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add more to external reference controller, service

This commit is contained in:
amentis 2023-10-25 12:42:34 +03:00
parent 079382556f
commit 7df098a010
15 changed files with 417 additions and 685 deletions
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5
dmp-backend/core/src/main/java/eu/eudat/audit/AuditableAction.java
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@ -36,4 +36,9 @@ public class AuditableAction {
public static final EventId Description_Persist = new EventId(6002, "Description_Persist"); public static final EventId Description_Persist = new EventId(6002, "Description_Persist");
public static final EventId Description_Delete = new EventId(6003, "Description_Delete"); public static final EventId Description_Delete = new EventId(6003, "Description_Delete");
public static final EventId External_Reference_Query = new EventId(7000, "External_Reference_Query");
public static final EventId External_Reference_Lookup = new EventId(7001, "External_Reference_Lookup");
public static final EventId External_Reference_Persist = new EventId(7002, "External_Reference_Persist");
public static final EventId External_Reference_Delete = new EventId(7003, "External_Reference_Delete");
} }

2
dmp-backend/core/src/main/java/eu/eudat/data/DmpExternalReferenceEntity.java
View File

@ -8,7 +8,7 @@ import jakarta.persistence.Table;
import java.util.UUID; import java.util.UUID;
@Entity @Entity
@Table(name = "\"ExternalReference\"") @Table(name = "\"DmpExternalReference\"")
public class DmpExternalReferenceEntity { public class DmpExternalReferenceEntity {
@Id @Id

11
dmp-backend/core/src/main/java/eu/eudat/model/ExternalReference.java
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@ -5,6 +5,7 @@ import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.SourceType; import eu.eudat.commons.enums.SourceType;
import java.time.Instant; import java.time.Instant;
import java.util.List;
import java.util.UUID; import java.util.UUID;
public class ExternalReference { public class ExternalReference {
@ -48,6 +49,9 @@ public class ExternalReference {
//private UserInfo createdBy; ToDo //private UserInfo createdBy; ToDo
//public static final String _createdBy = "createdBy"; //public static final String _createdBy = "createdBy";
private List<DmpExternalReference> dmpExternalReferences;
public static final String _dmpExternalReferences = "dmpExternalReferences";
public UUID getId() { public UUID getId() {
return id; return id;
} }
@ -144,4 +148,11 @@ public class ExternalReference {
this.updatedAt = updatedAt; this.updatedAt = updatedAt;
} }
public List<DmpExternalReference> getDmpExternalReferences() {
return dmpExternalReferences;
}
public void setDmpExternalReferences(List<DmpExternalReference> dmpExternalReferences) {
this.dmpExternalReferences = dmpExternalReferences;
}
} }

37
dmp-backend/core/src/main/java/eu/eudat/model/builder/ExternalReferenceBuilder.java
View File

@ -3,9 +3,13 @@ package eu.eudat.model.builder;
import eu.eudat.authorization.AuthorizationFlags; import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.convention.ConventionService; import eu.eudat.convention.ConventionService;
import eu.eudat.data.ExternalReferenceEntity; import eu.eudat.data.ExternalReferenceEntity;
import eu.eudat.model.DmpExternalReference;
import eu.eudat.model.ExternalReference; import eu.eudat.model.ExternalReference;
import eu.eudat.query.DmpExternalReferenceQuery;
import gr.cite.tools.data.builder.BuilderFactory; import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException; import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.fieldset.FieldSet; import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry; import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService; import gr.cite.tools.logging.LoggerService;
@ -16,20 +20,23 @@ import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component; import org.springframework.stereotype.Component;
import java.util.*; import java.util.*;
import java.util.stream.Collectors;
@Component @Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE) @Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class ExternalReferenceBuilder extends BaseBuilder<ExternalReference, ExternalReferenceEntity>{ public class ExternalReferenceBuilder extends BaseBuilder<ExternalReference, ExternalReferenceEntity>{
private final BuilderFactory builderFactory; private final BuilderFactory builderFactory;
private final QueryFactory queryFactory;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None); private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired @Autowired
public ExternalReferenceBuilder( public ExternalReferenceBuilder(
ConventionService conventionService, ConventionService conventionService,
BuilderFactory builderFactory) { BuilderFactory builderFactory, QueryFactory queryFactory) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(ExternalReferenceBuilder.class))); super(conventionService, new LoggerService(LoggerFactory.getLogger(ExternalReferenceBuilder.class)));
this.builderFactory = builderFactory; this.builderFactory = builderFactory;
this.queryFactory = queryFactory;
} }
public ExternalReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) { public ExternalReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
@ -43,7 +50,11 @@ public class ExternalReferenceBuilder extends BaseBuilder<ExternalReference, Ext
this.logger.trace(new DataLogEntry("requested fields", fields)); this.logger.trace(new DataLogEntry("requested fields", fields));
if (fields == null || data == null || fields.isEmpty()) if (fields == null || data == null || fields.isEmpty())
return new ArrayList<>(); return new ArrayList<>();
// FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(ExternalReference._createdBy));
//FieldSet userInfoFields = fields.extractPrefixed(this.asPrefix(ExternalReference._createdBy));
FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asPrefix(ExternalReference._dmpExternalReferences));
Map<UUID, List<DmpExternalReference>> dmpExternalReferenceMap = this.collectDmpExternalReferences(dmpExternalReferencesFields, data);
List<ExternalReference> models = new ArrayList<>(); List<ExternalReference> models = new ArrayList<>();
for (ExternalReferenceEntity d : data) { for (ExternalReferenceEntity d : data) {
@ -60,13 +71,31 @@ public class ExternalReferenceBuilder extends BaseBuilder<ExternalReference, Ext
if (fields.hasField(this.asIndexer(ExternalReference._source))) m.setSource(d.getSource()); if (fields.hasField(this.asIndexer(ExternalReference._source))) m.setSource(d.getSource());
if (fields.hasField(this.asIndexer(ExternalReference._sourceType))) m.setSourceType(d.getSourceType()); if (fields.hasField(this.asIndexer(ExternalReference._sourceType))) m.setSourceType(d.getSourceType());
if (fields.hasField(this.asIndexer(ExternalReference._type))) m.setType(d.getType()); if (fields.hasField(this.asIndexer(ExternalReference._type))) m.setType(d.getType());
// if (!userInfoFields.isEmpty() && d.getCreatedBy() != null){ // if (!userInfoFields.isEmpty() && d.getCreatedBy() != null){
// //Todo // //ToDo
// } // }
if (!dmpExternalReferenceMap.isEmpty() && dmpExternalReferenceMap != null && dmpExternalReferenceMap.containsKey(d.getId())) m.setDmpExternalReferences(dmpExternalReferenceMap.get(d.getId()));
models.add(m); models.add(m);
} }
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0)); this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models; return models;
} }
private Map<UUID, List<DmpExternalReference>> collectDmpExternalReferences(FieldSet fields, List<ExternalReferenceEntity> datas) throws MyApplicationException {
if (fields.isEmpty() || datas.isEmpty()) return null;
this.logger.debug("checking related - {}", DmpExternalReference.class.getSimpleName());
Map<UUID, List<DmpExternalReference>> itemMap = null;
FieldSet clone = new BaseFieldSet(fields.getFields()).ensure(this.asIndexer(DmpExternalReference._externalReference, ExternalReference._id));
DmpExternalReferenceQuery query = this.queryFactory.query(DmpExternalReferenceQuery.class).authorize(this.authorize).referenceIds(datas.stream().map(x -> x.getId()).distinct().collect(Collectors.toList()));
itemMap = this.builderFactory.builder(DmpExternalReferenceBuilder.class).authorize(this.authorize).authorize(this.authorize).asMasterKey(query, clone, x -> x.getExternalReference().getId());
if (!fields.hasField(this.asIndexer(DmpExternalReference._externalReference, ExternalReference._id))) {
itemMap.values().stream().flatMap(List::stream).filter(x -> x != null && x.getExternalReference() != null).map(x -> {
x.getExternalReference().setId(null);
return x;
}).collect(Collectors.toList());
}
return itemMap;
}
} }

