Updated `countZzzz` by model filter methods

src/main/java/org/genesys/catalog/model/filters/DatasetFilter.java

@@ -17,6 +17,7 @@ package org.genesys.catalog.model.filters;
 
 import static org.genesys.catalog.model.dataset.QDataset.dataset;
 
+import java.util.HashSet;
 import java.util.Set;
 
 import org.apache.commons.collections4.CollectionUtils;
@@ -124,4 +125,14 @@ public class DatasetFilter extends UuidModelFilter<DatasetFilter, Dataset> {
 
 		return and;
 	}
+
+	public DatasetFilter state(PublishState... state) {
+		if (this.state == null) {
+			this.state = new HashSet<>();
+		}
+		for (PublishState s : state) {
+			this.state.add(s);
+		}
+		return this;
+	}
 }

src/main/java/org/genesys/catalog/model/filters/DescriptorFilter.java

@@ -17,6 +17,7 @@ package org.genesys.catalog.model.filters;
 
 import static org.genesys.catalog.model.traits.QDescriptor.descriptor;
 
+import java.util.HashSet;
 import java.util.Set;
 
 import org.apache.commons.lang3.ArrayUtils;
@@ -171,4 +172,14 @@ public class DescriptorFilter extends UuidModelFilter<DescriptorFilter, Descript
 		return and;
 	}
 
+	public DescriptorFilter state(PublishState... state) {
+		if (this.state == null) {
+			this.state = new HashSet<>();
+		}
+		for (PublishState s : state) {
+			this.state.add(s);
+		}
+		return this;
+	}
+
 }

src/main/java/org/genesys/catalog/service/DatasetService.java

@@ -245,11 +245,12 @@ public interface DatasetService {
 	Dataset updateDatasetFile(Dataset dataset, RepositoryFile metadata) throws NoSuchRepositoryFileException;
 
 	/**
-	 * Count the number of published datasets
+	 * Count the number of published datasets.
 	 *
+	 * @param filter the filter
 	 * @return the number of published datasets
 	 */
-	long countPublished();
+	long countDatasets(DatasetFilter filter);
 
 	/**
 	 * Load data about last published datasets.

src/main/java/org/genesys/catalog/service/DescriptorService.java

@@ -174,9 +174,10 @@ public interface DescriptorService {
 	void exportDescriptors(DescriptorFilter filter, OutputStream outputStream) throws IOException;
 
 	/**
-	 * Cont published descriptors
+	 * Count published descriptors.
 	 *
+	 * @param filter the filter
 	 * @return the number of published descriptors
 	 */
-	long countPublished();
+	long countDescriptors(DescriptorFilter filter);
 }

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -15,7 +15,7 @@
  */
 package org.genesys.catalog.service.impl;
 
-import static org.genesys.catalog.model.dataset.QDataset.*;
+import static org.genesys.catalog.model.dataset.QDataset.dataset;
 
 import java.io.IOException;
 import java.nio.file.Paths;
@@ -267,8 +267,16 @@ public class DatasetServiceImpl implements DatasetService {
 	@Override
 	public Page<Dataset> listDatasets(final DatasetFilter filter, final Pageable page) {
 		Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-		Page res = datasetRepository.findAll(new BooleanBuilder().and(filter.buildQuery()).and(QDataset.dataset.state.in(PublishState.PUBLISHED)), markdownSortPageRequest);
-		return new PageImpl<Dataset>(res.getContent(), page, res.getTotalElements());
+		Page<Dataset> res = datasetRepository.findAll(new BooleanBuilder().and(filter.buildQuery()).and(QDataset.dataset.state.in(PublishState.PUBLISHED)), markdownSortPageRequest);
+		return new PageImpl<>(res.getContent(), page, res.getTotalElements());
+	}
+	
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	public long countDatasets(DatasetFilter filter) {
+		return datasetRepository.count(filter.buildQuery());
 	}
 
