Examples with DynamicEntity org.molgenis.data.support.DynamicEntity used on opensource projects

Example 61 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class VcfUtilsTest method beforeMethod.

@BeforeMethod
public void beforeMethod() throws IOException {
    /*
			 * 1 10050000 test21 G A . PASS AC=21;AN=22;GTC=0,1,10 1 10050001 test22 G A . PASS AC=22;AN=23;GTC=1,2,11 1
			 * 10050002 test23 G A . PASS AC=23;AN=24;GTC=2,3,12
			 */
    metaDataCanAnnotate.addAttribute(attributeChrom, ROLE_ID);
    metaDataCanAnnotate.addAttribute(attributePos);
    metaDataCanAnnotate.addAttribute(attributeRef);
    metaDataCanAnnotate.addAttribute(attributeAlt);
    metaDataCantAnnotate.addAttribute(attributeCantAnnotateChrom);
    metaDataCantAnnotate.addAttribute(attributePos);
    metaDataCantAnnotate.addAttribute(attributeRef);
    metaDataCantAnnotate.addAttribute(attributeAlt);
    entity = new DynamicEntity(metaDataCanAnnotate);
    entity1 = new DynamicEntity(metaDataCanAnnotate);
    entity2 = new DynamicEntity(metaDataCanAnnotate);
    entity3 = new DynamicEntity(metaDataCanAnnotate);
    entity4 = new DynamicEntity(metaDataCanAnnotate);
    metaDataCanAnnotate.addAttribute(attributeFactory.create().setName(ID).setDataType(STRING));
    metaDataCanAnnotate.addAttribute(attributeFactory.create().setName(QUAL).setDataType(STRING));
    metaDataCanAnnotate.addAttribute(attributeFactory.create().setName(FILTER).setDataType(STRING));
    metaDataCanAnnotate.addAttribute(attributeFactory.create().setName(EFFECT).setDataType(STRING).setDescription("EFFECT annotations: 'Alt_Allele | Gene_Name | Annotation | Putative_impact | Gene_ID | Feature_type | Feature_ID | Transcript_biotype | Rank_total | HGVS_c | HGVS_p | cDNA_position | CDS_position | Protein_position | Distance_to_feature | Errors'"));
    Attribute INFO = attributeFactory.create().setName("INFO").setDataType(COMPOUND);
    Attribute AC = attributeFactory.create().setName("AC").setDataType(STRING).setParent(INFO);
    Attribute AN = attributeFactory.create().setName("AN").setDataType(STRING).setParent(INFO);
    Attribute GTC = attributeFactory.create().setName("GTC").setDataType(STRING).setParent(INFO);
    metaDataCanAnnotate.addAttribute(INFO);
    metaDataCanAnnotate.addAttribute(AC);
    metaDataCanAnnotate.addAttribute(AN);
    metaDataCanAnnotate.addAttribute(GTC);
    annotatedEntityType.addAttribute(attributeChrom, ROLE_ID);
    annotatedEntityType.addAttribute(attributePos);
    annotatedEntityType.addAttribute(attributeRef);
    annotatedEntityType.addAttribute(attributeAlt);
    annotatedEntityType.addAttribute(attributeFactory.create().setName(ID).setDataType(STRING));
    annotatedEntityType.addAttribute(attributeFactory.create().setName(QUAL).setDataType(STRING));
    annotatedEntityType.addAttribute((attributeFactory.create().setName(FILTER).setDataType(STRING)).setDescription("Test that description is not: '" + VcfRepository.DEFAULT_ATTRIBUTE_DESCRIPTION + "'"));
    Attribute annoAttr = attributeFactory.create().setName("ANNO").setDataType(STRING).setParent(INFO);
    annotatedEntityType.addAttribute(INFO);
    annotatedEntityType.addAttribute(AC);
    annotatedEntityType.addAttribute(AN);
    annotatedEntityType.addAttribute(GTC);
    annotatedEntityType.addAttribute(annoAttr);
    metaDataCanAnnotate.addAttribute(annoAttr);
    entity1.set(VcfAttributes.CHROM, "1");
    entity1.set(VcfAttributes.POS, 10050000);
    entity1.set(VcfAttributes.ID, "test21");
    entity1.set(VcfAttributes.REF, "G");
    entity1.set(VcfAttributes.ALT, "A");
    entity1.set(VcfAttributes.QUAL, ".");
    entity1.set(VcfAttributes.FILTER, "PASS");
    entity1.set("AC", "21");
    entity1.set("AN", "22");
    entity1.set("GTC", "0,1,10");
    entity1.set(EFFECT, "A|TUBB8|missense_variant|MODERATE|TUBB8|transcript|NM_177987.2|Coding|4/4|c.1286C>T|p.Thr429Met|1286/1504|1286/1335|429/444||");
    entity2.set(VcfAttributes.CHROM, "1");
    entity2.set(VcfAttributes.POS, 10050001);
    entity2.set(VcfAttributes.ID, "test22");
    entity2.set(VcfAttributes.REF, "G");
    entity2.set(VcfAttributes.ALT, "A");
    entity2.set(VcfAttributes.QUAL, ".");
    entity2.set(VcfAttributes.FILTER, "PASS");
    entity2.set(EFFECT, "A|TUBB8|missense_variant|MODERATE|TUBB8|transcript|NM_177987.2|Coding|4/4|c.1286C>T|p.Thr429Met|1286/1504|1286/1335|429/444||,A|GEN2|missense_variant|MODERATE|GEN2|transcript|NM_177987.2|Coding|4/4|c.1286C>T|p.Thr429Met|1286/1504|1286/1335|429/444||");
    entity3.set(VcfAttributes.CHROM, "1");
    entity3.set(VcfAttributes.POS, 10050002);
    entity3.set(VcfAttributes.ID, "test23");
    entity3.set(VcfAttributes.REF, "G");
    entity3.set(VcfAttributes.ALT, "A");
    entity3.set(VcfAttributes.QUAL, ".");
    entity3.set(VcfAttributes.FILTER, "PASS");
    entities = new ArrayList<>();
    entities.add(entity1);
    entities.add(entity2);
    entities.add(entity3);
    expectedEffectsEntityType = entityTypeFactory.create("EFFECTannotations");
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("identifier").setDataType(STRING), ROLE_ID);
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Alt_Allele").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Gene_Name").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Annotation").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Putative_impact").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Gene_ID").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Feature_type").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Feature_ID").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Transcript_biotype").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Rank_total").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("HGVS_c").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("HGVS_p").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("cDNA_position").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("CDS_position").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Protein_position").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Distance_to_feature").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("Errors").setDataType(STRING));
    expectedEffectsEntityType.addAttribute(attributeFactory.create().setName("VARIANT").setDataType(XREF).setRefEntity(metaDataCanAnnotate));
}

