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

Example 86 with DynamicEntity

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

the class MetaDataServiceIT method testUpdateEntityType.

@WithMockUser(username = USERNAME)
@Test
public void testUpdateEntityType() {
    EntityType updatedEntityType = metaDataService.getEntityType(ENTITY_TYPE_ID);
    updatedEntityType.getAttribute(ATTR_STRING).setDataType(ENUM).setEnumOptions(asList("string0", "string1"));
    updatedEntityType.getAttribute(ATTR_BOOL).setDataType(STRING);
    updatedEntityType.getAttribute(ATTR_CATEGORICAL).setDataType(LONG).setRefEntity(null);
    updatedEntityType.getAttribute(ATTR_CATEGORICAL_MREF).setDataType(MREF);
    updatedEntityType.getAttribute(ATTR_DATE).setDataType(DATE_TIME);
    updatedEntityType.getAttribute(ATTR_DATETIME).setDataType(DATE);
    updatedEntityType.getAttribute(ATTR_EMAIL).setDataType(STRING);
    updatedEntityType.getAttribute(ATTR_DECIMAL).setDataType(INT);
    updatedEntityType.getAttribute(ATTR_HTML).setDataType(TEXT);
    updatedEntityType.getAttribute(ATTR_HYPERLINK).setDataType(STRING);
    updatedEntityType.getAttribute(ATTR_LONG).setDataType(DECIMAL);
    updatedEntityType.getAttribute(ATTR_INT).setDataType(LONG);
    updatedEntityType.getAttribute(ATTR_SCRIPT).setDataType(TEXT);
    updatedEntityType.getAttribute(ATTR_XREF).setDataType(CATEGORICAL);
    updatedEntityType.getAttribute(ATTR_MREF).setDataType(CATEGORICAL_MREF);
    updatedEntityType.getAttribute(ATTR_ENUM).setDataType(STRING).setEnumOptions(emptyList());
    metaDataService.updateEntityType(updatedEntityType);
    Entity expectedEntity = new DynamicEntity(updatedEntityType);
    expectedEntity.set(ATTR_ID, "0");
    expectedEntity.set(ATTR_STRING, "string1");
    expectedEntity.set(ATTR_BOOL, "true");
    expectedEntity.set(ATTR_CATEGORICAL, 0L);
    expectedEntity.set(ATTR_CATEGORICAL_MREF, singletonList(refEntities.get(0)));
    expectedEntity.set(ATTR_DATE, LocalDate.parse("2012-12-21").atStartOfDay(systemDefault()).toInstant());
    expectedEntity.set(ATTR_DATETIME, MolgenisDateFormat.parseLocalDate("1985-08-12T06:12:13Z"));
    expectedEntity.set(ATTR_EMAIL, "this.is@mail.address");
    // before update: 0.123
    expectedEntity.set(ATTR_DECIMAL, 0);
    expectedEntity.set(ATTR_HTML, null);
    expectedEntity.set(ATTR_HYPERLINK, "http://www.molgenis.org");
    expectedEntity.set(ATTR_LONG, 0.0);
    expectedEntity.set(ATTR_INT, 10L);
    expectedEntity.set(ATTR_SCRIPT, "/bin/blaat/script.sh");
    expectedEntity.set(ATTR_XREF, refEntities.get(0));
    expectedEntity.set(ATTR_MREF, singletonList(refEntities.get(0)));
    expectedEntity.set(ATTR_COMPOUND_CHILD_INT, 10);
    expectedEntity.set(ATTR_ENUM, "option1");
    expectedEntity = new EntityWithComputedAttributes(expectedEntity);
    assertTrue(EntityUtils.equals(dataService.findOneById(ENTITY_TYPE_ID, "0"), expectedEntity));
}

Example 87 with DynamicEntity

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

the class JobExecutionUpdaterImpl method update.

@Override
public void update(JobExecution jobExecution) {
    Entity copy = new DynamicEntity(jobExecution.getEntityType());
    copy.set(jobExecution);
    executorService.execute(() -> updateInternal(copy));
}

Example 88 with DynamicEntity

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

the class SortaJobProcessor method process.

public void process() {
    RunAsSystemAspect.runAsSystem(() -> {
        long maxCount = dataService.count(inputRepositoryName, new QueryImpl<>());
        progress.status("Matching " + maxCount + " input terms from " + inputRepositoryName + ".\nStoring results in " + resultRepositoryName);
        progress.setProgressMax((int) maxCount);
        // FIXME get rid of getApplicationContext reference
        MatchingTaskContentMetaData matchingTaskContentMetaData = getApplicationContext().getBean(MatchingTaskContentMetaData.class);
        // Match input terms with code
        List<Entity> entitiesToAdd = newArrayList();
        dataService.findAll(inputRepositoryName).forEach(inputRow -> {
            Entity resultEntity = new DynamicEntity(matchingTaskContentMetaData) {

                @Override
                protected void validateValueType(String attrName, Object value) {
                // FIXME enable validation by not overriding this method
                }
            };
            resultEntity.set(MatchingTaskContentMetaData.INPUT_TERM, inputRow);
            resultEntity.set(MatchingTaskContentMetaData.IDENTIFIER, idGenerator.generateId());
            resultEntity.set(MatchingTaskContentMetaData.VALIDATED, false);
            entitiesToAdd.add(resultEntity);
            Iterable<Entity> ontologyTermEntities = sortaService.findOntologyTermEntities(ontologyIri, inputRow);
            if (Iterables.size(ontologyTermEntities) > 0) {
                Entity firstMatchedOntologyTerm = Iterables.getFirst(ontologyTermEntities, new DynamicEntity(matchingTaskContentMetaData));
                resultEntity.set(MatchingTaskContentMetaData.MATCHED_TERM, firstMatchedOntologyTerm.get(OntologyTermMetaData.ONTOLOGY_TERM_IRI));
                resultEntity.set(MatchingTaskContentMetaData.SCORE, firstMatchedOntologyTerm.get(SCORE));
            } else {
                resultEntity.set(MatchingTaskContentMetaData.SCORE, 0.0);
            }
            // Add entity in batch
            if (entitiesToAdd.size() >= ADD_BATCH_SIZE) {
                dataService.add(resultRepositoryName, entitiesToAdd.stream());
                entitiesToAdd.clear();
            }
            // Increase the number of the progress
            counter.incrementAndGet();
            // Update the progress only when the progress proceeds the threshold
            if (counter.get() % PROGRESS_UPDATE_BATCH_SIZE == 0) {
                progress.progress(counter.get(), "Processed " + counter + " input terms.");
            }
        });
        // Add the rest
        if (!entitiesToAdd.isEmpty()) {
            dataService.add(resultRepositoryName, entitiesToAdd.stream());
        }
        progress.progress(counter.get(), "Processed " + counter + " input terms.");
        progress.setResultUrl(menuReaderService.getMenu().findMenuItemPath(SortaController.ID) + "/result/" + resultRepositoryName);
    });
}

Example 89 with DynamicEntity

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

the class SortaServiceImplTest method findOntologyTermEntities.

@Test
public void findOntologyTermEntities() {
    Attribute nameAttr = when(mock(Attribute.class).getName()).thenReturn("Name").getMock();
    when(nameAttr.getDataType()).thenReturn(STRING);
    Attribute omimAttr = when(mock(Attribute.class).getName()).thenReturn("OMIM").getMock();
    when(omimAttr.getDataType()).thenReturn(STRING);
    EntityType entityType = mock(EntityType.class);
    when(entityType.getAtomicAttributes()).thenReturn(asList(nameAttr, omimAttr));
    when(entityType.getAttribute("Name")).thenReturn(nameAttr);
    when(entityType.getAttribute("OMIM")).thenReturn(omimAttr);
    // Test one: match only the name of input with ontology terms
    Entity firstInput = new DynamicEntity(entityType);
    firstInput.set("Name", "hearing impairment");
    Iterable<Entity> ontologyTerms_test1 = sortaServiceImpl.findOntologyTermEntities(ONTOLOGY_IRI, firstInput);
    Iterator<Entity> iterator_test1 = ontologyTerms_test1.iterator();
    assertEquals(iterator_test1.hasNext(), true);
    Entity firstMatch_test1 = iterator_test1.next();
    assertEquals(firstMatch_test1.getDouble(COMBINED_SCORE).intValue(), 100);
    assertEquals(iterator_test1.hasNext(), true);
    Entity secondMatch_test1 = iterator_test1.next();
    assertEquals(secondMatch_test1.getDouble(COMBINED_SCORE).intValue(), new Double(85).intValue());
    assertEquals(iterator_test1.hasNext(), false);
    // Test two: match the database annotation of input with ontology terms
    Entity secondInput = new DynamicEntity(entityType);
    secondInput.set("Name", "input");
    secondInput.set("OMIM", "123456");
    Iterable<Entity> ontologyTerms_test2 = sortaServiceImpl.findOntologyTermEntities(ONTOLOGY_IRI, secondInput);
    Iterator<Entity> iterator_test2 = ontologyTerms_test2.iterator();
    assertEquals(iterator_test2.hasNext(), true);
    Entity firstMatch_test2 = iterator_test2.next();
    assertEquals(firstMatch_test2.getDouble(COMBINED_SCORE).intValue(), 100);
    assertEquals(iterator_test2.hasNext(), false);
    // Test three: match only the name of input with ontology terms, since the name contains multiple synonyms
    // therefore add up all the scores from synonyms
    Entity thirdInput = new DynamicEntity(entityType);
    thirdInput.set("Name", "proptosis, protruding eye, Exophthalmos ");
    Iterable<Entity> ontologyTerms_test3 = sortaServiceImpl.findOntologyTermEntities(ONTOLOGY_IRI, thirdInput);
    Iterator<Entity> iterator_test3 = ontologyTerms_test3.iterator();
    assertEquals(iterator_test3.hasNext(), true);
    Entity firstMatch_test3 = iterator_test3.next();
    assertEquals(firstMatch_test3.getDouble(COMBINED_SCORE).intValue(), 100);
    assertEquals(iterator_test3.hasNext(), false);
}

Example 90 with DynamicEntity

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

the class OneToManyCategoryAlgorithmGeneratorTest method init.