4
dmp-backend/core/src/main/java/eu/eudat/model/censorship/ExternalReferenceCensor.java
View File

@ -2,9 +2,7 @@ package eu.eudat.model.censorship;
import eu.eudat.authorization.Permission; import eu.eudat.authorization.Permission;
import eu.eudat.convention.ConventionService; import eu.eudat.convention.ConventionService;
import eu.eudat.model.DmpBlueprint;
import eu.eudat.model.ExternalReference; import eu.eudat.model.ExternalReference;
import eu.eudat.model.censorship.dmpblueprintdefinition.DefinitionCensor;
import gr.cite.commons.web.authz.service.AuthorizationService; import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.censor.CensorFactory; import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.fieldset.FieldSet; import gr.cite.tools.fieldset.FieldSet;
@ -40,6 +38,8 @@ public class ExternalReferenceCensor extends BaseCensor {
return; return;
this.authService.authorizeForce(Permission.BrowseExternalReference); this.authService.authorizeForce(Permission.BrowseExternalReference);
FieldSet dmpExternalReferencesFields = fields.extractPrefixed(this.asIndexerPrefix(ExternalReference._dmpExternalReferences));
this.censorFactory.censor(DmpExternalReferenceCensor.class).censor(dmpExternalReferencesFields, userId);
//ToDo //ToDo
//FieldSet definitionFields = fields.extractPrefixed(this.asIndexerPrefix(ExternalReference._createdBy)); //FieldSet definitionFields = fields.extractPrefixed(this.asIndexerPrefix(ExternalReference._createdBy));
//this.censorFactory.censor(UserInfo.class).censor(definitionFields, userId); //this.censorFactory.censor(UserInfo.class).censor(definitionFields, userId);

8
dmp-backend/core/src/main/java/eu/eudat/query/ExternalReferenceQuery.java
View File

@ -156,7 +156,9 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
predicates.add(inClause); predicates.add(inClause);
} }
if (this.like != null && !this.like.isEmpty()) { if (this.like != null && !this.like.isEmpty()) {
predicates.add(queryContext.CriteriaBuilder.like(queryContext.Root.get(ExternalReferenceEntity._label), this.like)); predicates.add(queryContext.CriteriaBuilder.or(queryContext.CriteriaBuilder.like(queryContext.Root.get(ExternalReferenceEntity._label), this.like),
queryContext.CriteriaBuilder.like(queryContext.Root.get(ExternalReferenceEntity._description), this.like)
));
} }
if (this.isActives != null) { if (this.isActives != null) {
CriteriaBuilder.In<IsActive> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._isActive)); CriteriaBuilder.In<IsActive> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._isActive));
@ -177,7 +179,7 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
predicates.add(inClause); predicates.add(inClause);
} }
if (this.excludedIds != null) { if (this.excludedIds != null) {
CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(DmpBlueprintEntity._id)); CriteriaBuilder.In<UUID> notInClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(ExternalReferenceEntity._id));
for (UUID item : this.excludedIds) for (UUID item : this.excludedIds)
notInClause.value(item); notInClause.value(item);
predicates.add(notInClause.not()); predicates.add(notInClause.not());
@ -205,7 +207,7 @@ public class ExternalReferenceQuery extends QueryBase<ExternalReferenceEntity> {
item.setSource(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._source, String.class)); item.setSource(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._source, String.class));
item.setSourceType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._sourceType, SourceType.class)); item.setSourceType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._sourceType, SourceType.class));
item.setType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._type, ExternalReferencesType.class)); item.setType(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._type, ExternalReferencesType.class));
//item.setCreatedBy(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._createdBy, UUID.class)); item.setCreatedBy(QueryBase.convertSafe(tuple, columns, ExternalReferenceEntity._createdBy, UUID.class));
return item; return item;
} }

171
dmp-backend/web/src/main/java/eu/eudat/controllers/v2/ExternalReferenceController.java Normal file
View File

