changes for remote fetcher
This commit is contained in:
parent
2a4e61f08f
commit
0b3178177a
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@ -0,0 +1,37 @@
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package eu.eudat.commons.enums;
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import java.util.Map;
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public enum ExternalReferencesType {
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Taxonomies((short) 0),
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Licenses((short) 1),
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Publications((short) 2),
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Journals((short) 3),
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PubRepositories((short) 4),
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DataRepositories((short) 5),
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Registries((short) 6),
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Services((short) 7),
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Project((short) 8),
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Founder((short) 8),
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Datasets((short) 9),
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Organizations((short) 10),
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Grants((short) 11),
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Prefillings((short) 12),
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Validators((short) 13),
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Researcher((short) 14);
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private final Short value;
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ExternalReferencesType(Short value) {
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this.value = value;
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}
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public Short getValue() {
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return value;
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}
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private static final Map<Short, IsActive> map = EnumUtils.getEnumValueMap(IsActive.class);
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public static IsActive of(Short i) {
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return map.get(i);
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}
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}
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@ -38,6 +38,8 @@ import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.MessageSource;
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import org.springframework.context.i18n.LocaleContextHolder;
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import org.springframework.stereotype.Component;
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import org.springframework.stereotype.Service;
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import javax.management.InvalidApplicationException;
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import java.time.Instant;
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@ -46,6 +48,7 @@ import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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@Service
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public class EntityDoiServiceImpl implements EntityDoiService {
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private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(EntityDoiServiceImpl.class));
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@ -1,6 +1,7 @@
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package eu.eudat.controllers.v2;
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import eu.eudat.authorization.Permission;
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import eu.eudat.commons.enums.ExternalReferencesType;
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import eu.eudat.controllers.BaseController;
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import eu.eudat.data.query.items.item.funder.FunderCriteriaRequest;
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import eu.eudat.data.query.items.item.project.ProjectCriteriaRequest;
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@ -50,27 +51,28 @@ public class ExternalReferencesController extends BaseController {
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this.authorizationService = authorizationService;
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}
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@PostMapping(path = {"funders"}, consumes = "application/json", produces = "application/json")
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public @ResponseBody ResponseEntity<ResponseItem<List<Funder>>> getWithExternal(@RequestBody FunderCriteriaRequest funderCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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List<Funder> dataTable = this.funderService.getCriteriaWithExternal(funderCriteria);
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Funder>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
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}
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@PostMapping(path = {"projects"}, consumes = "application/json", produces = "application/json")
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public @ResponseBody
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ResponseEntity<ResponseItem<List<Project>>> getWithExternal(@RequestBody ProjectCriteriaRequest projectCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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List<Project> dataTable = this.projectService.getCriteriaWithExternal(projectCriteria);
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Project>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
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}
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// @PostMapping(path = {"funders"}, consumes = "application/json", produces = "application/json")
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// public @ResponseBody ResponseEntity<ResponseItem<List<Funder>>> getWithExternal(@RequestBody FunderCriteriaRequest funderCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
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// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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//
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// List<Funder> dataTable = this.funderService.getCriteriaWithExternal(funderCriteria);
