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curation-279-sync-publications-ondemand changes to sendmessage on adh… #280

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curation-279-sync-publications-ondemand changes to sendmessage on adh… #280

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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/spot/gwas/curation/constants/DepositionCurationConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ public class DepositionCurationConstants {

public static final String API_PUBLICATION = "/publications";
public static final String API_PUBLICATION_AUDIT_ENTRIES = "/publication-audit-entries";

public static final String API_SYNC_PUBLICATION = "/sync-publication";
public static final String PARAM_PUBID = "publicationId";

}
8 changes: 8 additions & 0 deletions src/main/java/uk/ac/ebi/spot/gwas/curation/rest/PublicationsController.java
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Expand Up @@ -94,6 +94,14 @@ public List<PublicationStatusReport> createPublication(@PathVariable List<String
return statusReports;
}

@ResponseStatus(HttpStatus.OK)
@PostMapping(value = "/{pmid}" + DepositionCurationConstants.API_SYNC_PUBLICATION,produces = MediaType.APPLICATION_JSON_VALUE)
@PreAuthorize("hasRole('self.GWAS_Curator')")
public void syncPublication(@PathVariable String pmid, HttpServletRequest request) {
User user = userService.findUser(jwtService.extractUser(CurationUtil.parseJwt(request)), false);
publicationService.syncPublication(pmid, user);
}

@ResponseStatus(HttpStatus.OK)
@GetMapping(value = "/{pmid}/linked-submissions",produces = MediaType.APPLICATION_JSON_VALUE)
@PreAuthorize("hasRole('self.GWAS_Curator')")
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8 changes: 4 additions & 4 deletions src/main/java/uk/ac/ebi/spot/gwas/curation/service/PublicationService.java
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Expand Up @@ -11,6 +11,7 @@
import uk.ac.ebi.spot.gwas.deposition.dto.curation.SearchPublicationDTO;
import uk.ac.ebi.spot.gwas.deposition.solr.SOLRPublication;

import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.util.List;

Expand All @@ -24,15 +25,12 @@ public interface PublicationService {

SOLRPublication getPublicationFromSolr(String id);

List<PublicationStatusReport> createPublication(List<String> pmids, User user);

List<PublicationStatusReport> createPublication(List<String> pmids, User user) ;
Page<MatchPublicationReport> matchPublication(String pmid, Pageable pageable);



PublicationDto patchPublication(String pmid, PublicationDto publicationDto, User user);


void linkSubmission(String pmid, String submissionId);

void fillSubmitterForOldPublications();
Expand All @@ -44,4 +42,6 @@ public interface PublicationService {
String getCuratorEventDetails(PublicationDto publicationDto);

List<Publication> getTotalPublications();

void syncPublication(String pmid, User user);
}
17 changes: 17 additions & 0 deletions src/main/java/uk/ac/ebi/spot/gwas/curation/service/impl/PublicationServiceImpl.java
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Expand Up @@ -40,6 +40,7 @@
import uk.ac.ebi.spot.gwas.deposition.exception.PubmedLookupException;
import uk.ac.ebi.spot.gwas.deposition.solr.SOLRPublication;

import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -346,6 +347,7 @@ public List<PublicationStatusReport> createPublication(List<String> pmids, User
statusReport.setPmid(pmid);
statusReport.setPublicationDto(publicationDtoAssembler.assemble(publication, user));
statusReport.setStatus("PMID already exists");
log.info("PMID already exists {}", pmid);
reports.add(statusReport);
} else {

Expand All @@ -361,16 +363,19 @@ public List<PublicationStatusReport> createPublication(List<String> pmids, User
statusReport.setPmid(pmid);
statusReport.setPublicationDto(publicationDtoAssembler.assemble(publicationImported, user));
statusReport.setStatus("PMID saved");
log.info("PMID saved {}", pmid);
reports.add(statusReport);
} catch (EuropePMCException ex){
PublicationStatusReport statusReport = new PublicationStatusReport();
statusReport.setPmid(pmid);
statusReport.setStatus("Couldn't contact EPMC API");
log.info("Couldn't contact EPMC API {}", pmid);
reports.add(statusReport);
}catch (PubmedLookupException ex) {
PublicationStatusReport statusReport = new PublicationStatusReport();
statusReport.setPmid(pmid);
statusReport.setStatus("PMID not found in EPMC");
log.info("PMID not found in EPMC {}", pmid);
reports.add(statusReport);
}

Expand All @@ -380,6 +385,18 @@ public List<PublicationStatusReport> createPublication(List<String> pmids, User
return reports;
}

public void syncPublication(String pmid, User user) {
Publication publication = getPublicationDetailsByPmidOrPubId(pmid, true);
if(publication != null) {
Map<Integer, PublicationAuthor> authortSortMap = publicationRabbitMessageService.
getAuthorDetails(publication.getAuthors(), publication.getId());
PublicationAuthor firstAuthor = publicationRabbitMessageService.
getFirstAuthor(publication.getFirstAuthorId());
publicationMQProducer.send(publicationRabbitMessageAssembler.assemble(publication, authortSortMap,
firstAuthor, user));
}
}

@Override
public PublicationDto patchPublication(String pubmedId, PublicationDto publicationDto, User user) {
Publication publication = publicationRepository
Expand Down