@ -0,0 +1,171 @@
package eu.eudat.controllers.v2;
import eu.eudat.audit.AuditableAction;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.enums.ExternalReferencesType;
import eu.eudat.controllers.BaseController;
import eu.eudat.data.ExternalReferenceEntity;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.externalreferences.ExternalReferenceService;
import eu.eudat.model.ExternalReference;
import eu.eudat.model.builder.ExternalReferenceBuilder;
import eu.eudat.model.censorship.ExternalReferenceCensor;
import eu.eudat.model.result.QueryResult;
import eu.eudat.models.data.FetcherExternalReference;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.query.ExternalReferenceQuery;
import eu.eudat.query.lookup.ExternalReferenceLookup;
import eu.eudat.types.ApiMessageCode;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.auditing.AuditService;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.exception.MyForbiddenException;
import gr.cite.tools.exception.MyNotFoundException;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.LoggerService;
import gr.cite.tools.logging.MapLogEntry;
import jakarta.transaction.Transactional;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.context.i18n.LocaleContextHolder;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import javax.management.InvalidApplicationException;
import java.util.AbstractMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
@RestController
@RequestMapping(path = {"api/external-references"})
public class ExternalReferenceController extends BaseController {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceController.class));
private final BuilderFactory builderFactory;
private final AuditService auditService;
private final ExternalReferenceService externalReferenceService;
private final CensorFactory censorFactory;
private final QueryFactory queryFactory;
private final MessageSource messageSource;
private final AuthorizationService authorizationService;
@Autowired
public ExternalReferenceController(
ApiContext apiContext,
BuilderFactory builderFactory,
ExternalReferenceService externalReferenceService,
AuditService auditService,
CensorFactory censorFactory,
QueryFactory queryFactory,
MessageSource messageSource, AuthorizationService authorizationService) {
super(apiContext);
this.builderFactory = builderFactory;
this.externalReferenceService = externalReferenceService;
this.auditService = auditService;
this.censorFactory = censorFactory;
this.queryFactory = queryFactory;
this.messageSource = messageSource;
this.authorizationService = authorizationService;
}
@PostMapping("query")
public QueryResult<ExternalReference> query(@RequestBody ExternalReferenceLookup lookup) throws MyApplicationException, MyForbiddenException {
logger.debug("querying {}", ExternalReference.class.getSimpleName());
this.censorFactory.censor(ExternalReferenceCensor.class).censor(lookup.getProject(), null);
ExternalReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrPermission);
List<ExternalReferenceEntity> datas = query.collectAs(lookup.getProject());
List<ExternalReference> models = this.builderFactory.builder(ExternalReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(lookup.getProject(), datas);
long count = (lookup.getMetadata() != null && lookup.getMetadata().getCountAll()) ? query.count() : models.size();
this.auditService.track(AuditableAction.External_Reference_Query, "lookup", lookup);
return new QueryResult(models, count);
}
@GetMapping("{id}")
public ExternalReference get(@PathVariable("id") UUID id, FieldSet fieldSet) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
logger.debug(new MapLogEntry("retrieving" + eu.eudat.model.ExternalReference.class.getSimpleName()).And("id", id).And("fields", fieldSet));
this.censorFactory.censor(ExternalReferenceCensor.class).censor(fieldSet, null);
ExternalReferenceQuery query = this.queryFactory.query(ExternalReferenceQuery.class).authorize(AuthorizationFlags.OwnerOrPermission).ids(id);
ExternalReference model = this.builderFactory.builder(ExternalReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrPermission).build(fieldSet, query.firstAs(fieldSet));
if (model == null)
throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{id, eu.eudat.model.ExternalReference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
this.auditService.track(AuditableAction.External_Reference_Lookup, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("id", id),
new AbstractMap.SimpleEntry<String, Object>("fields", fieldSet)
));
return model;
}
@GetMapping(path = {"search/{externalType}"}, produces = "application/json")
public @ResponseBody ResponseEntity<ResponseItem<List<FetcherExternalReference>>> searchExternalReference(@PathVariable(value = "externalType") int externalType,
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "type", required = false) String type
) throws HugeResultSet, NoURLFound, InvalidApplicationException {
this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
ExternalReferencesType externalReferencesType = ExternalReferencesType.of((short) externalType);
List<FetcherExternalReference> fetcherExternalReferences = this.externalReferenceService.searchExternalReference(externalReferencesType, query, type);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<FetcherExternalReference>>().status(ApiMessageCode.NO_MESSAGE).payload(fetcherExternalReferences));
}
@DeleteMapping("{id}")
@Transactional
public void delete(@PathVariable("id") UUID id) throws MyForbiddenException, InvalidApplicationException {
logger.debug(new MapLogEntry("retrieving" + ExternalReference.class.getSimpleName()).And("id", id));
this.externalReferenceService.deleteAndSave(id);
this.auditService.track(AuditableAction.External_Reference_Delete, "id", id);
}
// @Transactional
// @PostMapping(path = {"persist"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody
// ResponseEntity<ResponseItem<ExternalReference>> createExternalReferecnes(@RequestBody ExternalReference externalReference) throws Exception {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// ExternalReference newExternalReference = this.externalReferencesService.createDataRepo(externalReference);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
// }
// @GetMapping(path = {"{externalType}"}, produces = "application/json")
// public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference2>>> listExternalReferecnes2(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
// @RequestParam(value = "type", required = false) String type
// ) throws HugeResultSet, NoURLFound, InvalidApplicationException {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// List<ExternalReference2> externalReferences = this.externalReferencesService.getExternalReference2(externalType, query, type);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference2>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
// }
//
// @Transactional
// @PostMapping(value = {"{externalType}/persist"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody
// ResponseEntity<ResponseItem<ExternalReference2>> create(@RequestBody ExternalReference2 externalReference) throws Exception {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// ExternalReference2 newExternalReference = this.externalReferencesService.create(externalReference);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference2>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
// }
}

111
dmp-backend/web/src/main/java/eu/eudat/controllers/v2/ExternalReferencesController.java
View File