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// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Funder>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
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// }
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//
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// @PostMapping(path = {"projects"}, consumes = "application/json", produces = "application/json")
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// public @ResponseBody
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// ResponseEntity<ResponseItem<List<Project>>> getWithExternal(@RequestBody ProjectCriteriaRequest projectCriteria) throws NoURLFound, InstantiationException, HugeResultSet, IllegalAccessException, InvalidApplicationException {
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// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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//
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// List<Project> dataTable = this.projectService.getCriteriaWithExternal(projectCriteria);
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// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Project>>().payload(dataTable).status(ApiMessageCode.NO_MESSAGE));
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// }
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@GetMapping(path = {"data-repo/{externalType}"}, produces = "application/json")
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public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference>>> listExternalReferecnes(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
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public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference>>> listExternalReferecnes(@RequestParam(value = "externalType") ExternalReferencesType externalType,
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@RequestParam(value = "query", required = false) String query,
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@RequestParam(value = "type", required = false) String type
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) throws HugeResultSet, NoURLFound, InvalidApplicationException {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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@ -79,37 +81,37 @@ public class ExternalReferencesController extends BaseController {
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
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}
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@Transactional
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@PostMapping(path = {"data-repo/persist"}, consumes = "application/json", produces = "application/json")
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public @ResponseBody
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ResponseEntity<ResponseItem<ExternalReference>> createExternalReferecnes(@RequestBody ExternalReference externalReference) throws Exception {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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ExternalReference newExternalReference = this.externalReferencesService.createDataRepo(externalReference);
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
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}
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// @Transactional
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// @PostMapping(path = {"data-repo/persist"}, consumes = "application/json", produces = "application/json")
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// public @ResponseBody
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// ResponseEntity<ResponseItem<ExternalReference>> createExternalReferecnes(@RequestBody ExternalReference externalReference) throws Exception {
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// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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//
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// ExternalReference newExternalReference = this.externalReferencesService.createDataRepo(externalReference);
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// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
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// }
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@GetMapping(path = {"{externalType}"}, produces = "application/json")
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public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference2>>> listExternalReferecnes2(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
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@RequestParam(value = "type", required = false) String type
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) throws HugeResultSet, NoURLFound, InvalidApplicationException {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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List<ExternalReference2> externalReferences = this.externalReferencesService.getExternalReference2(externalType, query, type);
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference2>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
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}
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@Transactional
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@PostMapping(value = {"{externalType}/persist"}, consumes = "application/json", produces = "application/json")
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public @ResponseBody
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ResponseEntity<ResponseItem<ExternalReference2>> create(@RequestBody ExternalReference2 externalReference) throws Exception {
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this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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ExternalReference2 newExternalReference = this.externalReferencesService.create(externalReference);
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return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference2>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
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}
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// @GetMapping(path = {"{externalType}"}, produces = "application/json")
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// public @ResponseBody ResponseEntity<ResponseItem<List<ExternalReference2>>> listExternalReferecnes2(@RequestParam(value = "externalType") String externalType, @RequestParam(value = "query", required = false) String query,
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// @RequestParam(value = "type", required = false) String type
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// ) throws HugeResultSet, NoURLFound, InvalidApplicationException {
