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

Example 6 with BioObject

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

the class ObjectAnnotationSimilarityPredicateTest method shouldBeSimilarBasedOnBioObjectAccessionEquals.

@Test
public void shouldBeSimilarBasedOnBioObjectAccessionEquals() throws Exception {
    AnnotationSimilarityPredicate predicateBasedOnBioObjectAccessionEquals = new ObjectSimilarityPredicate(Annotation::getBioObject, (o1, o2) -> Objects.equals(((BioObject) o1).getAccession(), ((BioObject) o2).getAccession()));
    Assert.assertTrue(predicateBasedOnBioObjectAccessionEquals.isSimilar(mockAnnotationWithBioObject("toto", BioObject.BioType.CHEMICAL), mockAnnotationWithBioObject("toto", BioObject.BioType.GROUP)));
}

Example 7 with BioObject

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

the class ObjectAnnotationSimilarityPredicateTest method mockAnnotationWithBioObject.

public static Annotation mockAnnotationWithBioObject(String accession, BioObject.BioType type) {
    Annotation annotation = Mockito.mock(Annotation.class);
    BioObject bioObject = Mockito.mock(BioObject.class);
    when(bioObject.getAccession()).thenReturn(accession);
    when(bioObject.getBioType()).thenReturn(type);
    when(annotation.getBioObject()).thenReturn(bioObject);
    return annotation;
}

Example 8 with BioObject

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

the class AnnotationSimilarityPredicateTest method mockAnnotation.

private static Annotation mockAnnotation(String accession, String database) {
    Annotation annot = Mockito.mock(Annotation.class);
    BioObject bo = Mockito.mock(BioObject.class);
    Mockito.when(bo.getAccession()).thenReturn(accession);
    Mockito.when(bo.getDatabase()).thenReturn(database);
    Mockito.when(annot.getBioObject()).thenReturn(bo);
    return annot;
}

Example 9 with BioObject

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

the class StatementAnnotationBuilder method buildAnnotationList.