@ -1,111 +0,0 @@
package eu.eudat.controllers.v2;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.enums.ExternalReferencesType;
import eu.eudat.controllers.BaseController;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.externalreferences.ExternalReferencesService;
import eu.eudat.logic.services.externalreferences.FunderService;
import eu.eudat.logic.services.externalreferences.ProjectService;
import eu.eudat.models.data.ExternalReference;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.types.ApiMessageCode;
import gr.cite.commons.web.authz.service.AuthorizationService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import javax.management.InvalidApplicationException;
import java.util.List;
@RestController
@RequestMapping(path = {"api/external-references"})
public class ExternalReferencesController extends BaseController {
private final FunderService funderService;
private final ExternalReferencesService externalReferencesService;
private final ProjectService projectService;
private final AuthorizationService authorizationService;
@Autowired
public ExternalReferencesController(
ApiContext apiContext,
FunderService funderService,
ExternalReferencesService externalReferencesService,
ProjectService projectService,
AuthorizationService authorizationService) {
super(apiContext);
this.funderService = funderService;
this.externalReferencesService = externalReferencesService;
this.projectService = projectService;
this.authorizationService = authorizationService;
}
// @PostMapping(path = {"funders"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody ResponseEntity<ResponseItem<List<Funder>>> getWithExternal(@RequestBody FunderCriteriaRequest funderCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// List<Funder> dataTable = this.funderService.getCriteriaWithExternal(funderCriteria);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Funder>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
// }
//
// @PostMapping(path = {"projects"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody
// ResponseEntity<ResponseItem<List<Project>>> getWithExternal(@RequestBody ProjectCriteriaRequest projectCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// List<Project> dataTable = this.projectService.getCriteriaWithExternal(projectCriteria);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Project>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
// }
@GetMapping(path = {"{externalType}"}, produces = "application/json")
public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference>>> listExternalReferecnes(@PathVariable(value = "externalType") int externalType,
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "type", required = false) String type
) throws HugeResultSet, NoURLFound, InvalidApplicationException {
this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
ExternalReferencesType externalReferencesType = ExternalReferencesType.of((short) externalType);
List<ExternalReference> externalReferences = this.externalReferencesService.getExternalReference(externalReferencesType, query, type);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
}
// @Transactional
// @PostMapping(path = {"data-repo/persist"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody
// ResponseEntity<ResponseItem<ExternalReference>> createExternalReferecnes(@RequestBody ExternalReference externalReference) throws Exception {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// ExternalReference newExternalReference = this.externalReferencesService.createDataRepo(externalReference);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
// }
// @GetMapping(path = {"{externalType}"}, produces = "application/json")
// public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference2>>> listExternalReferecnes2(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
// @RequestParam(value = "type", required = false) String type
// ) throws HugeResultSet, NoURLFound, InvalidApplicationException {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// List<ExternalReference2> externalReferences = this.externalReferencesService.getExternalReference2(externalType, query, type);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference2>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
// }
//
// @Transactional
// @PostMapping(value = {"{externalType}/persist"}, consumes = "application/json", produces = "application/json")
// public @ResponseBody
// ResponseEntity<ResponseItem<ExternalReference2>> create(@RequestBody ExternalReference2 externalReference) throws Exception {
// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
//
// ExternalReference2 newExternalReference = this.externalReferencesService.create(externalReference);
// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference2>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
// }
}

163
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package eu.eudat.logic.services.externalreferences;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.enums.ExternalReferencesType;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.dao.criteria.DataRepositoryCriteria;
import eu.eudat.data.dao.criteria.ExternalDatasetCriteria;
import eu.eudat.data.dao.criteria.RegistryCriteria;
import eu.eudat.data.dao.criteria.ServiceCriteria;
import eu.eudat.data.old.DataRepository;
import eu.eudat.data.old.ExternalDataset;
import eu.eudat.data.old.Registry;
import eu.eudat.data.old.Service;
import eu.eudat.logic.builders.model.criteria.ExternalDatasetCriteriaBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.model.deleter.ExternalReferenceDeleter;
import eu.eudat.models.data.FetcherExternalReference;
import eu.eudat.queryable.QueryableList;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.deleter.DeleterFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyForbiddenException;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager;
import org.slf4j.LoggerFactory;
import org.springframework.context.MessageSource;
import javax.management.InvalidApplicationException;
import java.util.*;
import java.util.stream.Collectors;
@org.springframework.stereotype.Service
public class ExternalReferenceService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(ExternalReferenceService.class));
private final ApiContext apiContext;
private final UserScope userScope;
private final RemoteFetcher remoteFetcher;
private final EntityManager entityManager;
private final AuthorizationService authorizationService;
private final DeleterFactory deleterFactory;
private final BuilderFactory builderFactory;
private final ConventionService conventionService;
private final MessageSource messageSource;
private final QueryFactory queryFactory;
public ExternalReferenceService(ApiContext apiContext,
UserScope userScope,
RemoteFetcher remoteFetcher,
EntityManager entityManager,
AuthorizationService authorizationService,
DeleterFactory deleterFactory,
BuilderFactory builderFactory,
ConventionService conventionService,
MessageSource messageSource,
QueryFactory queryFactory) {
this.apiContext = apiContext;
this.userScope = userScope;
this.remoteFetcher = remoteFetcher;
this.entityManager = entityManager;
this.authorizationService = authorizationService;
this.deleterFactory = deleterFactory;
this.builderFactory = builderFactory;
this.conventionService = conventionService;
this.messageSource = messageSource;
this.queryFactory = queryFactory;
}
public void deleteAndSave(UUID id) throws MyForbiddenException, InvalidApplicationException {
logger.debug("deleting : {}", id);
this.authorizationService.authorizeForce(Permission.DeleteExternalReference);
this.deleterFactory.deleter(ExternalReferenceDeleter.class).deleteAndSaveByIds(List.of(id));
}
// external references:
// taxonomies,
// licenses,
// publications,
// journals,
// pubRepositories,
// dataRepositories
// registries,
// services
public List<FetcherExternalReference> searchExternalReference(ExternalReferencesType externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
List<Map<String, String>> remoteRepos = null;
if (externalType.equals(ExternalReferencesType.Datasets)){
remoteRepos = remoteFetcher.getDatasets(externalUrlCriteria, type);
}else {
remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
}
List<FetcherExternalReference> list = this.fetchFromDb(externalType, query, type, remoteRepos);
list.addAll(remoteRepos.stream().map(FetcherExternalReference::fromRemoteModel).toList());
list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList());
list.sort(Comparator.comparing(FetcherExternalReference::getName));
return list;
}
private List<FetcherExternalReference> fetchFromDb(ExternalReferencesType externalType, String query, String type, List<Map<String, String>> remoteRepos) throws InvalidApplicationException {
List<FetcherExternalReference> list = new LinkedList<>();
switch (externalType) {
case DataRepositories:
case PubRepositories:
case Journals: {
DataRepositoryCriteria criteria = new DataRepositoryCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<DataRepository> dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList();
list = dataRepositoryList.stream().map(item -> new FetcherExternalReference().fromDataRepository(item)).collect(Collectors.toList());
}
}
case Registries: {
RegistryCriteria criteria = new RegistryCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<Registry> registryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao().getWithCriteria(criteria)).toList();
list = registryList.stream().map(item -> new FetcherExternalReference().fromRegistry(item)).collect(Collectors.toList());
}
}
case Services:
{
ServiceCriteria criteria = new ServiceCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<Service> serviceList = (this.apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().getWithCriteria(criteria)).toList();
list = serviceList.stream().map(item -> new FetcherExternalReference().fromService(item)).collect(Collectors.toList());
}
}
case Datasets:{
ExternalDatasetCriteria criteria = apiContext.getOperationsContext().getBuilderFactory().getBuilder(ExternalDatasetCriteriaBuilder.class).like(query).build();
criteria.setCreationUserId(this.userScope.getUserId());
QueryableList<ExternalDataset> items = apiContext.getOperationsContext().getDatabaseRepository().getExternalDatasetDao().getWithCriteria(criteria);
list = items.select(item -> new FetcherExternalReference().fromDataset(item));
}
case Taxonomies:
case Publications:
case Licenses:
break;
}
return list;
}
}