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// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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//
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// List<ExternalReference2> externalReferences = this.externalReferencesService.getExternalReference2(externalType, query, type);
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// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<ExternalReference2>>().status(ApiMessageCode.NO_MESSAGE).payload(externalReferences));
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// }
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//
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// @Transactional
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// @PostMapping(value = {"{externalType}/persist"}, consumes = "application/json", produces = "application/json")
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// public @ResponseBody
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// ResponseEntity<ResponseItem<ExternalReference2>> create(@RequestBody ExternalReference2 externalReference) throws Exception {
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// this.authorizationService.authorizeForce(Permission.AuthenticatedRole);
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//
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// ExternalReference2 newExternalReference = this.externalReferencesService.create(externalReference);
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// return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalReference2>().payload(newExternalReference).status(ApiMessageCode.SUCCESS_MESSAGE));
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// }
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}
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@ -5,6 +5,7 @@ import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.jayway.jsonpath.DocumentContext;
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import com.jayway.jsonpath.JsonPath;
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import eu.eudat.commons.enums.ExternalReferencesType;
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import eu.eudat.logic.proxy.config.*;
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import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
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import eu.eudat.logic.proxy.config.entities.GenericUrls;
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@ -50,55 +51,37 @@ public class RemoteFetcher {
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).clientConnector(new ReactorClientHttpConnector(HttpClient.create().followRedirect(true))).build();
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}
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public List<Map<String, String>> get(String externalType, ExternalUrlCriteria externalUrlCriteria, String key) throws NoURLFound, HugeResultSet {
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List<UrlConfiguration> urlConfigs = null;
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public List<Map<String, String>> get(ExternalReferencesType externalType, ExternalUrlCriteria externalUrlCriteria, String key) throws NoURLFound, HugeResultSet {
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FetchStrategy fetchStrategy = null;
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switch (externalType){
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case "taxonomies":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getTaxonomies().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getTaxonomies().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getTaxonomies().getFetchMode();
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break;
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case "licenses":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getLicenses().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getLicenses().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getLicenses().getFetchMode();
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break;
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case "publications":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getPublications().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getPublications().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getPublications().getFetchMode();
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break;
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case "journals":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getJournals().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getJournals().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getJournals().getFetchMode();
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break;
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case "pubRepositories":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getPubRepositories().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getPubRepositories().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getPubRepositories().getFetchMode();
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break;
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case "dataRepositories":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getRepositories().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getRepositories().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getRepositories().getFetchMode();
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break;
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case "registries":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getRegistries().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getRegistries().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getRegistries().getFetchMode();
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break;
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case "services":
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urlConfigs = key != null && !key.isEmpty() ? configLoader.getExternalUrls().getServices().getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: configLoader.getExternalUrls().getServices().getUrls();
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fetchStrategy = configLoader.getExternalUrls().getServices().getFetchMode();
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break;
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}
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GenericUrls exGenericUrls = this.getExternalUrls(externalType);
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List<UrlConfiguration> urlConfigs = key != null && !key.isEmpty() ? exGenericUrls.getUrls().stream().filter(item -> item.getKey().equals(key)).collect(Collectors.toList())
