Examples with Entity org.molgenis.data.Entity used on opensource projects

Example 66 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testApply.

@Test(dataProvider = "testApplyProvider")
public void testApply(AttributeType sourceAttributeType, Object sourceAttributeValue, String algorithm, AttributeType targetAttributeType, Object expected, String message) {
    String idAttrName = "id";
    EntityType entityType = entityTypeFactory.create("LL");
    entityType.addAttribute(attrMetaFactory.create().setName(idAttrName).setDataType(INT), ROLE_ID);
    entityType.addAttribute(attrMetaFactory.create().setName("source").setDataType(sourceAttributeType));
    Entity source = new DynamicEntity(entityType);
    source.set(idAttrName, 1);
    source.set("source", sourceAttributeValue);
    Attribute targetAttribute = attrMetaFactory.create().setName("target");
    targetAttribute.setDataType(targetAttributeType);
    AttributeMapping attributeMapping = new AttributeMapping(targetAttribute);
    attributeMapping.setAlgorithm(algorithm);
    Object result = algorithmService.apply(attributeMapping, source, entityType);
    assertEquals(result, expected, message);
}

Example 67 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testDotAnnotationWithXref.

@Test
public void testDotAnnotationWithXref() throws ParseException {
    EntityType referenceEntityType = entityTypeFactory.create("reference");
    referenceEntityType.addAttribute(attrMetaFactory.create().setName("id"), ROLE_ID);
    referenceEntityType.addAttribute(attrMetaFactory.create().setName("label"));
    Entity referenceEntity = new DynamicEntity(referenceEntityType);
    referenceEntity.set("id", "1");
    referenceEntity.set("label", "label 1");
    EntityType sourceEntityType = entityTypeFactory.create("source");
    sourceEntityType.addAttribute(attrMetaFactory.create().setName("id"), ROLE_ID);
    sourceEntityType.addAttribute(attrMetaFactory.create().setName("source_xref").setDataType(XREF));
    Entity sourceEntity = new DynamicEntity(sourceEntityType);
    sourceEntity.set("id", "1");
    sourceEntity.set("source_xref", referenceEntity);
    Attribute targetAttribute = attrMetaFactory.create().setName("target_label");
    AttributeMapping attributeMapping = new AttributeMapping(targetAttribute);
    attributeMapping.setAlgorithm("$('source_xref.label').value()");
    Object result = algorithmService.apply(attributeMapping, sourceEntity, sourceEntityType);
    assertEquals(result, "label 1");
}

Example 68 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testApplyMrefNillable.

@Test
public void testApplyMrefNillable() throws ParseException {
    String refEntityName = "refEntity";
    String refEntityIdAttrName = "id";
    String refEntityLabelAttrName = "label";
    String sourceEntityName = "source";
    String sourceEntityAttrName = "mref-source";
    String targetEntityAttrName = "mref-target";
    // ref entities
    EntityType refEntityType = entityTypeFactory.create(refEntityName);
    refEntityType.addAttribute(attrMetaFactory.create().setName(refEntityIdAttrName), ROLE_ID);
    refEntityType.addAttribute(attrMetaFactory.create().setName(refEntityLabelAttrName), ROLE_LABEL);
    // mapping
    Attribute targetAttribute = attrMetaFactory.create().setName(targetEntityAttrName);
    targetAttribute.setDataType(MREF).setNillable(true).setRefEntity(refEntityType);
    AttributeMapping attributeMapping = new AttributeMapping(targetAttribute);
    attributeMapping.setAlgorithm("$('" + sourceEntityAttrName + "').value()");
    // source Entity
    EntityType entityTypeSource = entityTypeFactory.create(sourceEntityName);
    entityTypeSource.addAttribute(attrMetaFactory.create().setName(refEntityIdAttrName).setDataType(INT).setAuto(true), ROLE_ID);
    entityTypeSource.addAttribute(attrMetaFactory.create().setName(sourceEntityAttrName).setDataType(MREF).setNillable(true).setRefEntity(refEntityType));
    Entity source = new DynamicEntity(entityTypeSource);
    source.set(sourceEntityAttrName, emptyList());
    Object result = algorithmService.apply(attributeMapping, source, entityTypeSource);
    assertEquals(result, emptyList());
}

Example 69 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testApplyMref.

@Test
public void testApplyMref() throws ParseException {
    String refEntityName = "refEntity";
    String refEntityIdAttrName = "id";
    String refEntityLabelAttrName = "label";
    String refEntityId0 = "id0";
    String refEntityId1 = "id1";
    String sourceEntityName = "source";
    String sourceEntityAttrName = "mref-source";
    String targetEntityAttrName = "mref-target";
    // ref entities
    EntityType refEntityType = entityTypeFactory.create(refEntityName);
    refEntityType.addAttribute(attrMetaFactory.create().setName(refEntityIdAttrName), ROLE_ID);
    refEntityType.addAttribute(attrMetaFactory.create().setName(refEntityLabelAttrName).setDataType(STRING), ROLE_LABEL);
    Entity refEntity0 = new DynamicEntity(refEntityType);
    refEntity0.set(refEntityIdAttrName, refEntityId0);
    refEntity0.set(refEntityLabelAttrName, "label0");
    Entity refEntity1 = new DynamicEntity(refEntityType);
    refEntity1.set(refEntityIdAttrName, refEntityId1);
    refEntity1.set(refEntityLabelAttrName, "label1");
    // mapping
    Attribute targetAttribute = attrMetaFactory.create().setName(targetEntityAttrName);
    targetAttribute.setDataType(MREF).setNillable(false).setRefEntity(refEntityType);
    AttributeMapping attributeMapping = new AttributeMapping(targetAttribute);
    attributeMapping.setAlgorithm("$('" + sourceEntityAttrName + "').value()");
    when(entityManager.getReference(refEntityType, refEntityId0)).thenReturn(refEntity0);
    when(entityManager.getReference(refEntityType, refEntityId1)).thenReturn(refEntity1);
    // source Entity
    EntityType entityTypeSource = entityTypeFactory.create(sourceEntityName);
    entityTypeSource.addAttribute(attrMetaFactory.create().setName(refEntityIdAttrName).setDataType(INT).setAuto(true), ROLE_ID);
    entityTypeSource.addAttribute(attrMetaFactory.create().setName(sourceEntityAttrName).setDataType(MREF).setNillable(false).setRefEntity(refEntityType));
    Entity source = new DynamicEntity(entityTypeSource);
    source.set(sourceEntityAttrName, Arrays.asList(refEntity0, refEntity1));
    Object result = algorithmService.apply(attributeMapping, source, entityTypeSource);
    assertEquals(result, Arrays.asList(refEntity0, refEntity1));
}

Example 70 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testGetAgeScript.

@Test
public void testGetAgeScript() throws ParseException {
    String idAttrName = "id";
    EntityType entityType = entityTypeFactory.create("LL");
    entityType.addAttribute(attrMetaFactory.create().setName(idAttrName).setDataType(INT), ROLE_ID);
    entityType.addAttribute(attrMetaFactory.create().setName("dob").setDataType(DATE));
    Entity source = new DynamicEntity(entityType);
    source.set(idAttrName, 1);
    source.set("dob", LocalDate.of(1973, Month.AUGUST, 28));
    Attribute targetAttribute = attrMetaFactory.create().setName("age");
    targetAttribute.setDataType(INT);
    AttributeMapping attributeMapping = new AttributeMapping(targetAttribute);
    attributeMapping.setAlgorithm("Math.floor((new Date(2015, 2, 12) - $('dob').value())/(365.2425 * 24 * 60 * 60 * 1000))");
    Object result = algorithmService.apply(attributeMapping, source, entityType);
    assertEquals(result, 41);
}