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dmp-backend/web/src/main/java/eu/eudat/logic/services/externalreferences/ExternalReferencesService.java
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package eu.eudat.logic.services.externalreferences;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.commons.enums.ExternalReferencesType;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.data.dao.criteria.DataRepositoryCriteria;
import eu.eudat.data.dao.criteria.ExternalDatasetCriteria;
import eu.eudat.data.dao.criteria.RegistryCriteria;
import eu.eudat.data.dao.criteria.ServiceCriteria;
import eu.eudat.data.old.DataRepository;
import eu.eudat.data.old.ExternalDataset;
import eu.eudat.data.old.Registry;
import eu.eudat.data.old.Service;
import eu.eudat.logic.builders.model.criteria.ExternalDatasetCriteriaBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.ExternalReference;
import eu.eudat.queryable.QueryableList;
import javax.management.InvalidApplicationException;
import java.util.Comparator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@org.springframework.stereotype.Service
public class ExternalReferencesService {
private final ApiContext apiContext;
private final UserScope userScope;
private final RemoteFetcher remoteFetcher;
public ExternalReferencesService(ApiContext apiContext, UserScope userScope, RemoteFetcher remoteFetcher) {
this.apiContext = apiContext;
this.userScope = userScope;
this.remoteFetcher = remoteFetcher;
}
// external references:
// taxonomies,
// licenses,
// publications,
// journals,
// pubRepositories,
// dataRepositories
// public ExternalReference createDataRepo(ExternalReference externalReference) throws Exception {
// // only dataRepositories, pubRepositories, journals
// DataRepository dataRepository = externalReference.toDataModel();
// dataRepository.getCreationUser().setId(this.userScope.getUserId());
//
// dataRepository = apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().createOrUpdate(dataRepository);
// return new ExternalReference().fromDataModel(dataRepository);
// }
// public List<ExternalReference> getExternalReference(String externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
// ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
// List<Map<String, String>> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
//
// DataRepositoryCriteria criteria = new DataRepositoryCriteria();
// if (!query.isEmpty()) criteria.setLike(query);
//
// List<ExternalReference> list = new LinkedList<>();
// if((externalType.equals("dataRepositories") || externalType.equals("pubRepositories") || externalType.equals("journals"))){
// criteria.setCreationUserId(this.userScope.getUserId());
// if (type.equals("")) {
// List<DataRepository> dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList();
// list = dataRepositoryList.stream().map(item -> new ExternalReference().fromDataModel(item)).collect(Collectors.toList());
// }
// }
//
// ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
// list.addAll(remoteRepos.stream().map(item -> mapper.convertValue(item, ExternalReference.class)).collect(Collectors.toList()));
// list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList());
// return list;
// }
// external references2:
// registries,
// services
// public ExternalReference2 create(ExternalReference2 externalReference) throws Exception {
// if (externalReference.getLabel() == null || externalReference.getAbbreviation() == null || externalReference.getUri() == null) {
// throw new Exception("Missing mandatory entity.");
// }
//
// ExternalReference2 newExternalReference = null;
// if(externalReference.getExternalType().equals("registries")){
// Registry registry = externalReference.toDataModelRegistry();
// registry.getCreationUser().setId(this.userScope.getUserId());
// registry = apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao().createOrUpdate(registry);
// newExternalReference = new ExternalReference2().fromDataModel(registry);
// } else if (externalReference.getExternalType().equals("services")) {
// Service service = externalReference.toDataModelService();
// service.getCreationUser().setId(this.userScope.getUserId());
// service = apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().createOrUpdate(service);
// newExternalReference = new ExternalReference2().fromDataModel(service);
// }
//
// return newExternalReference;
// }
//
//
// public List<ExternalReference2> getExternalReference2(String externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
// ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
// List<Map<String, String>> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType,externalUrlCriteria, type);
//
// List<ExternalReference2> list = new LinkedList<>();
//
// if (externalType.equals("registries")){
// RegistryCriteria criteria = new RegistryCriteria();
//
// if (!query.isEmpty()) criteria.setLike(query);
// criteria.setCreationUserId(this.userScope.getUserId());
//
// if (type.equals("")) {
// List<Registry> registryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao().getWithCriteria(criteria)).toList();
// list = registryList.stream().map(item -> new ExternalReference2().fromDataModel(item)).collect(Collectors.toList());
// }
// } else if (externalType.equals("services")) {
// ServiceCriteria criteria = new ServiceCriteria();
//
// if (!query.isEmpty()) criteria.setLike(query);
// criteria.setCreationUserId(this.userScope.getUserId());
//
// if (type.equals("")) {
// List<Service> serviceList = (this.apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().getWithCriteria(criteria)).toList();
// list = serviceList.stream().map(item -> new ExternalReference2().fromDataModel(item)).collect(Collectors.toList());
// }
// }
//
// ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
// list.addAll(remoteRepos.stream().map(item -> mapper.convertValue(item, ExternalReference2.class)).collect(Collectors.toList()));
//
// return list;
// }
public List<ExternalReference> getExternalReference(ExternalReferencesType externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
List<Map<String, String>> remoteRepos = null;
if (externalType.equals(ExternalReferencesType.Datasets)){
remoteRepos = remoteFetcher.getDatasets(externalUrlCriteria, type);
}else {
remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
}
List<ExternalReference> list = this.fetchFromDb(externalType, query, type, remoteRepos);
list.addAll(remoteRepos.stream().map(ExternalReference::fromRemoteModel).toList());
list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList());
list.sort(Comparator.comparing(ExternalReference::getName));
return list;
}
private List<ExternalReference> fetchFromDb(ExternalReferencesType externalType, String query, String type, List<Map<String, String>> remoteRepos) throws InvalidApplicationException {
List<ExternalReference> list = new LinkedList<>();
switch (externalType) {
case DataRepositories:
case PubRepositories:
case Journals: {
DataRepositoryCriteria criteria = new DataRepositoryCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<DataRepository> dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList();
list = dataRepositoryList.stream().map(item -> new ExternalReference().fromDataRepository(item)).collect(Collectors.toList());
}
}
case Registries: {
RegistryCriteria criteria = new RegistryCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<Registry> registryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao().getWithCriteria(criteria)).toList();
list = registryList.stream().map(item -> new ExternalReference().fromRegistry(item)).collect(Collectors.toList());
}
}
case Services:
{
ServiceCriteria criteria = new ServiceCriteria();
if (!query.isEmpty()) criteria.setLike(query);
criteria.setCreationUserId(this.userScope.getUserId());
if (type.equals("")) {
List<Service> serviceList = (this.apiContext.getOperationsContext().getDatabaseRepository().getServiceDao().getWithCriteria(criteria)).toList();
list = serviceList.stream().map(item -> new ExternalReference().fromService(item)).collect(Collectors.toList());
}
}
case Datasets:{
ExternalDatasetCriteria criteria = apiContext.getOperationsContext().getBuilderFactory().getBuilder(ExternalDatasetCriteriaBuilder.class).like(query).build();
criteria.setCreationUserId(this.userScope.getUserId());
QueryableList<ExternalDataset> items = apiContext.getOperationsContext().getDatabaseRepository().getExternalDatasetDao().getWithCriteria(criteria);
list = items.select(item -> new ExternalReference().fromDataset(item));
}
case Taxonomies:
case Publications:
case Licenses:
break;
}
return list;
}
}