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: exGenericUrls.getUrls();
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return getAll(urlConfigs, fetchStrategy, externalUrlCriteria);
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}
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public GenericUrls getExternalUrls(ExternalReferencesType externalType) {
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switch (externalType){
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case Taxonomies: return configLoader.getExternalUrls().getTaxonomies();
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case Licenses: return configLoader.getExternalUrls().getLicenses();
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case Publications: return configLoader.getExternalUrls().getPublications();
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case Journals: return configLoader.getExternalUrls().getJournals();
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case PubRepositories: return configLoader.getExternalUrls().getPubRepositories();
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case DataRepositories: return configLoader.getExternalUrls().getRepositories();
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case Registries: return configLoader.getExternalUrls().getRegistries();
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case Services: return configLoader.getExternalUrls().getServices();
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case Grants: return configLoader.getExternalUrls().getGrants();
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case Organizations: return configLoader.getExternalUrls().getOrganisations();
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case Datasets: return configLoader.getExternalUrls().getDatasets();
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case Founder: return configLoader.getExternalUrls().getFunders();
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case Project: return configLoader.getExternalUrls().getProjects();
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case Researcher: return configLoader.getExternalUrls().getResearchers();
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case Validators: return configLoader.getExternalUrls().getValidations();
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// case Prefillings: return configLoader.getExternalUrls().getPrefillings();
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default: throw new IllegalArgumentException("Type not found" + externalType);
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}
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}
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@Cacheable(value = "repositories", keyGenerator = "externalUrlsKeyGenerator")
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public List<Map<String, String>> getRepositories(ExternalUrlCriteria externalUrlCriteria, String key) throws NoURLFound, HugeResultSet {
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List<UrlConfiguration> urlConfigs =
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@ -2,6 +2,7 @@ package eu.eudat.logic.services.externalreferences;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.eudat.commons.enums.ExternalReferencesType;
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import eu.eudat.commons.scope.user.UserScope;
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import eu.eudat.data.dao.criteria.DataRepositoryCriteria;
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import eu.eudat.data.dao.criteria.RegistryCriteria;
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@ -15,9 +16,9 @@ import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
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import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
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import eu.eudat.logic.services.ApiContext;
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import eu.eudat.models.data.ExternalReference;
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import eu.eudat.models.data.ExternalReference2;
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import javax.management.InvalidApplicationException;
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import java.util.Comparator;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.Map;
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@ -42,36 +43,36 @@ public class ExternalReferencesService {//implements ExternalReferencesService{
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// pubRepositories,
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// dataRepositories
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public ExternalReference createDataRepo(ExternalReference externalReference) throws Exception {
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// only dataRepositories, pubRepositories, journals
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DataRepository dataRepository = externalReference.toDataModel();
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dataRepository.getCreationUser().setId(this.userScope.getUserId());
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// public ExternalReference createDataRepo(ExternalReference externalReference) throws Exception {
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// // only dataRepositories, pubRepositories, journals
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// DataRepository dataRepository = externalReference.toDataModel();
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// dataRepository.getCreationUser().setId(this.userScope.getUserId());
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//
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// dataRepository = apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().createOrUpdate(dataRepository);
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// return new ExternalReference().fromDataModel(dataRepository);
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// }
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dataRepository = apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().createOrUpdate(dataRepository);
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return new ExternalReference().fromDataModel(dataRepository);
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}
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public List<ExternalReference> getExternalReference(String externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
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ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
