Examples with StatementSimpleWhereClauseQueryDSL org.nextprot.api.core.dao.impl.StatementSimpleWhereClauseQueryDSL used on opensource projects

Example 1 with StatementSimpleWhereClauseQueryDSL

use of org.nextprot.api.core.dao.impl.StatementSimpleWhereClauseQueryDSL in project nextprot-api by calipho-sib.

the class ConsistencyResourceTest method shouldFindAllPublications.

@Test
public void shouldFindAllPublications() {
    boolean missingPublications = false;
    List<String> pubmedIds = statementDao.findAllDistinctValuesforFieldWhereFieldEqualsValues(StatementField.REFERENCE_ACCESSION, new StatementSimpleWhereClauseQueryDSL(StatementField.REFERENCE_DATABASE, "PubMed"));
    System.out.println("Found " + pubmedIds.size() + " distinct pubmeds");
    for (String p : pubmedIds) {
        if (p != null) {
            String pubmedId = p.replace("(PubMed,", "").replace(")", "");
            Publication pub = publicationService.findPublicationByDatabaseAndAccession("PubMed", pubmedId);
            // TODO: remove the following line after next release data jan 2018
            if (!"23248292".equals(pubmedId)) {
                if (pub == null) {
                    System.err.println("Can t find publication for " + pubmedId);
                    missingPublications = true;
                }
            } else {
                System.err.println("FOUND EMPTY PUBLICATION " + pubmedId + ", FIX THIS IN NEXT RELEASE !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Probably related to: https://issues.isb-sib.ch/browse/NEXTPROT-1369");
            }
        }
    }
    ;
    if (missingPublications)
        Assert.fail();
}

Example 2 with StatementSimpleWhereClauseQueryDSL

use of org.nextprot.api.core.dao.impl.StatementSimpleWhereClauseQueryDSL in project nextprot-api by calipho-sib.

the class PublicationServiceImpl method findPublicationsByEntryName.

// TODO: Publications are already cached in publications-get-by-id - even worse, some publication are linked to more than 10000 entries!!!)
// almost 5GB of cache here !!!
@Override
@Cacheable("publications")
public List<Publication> findPublicationsByEntryName(String uniqueName) {
    Long masterId = masterIdentifierService.findIdByUniqueName(uniqueName);
    List<Publication> publications = publicationDao.findSortedPublicationsByMasterId(masterId);
    Map<Long, List<PublicationDbXref>> npPublicationsXrefs = updateMissingPublicationFields(publications);
    // Getting publications from nx flat database
    List<Publication> nxflatPublications = new ArrayList<>();
    Arrays.asList(XrefDatabase.DOI, XrefDatabase.PUB_MED).forEach(db -> {
        List<String> referenceIds = this.statementDao.findAllDistinctValuesforFieldWhereFieldEqualsValues(StatementField.REFERENCE_ACCESSION, new StatementSimpleWhereClauseQueryDSL(StatementField.ENTRY_ACCESSION, uniqueName), new StatementSimpleWhereClauseQueryDSL(StatementField.REFERENCE_DATABASE, db.getName()));
        nxflatPublications.addAll(getPublicationsFromDBReferenceIds(referenceIds, db.getName(), npPublicationsXrefs));
    });
    updateMissingPublicationFields(nxflatPublications);
    publications.addAll(nxflatPublications);
    Comparator<Publication> comparator = PublicationComparator.StringComparator(Publication::getPublicationYear).reversed().thenComparing(Comparator.comparing(Publication::getPublicationType)).thenComparing(PublicationComparator.StringComparator(Publication::getPublicationLocatorName)).thenComparing(PublicationComparator.FormattedNumberComparator(Publication::getVolume)).thenComparing(PublicationComparator.FormattedNumberComparator(Publication::getFirstPage));
    // sort according to order with criteria defined in publication-sorted-for-master.sql
    publications.sort(comparator);
    // returns a immutable list when the result is cacheable (this prevents modifying the cache, since the cache returns a reference) copy on read and copy on write is too much time consuming
    return new ImmutableList.Builder<Publication>().addAll(publications).build();
}

Example 3 with StatementSimpleWhereClauseQueryDSL

use of org.nextprot.api.core.dao.impl.StatementSimpleWhereClauseQueryDSL in project nextprot-api by calipho-sib.

the class ConsistencyServiceImpl method findMissingPublications.

@Override
public List<String> findMissingPublications() {
    List<String> missingPublications = new ArrayList<>();
    Arrays.asList(XrefDatabase.PUB_MED, XrefDatabase.DOI).forEach(referenceDB -> {
        List<String> ids = statementDao.findAllDistinctValuesforFieldWhereFieldEqualsValues(StatementField.REFERENCE_ACCESSION, new StatementSimpleWhereClauseQueryDSL(StatementField.REFERENCE_DATABASE, referenceDB.getName()));
        for (String id : ids) {
            if (id != null) {
                Publication pub = publicationService.findPublicationByDatabaseAndAccession(referenceDB.getName(), id);
                if (pub == null) {
                    missingPublications.add(referenceDB + id);
                }
            }
        }
        ;
    });
    return missingPublications;
}