Examples with DbXref org.nextprot.api.core.domain.DbXref used on opensource projects

Example 51 with DbXref

use of org.nextprot.api.core.domain.DbXref in project nextprot-api by calipho-sib.

the class WebInfoXrefResolverTest method testResolve.

@Test
public void testResolve() throws Exception {
    DefaultDbXrefURLResolver resolver = new WebInfoXrefURLResolver();
    DbXref xref = DbXrefURLResolverDelegateTest.createDbXref("babebibobu", "WEBINFO", "");
    Assert.assertEquals("babebibobu", resolver.resolve(xref));
}

Example 52 with DbXref

use of org.nextprot.api.core.domain.DbXref in project nextprot-api by calipho-sib.

the class DbXrefServiceImpl method newAnnotationEvidence.

private AnnotationEvidence newAnnotationEvidence(Annotation xrefAnnotation) {
    AnnotationEvidence evidence = new AnnotationEvidence();
    DbXref pxref = xrefAnnotation.getParentXref();
    evidence.setAnnotationId(xrefAnnotation.getAnnotationId());
    Xref2Annotation xam = Xref2Annotation.getByDatabaseName(pxref.getDatabaseName());
    evidence.setEvidenceId(xrefAnnotation.getAnnotationId() + IdentifierOffset.XREF_ANNOTATION_EVIDENCE_OFFSET);
    evidence.setAssignedBy(xam.getSrcName());
    evidence.setResourceId(pxref.getDbXrefId());
    evidence.setResourceAccession(pxref.getAccession());
    evidence.setResourceDb(pxref.getDatabaseName());
    evidence.setResourceAssociationType("evidence");
    evidence.setResourceType("database");
    evidence.setEvidenceCodeOntology(xam.getEcoOntology());
    evidence.setNegativeEvidence(false);
    evidence.setExperimentalContextId(null);
    evidence.setResourceDescription(null);
    evidence.setProperties(new ArrayList<>());
    evidence.setQualifierType(xam.getQualifierType());
    evidence.setQualityQualifier(xam.getQualityQualifier());
    evidence.setAssignmentMethod(xam.getAssignmentMethod());
    evidence.setEvidenceCodeAC(xam.getEcoAC());
    evidence.setEvidenceCodeName(xam.getEcoName());
    return evidence;
}

Example 53 with DbXref

use of org.nextprot.api.core.domain.DbXref in project nextprot-api by calipho-sib.

the class EmblDbXrefConverterTest method testConvertFromMultipleProps.

@Test
public void testConvertFromMultipleProps() {
    EmblDbXrefConverter converter = new EmblDbXrefConverter();
    DbXref xref = createDbXref("AY899304", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena");
    xref.setProperties(Arrays.asList(createDbXrefProperty(1935564, "genomic sequence ID", "M27429"), createDbXrefProperty(1935565, "genomic sequence ID", "M27428"), createDbXrefProperty(1935566, "genomic sequence ID", "M27427"), createDbXrefProperty(1935567, "genomic sequence ID", "M27426"), createDbXrefProperty(1935568, "genomic sequence ID", "M27425"), createDbXrefProperty(1935569, "genomic sequence ID", "M27424"), createDbXrefProperty(1935570, "genomic sequence ID", "M27423"), createDbXrefProperty(1935571, "molecule type", "protein"), createDbXrefProperty(1935572, "genomic sequence ID", "M27430")));
    List<DbXref> xrefs = converter.convert(xref);
    Assert.assertEquals(8, xrefs.size());
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935564, "M27429", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27429");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935565, "M27428", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27428");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935566, "M27427", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27427");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935567, "M27426", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27426");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935568, "M27425", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27425");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935569, "M27424", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27424");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935570, "M27423", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27423");
    assertProducedXrefListContains(xrefs, IdentifierOffset.XREF_PROPERTY_OFFSET + 1935572, "M27430", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "Sequence databases", "http://www.ebi.ac.uk/ena", "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena/data/view/M27430");
}

Example 54 with DbXref

use of org.nextprot.api.core.domain.DbXref in project nextprot-api by calipho-sib.

the class EmblDbXrefConverterTest method testConvertEx2.

@Test
public void testConvertEx2() {
    EmblDbXrefConverter converter = new EmblDbXrefConverter();
    DbXref xref = createDbXref("AY899304", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena");
    xref.setProperties(Collections.singletonList(createDbXrefProperty(1724230, "protein sequence ID", "AAW83741.1")));
    List<DbXref> xrefs = converter.convert(xref);
    Assert.assertEquals(1, xrefs.size());
    DbXref ref = xrefs.get(0);
    Assert.assertEquals(IdentifierOffset.XREF_PROPERTY_OFFSET + 1724230, ref.getDbXrefId().longValue());
    Assert.assertEquals("AAW83741.1", ref.getAccession());
    Assert.assertTrue(ref.getProperties().isEmpty());
    Assert.assertEquals("Sequence databases", ref.getDatabaseCategory());
    Assert.assertEquals(XrefDatabase.EMBL.getName(), ref.getDatabaseName());
    Assert.assertEquals("http://www.ebi.ac.uk/ena/data/view/%s", ref.getLinkUrl());
    Assert.assertEquals("http://www.ebi.ac.uk/ena/data/view/AAW83741", ref.getResolvedUrl());
    Assert.assertEquals("http://www.ebi.ac.uk/ena", ref.getUrl());
}

Example 55 with DbXref

use of org.nextprot.api.core.domain.DbXref in project nextprot-api by calipho-sib.

the class EmblDbXrefConverterTest method testConvertEx1.

@Test
public void testConvertEx1() {
    EmblDbXrefConverter converter = new EmblDbXrefConverter();
    DbXref xref = createDbXref("AAA59172.1", DbXrefURLResolverSupplier.EMBL.getXrefDatabase().getName(), "http://www.ebi.ac.uk/ena/data/view/%s", "http://www.ebi.ac.uk/ena");
    xref.setProperties(Collections.singletonList(createDbXrefProperty(1724225, "genomic sequence ID", "J00265")));
    List<DbXref> xrefs = converter.convert(xref);
    Assert.assertEquals(1, xrefs.size());
    DbXref ref = xrefs.get(0);
    Assert.assertEquals(IdentifierOffset.XREF_PROPERTY_OFFSET + 1724225, ref.getDbXrefId().longValue());
    Assert.assertEquals("J00265", ref.getAccession());
    Assert.assertTrue(ref.getProperties().isEmpty());
    Assert.assertEquals("Sequence databases", ref.getDatabaseCategory());
    Assert.assertEquals(XrefDatabase.EMBL.getName(), ref.getDatabaseName());
    Assert.assertEquals("http://www.ebi.ac.uk/ena/data/view/%s", ref.getLinkUrl());
    Assert.assertEquals("http://www.ebi.ac.uk/ena/data/view/J00265", ref.getResolvedUrl());
    Assert.assertEquals("http://www.ebi.ac.uk/ena", ref.getUrl());
}