Merge branch '359-upgrade-to-data-provider' into 'master'

Resolve "Upgrade to Data Provider"

Closes #359

See merge request genesys-pgr/genesys-server!260

src/main/java/org/genesys/catalog/model/Partner.java

@@ -24,10 +24,12 @@ import org.genesys.blocks.security.model.AclAwareModel;
 import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys.catalog.model.traits.DescriptorList;
 import org.genesys.catalog.model.vocab.ControlledVocabulary;
+import org.genesys2.server.model.impl.FaoInstitute;
 import org.springframework.data.elasticsearch.annotations.Document;
 
 import javax.persistence.*;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -78,10 +80,9 @@ public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
 	private Set<URL> urls;
 
 	/// FAO WIEWS codes associated with this partner
-	@ElementCollection
-	@CollectionTable(name = "partner_wiews", joinColumns = @JoinColumn(name = "partnerId"))
-	@Column(name = "wiews")
-	private Set<String> wiewsCodes;
+    @JsonIgnore
+	@OneToMany(mappedBy = "owner", fetch = FetchType.LAZY)
+	private List<FaoInstitute> institutes;
 
 	@ElementCollection
 	@CollectionTable(name = "partner_country", joinColumns = @JoinColumn(name = "partnerId"), uniqueConstraints = { @UniqueConstraint(columnNames = { "partnerId", "code" }) })
@@ -121,7 +122,7 @@ public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
 	 * @param partner the partner
 	 */
 	public Partner(final Partner partner) {
-		this(partner.getShortName(), partner.getName(), partner.getUrls(), partner.getWiewsCodes(), partner.getDescriptors(), partner.getVocabularies(), partner
+		this(partner.getShortName(), partner.getName(), partner.getUrls(), partner.getInstitutes(), partner.getDescriptors(), partner.getVocabularies(), partner
 			.getDescriptorList());
 	}
 
@@ -131,20 +132,20 @@ public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
 	 * @param shortName the short name
 	 * @param name the name
 	 * @param urls the urls
-	 * @param wiewsCodes the wiews codes
+	 * @param institutes the institutes
 	 * @param descriptors the descriptors
 	 * @param vocabularies the vocabularies
 	 * @param descriptorList the descriptor list
 	 */
-	public Partner(final String shortName, final String name, final Set<URL> urls, final Set<String> wiewsCodes, final List<Descriptor> descriptors,
+	public Partner(final String shortName, final String name, final Set<URL> urls, final List<FaoInstitute> institutes, final List<Descriptor> descriptors,
                    final List<ControlledVocabulary> vocabularies, final List<DescriptorList> descriptorList) {
 		this.shortName = shortName;
 		this.name = name;
 		if (urls != null) {
 			this.urls = new HashSet<>(urls);
 		}
-		if (wiewsCodes != null) {
-			this.wiewsCodes = new HashSet<>(wiewsCodes);
+		if (institutes != null) {
+			this.institutes = new ArrayList<>(institutes);
 		}
 		this.descriptors = descriptors;
 		this.vocabularies = vocabularies;
@@ -223,22 +224,12 @@ public class Partner extends UuidModel implements SelfCleaning, AclAwareModel {
 		this.urls = urls;
 	}
 
-	/**
-	 * Gets the wiews codes.
-	 *
-	 * @return the wiewsCodes
-	 */
-	public Set<String> getWiewsCodes() {
-		return wiewsCodes;
+	public List<FaoInstitute> getInstitutes() {
+		return institutes;
 	}
 
-	/**
-	 * Sets the wiews codes.
-	 *
-	 * @param wiewsCodes the wiewsCodes to set
-	 */
-	public void setWiewsCodes(final Set<String> wiewsCodes) {
-		this.wiewsCodes = wiewsCodes;
+	public void setInstitutes(List<FaoInstitute> institutes) {
+		this.institutes = institutes;
 	}
 
 	/**

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

@@ -70,7 +70,7 @@ public class PartnerFilter extends UuidModelFilter<PartnerFilter, Partner> {
 			and.and(description.buildQuery(partnerPath.description));
 		}
 		if (CollectionUtils.isNotEmpty(wiewsCodes)) {
-			and.and(partnerPath.wiewsCodes.any().in(wiewsCodes));
+			and.and(partnerPath.institutes.any().code.in(wiewsCodes));
 		}
 		return and;
 	}

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

@@ -17,9 +17,12 @@ package org.genesys.catalog.service;
 
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.filters.PartnerFilter;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.filter.InstituteFilter;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 
+import java.util.Set;
 import java.util.UUID;
 
 /**
@@ -61,6 +64,14 @@ public interface PartnerService {
 	 */
 	Partner loadPartner(UUID uuid);
 
+	/**
+	 * Load partners institutes by uuid of partner.
+	 *
+	 * @param uuid uuid of partner
+	 * @return partners institutes
+	 */
+	Page<FaoInstitute> loadPartnerInstitutes(UUID uuid, InstituteFilter filter, Pageable page);
+
 	/**
 	 * Load partner.
 	 *
@@ -96,6 +107,25 @@ public interface PartnerService {
 	 */
 	Page<Partner> listPartners(PartnerFilter partnerFilter, Pageable page);
 
+
+	/**
+	 * Adds the institutes to partner
+	 *
+	 * @param partner the partner
+	 * @param instituteCodes the institute codes
+	 * @return the partner
+	 */
+	Partner addInstitutes(Partner partner, Set<String> instituteCodes);
+
+	/**
+	 * Removes the institutes from partner
+	 *
+	 * @param partner the partner
+	 * @param instituteCodes the institute codes
+	 * @return the partner
+	 */
+	Partner removeInstitutes(Partner partner, Set<String> instituteCodes);
+
 	/**
 	 * Method for copy values of source to target.
 	 *

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

@@ -17,15 +17,24 @@ package org.genesys.catalog.service.impl;
 
 import static org.genesys.catalog.model.QPartner.partner;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
 import java.util.HashSet;
 import java.util.UUID;
 
+import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.filters.PartnerFilter;
 import org.genesys.catalog.persistence.PartnerRepository;
 import org.genesys.catalog.service.PartnerService;
+import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.UserRole;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.model.impl.QFaoInstitute;
+import org.genesys2.server.persistence.FaoInstituteRepository;
 import org.genesys2.server.security.SecurityUtils;
+import org.genesys2.server.service.filter.InstituteFilter;
 import org.genesys2.util.JPAUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -55,9 +64,15 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 	@Autowired
 	private PartnerRepository partnerRepository;
 
+	@Autowired
+	private FaoInstituteRepository instituteRepository;
+
 	@Autowired
 	private SecurityUtils securityUtils;
 
+	@Autowired
+	private CustomAclService aclService;
+
 	@Value("${partner.primary.uuid}")
 	private UUID primaryPartnerUuid;
 
@@ -163,14 +178,52 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 		return new PageImpl<>(res.getContent(), page, res.getTotalElements());
 	}
 
+	@Override
+	@Transactional
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	public Partner addInstitutes(Partner partner, Set<String> instituteCodes) {
+		final Partner savedPartner = loadPartner(partner.getUuid());
+
+		List<FaoInstitute> institutes = instituteRepository.findAllByCodes(instituteCodes);
+		institutes.forEach((inst) -> inst.setOwner(savedPartner));
+		institutes.forEach((institute -> aclService.createOrUpdatePermissions(institute)));
+		savedPartner.getInstitutes().addAll(institutes);
+
+		return lazyLoad(partnerRepository.save(savedPartner));
+	}
+
+	@Override
+	@Transactional
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	public Partner removeInstitutes(Partner partner, Set<String> instituteCodes) {
+		partner = loadPartner(partner.getUuid());
+
+		List<FaoInstitute> institutesToRemove = instituteRepository.findAllByCodes(instituteCodes);
+		institutesToRemove.forEach((institute -> institute.setOwner(null)));
+		institutesToRemove.forEach((institute -> aclService.createOrUpdatePermissions(institute)));
+		instituteRepository.save(institutesToRemove);
+
+		partner.getInstitutes().removeAll(institutesToRemove);
+ 		return lazyLoad(partnerRepository.save(partner));
+	}
+
 	/**
 	 * {@inheritDoc}
 	 */
 	@Override
 	public Partner loadPartner(final UUID uuid) {
-		return lazyLoad(partnerRepository.findByUuid(uuid));
+		Partner partner = partnerRepository.findByUuid(uuid);
+		if (partner == null) {
+			throw new NotFoundElement("No partner with uuid=" + uuid);
+		}
+		return lazyLoad(partner);
 	}
 
+	@Override
+	public Page<FaoInstitute> loadPartnerInstitutes(UUID uuid, InstituteFilter filter, Pageable page) {
+        return instituteRepository.findAll(QFaoInstitute.faoInstitute.owner.uuid.eq(uuid).and(filter.buildQuery()), page);
+    }
+
 	/**
 	 * {@inheritDoc}
 	 */
@@ -197,9 +250,9 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 			target.getUrls().addAll(source.getUrls());
 		}
 
-		target.setWiewsCodes(new HashSet<>());
-		if (source.getWiewsCodes() != null) {
-			target.getWiewsCodes().addAll(source.getWiewsCodes());
+		target.setInstitutes(new ArrayList<>());
+		if (source.getInstitutes() != null) {
+			target.getInstitutes().addAll(source.getInstitutes());
 		}
 
 		target.setCountryCodes(new HashSet<>());
@@ -236,8 +289,8 @@ public class PartnerServiceImpl implements PartnerService, InitializingBean {
 			if (partner.getUrls() != null) {
 				partner.getUrls().size();
 			}
-			if (partner.getWiewsCodes() != null) {
-				partner.getWiewsCodes().size();
+			if (partner.getInstitutes() != null) {
+				partner.getInstitutes().size();
 			}
 			if (partner.getCountryCodes() != null) {
 				partner.getCountryCodes().size();

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

@@ -17,6 +17,7 @@
 package org.genesys2.server.api.v1;
 
 import java.io.IOException;
+import java.util.Set;
 import java.util.UUID;
 
 import io.swagger.annotations.Api;
@@ -29,6 +30,8 @@ import org.genesys.catalog.service.ShortFilterService.FilterInfo;
 import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.api.FilteredPage;
 import org.genesys2.server.api.Pagination;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.filter.InstituteFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -109,6 +112,36 @@ public class PartnerController {
 		return partnerService.updatePartner(source);
 	}
 
+	/**
+	 * Adds the institutes to the Partner with provided uuid. Existing
+	 * {@link FaoInstitute#owner} is force-set to this partner.
+	 *
+	 * @param uuid the uuid
+	 * @param instituteCodes the institute codes
+	 * @return the partner
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@PostMapping(value = "/addInstitutes/{UUID}")
+	public Partner addInstitutes(@PathVariable("UUID") UUID uuid, @RequestBody Set<String> instituteCodes) {
+		Partner partner = partnerService.loadPartner(uuid);
+		return partnerService.addInstitutes(partner, instituteCodes);
+	}
+
+	/**
+	 * Removes the institutes from the Partner with provided uuid. Effectively this
+	 * sets {@link FaoInstitute#owner} to null.
+	 *
+	 * @param uuid the uuid
+	 * @param instituteCodes the institute codes
+	 * @return the partner
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@PostMapping(value = "/removeInstitutes/{UUID}")
+	public Partner removeInstitutes(@PathVariable("UUID") UUID uuid, @RequestBody Set<String> instituteCodes) {
+		Partner partner = partnerService.loadPartner(uuid);
+		return partnerService.removeInstitutes(partner, instituteCodes);
+	}
+
 	/**
 	 * List partners.
 	 *
@@ -131,6 +164,18 @@ public class PartnerController {
 		return new FilteredPage<>(filterInfo.filterCode, filterInfo.filter, partnerService.listPartners(filterInfo.filter, page.toPageRequest(100)));
 	}
 
+	/**
+	 * Gets partners institutes.
+	 *
+	 * @param uuid the uuid
+	 * @return the partner
+	 */
+	@PostMapping(value = "/{UUID}/institutes")
+	public Page<FaoInstitute> listInstitutes(@PathVariable("UUID") final UUID uuid,
+			@RequestBody(required = false) InstituteFilter filter, Pagination page) {
+		return partnerService.loadPartnerInstitutes(uuid, filter, page.toPageRequest(100));
+	}
+
 	/**
 	 * My partners.
 	 *

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

@@ -64,7 +64,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	@MapsId
 	@OneToOne(cascade = { CascadeType.PERSIST, CascadeType.MERGE }, fetch = FetchType.EAGER, optional = false, orphanRemoval = false)
 	@JoinColumn(name = "id")
-    @JsonUnwrapped
+	@JsonUnwrapped
 	@Field(type=FieldType.Auto)
 	private AccessionId accessionId;
 

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

@@ -25,24 +25,14 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import javax.persistence.Cacheable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.MapKey;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import javax.persistence.*;
 
 import org.apache.commons.lang3.StringUtils;
 import org.genesys.blocks.model.BasicModel;
 import org.genesys.blocks.model.EntityId;
 import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.security.model.AclAwareModel;
+import org.genesys.catalog.model.Partner;
 import org.genesys.custom.elasticsearch.IgnoreField;
 import org.genesys2.server.model.genesys.PDCIStatistics;
 import org.springframework.data.elasticsearch.annotations.Field;
@@ -118,6 +108,12 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
 	private List<Organization> networks;
 