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dmp-backend/web/src/main/java/eu/eudat/logic/services/externalreferences/FunderService.java
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package eu.eudat.logic.services.externalreferences;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.data.old.UserInfo;
import eu.eudat.data.query.items.item.funder.FunderCriteriaRequest;
import eu.eudat.logic.builders.model.models.FunderBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.utilities.helpers.ListHelper;
import eu.eudat.models.data.external.ExternalSourcesItemModel;
import eu.eudat.models.data.external.FundersExternalSourcesModel;
import eu.eudat.models.data.funder.Funder;
import eu.eudat.queryable.QueryableList;
import org.springframework.stereotype.Service;
import javax.management.InvalidApplicationException;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@Service
public class FunderService {
private ApiContext apiContext;
private RemoteFetcher remoteFetcher;
private ListHelper listHelper;
private final UserScope userScope;
public FunderService(ApiContext apiContext, RemoteFetcher remoteFetcher, ListHelper listHelper, UserScope userScope) {
this.apiContext = apiContext;
this.remoteFetcher = remoteFetcher;
this.listHelper = listHelper;
this.userScope = userScope;
}
public List<Funder> getCriteriaWithExternal(FunderCriteriaRequest funderCriteria) throws HugeResultSet, NoURLFound, InvalidApplicationException {
UserInfo userInfo = new UserInfo();
userInfo.setId(this.userScope.getUserId());
funderCriteria.getCriteria().setReference("dmp:");
QueryableList<eu.eudat.data.old.Funder> items = apiContext.getOperationsContext().getDatabaseRepository().getFunderDao().getWithCritetia(funderCriteria.getCriteria());
QueryableList<eu.eudat.data.old.Funder> authItems = apiContext.getOperationsContext().getDatabaseRepository().getFunderDao().getAuthenticated(items, userInfo);
List<Funder> funders = authItems.select(item -> new Funder().fromDataModel(item));
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(funderCriteria.getCriteria().getLike());
List<Map<String, String>> remoteRepos = remoteFetcher.getFunders(externalUrlCriteria);
FundersExternalSourcesModel fundersExternalSourcesModel = new FundersExternalSourcesModel().fromExternalItem(remoteRepos);
for (ExternalSourcesItemModel externalListingItem : fundersExternalSourcesModel) {
Funder funder = apiContext.getOperationsContext().getBuilderFactory().getBuilder(FunderBuilder.class)
.reference(externalListingItem.getRemoteId()).label(externalListingItem.getName())
.status(eu.eudat.data.old.Funder.Status.fromInteger(0))
.key(externalListingItem.getKey())
.source(externalListingItem.getTag())
.build();
if (externalListingItem.getSource() != null) {
funder.setSource(externalListingItem.getSource());
} else {
funder.setSource(externalListingItem.getTag());
}
funders.add(funder);
}
funders.sort(Comparator.comparing(Funder::getLabel));
funders = funders.stream().filter(listHelper.distinctByKey(Funder::getLabel)).collect(Collectors.toList());
return funders;
}
}