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List<Map<String, String>> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
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DataRepositoryCriteria criteria = new DataRepositoryCriteria();
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if (!query.isEmpty()) criteria.setLike(query);
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List<ExternalReference> list = new LinkedList<>();
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if((externalType.equals("dataRepositories") || externalType.equals("pubRepositories") || externalType.equals("journals"))){
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criteria.setCreationUserId(this.userScope.getUserId());
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if (type.equals("")) {
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List<DataRepository> dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList();
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list = dataRepositoryList.stream().map(item -> new ExternalReference().fromDataModel(item)).collect(Collectors.toList());
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}
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}
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ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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list.addAll(remoteRepos.stream().map(item -> mapper.convertValue(item, ExternalReference.class)).collect(Collectors.toList()));
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list = list.stream().filter(x -> x.getName().toLowerCase().contains(query.toLowerCase())).collect(Collectors.toList());
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return list;
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}
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// public List<ExternalReference> getExternalReference(String externalType, String query, String type) throws HugeResultSet, NoURLFound, InvalidApplicationException {
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// ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
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// List<Map<String, String>> remoteRepos = this.apiContext.getOperationsContext().getRemoteFetcher().get(externalType, externalUrlCriteria, type);
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//
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// DataRepositoryCriteria criteria = new DataRepositoryCriteria();
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// if (!query.isEmpty()) criteria.setLike(query);
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//
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// List<ExternalReference> list = new LinkedList<>();
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// if((externalType.equals("dataRepositories") || externalType.equals("pubRepositories") || externalType.equals("journals"))){
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// criteria.setCreationUserId(this.userScope.getUserId());
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// if (type.equals("")) {
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// List<DataRepository> dataRepositoryList = (this.apiContext.getOperationsContext().getDatabaseRepository().getDataRepositoryDao().getWithCriteria(criteria)).toList();
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// list = dataRepositoryList.stream().map(item -> new ExternalReference().fromDataModel(item)).collect(Collectors.toList());
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// }
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// }
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//
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// 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;
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
|
@ -79,45 +80,99 @@ public class ExternalReferencesService {//implements ExternalReferencesService{
|
|||
// 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.");
|
||||
}
|
||||
// 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;
|
||||
// }
|
||||
|
||||
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 {
|
||||
public List<ExternalReference> getExternalReference(ExternalReferencesType 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<>();
|
||||
List<ExternalReference> list = this.fetchFromDb(externalType, query, type);
|
||||
|
||||
if (externalType.equals("registries")){
|
||||
RegistryCriteria criteria = new RegistryCriteria();
|
||||
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) 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 ExternalReference2().fromDataModel(item)).collect(Collectors.toList());
|
||||
list = registryList.stream().map(item -> new ExternalReference().fromRegistry(item)).collect(Collectors.toList());
|
||||
}
|
||||
} else if (externalType.equals("services")) {
|
||||
}
|
||||
case Services:
|
||||
{
|
||||
ServiceCriteria criteria = new ServiceCriteria();
|
||||
|
||||
if (!query.isEmpty()) criteria.setLike(query);
|
||||
|
|
@ -125,12 +180,14 @@ public class ExternalReferencesService {//implements ExternalReferencesService{
|
|||
|
||||
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());
|
||||
list = serviceList.stream().map(item -> new ExternalReference().fromService(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()));
|
||||
case Taxonomies:
|
||||
case Publications:
|
||||
case Licenses:
|
||||
break;
|
||||
}
|
||||
|
||||
return list;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,34 +1,64 @@
|
|||
package eu.eudat.models.data;
|
||||
|
||||
|
||||
|
||||
import eu.eudat.data.old.DataRepository;
|
||||
import eu.eudat.data.old.Registry;
|
||||
import eu.eudat.data.old.Service;
|
||||
import eu.eudat.data.old.UserInfo;
|
||||
import eu.eudat.models.data.datarepository.DataRepositoryModel;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
|
||||
public class ExternalReference {
|
||||
private UUID id;
|
||||
private String name;
|
||||
private String pid;
|
||||
private String abbreviation;
|
||||
private String uri;
|
||||
private Date created;
|
||||
private Date modified;
|
||||
private String tag; // Api fetching the data
|
||||
private String source; // Actual harvested source
|
||||
|
||||
public UUID getId() {
|
||||
private String id;
|
||||
private String name;
|
||||
private String abbreviation;
|
||||
private String pid;
|
||||
private String originalId;
|
||||
private String key;
|
||||
private String pidTypeField;
|
||||
private String uri;
|
||||
private String description;
|
||||
private String source;
|
||||
private String count;
|
||||
private String path;
|
||||
private String host;
|
||||
private String types;
|
||||
private String firstName;
|
||||
private String lastName;
|
||||
private String tag;
|
||||
|
||||
