory;
+
+/**
+ * GeoRegion service.
+ */
 @Service
 @Transactional(readOnly = true)
 public class GeoRegionServiceImpl implements GeoRegionService {
 
+	/** The Constant LOG. */
 	private static final Logger LOG = LoggerFactory.getLogger(GeoRegionServiceImpl.class);
 
+	/** The country repository. */
 	@Autowired
 	CountryRepository countryRepository;
 
+	/** The geo region repository. */
 	@Autowired
 	GeoRegionRepository geoRegionRepository;
 
+	/** The geo region data CLDR. */
 	@Autowired
 	GeoRegionDataCLDR geoRegionDataCLDR;
 
+	/** The jpa query factory. */
+	@Autowired
+	private JPAQueryFactory jpaQueryFactory;
+
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.GeoRegionService#find(java.lang.String)
+	 */
 	@Override
 	public GeoRegion find(String regionIsoCode) {
 		GeoRegion geoRegion = geoRegionRepository.findByIsoCode(regionIsoCode);
@@ -47,18 +82,27 @@ public class GeoRegionServiceImpl implements GeoRegionService {
 		return geoRegion;
 	}
 
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.GeoRegionService#save(org.genesys2.server.model.impl.GeoRegion)
+	 */
 	@Override
 	@Transactional(readOnly = false)
 	public void save(GeoRegion geoRegion) {
 		geoRegionRepository.save(geoRegion);
 	}
 
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.GeoRegionService#delete(org.genesys2.server.model.impl.GeoRegion)
+	 */
 	@Override
 	@Transactional(readOnly = false)
 	public void delete(GeoRegion geoRegion) {
 		geoRegionRepository.delete(geoRegion);
 	}
 
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.GeoRegionService#getRegion(org.genesys2.server.model.impl.Country)
+	 */