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

Example 21 with CvTerm

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

the class AnnotationBuilderBastUnitTest method init.

@Before
public void init() throws FileNotFoundException, DataSetException {
    MockitoAnnotations.initMocks(this);
    CvTerm cvterm = new CvTerm();
    cvterm.setName("eco-name-1");
    cvterm.setOntology("eco-ontology-cv");
    cvterm.setDescription("some description");
    Mockito.when(terminologyService.findCvTermByAccession(Matchers.anyString())).thenReturn(cvterm);
    Publication pub = new Publication();
    pub.setId(999);
    Mockito.when(publicationService.findPublicationByDatabaseAndAccession("PubMed", "000")).thenReturn(null);
    Mockito.when(publicationService.findPublicationByDatabaseAndAccession("PubMed", "123")).thenReturn(pub);
    // unused in tests yet
    Mockito.when(mainNamesService.findIsoformOrEntryMainName()).thenReturn(null);
}

Example 22 with CvTerm

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

the class CVFieldBuilder method init.

@Override
protected void init(Entry entry) {
    Set<String> cv_acs = new HashSet<String>();
    Set<String> cv_ancestors_acs = new HashSet<String>();
    Set<String> cv_synonyms = new HashSet<String>();
    // top level ancestors (Annotation, feature, and ROI)
    Set<String> top_acs = new HashSet<>(Arrays.asList("CVAN_0001", "CVAN_0002", "CVAN_0011"));
    // CV accessions
    List<Annotation> annots = entry.getAnnotations();
    boolean allnegative;
    for (Annotation currannot : annots) {
        String category = currannot.getCategory();
        if (!category.equals("tissue specificity")) {
            // tissue-specific CVs are indexed under 'expression'
            String cvac = currannot.getCvTermAccessionCode();
            if (cvac == null)
                continue;
            if (cvac.isEmpty())
                logger.warn("CVterm accession empty in " + category + " for " + entry.getUniqueName());
            else {
                if (category.startsWith("go ")) {
                    allnegative = true;
                    List<AnnotationEvidence> evlist = currannot.getEvidences();
                    // We don't index negative annotations
                    for (AnnotationEvidence ev : evlist) allnegative = allnegative & ev.isNegativeEvidence();
                    if (allnegative == true)
                        continue;
                }
                if (!this.isGold() || currannot.getQualityQualifier().equals("GOLD")) {
                    addField(Fields.CV_ACS, cvac);
                    // No duplicates: this is a Set, will be used for synonyms and ancestors
                    cv_acs.add(cvac);
                    addField(Fields.CV_NAMES, currannot.getCvTermName());
                }
            }
        }
    }
    // Families (why not part of Annotations ?)
    for (Family family : entry.getOverview().getFamilies()) {
        addField(Fields.CV_ACS, family.getAccession());
        addField(Fields.CV_NAMES, family.getName() + " family");
        cv_acs.add(family.getAccession());
    }
    // Final CV acs, ancestors and synonyms
    for (String cvac : cv_acs) {
        CvTerm term = this.terminologyservice.findCvTermByAccession(cvac);
        if (null == term) {
            logger.error(entry.getUniqueName() + " - term with accession |" + cvac + "| not found with findCvTermByAccession()");
            continue;
        }
        List<String> ancestors = terminologyservice.getAllAncestorsAccession(term.getAccession());
        if (ancestors != null) {
            for (String ancestor : ancestors) cv_ancestors_acs.add(ancestor);
        }
        List<String> synonyms = term.getSynonyms();
        if (synonyms != null) {
            // No duplicate: this is a Set
            for (String synonym : synonyms) cv_synonyms.add(synonym.trim());
        }
    }
    // Remove uninformative top level ancestors (Annotation, feature, and ROI)
    cv_ancestors_acs.removeAll(top_acs);
    // Index generated sets
    for (String ancestorac : cv_ancestors_acs) {
        addField(Fields.CV_ANCESTORS_ACS, ancestorac);
        addField(Fields.CV_ANCESTORS, this.terminologyservice.findCvTermByAccession(ancestorac).getName());
    }
    for (String synonym : cv_synonyms) {
        addField(Fields.CV_SYNONYMS, synonym);
    }
    List<CvTerm> enzymes = entry.getEnzymes();
    String ec_names = "";
    for (CvTerm currenzyme : enzymes) {
        cv_acs.add(currenzyme.getAccession());
        addField(Fields.CV_NAMES, currenzyme.getName());
        if (ec_names != "")
            ec_names += ", ";
        ec_names += "EC " + currenzyme.getAccession();
        List<String> synonyms = currenzyme.getSynonyms();
        if (synonyms != null)
            for (String synonym : synonyms) {
                addField(Fields.CV_SYNONYMS, synonym.trim());
            }
    }
    addField(Fields.EC_NAME, ec_names);
}

Example 23 with CvTerm

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

the class ExpressionFieldBuilder method init.