public String getOriginalId() {
|
||||
return originalId;
|
||||
}
|
||||
|
||||
public void setOriginalId(String originalId) {
|
||||
this.originalId = originalId;
|
||||
}
|
||||
|
||||
public String getKey() {
|
||||
return key;
|
||||
}
|
||||
|
||||
public void setKey(String key) {
|
||||
this.key = key;
|
||||
}
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
public void setId(UUID id) {
|
||||
|
||||
public void setId(String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
|
@ -36,58 +66,136 @@ public class ExternalReference {
|
|||
public String getPid() {
|
||||
return pid;
|
||||
}
|
||||
|
||||
public void setPid(String pid) {
|
||||
this.pid = pid;
|
||||
}
|
||||
|
||||
public String getAbbreviation() {
|
||||
return abbreviation;
|
||||
public String getPidTypeField() {
|
||||
return pidTypeField;
|
||||
}
|
||||
public void setAbbreviation(String abbreviation) {
|
||||
this.abbreviation = abbreviation;
|
||||
|
||||
public void setPidTypeField(String pidTypeField) {
|
||||
this.pidTypeField = pidTypeField;
|
||||
}
|
||||
|
||||
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 String getDescription() {
|
||||
return description;
|
||||
}
|
||||
|
||||
public Date getModified() {
|
||||
return modified;
|
||||
}
|
||||
public void setModified(Date modified) {
|
||||
this.modified = modified;
|
||||
}
|
||||
|
||||
public String getTag() {
|
||||
return tag;
|
||||
}
|
||||
public void setTag(String tag) {
|
||||
this.tag = tag;
|
||||
public void setDescription(String description) {
|
||||
this.description = description;
|
||||
}
|
||||
|
||||
public String getSource() {
|
||||
return source;
|
||||
}
|
||||
|
||||
public void setSource(String source) {
|
||||
this.source = source;
|
||||
}
|
||||
|
||||
public String getCount() {
|
||||
return count;
|
||||
}
|
||||
|
||||
public ExternalReference fromDataModel(DataRepository entity) {
|
||||
public void setCount(String count) {
|
||||
this.count = count;
|
||||
}
|
||||
|
||||
public String getPath() {
|
||||
return path;
|
||||
}
|
||||
|
||||
public void setPath(String path) {
|
||||
this.path = path;
|
||||
}
|
||||
|
||||
public String getHost() {
|
||||
return host;
|
||||
}
|
||||
|
||||
public void setHost(String host) {
|
||||
this.host = host;
|
||||
}
|
||||
|
||||
public String getTypes() {
|
||||
return types;
|
||||
}
|
||||
|
||||
public void setTypes(String types) {
|
||||
this.types = types;
|
||||
}
|
||||
|
||||
public String getFirstName() {
|
||||
return firstName;
|
||||
}
|
||||
|
||||
public void setFirstName(String firstName) {
|
||||
this.firstName = firstName;
|
||||
}
|
||||
|
||||
public String getLastName() {
|
||||
return lastName;
|
||||
}
|
||||
|
||||
public void setLastName(String lastName) {
|
||||
this.lastName = lastName;
|
||||
}
|
||||
|
||||
public String getTag() {
|
||||
return tag;
|
||||
}
|
||||
|
||||
public void setTag(String tag) {
|
||||
this.tag = tag;
|
||||
}
|
||||
|
||||
public String getAbbreviation() {
|
||||
return abbreviation;
|
||||
}
|
||||
|
||||
public void setAbbreviation(String abbreviation) {
|
||||
this.abbreviation = abbreviation;
|
||||
}
|
||||
|
||||
public static ExternalReference fromRemoteModel(Map<String, String> data) {
|
||||
ExternalReference externalReference = new ExternalReference();
|
||||
if (data == null) return externalReference;
|
||||
|
||||
externalReference.setId(data.getOrDefault("id", null));
|
||||
externalReference.setName(data.getOrDefault("name", null));
|
||||
externalReference.setAbbreviation(data.getOrDefault("abbreviation", null));
|
||||
externalReference.setPid(data.getOrDefault("pid", null));
|
||||
externalReference.setOriginalId(data.getOrDefault("originalId", null));
|
||||
externalReference.setKey(data.getOrDefault("key", null));
|
||||
externalReference.setPidTypeField(data.getOrDefault("pidTypeField", null));
|
||||
externalReference.setUri(data.getOrDefault("uri", null));
|
||||
externalReference.setDescription(data.getOrDefault("description", null));
|
||||
externalReference.setSource(data.getOrDefault("source", null));
|
||||
externalReference.setCount(data.getOrDefault("count", null));
|
||||
externalReference.setPath(data.getOrDefault("path", null));
|
||||
externalReference.setHost(data.getOrDefault("host", null));
|
||||
externalReference.setTypes(data.getOrDefault("types", null));
|
||||
externalReference.setFirstName(data.getOrDefault("firstName", null));
|
||||
externalReference.setLastName(data.getOrDefault("lastName", null));
|
||||
externalReference.setTag(data.getOrDefault("tag", null));
|
||||
return externalReference;
|
||||
}
|
||||
|
||||
public ExternalReference fromDataRepository(DataRepository entity) {
|
||||
this.setAbbreviation(entity.getAbbreviation());
|
||||
this.setName(entity.getLabel());
|
||||
this.setUri(entity.getUri());
|
||||
this.setId(entity.getId());
|
||||
this.setId(entity.getId().toString());
|
||||
this.setPid(entity.getReference());
|
||||
String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":"));
|
||||
if (source1.equals("dmp")) {
|
||||
|
|
@ -98,29 +206,37 @@ public class ExternalReference {
|
|||
return this;
|
||||
}
|
||||
|
||||
public DataRepository toDataModel() throws Exception {
|
||||
DataRepository dataRepository = new DataRepository();
|
||||
dataRepository.setId(this.id != null ? this.id : UUID.randomUUID());
|
||||
dataRepository.setAbbreviation(this.abbreviation);
|
||||
dataRepository.setCreated(this.created != null ? this.created : new Date());
|
||||
dataRepository.setModified(new Date());
|
||||
dataRepository.setLabel(this.name);
|
||||
if (this.source != null) {
|
||||
if (this.source.equals("Internal") || this.source.equals(this.id.toString().substring(0, this.source.length()))) {
|
||||
dataRepository.setReference(this.id.toString());
|
||||
public ExternalReference fromRegistry(Registry entity){
|
||||
this.id = entity.getId().toString();
|
||||
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 {
|
||||
dataRepository.setReference(this.source + ":" + dataRepository.getId());
|
||||
this.source = source1;
|
||||
}
|
||||
// this.reference = entity.getReference();
|
||||
return this;
|
||||
}
|
||||
public ExternalReference fromService(Service entity) {
|
||||
this.abbreviation = entity.getAbbreviation();
|
||||
// this.created = entity.getCreated();
|
||||
this.id = entity.getId().toString();
|
||||
// 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 {
|
||||
dataRepository.setReference("dmp:" + dataRepository.getId());
|
||||
this.source = source;
|
||||
}
|
||||
dataRepository.setUri(this.uri);
|
||||
dataRepository.setStatus((short) 0);
|
||||
dataRepository.setCreationUser(new UserInfo());
|
||||
return dataRepository;
|
||||
}
|
||||
|
||||
public String getHint() {
|
||||
return null;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue