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

Example 6 with Family

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

the class NXVelocityUtilsTest method testGetFamilyHierarchyFromRoot.

@Test
public void testGetFamilyHierarchyFromRoot() throws Exception {
    Family superfamily = new Family();
    superfamily.setName("ba superfamily");
    Family family = new Family();
    family.setName("be family");
    Family subfamily = new Family();
    subfamily.setName("bi subfamily");
    subfamily.setParent(family);
    family.setParent(superfamily);
    Assert.assertEquals(Arrays.asList(superfamily, family, subfamily), NXVelocityUtils.getFamilyHierarchyFromRoot(subfamily));
}

Example 7 with Family

use of org.nextprot.api.core.domain.Family 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 8 with Family

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

the class FamilyServiceImpl method findFamilies.

@Override
@Cacheable("families")
public List<Family> findFamilies(String uniqueName) {
    List<Family> families = familyDao.findFamilies(uniqueName);
    for (Family child : families) {
        while (true) {
            Long childId = child.getFamilyId();
            // TODO can this be done with one query???
            Family parent = familyDao.findParentOfFamilyId(childId);
            if (parent == null)
                break;
            child.setParent(parent);
            // TODO setting a reference inside a for loop????
            child = parent;
        }
    }
    Collections.sort(families, FAMILY_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<Family>().addAll(families).build();
}

Example 9 with Family

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

the class FamilyDaoIntegrationTest method shouldReturn_1_Parent_Family.

@Test
public void shouldReturn_1_Parent_Family() {
    List<Family> families = familyDao.findFamilies("NX_Q3SY69");
    Long familyId = families.get(0).getFamilyId();
    Family fam = familyDao.findParentOfFamilyId(64506L);
    assertTrue(fam.getAccession() != null);
    // always null (region comes from annotation)
    assertTrue(fam.getDescription() == null);
    assertTrue(fam.getName() != null);
    // always null (region comes from annotation)
    assertTrue(fam.getRegion() == null);
    assertTrue(fam.getFamilyId() > 0);
    // the parent (if any) is set later in the family service
    assertTrue(fam.getParent() == null);
}

Example 10 with Family

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

the class FamilyDaoIntegrationTest method shouldReturn_No_Parent_Family.

@Test
public void shouldReturn_No_Parent_Family() {
    // random id
    Long familyId = 872345298725L;
    Family fam = familyDao.findParentOfFamilyId(familyId);
    assertTrue(fam == null);
}