+
+	@ManyToOne(cascade = {})
+	@JoinColumn(name = "partnerId")
+	@JsonView({ JsonViews.Public.class })
+	private Partner owner;
+
 	private long accessionCount;
 	private boolean pgrActivity;
 	private boolean maintainsCollection;
@@ -132,6 +128,12 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 	@Column(name = "pdciHistogram")
 	private String pdciHistogram;
 
+
+	@Override
+	public AclAwareModel aclParentObject(){
+		return this.owner;
+	}
+
 	public FaoInstitute() {
 	}
 
@@ -340,6 +342,14 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 		this.pdciHistogram = pdciHistogram;
 	}
 
+	public Partner getOwner() {
+		return owner;
+	}
+
+	public void setOwner(Partner owner) {
+		this.owner = owner;
+	}
+
 	public PDCIStatistics getStatisticsPDCI() {
 		if (this.pdciMin == null || this.pdciMax == null || this.pdciAvg == null) {
 			return null;

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -4468,6 +4468,56 @@ databaseChangeLog:
         referencedColumnNames:  id
 
 
+- changeSet:
+      id:                 1539274052727-1
+      author:             vpavlov
+      comment:            partnerId to faoinstitute
+      changes:
+      - addColumn:
+            columns:
+            - column:
+                  name:  partnerId
+                  type:  bigint(20)
+            tableName: faoinstitute
+
+
+- changeSet:
+      id: 1539274052727-2
+      author: vpavlov
+      comment: added foreign key faoinstitute(partnerId)-partner(id)
+      changes:
+      - addForeignKeyConstraint:
+            baseColumnNames: partnerId
+            baseTableName: faoinstitute
+            constraintName: FK_103537ceb0f6f88fee69bbf23
+            deferrable: false
+            initiallyDeferred: false
+            onDelete: NO ACTION
+            onUpdate: NO ACTION
+            referencedColumnNames: id
+            referencedTableName: partner
+
+
+- changeSet:
+      id: 1539274052727-3
+      author: vpavlov
+      comment: Migrate data from partner_wiews to faoinstitute (partnerId)
+      changes:
+      - sql:
+            sql: >-
+                update faoinstitute f
+                    inner join partner_wiews pw on
+                    f.code = pw.wiews
+                    set f.partnerId = pw.partnerId;
+
+- changeSet:
+      id: 1539274052727-4
+      author: vpavlov
+      comment: drop partner_wiews
+      changes:
+      - dropTable:
+            tableName:                     partner_wiews
+
 # ENABLE AFTER SOME TIME
 # - changeSet:
 #     id:                        1537463144763-folder

src/test/java/org/genesys/test/base/AbstractApiTest.java

@@ -17,6 +17,7 @@ package org.genesys.test.base;
 
 import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.documentationConfiguration;
 
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.UUID;
 
@@ -121,7 +122,7 @@ public abstract class AbstractApiTest extends AbstractTest {
 		partner.setActive(isActive);
 		partner.setShortName(shortName);
 		partner.setUuid(uuid);
-		partner.setWiewsCodes(new HashSet<>());
+		partner.setInstitutes(new ArrayList<>());
 		partner.setUrls(new HashSet<>());
 		return partnerRepository.save(partner);
 	}

src/test/java/org/genesys/test/catalog/services/CatalogServiceTest.java

@@ -17,6 +17,7 @@ package org.genesys.test.catalog.services;
 
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
@@ -85,6 +86,12 @@ public abstract class CatalogServiceTest extends AbstractServiceTest {
 	@Autowired
 	protected PartnerRepository partnerRepository;
 
+	@Autowired
+	protected InstituteService instituteService;
+
+	@Autowired
+	protected FaoInstituteRepository instituteRepository;
+
 	@Autowired
 	protected DescriptorListService descriptorListService;
 
@@ -109,18 +116,12 @@ public abstract class CatalogServiceTest extends AbstractServiceTest {
 	@Autowired
 	protected ShortFilterRepository shortFilterRepository;
 
-	@Autowired
-	private InstituteService instituteService;
-
 	@Autowired
 	private AccessionUploader accessionUploader;
 
 	@Autowired
 	protected AccessionRepository accessionRepository;
 
-	@Autowired
-	protected FaoInstituteRepository instituteRepository;
-
 	protected Partner partner;
 	protected Partner partner2;