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dmp-backend/web/src/main/java/eu/eudat/logic/services/externalreferences/ProjectService.java
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package eu.eudat.logic.services.externalreferences;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.data.query.items.item.project.ProjectCriteriaRequest;
import eu.eudat.logic.builders.model.models.ProjectBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.utilities.helpers.ListHelper;
import eu.eudat.models.data.external.ExternalSourcesItemModel;
import eu.eudat.models.data.external.ProjectsExternalSourcesModel;
import eu.eudat.models.data.project.Project;
import eu.eudat.queryable.QueryableList;
import org.springframework.stereotype.Service;
import javax.management.InvalidApplicationException;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@Service
public class ProjectService {
private ApiContext apiContext;
private RemoteFetcher remoteFetcher;
private ListHelper listHelper;
private final UserScope userScope;
public ProjectService(ApiContext apiContext, ListHelper listHelper, UserScope userScope) {
this.apiContext = apiContext;
this.remoteFetcher = apiContext.getOperationsContext().getRemoteFetcher();
this.listHelper = listHelper;
this.userScope = userScope;
}
public List<Project> getCriteriaWithExternal(ProjectCriteriaRequest projectCriteria) throws HugeResultSet, NoURLFound, InvalidApplicationException {
eu.eudat.data.old.UserInfo userInfo = new eu.eudat.data.old.UserInfo();
userInfo.setId(this.userScope.getUserId());
projectCriteria.getCriteria().setReference("dmp:");
QueryableList<eu.eudat.data.old.Project> items = apiContext.getOperationsContext().getDatabaseRepository().getProjectDao().getWithCritetia(projectCriteria.getCriteria());
QueryableList<eu.eudat.data.old.Project> authItems = apiContext.getOperationsContext().getDatabaseRepository().getProjectDao().getAuthenticated(items, userInfo);
List<Project> projects = authItems.select(item -> new Project().fromDataModel(item));
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(projectCriteria.getCriteria().getLike());
List<Map<String, String>> remoteRepos = remoteFetcher.getProjects(externalUrlCriteria);
ProjectsExternalSourcesModel projectsExternalSourcesModel = new ProjectsExternalSourcesModel().fromExternalItem(remoteRepos);
for (ExternalSourcesItemModel externalListingItem : projectsExternalSourcesModel) {
Project project = apiContext.getOperationsContext().getBuilderFactory().getBuilder(ProjectBuilder.class)
.reference(externalListingItem.getRemoteId()).label(externalListingItem.getName())
.description(externalListingItem.getDescription()).uri(externalListingItem.getUri())
.abbreviation(externalListingItem.getAbbreviation()).status(eu.eudat.data.old.Project.Status.fromInteger(0))
.key(externalListingItem.getKey())
.source(externalListingItem.getTag())
.build();
projects.add(project);
}
projects.sort(Comparator.comparing(Project::getLabel));
projects = projects.stream().filter(listHelper.distinctByKey(Project::getLabel)).collect(Collectors.toList());
return projects;
}
}

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dmp-backend/web/src/main/java/eu/eudat/models/data/ExternalReference2.java
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@ -1,188 +0,0 @@
package eu.eudat.models.data;
import eu.eudat.data.old.Registry;
import eu.eudat.data.old.Service;
import eu.eudat.data.old.UserInfo;
import java.util.Date;
import java.util.UUID;
public class ExternalReference2 {
private UUID id;
private String label;
private String name;
private String pid;
private String abbreviation;
private String uri;
private Date created;
private Date modified;
private String reference;
private String tag;
private String source;
private String externalType;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getPid() {
return pid;
}
public void setPid(String pid) {
this.pid = pid;
}
public String getAbbreviation() {
return abbreviation;
}
public void setAbbreviation(String abbreviation) {
this.abbreviation = abbreviation;
}
public String getUri() {
return uri;
}
public void setUri(String uri) {
this.uri = uri;
}
public Date getCreated() {
return created;
}
public void setCreated(Date created) {
this.created = created;
}
public Date getModified() {
return modified;
}
public void setModified(Date modified) {
this.modified = modified;
}
public String getReference() {
return reference;
}
public void setReference(String reference) {
this.reference = reference;
}
public String getTag() {
return tag;
}
public void setTag(String tag) {
this.tag = tag;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public String getExternalType() {return externalType;}
public void setExternalType(String externalType) {this.externalType = externalType;}
public ExternalReference2 fromDataModel(Service entity) {
this.abbreviation = entity.getAbbreviation();
this.created = entity.getCreated();
this.id = entity.getId();
this.label = entity.getLabel();
this.name = entity.getLabel();
this.modified = entity.getModified();
this.uri = entity.getUri();
String source = entity.getReference().substring(0, entity.getReference().indexOf(":"));
if (source.equals("dmp")) {
this.source = "Internal";
} else {
this.source = source;
}
this.externalType = "services";
return this;
}
public ExternalReference2 fromDataModel(Registry entity) {
this.id = entity.getId();
this.abbreviation = entity.getAbbreviation();
this.created = entity.getCreated();
this.label = entity.getLabel();
this.name = entity.getLabel();
this.modified = entity.getModified();
this.uri = entity.getUri();
String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":"));
if (source1.equals("dmp")) {
this.source = "Internal";
} else {
this.source = source1;
}
this.reference = entity.getReference();
this.externalType = "registries";
return this;
}
public Service toDataModelService() throws Exception {
Service service = new Service();
service.setId(this.id != null ? this.id : UUID.randomUUID());
service.setAbbreviation(this.abbreviation);
service.setCreated(this.created != null ? this.created : new Date());
service.setLabel(this.label != null ? this.label : this.name);
service.setModified(new Date());
service.setUri(this.uri);
if (this.source == null) this.source = "dmp";
if (this.reference == null) this.reference = service.getId().toString();
if (this.source.equals(this.reference.substring(0, this.source.length()))) {
service.setReference(this.reference);
} else {
service.setReference(this.source + ":" + this.reference);
}
service.setModified(new Date());
service.setStatus((short) 0);
service.setCreationUser(new UserInfo());
return service;
}
public Registry toDataModelRegistry() throws Exception {
Registry registry = new Registry();
registry.setAbbreviation(this.abbreviation);
registry.setCreated(this.created != null ? this.created : new Date());
registry.setId(this.id != null ? this.id : UUID.randomUUID());
registry.setLabel(this.label != null ? this.label : this.name);
registry.setUri(this.uri);
registry.setModified(new Date());
if (this.source == null) this.source = "dmp";
if (this.source.equals(registry.getId().toString().substring(0, this.source.length()))) {
registry.setReference(registry.getId().toString());
} else {
registry.setReference(this.source + ":" + registry.getId());
}
registry.setStatus((short)0);
registry.setCreationUser(new UserInfo());
return registry;
}
public String getHint() {
return null;
}
}

50
dmp-backend/web/src/main/java/eu/eudat/models/data/ExternalReference.java → dmp-backend/web/src/main/java/eu/eudat/models/data/FetcherExternalReference.java
View File

@ -4,7 +4,7 @@ import eu.eudat.data.old.*;
import java.util.Map; import java.util.Map;
public class ExternalReference { public class FetcherExternalReference {
private String id; private String id;
private String name; private String name;
@ -133,28 +133,28 @@ public class ExternalReference {
this.tag = tag; this.tag = tag;
} }
public static ExternalReference fromRemoteModel(Map<String, String> data) { public static FetcherExternalReference fromRemoteModel(Map<String, String> data) {
ExternalReference externalReference = new ExternalReference(); FetcherExternalReference fetcherExternalReference = new FetcherExternalReference();
if (data == null) return externalReference; if (data == null) return fetcherExternalReference;
externalReference.setId(data.getOrDefault("id", null)); fetcherExternalReference.setId(data.getOrDefault("id", null));
externalReference.setName(data.getOrDefault("name", null)); fetcherExternalReference.setName(data.getOrDefault("name", null));
externalReference.setPid(data.getOrDefault("pid", null)); fetcherExternalReference.setPid(data.getOrDefault("pid", null));
externalReference.setPidTypeField(data.getOrDefault("pidTypeField", null)); fetcherExternalReference.setPidTypeField(data.getOrDefault("pidTypeField", null));
externalReference.setUri(data.getOrDefault("uri", null)); fetcherExternalReference.setUri(data.getOrDefault("uri", null));
externalReference.setDescription(data.getOrDefault("description", null)); fetcherExternalReference.setDescription(data.getOrDefault("description", null));
externalReference.setSource(data.getOrDefault("source", null)); fetcherExternalReference.setSource(data.getOrDefault("source", null));
externalReference.setCount(data.getOrDefault("count", null)); fetcherExternalReference.setCount(data.getOrDefault("count", null));
externalReference.setPath(data.getOrDefault("path", null)); fetcherExternalReference.setPath(data.getOrDefault("path", null));
externalReference.setHost(data.getOrDefault("host", null)); fetcherExternalReference.setHost(data.getOrDefault("host", null));
externalReference.setTypes(data.getOrDefault("types", null)); fetcherExternalReference.setTypes(data.getOrDefault("types", null));
externalReference.setFirstName(data.getOrDefault("firstName", null)); fetcherExternalReference.setFirstName(data.getOrDefault("firstName", null));
externalReference.setLastName(data.getOrDefault("lastName", null)); fetcherExternalReference.setLastName(data.getOrDefault("lastName", null));
externalReference.setTag(data.getOrDefault("tag", null)); fetcherExternalReference.setTag(data.getOrDefault("tag", null));
return externalReference; return fetcherExternalReference;
} }
public ExternalReference fromDataRepository(DataRepository entity) { public FetcherExternalReference fromDataRepository(DataRepository entity) {
// this.setAbbreviation(entity.getAbbreviation()); // this.setAbbreviation(entity.getAbbreviation());
this.setName(entity.getLabel()); this.setName(entity.getLabel());
this.setUri(entity.getUri()); this.setUri(entity.getUri());
@ -169,7 +169,7 @@ public class ExternalReference {
return this; return this;
} }
public ExternalReference fromRegistry(Registry entity){ public FetcherExternalReference fromRegistry(Registry entity){
this.id = entity.getId().toString(); this.id = entity.getId().toString();
// this.abbreviation = entity.getAbbreviation(); // this.abbreviation = entity.getAbbreviation();
// this.created = entity.getCreated(); // this.created = entity.getCreated();
@ -186,7 +186,7 @@ public class ExternalReference {
// this.reference = entity.getReference(); // this.reference = entity.getReference();
return this; return this;
} }
public ExternalReference fromService(Service entity) { public FetcherExternalReference fromService(Service entity) {
// this.abbreviation = entity.getAbbreviation(); // this.abbreviation = entity.getAbbreviation();
// this.created = entity.getCreated(); // this.created = entity.getCreated();
this.id = entity.getId().toString(); this.id = entity.getId().toString();
@ -203,7 +203,7 @@ public class ExternalReference {
return this; return this;
} }
public ExternalReference fromResearcher(Researcher entity){ public FetcherExternalReference fromResearcher(Researcher entity){
this.id = entity.getId().toString(); this.id = entity.getId().toString();
this.name = entity.getLabel(); this.name = entity.getLabel();
String refParts[] = entity.getReference().split(":"); String refParts[] = entity.getReference().split(":");
@ -216,7 +216,7 @@ public class ExternalReference {
return this; return this;
} }
public ExternalReference fromOrganisation(Organisation entity){ public FetcherExternalReference fromOrganisation(Organisation entity){
this.id = entity.getId().toString(); this.id = entity.getId().toString();
this.name = entity.getLabel(); this.name = entity.getLabel();
String refParts[] = entity.getReference().split(":"); String refParts[] = entity.getReference().split(":");
@ -229,7 +229,7 @@ public class ExternalReference {
return this; return this;
} }
public ExternalReference fromDataset(ExternalDataset entity){ public FetcherExternalReference fromDataset(ExternalDataset entity){
this.id = entity.getId().toString(); this.id = entity.getId().toString();
this.name = entity.getLabel(); this.name = entity.getLabel();
String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":")); String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":"));

2
dmp-frontend/src/app/core/services/external-sources/external-sources.service.ts
View File

@ -60,7 +60,7 @@ export class ExternalSourcesService {
} }
public listExternal(externalType: ExternalReferencesType, query: string, type: string): Observable<ExternalReference[]> { public listExternal(externalType: ExternalReferencesType, query: string, type: string): Observable<ExternalReference[]> {
const url = this.configurationService.server + `external-references/${externalType}`; const url = this.configurationService.server + `external-references/search/${externalType}`;
const options = { params: { query: query, type: type } }; const options = { params: { query: query, type: type } };
return this.http.get<ExternalReference[]>(url, options); return this.http.get<ExternalReference[]>(url, options);