Example 62 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class EntityManagerImpl method create.

private Entity create(EntityType entityType, Fetch fetch, CreationMode creationMode) {
    Entity entity = new DynamicEntity(entityType);
    if (fetch != null) {
        // create partial entity that loads attribute values not contained in the fetch on demand.
        entity = new PartialEntity(entity, fetch, this);
    }
    if (entityType.hasAttributeWithExpression()) {
        // create entity that computed values based on expressions defined in meta data
        entity = new EntityWithComputedAttributes(entity);
    }
    if (creationMode == POPULATE) {
        entityPopulator.populate(entity);
    }
    EntityFactory<? extends Entity, ?> entityFactory = entityFactoryRegistry.getEntityFactory(entityType);
    if (entityFactory != null) {
        // create static entity (e.g. Tag, Language, Package) that wraps the constructed dynamic or partial entity.
        return entityFactory.create(entity);
    }
    return entity;
}

Example 63 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class OmimResultFilter method filterResults.

@Override
public Optional<Entity> filterResults(Iterable<Entity> results, Entity annotatedEntity, boolean updateMode) {
    if (updateMode == true) {
        throw new MolgenisDataException("This annotator/filter does not support updating of values");
    }
    Optional<Entity> firstResult = FluentIterable.from(results).first();
    // FIXME 4714 refactor to work with auto id, setPackage() and setName()
    EntityType emd = entityTypeFactory.create().setId(OmimAnnotator.NAME);
    emd.addAttributes(Arrays.asList(omimAnnotator.getPhenotypeAttr(), omimAnnotator.getMimNumberAttr(), omimAnnotator.getOmimLocationAttr(), omimAnnotator.getEntryAttr(), omimAnnotator.getTypeAttr()));
    return firstResult.transform(e -> {
        Entity result = new DynamicEntity(emd);
        result.set(OMIM_DISORDER, e.get(OmimRepository.OMIM_PHENOTYPE_COL_NAME));
        result.set(OMIM_CAUSAL_IDENTIFIER, e.get(OmimRepository.OMIM_MIM_NUMBER_COL_NAME));
        result.set(OMIM_CYTO_LOCATIONS, e.get(OmimRepository.OMIM_CYTO_LOCATION_COL_NAME));
        result.set(OMIM_TYPE, e.get(OmimRepository.OMIM_TYPE_COL_NAME).toString());
        result.set(OMIM_ENTRY, e.get(OmimRepository.OMIM_ENTRY_COL_NAME).toString());
        return result;
    });
}

Example 64 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class EntityTestHarness method createEntity.

public Entity createEntity(EntityType entityType, int id, Entity refEntity) {
    Entity entity = new DynamicEntity(entityType);
    entity.set(ATTR_ID, "" + id);
    entity.set(ATTR_STRING, "string1");
    entity.set(ATTR_BOOL, id % 2 == 0);
    entity.set(ATTR_CATEGORICAL, refEntity);
    entity.set(ATTR_CATEGORICAL_MREF, refEntity == null ? emptyList() : singletonList(refEntity));
    entity.set(ATTR_DATE, date);
    entity.set(ATTR_DATETIME, dateTime);
    entity.set(ATTR_EMAIL, "this.is@mail.address");
    entity.set(ATTR_DECIMAL, id + 0.123);
    entity.set(ATTR_HTML, id % 2 == 1 ? "<html>where is my head and where is my body</html>" : null);
    entity.set(ATTR_HYPERLINK, "http://www.molgenis.org");
    entity.set(ATTR_LONG, id * 1000000L);
    entity.set(ATTR_INT, 10 + id);
    entity.set(ATTR_SCRIPT, "/bin/blaat/script.sh");
    entity.set(ATTR_XREF, refEntity);
    entity.set(ATTR_MREF, refEntity == null ? emptyList() : singletonList(refEntity));
    entity.set(ATTR_COMPOUND_CHILD_INT, 10 + id);
    entity.set(ATTR_ENUM, id % 2 == 0 ? "option1" : "option2");
    return new EntityWithComputedAttributes(entity);
}

Example 65 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class JsMagmaScriptEvaluatorTest method testNull.

@Test
public void testNull() {
    Entity person0 = new DynamicEntity(personBirthDateMeta);
    person0.set("birthdate", LocalDate.now());
    String script = "$('birthdate').age().value() < 18  || $('birthdate').value() != null";
    Object result = jsMagmaScriptEvaluator.eval(script, person0, 3);
    assertEquals(result, true);
    Entity person1 = new DynamicEntity(personBirthDateMeta);
    person1.set("birthdate", null);
    result = jsMagmaScriptEvaluator.eval(script, person1, 3);
    assertEquals(result, false);
}