 	/**
@@ -278,13 +286,13 @@ public class DatasetServiceImpl implements DatasetService {
 	public Page<Dataset> listDatasetsForCurrentUser(final DatasetFilter filter, final Pageable page) {
 		if (securityUtils.hasRole(UserRole.ADMINISTRATOR)) {
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-			Page res = datasetRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
-			return new PageImpl<Dataset>(res.getContent(), page, res.getTotalElements());
+			Page<Dataset> res = datasetRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		} else {
 			final HashSet<Long> partners = new HashSet<>(securityUtils.listObjectIdentityIdsForCurrentUser(Partner.class, BasePermission.WRITE));
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-			Page res = datasetRepository.findAll(dataset.owner.id.in(partners).and(filter.buildQuery()), markdownSortPageRequest);
-			return new PageImpl<Dataset>(res.getContent(), page, res.getTotalElements());
+			Page<Dataset> res = datasetRepository.findAll(dataset.owner.id.in(partners).and(filter.buildQuery()), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		}
 	}
 
@@ -528,14 +536,6 @@ public class DatasetServiceImpl implements DatasetService {
 		return lazyLoad(datasetRepository.save(loaded));
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
-	@Override
-	public long countPublished() {
-		return datasetRepository.count(dataset.state.in(PublishState.PUBLISHED));
-	}
-
 	/**
 	 * {@inheritDoc}
 	 */

src/main/java/org/genesys/catalog/service/impl/DescriptorServiceImpl.java

@@ -26,7 +26,6 @@ import java.util.UUID;
 
 import javax.persistence.EntityManager;
 
-import com.querydsl.core.types.Predicate;
 import org.genesys.catalog.exceptions.InvalidApiUsageException;
 import org.genesys.catalog.exceptions.NotFoundElement;
 import org.genesys.catalog.model.Partner;
@@ -62,6 +61,7 @@ import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
 import com.querydsl.core.BooleanBuilder;
+import com.querydsl.core.types.Predicate;
 
 /**
  * The Class DescriptorServiceImpl.
@@ -226,13 +226,13 @@ public class DescriptorServiceImpl implements DescriptorService {
 	public Page<Descriptor> listDescriptorsForCurrentUser(final DescriptorFilter filter, final Pageable page) {
 		if (securityUtils.hasRole(UserRole.ADMINISTRATOR)) {
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-			Page res = descriptorRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
-			return new PageImpl<Descriptor>(res.getContent(), page, res.getTotalElements());
+			Page<Descriptor> res = descriptorRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		} else {
 			final HashSet<Long> partners = new HashSet<>(securityUtils.listObjectIdentityIdsForCurrentUser(Partner.class, BasePermission.WRITE));
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-			Page res = descriptorRepository.findAll(descriptor.owner.id.in(partners).and(filter.buildQuery()), markdownSortPageRequest);
-			return new PageImpl<Descriptor>(res.getContent(), page, res.getTotalElements());
+			Page<Descriptor> res = descriptorRepository.findAll(descriptor.owner.id.in(partners).and(filter.buildQuery()), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		}
 	}
 
@@ -242,8 +242,8 @@ public class DescriptorServiceImpl implements DescriptorService {
 	@Override
 	public Page<Descriptor> listDescriptors(final DescriptorFilter descriptorFilter, final Pageable page) {
 		Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "title");
-		Page res = descriptorRepository.findAll(new BooleanBuilder().and(descriptorFilter.buildQuery()).and(QDescriptor.descriptor.state.in(PublishState.PUBLISHED)), markdownSortPageRequest);
-		return new PageImpl<Descriptor>(res.getContent(), page, res.getTotalElements());
+		Page<Descriptor> res = descriptorRepository.findAll(new BooleanBuilder().and(descriptorFilter.buildQuery()).and(QDescriptor.descriptor.state.in(PublishState.PUBLISHED)), markdownSortPageRequest);
+		return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 	}
 
 	/**
@@ -458,8 +458,8 @@ public class DescriptorServiceImpl implements DescriptorService {
     }
 
 	@Override
-	public long countPublished() {
-		return descriptorRepository.count(descriptor.state.eq(PublishState.PUBLISHED));
+	public long countDescriptors(DescriptorFilter filter) {
+		return descriptorRepository.count(filter.buildQuery());
 	}
 
 }

src/main/java/org/genesys/catalog/service/impl/PartnerServiceImpl.java

@@ -26,7 +26,6 @@ import org.genesys.catalog.persistence.PartnerRepository;
 import org.genesys.catalog.service.PartnerService;
 import org.genesys2.server.model.UserRole;
 import org.genesys2.server.security.SecurityUtils;
-import org.genesys2.server.service.ElasticsearchService;
 import org.genesys2.util.JPAUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -59,9 +58,6 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 	@Autowired
 	private SecurityUtils securityUtils;
 