public List<T> buildAnnotationList(String isoformName, List<Statement> flatStatements) {
    List<T> annotations = new ArrayList<>();
    Map<String, List<Statement>> flatStatementsByAnnotationHash = flatStatements.stream().collect(Collectors.groupingBy(rs -> rs.getValue(StatementField.ANNOTATION_ID)));
    flatStatementsByAnnotationHash.forEach((key, statements) -> {
        T annotation = get();
        Statement firstStatement = statements.get(0);
        annotation.setAnnotationHash(firstStatement.getValue(StatementField.ANNOTATION_ID));
        // annotation.setAnnotationName(firstStatement.getValue(StatementField.ANNOTATION_NAME));
        AnnotationCategory category = AnnotationCategory.getDecamelizedAnnotationTypeName(StringUtils.camelToKebabCase(firstStatement.getValue(StatementField.ANNOTATION_CATEGORY)));
        annotation.setAnnotationCategory(category);
        if (category.equals(AnnotationCategory.VARIANT) || category.equals(AnnotationCategory.MUTAGENESIS)) {
            setVariantAttributes(annotation, firstStatement);
        }
        setIsoformTargeting(annotation, firstStatement);
        setIsoformName(annotation, isoformName);
        annotation.setDescription(firstStatement.getValue(StatementField.ANNOT_DESCRIPTION));
        String cvTermAccession = firstStatement.getValue(StatementField.ANNOT_CV_TERM_ACCESSION);
        // Set the evidences if not Mammalian phenotype or Protein Property https://issues.isb-sib.ch/browse/BIOEDITOR-466
        if (!ANNOT_CATEGORIES_WITHOUT_EVIDENCES.contains(category)) {
            annotation.setEvidences(buildAnnotationEvidences(statements));
            // TODO Remove this when you are able to do XREFs
            if (((annotation.getEvidences() == null) || ((annotation.getEvidences().isEmpty()))) && (category.equals(AnnotationCategory.VARIANT) || category.equals(AnnotationCategory.MUTAGENESIS))) {
                // All variants from BED are GOLD, and this is a special case when we don't have evidences for VDs.
                annotation.setQualityQualifier("GOLD");
            } else {
                annotation.setQualityQualifier(AnnotationUtils.computeAnnotationQualityBasedOnEvidences(annotation.getEvidences()).name());
            }
        } else {
            // Case of Protein propert and mammalian phenotypes
            annotation.setEvidences(new ArrayList<AnnotationEvidence>());
            boolean foundGold = statements.stream().anyMatch(s -> s.getValue(StatementField.EVIDENCE_QUALITY).equalsIgnoreCase("GOLD"));
            if (foundGold) {
                annotation.setQualityQualifier("GOLD");
            } else {
                annotation.setQualityQualifier("SILVER");
            }
        }
        if (cvTermAccession != null && !cvTermAccession.isEmpty()) {
            annotation.setCvTermAccessionCode(cvTermAccession);
            CvTerm cvTerm = terminologyService.findCvTermByAccession(cvTermAccession);
            if (cvTerm != null) {
                annotation.setCvTermName(cvTerm.getName());
                annotation.setCvApiName(cvTerm.getOntology());
                annotation.setCvTermDescription(cvTerm.getDescription());
                if (category.equals(AnnotationCategory.PROTEIN_PROPERTY)) {
                    // according to https://issues.isb-sib.ch/browse/BIOEDITOR-466
                    annotation.setDescription(cvTerm.getDescription());
                } else if (category.equals(AnnotationCategory.MAMMALIAN_PHENOTYPE)) {
                    annotation.setDescription("Relative to modification-effect annotations");
                }
            } else {
                LOGGER.error("cv term was expected to be found " + cvTermAccession);
                annotation.setCvTermName(firstStatement.getValue(StatementField.ANNOT_CV_TERM_NAME));
                annotation.setCvApiName(firstStatement.getValue(StatementField.ANNOT_CV_TERM_TERMINOLOGY));
            }
        }
        annotation.setAnnotationHash(firstStatement.getValue(StatementField.ANNOTATION_ID));
        annotation.setAnnotationName(firstStatement.getValue(StatementField.ANNOTATION_NAME));
        // Check this with PAM (does it need to be a human readable stuff)
        // Does it need a name?
        annotation.setUniqueName(firstStatement.getValue(StatementField.ANNOTATION_ID));
        String bioObjectAnnotationHash = firstStatement.getValue(StatementField.OBJECT_ANNOTATION_IDS);
        String bioObjectAccession = firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_ACCESSION);
        String bot = firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_TYPE);
        if ((bioObjectAnnotationHash != null) && (bioObjectAnnotationHash.length() > 0) || (bioObjectAccession != null && (bioObjectAccession.length() > 0))) {
            BioObject bioObject;
            if (AnnotationCategory.BINARY_INTERACTION.equals(annotation.getAPICategory())) {
                if (bioObjectAccession.startsWith("NX_") && BioType.PROTEIN.name().equalsIgnoreCase(bot)) {
                    // note that if we handle BioType.PROTEIN_ISOFORM in the future, we should
                    // add the property isoformName as well, see how it's done in BinaryInteraction2Annotation.newBioObject()
                    bioObject = BioObject.internal(BioType.PROTEIN);
                    // // TODO: REMOVE THIS HACK WHEN ISSUE https://issues.isb-sib.ch/browse/NEXTPROT-1513 will be fixed
                    // // NX_P62158 was split in 3 accessions: NX_P0DP23/CALM1, NX_P0DP24/CALM2 and NX_P0DP25/CALM3
                    // // BEGIN DIRTY HACK
                    /*
                        if (bioObjectAccession.equals("NX_P62158")) {
                            switch (isoformName) {
                                case "NX_P35499":
                                    bioObjectAccession = "NX_P0DP23";
                                    break;
                                case "NX_Q99250":
                                    bioObjectAccession = "NX_P0DP23";
                                    break;
                                case "NX_Q9UQD0":
                                    bioObjectAccession = "NX_P0DP23";
                                    break;
                                case "NX_Q9Y5Y9":
                                    bioObjectAccession = "NX_P0DP23";
                                    break;
                            }
                        }
                        */
                    // /// END OF HACK
                    bioObject.setAccession(bioObjectAccession);
                    bioObject.putPropertyNameValue("geneName", firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_NAME));
                    String proteinName = mainNamesService.findIsoformOrEntryMainName(bioObjectAccession).orElseThrow(() -> new NextProtException("Cannot create a binary interaction with " + isoformName + ": unknown protein accession " + bioObject.getAccession())).getName();
                    bioObject.putPropertyNameValue("proteinName", proteinName);
                    bioObject.putPropertyNameValue("url", "https://www.nextprot.org/entry/" + bioObjectAccession + "/interactions");
                } else {
                    throw new NextProtException("Binary Interaction only expects to be a nextprot entry NX_ and found " + bioObjectAccession + " with type " + bot);
                }
            } else if (AnnotationCategory.PHENOTYPIC_VARIATION.equals(annotation.getAPICategory())) {
                bioObject = BioObject.internal(BioType.ENTRY_ANNOTATION);
                bioObject.setAnnotationHash(bioObjectAnnotationHash);
            } else {
                throw new NextProtException("Category not expected for bioobject " + annotation.getAPICategory());
            }
            annotation.setBioObject(bioObject);
        }
        annotations.add(annotation);
    });
    return annotations;
}

Example 10 with BioObject

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

the class AnnotationUtils method newExternalChemicalBioObject.

static BioObject newExternalChemicalBioObject(AnnotationEvidence evi) {
    BioObject bo = BioObject.external(BioObject.BioType.CHEMICAL, evi.getResourceDb());
    bo.setId(evi.getResourceId());
    bo.setAccession(evi.getResourceAccession());
    String chemicalName = evi.getPropertyValue("name");
    if (chemicalName != null)
        bo.getProperties().put("chemical name", chemicalName);
    return bo;
}