@Override
protected void init(Entry entry) {
    // Extract the tissues where there is expression ....
    Set<String> cv_tissues = new HashSet<String>();
    for (Annotation currannot : entry.getAnnotations()) {
        if (currannot.getCategory().equals("tissue specificity")) {
            // Check there is a detected expression
            boolean allnegative = true;
            for (AnnotationEvidence ev : currannot.getEvidences()) if (!ev.isNegativeEvidence() && (!this.isGold() || ev.getQualityQualifier().equals("GOLD"))) // Only a GOLD positive evidence can invalidate allnegative in the GOLD index
            {
                allnegative = false;
                break;
            }
            if (!allnegative) {
                // No duplicates this is a Set
                if (!this.isGold() || currannot.getQualityQualifier().equals("GOLD")) {
                    cv_tissues.add(currannot.getCvTermAccessionCode());
                    cv_tissues.add(currannot.getCvTermName());
                }
            }
        // else System.err.println("No expression: " + currannot.getCvTermAccessionCode());
        }
    }
    // Expression (without stages and expression_levels)
    SortedSet<String> cv_tissues_final = new TreeSet<String>();
    for (String cv : cv_tissues) {
        cv_tissues_final.add(cv);
        if (cv.startsWith("TS-")) {
            CvTerm term = terminologyservice.findCvTermByAccession(cv);
            if (null == term) {
                // there is nothing more we can add to indexed fields (ancestors, synonyms), so let's return
                logger.error(entry.getUniqueName() + " - term with accession |" + cv + "| not found with findCvTermByAccession()");
                continue;
            }
            List<String> ancestors = terminologyservice.getAllAncestorsAccession(term.getAccession());
            if (ancestors != null)
                for (String ancestorac : ancestors) {
                    cv_tissues_final.add(ancestorac);
                    cv_tissues_final.add(terminologyservice.findCvTermByAccession(ancestorac).getName());
                }
            List<String> synonyms = term.getSynonyms();
            if (synonyms != null)
                for (String synonym : synonyms) cv_tissues_final.add(synonym);
        }
    }
    for (String cv : cv_tissues_final) {
        addField(Fields.EXPRESSION, cv.trim());
    }
}

Example 24 with CvTerm

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

the class AnnotationFieldBuilder method handleAnnotationTerm.

protected void handleAnnotationTerm(Annotation currannot, Entry entry) {
    String quality = currannot.getQualityQualifier();
    String cvac = currannot.getCvTermAccessionCode();
    if (cvac != null && !cvac.isEmpty()) {
        if (cvac.startsWith("GO:")) {
            boolean allnegative = true;
            // We don't index negative annotations
            for (AnnotationEvidence ev : currannot.getEvidences()) allnegative = allnegative & ev.isNegativeEvidence();
            if (allnegative == true) {
                return;
            }
        }
        if (!this.isGold() || quality.equals("GOLD")) {
            addField(Fields.ANNOTATIONS, cvac);
            addField(Fields.ANNOTATIONS, currannot.getCvTermName());
            CvTerm term = this.terminologyservice.findCvTermByAccession(cvac);
            if (null == term) {
                // there is nothing more we can add to indexed fields (ancestors, synonyms), so let's return
                logger.error(entry.getUniqueName() + " - term with accession |" + cvac + "| not found with findCvTermByAccession()");
                return;
            }
            List<String> synonyms = this.terminologyservice.findCvTermByAccession(cvac).getSynonyms();
            if (synonyms != null) {
                String allsynonyms = "";
                for (String synonym : synonyms) {
                    if (!allsynonyms.isEmpty())
                        allsynonyms += " | ";
                    allsynonyms += synonym.trim();
                }
                addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(allsynonyms));
            }
            List<String> ancestors = terminologyservice.getAllAncestorsAccession(cvac);
            String allancestors = "";
            for (String ancestor : ancestors) {
                if (!allancestors.isEmpty())
                    allancestors += " | ";
                // adding Ac
                allancestors += ancestor + " | ";
                String ancestorname = this.terminologyservice.findCvTermByAccession(ancestor).getName();
                allancestors += ancestorname;
            }
            if (allancestors.endsWith(" domain"))
                // don't index generic top
                allancestors = "domain";
            else // level ancestors
            if (allancestors.endsWith("zinc finger region"))
                // don't index
                allancestors = "zinc finger region";
            else // ancestors
            if (allancestors.endsWith("repeat"))
                // don't index generic top
                allancestors = "repeat";
            // level ancestors
            if (allancestors.length() > 1)
                addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(allancestors));
        }
    }
}