-	@Autowired
-	private ElasticsearchService elasticsearchService;
-
 	@Value("${partner.primary.uuid}")
 	private UUID primaryPartnerUuid;
 
@@ -147,13 +143,13 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 	public Page<Partner> listPartnersForCurrentUser(final PartnerFilter filter, final Pageable page) {
 		if (securityUtils.hasRole(UserRole.ADMINISTRATOR)) {
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "name");
-			Page res = partnerRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
-			return new PageImpl<Partner>(res.getContent(), page, res.getTotalElements());
+			Page<Partner> res = partnerRepository.findAll(filter.buildQuery(), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		} else {
 			final HashSet<Long> ids = new HashSet<>(securityUtils.listObjectIdentityIdsForCurrentUser(Partner.class, BasePermission.WRITE));
 			Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "name");
-			Page res = partnerRepository.findAll(partner.id.in(ids).and(filter.buildQuery()), markdownSortPageRequest);
-			return new PageImpl<Partner>(res.getContent(), page, res.getTotalElements());
+			Page<Partner> res = partnerRepository.findAll(partner.id.in(ids).and(filter.buildQuery()), markdownSortPageRequest);
+			return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 		}
 	}
 
@@ -163,8 +159,8 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 	@Override
 	public Page<Partner> listPartners(final PartnerFilter partnerFilter, final Pageable page) {
 		Pageable markdownSortPageRequest = JPAUtils.toMarkdownSort(page, "name");
-		Page res = partnerRepository.findAll(partnerFilter.buildQuery(), markdownSortPageRequest);
-		return new PageImpl<Partner>(res.getContent(), page, res.getTotalElements());
+		Page<Partner> res = partnerRepository.findAll(partnerFilter.buildQuery(), markdownSortPageRequest);
+		return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 	}
 
 	/**
@@ -226,14 +222,7 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 
 	@Override
 	public long countPartners(PartnerFilter filter) {
-		long total = elasticsearchService.count(Partner.class, filter);
-
-		if (total < 10000) {
-			// If total is below 10K, use actual count
-			total = partnerRepository.count(filter.buildQuery());
-		}
-
-		return total;
+		return partnerRepository.count(filter.buildQuery());
 	}
 
 	/**

src/main/java/org/genesys2/server/api/v1/ApiInfoController.java

 package org.genesys2.server.api.v1;
 
-import io.swagger.annotations.Api;
+import org.genesys.catalog.model.filters.DatasetFilter;
+import org.genesys.catalog.model.filters.DescriptorFilter;
 import org.genesys.catalog.model.filters.PartnerFilter;
 import org.genesys.catalog.service.DatasetService;
 import org.genesys.catalog.service.DescriptorService;
 import org.genesys.catalog.service.PartnerService;
 import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.model.PublishState;
 import org.genesys2.server.service.AccessionService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.SubsetService;
 import org.genesys2.server.service.filter.AccessionFilter;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.InitializingBean;
+import org.genesys2.server.service.filter.SubsetFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -20,7 +20,7 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
 
-import java.net.UnknownHostException;
+import io.swagger.annotations.Api;
 
 /**
  * Accession API v1
@@ -31,8 +31,6 @@ import java.net.UnknownHostException;
 @Api(tags = { "api-info" })
 public class ApiInfoController {
 
-    private static final Logger LOG = LoggerFactory.getLogger(ApiInfoController.class);
-
     public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/info";
 
     @Value("${build.version}")
@@ -44,6 +42,9 @@ public class ApiInfoController {
     @Value("${build.revision}")
     private String revision;
 
+    @Value("${base.url}")
+    private String baseUrl;
+
     @Value("${cdn.servers}")
     private String[] cdnServers;
 
@@ -67,25 +68,17 @@ public class ApiInfoController {
      */
     @RequestMapping(value = "/version", method = RequestMethod.GET)
     public ApiInfo apiInfo() {
-        String hN;
-        try {
-            hN = java.net.InetAddress.getLocalHost().getHostName();
-        } catch (final UnknownHostException e) {
-            LOG.error("Error getting Host Name");
-            hN = "";
-        }
-
-        ApiInfo apiInfo = new ApiInfo();
+       ApiInfo apiInfo = new ApiInfo();
         apiInfo.version = this.version;
         apiInfo.artifactId = this.artifactId;
         apiInfo.revision = this.revision;
         apiInfo.cdnServers = this.cdnServers;
-        apiInfo.hostName = hN;
-        apiInfo.accessionCount = accessionService.countAccessions(new AccessionFilter());
-        apiInfo.datasetCount = datasetService.countPublished();
-        apiInfo.subsetCount = subsetService.countPublished();
+        apiInfo.baseUrl = this.baseUrl;
+        apiInfo.accessionCount = accessionService.countAccessions(new AccessionFilter().historic(false));
+        apiInfo.datasetCount = datasetService.countDatasets(new DatasetFilter().state(PublishState.PUBLISHED));
+        apiInfo.subsetCount = subsetService.countSubsets(new SubsetFilter().state(PublishState.PUBLISHED));
         apiInfo.instituteCount = instituteService.countActive();
-        apiInfo.descriptorCount = descriptorService.countPublished();
+        apiInfo.descriptorCount = descriptorService.countDescriptors(new DescriptorFilter().state(PublishState.PUBLISHED));
         apiInfo.partnerCount = partnerService.countPartners(new PartnerFilter());
 
         return apiInfo;
@@ -98,7 +91,7 @@ public class ApiInfoController {
         public String artifactId;
         public String version;
         public String revision;
-        public String hostName;
+        public String baseUrl;
 
         public String[] cdnServers;
         public long accessionCount;

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

@@ -43,11 +43,12 @@ public interface SubsetService {
     Page<Subset> list(SubsetFilter filter, Pageable page);
 
     /**
-     * Cont published subsets
+     * Count published subsets.
      *
+     * @param filter the filter
      * @return the number of published subsets
      */
-    long countPublished();
+    long countSubsets(SubsetFilter filter);
 
     /**
      * List current user's subsets matching the filter.

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

@@ -15,7 +15,7 @@
  */
 package org.genesys2.server.service.filter;
 
-import static org.genesys2.server.model.genesys.QAccession.*;
+import static org.genesys2.server.model.genesys.QAccession.accession;
 
 import java.util.Set;
 import java.util.UUID;
@@ -169,4 +169,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 		}
 	}
 
+	public AccessionFilter historic(Boolean historic) {
+		this.historic = historic;
+		return this;
+	}
+
 }

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

@@ -17,6 +17,7 @@ package org.genesys2.server.service.filter;
 
 import static org.genesys2.server.model.impl.QSubset.subset;
 
+import java.util.HashSet;
 import java.util.Set;
 
 import org.genesys.blocks.model.filters.StringFilter;
@@ -93,4 +94,14 @@ public class SubsetFilter extends UuidModelFilter<SubsetFilter, Subset> {
         }
         return and;
     }
+
+	public SubsetFilter state(PublishState ... state) {
+		if (this.state == null) {
+			this.state = new HashSet<>();
+		}
+		for (PublishState s : state) {
+			this.state.add(s);
+		}
+		return this;
+	}
 }

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

@@ -16,10 +16,12 @@
 
 package org.genesys2.server.service.impl;
 
+import org.genesys2.server.model.PublishState;
 import org.genesys2.server.model.genesys.PDCIStatistics;
 import org.genesys2.server.model.genesys.PhenoStatistics;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
+import org.genesys.catalog.model.filters.DatasetFilter;
 import org.genesys.catalog.service.DatasetService;
 import org.genesys2.server.persistence.PDCIRepository;
 import org.genesys2.server.service.GenesysService;
@@ -88,7 +90,7 @@ public class StatisticsServiceImpl implements StatisticsService {
 	@Override
 	@Cacheable(value = "statistics", key = "'stats.' + #root.methodName")
 	public long numberOfPublishedDatasets() {
-		return datasetService.countPublished();
+		return datasetService.countDatasets(new DatasetFilter().state(PublishState.PUBLISHED));
 	}
 
 	@Override

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

@@ -99,8 +99,8 @@ public class SubsetServiceImpl implements SubsetService {
 	}
 
 	@Override
-	public long countPublished() {
-		return subsetRepository.count(QSubset.subset.state.eq(PublishState.PUBLISHED));
+	public long countSubsets(SubsetFilter filter) {
+		return subsetRepository.count(filter.buildQuery());
 	}
 
 	@Override