Example 25 with CvTerm

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

the class StatementAnnotationBuilder method buildAnnotationEvidences.

protected List<AnnotationEvidence> buildAnnotationEvidences(List<Statement> Statements) {
    // Ensures there is no repeated evidence!
    Set<AnnotationEvidence> evidencesSet = Statements.stream().map(s -> {
        AnnotationEvidence evidence = new AnnotationEvidence();
        // TODO to be checked with Amos and Lydie
        evidence.setResourceType("database");
        evidence.setResourceAssociationType("evidence");
        evidence.setQualityQualifier(s.getValue(StatementField.EVIDENCE_QUALITY));
        evidence.setResourceId(findPublicationId(s));
        AnnotationEvidenceProperty evidenceProperty = addPropertyIfPresent(s.getValue(StatementField.EVIDENCE_INTENSITY), "intensity");
        AnnotationEvidenceProperty expContextSubjectProteinOrigin = addPropertyIfPresent(s.getValue(StatementField.ANNOTATION_SUBJECT_SPECIES), "subject-protein-origin");
        AnnotationEvidenceProperty expContextObjectProteinOrigin = addPropertyIfPresent(s.getValue(StatementField.ANNOTATION_OBJECT_SPECIES), "object-protein-origin");
        // Set properties which are not null
        evidence.setProperties(Arrays.asList(evidenceProperty, expContextSubjectProteinOrigin, expContextObjectProteinOrigin).stream().filter(p -> p != null).collect(Collectors.toList()));
        String statementEvidenceCode = s.getValue(StatementField.EVIDENCE_CODE);
        evidence.setEvidenceCodeAC(statementEvidenceCode);
        evidence.setAssignedBy(s.getValue(StatementField.ASSIGNED_BY));
        evidence.setAssignmentMethod(s.getValue(StatementField.ASSIGMENT_METHOD));
        evidence.setResourceType(s.getValue(StatementField.RESOURCE_TYPE));
        evidence.setEvidenceCodeOntology("evidence-code-ontology-cv");
        evidence.setNegativeEvidence("true".equalsIgnoreCase(s.getValue(StatementField.IS_NEGATIVE)));
        if (statementEvidenceCode != null) {
            CvTerm term = terminologyService.findCvTermByAccession(statementEvidenceCode);
            if (term != null) {
                evidence.setEvidenceCodeName(term.getName());
            } else {
                throw new NextProtException("Not found " + statementEvidenceCode + " in the database");
            }
        }
        evidence.setNote(s.getValue(StatementField.EVIDENCE_NOTE));
        return evidence;
    }).collect(Collectors.toSet());
    // Ensures there is no repeated evidence!
    evidencesSet.forEach(e -> {
        long generatedEvidenceId = IdentifierOffset.EVIDENCE_ID_COUNTER_FOR_STATEMENTS.incrementAndGet();
        e.setEvidenceId(generatedEvidenceId);
    });
    List<AnnotationEvidence> evidencesFiltered = evidencesSet.stream().filter(e -> e.getResourceId() != -2).collect(Collectors.toList());
    if (evidencesFiltered.size() < evidencesSet.size()) {
        int total = evidencesSet.size();
        int removed = total - evidencesFiltered.size();
        LOGGER.debug("Removed " + removed + " evidence because no resource id from a total of " + total);
    }
    return new ArrayList<>(evidencesFiltered);
}