@BeforeMethod
public void init() {
    DataService dataService = Mockito.mock(DataService.class);
    categoryAlgorithmGenerator = new OneToManyCategoryAlgorithmGenerator(dataService);
    EntityType targetRefEntityType = entityTypeFactory.create("POTATO_REF");
    Attribute targetCodeAttribute = attrMetaFactory.create().setName("code").setDataType(INT);
    Attribute targetLabelAttribute = attrMetaFactory.create().setName("label");
    targetRefEntityType.addAttribute(targetCodeAttribute, ROLE_ID);
    targetRefEntityType.addAttribute(targetLabelAttribute, ROLE_LABEL);
    targetAttribute = attrMetaFactory.create().setName("Current Consumption Frequency of Potatoes").setDataType(CATEGORICAL);
    targetAttribute.setRefEntity(targetRefEntityType);
    Entity targetEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Almost daily + daily"));
    Entity targetEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "Several times a week"));
    Entity targetEntity3 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "About once a week"));
    Entity targetEntity4 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "Never + fewer than once a week"));
    Entity targetEntity5 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
    Mockito.when(dataService.findAll(targetRefEntityType.getId())).thenAnswer(invocation -> Stream.of(targetEntity1, targetEntity2, targetEntity3, targetEntity4, targetEntity5));
    targetEntityType = entityTypeFactory.create("target");
    targetEntityType.addAttribute(targetAttribute);
    EntityType sourceRefEntityType = createEntityType("LifeLines_POTATO_REF");
    sourceAttribute = attrMetaFactory.create().setName("MESHED_POTATO").setDataType(CATEGORICAL);
    sourceAttribute.setLabel("How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
    sourceAttribute.setRefEntity(sourceRefEntityType);
    Entity sourceEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Not this month"));
    Entity sourceEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1 day per month"));
    Entity sourceEntity3 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "2-3 days per month"));
    Entity sourceEntity4 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "1 day per week"));
    Entity sourceEntity5 = new DynamicEntity(targetRefEntityType, of("code", 5, "label", "2-3 days per week"));
    Entity sourceEntity6 = new DynamicEntity(targetRefEntityType, of("code", 6, "label", "4-5 days per week"));
    Entity sourceEntity7 = new DynamicEntity(targetRefEntityType, of("code", 7, "label", "6-7 days per week"));
    Mockito.when(dataService.findAll(sourceRefEntityType.getId())).thenAnswer(invocation -> Stream.of(sourceEntity1, sourceEntity2, sourceEntity3, sourceEntity4, sourceEntity5, sourceEntity6, sourceEntity7));
    EntityType sourceRefEntityType1 = createEntityType("Mitchelstown_POTATO_REF");
    sourceAttribute1 = attrMetaFactory.create().setName("MESHED_POTATO_1").setDataType(CATEGORICAL);
    sourceAttribute1.setLabel("How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
    sourceAttribute1.setRefEntity(sourceRefEntityType1);
    Entity sourceEntity8 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "never/less than 1 per month"));
    Entity sourceEntity9 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1-3 per month"));
    Entity sourceEntity10 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "once a week"));
    Entity sourceEntity11 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "2-4 per week"));
    Entity sourceEntity12 = new DynamicEntity(targetRefEntityType, of("code", 5, "label", "5-6 per week"));
    Entity sourceEntity13 = new DynamicEntity(targetRefEntityType, of("code", 6, "label", "once a day"));
    Entity sourceEntity14 = new DynamicEntity(targetRefEntityType, of("code", 7, "label", "2-3 per day"));
    Entity sourceEntity15 = new DynamicEntity(targetRefEntityType, of("code", 8, "label", "4-5 per day"));
    Entity sourceEntity16 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "6+ per day"));
    Mockito.when(dataService.findAll(sourceRefEntityType1.getId())).thenAnswer(invocation -> Stream.of(sourceEntity8, sourceEntity9, sourceEntity10, sourceEntity11, sourceEntity12, sourceEntity13, sourceEntity14, sourceEntity15, sourceEntity16));
    EntityType sourceRefEntityType2 = createEntityType("Mitchelstown_Stroke_REF");
    sourceAttribute2 = attrMetaFactory.create().setName("Stroke").setDataType(CATEGORICAL);
    sourceAttribute2.setLabel("History of stroke");
    sourceAttribute2.setRefEntity(sourceRefEntityType2);
    Entity sourceEntity17 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "yes"));
    Entity sourceEntity18 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "no"));
    Entity sourceEntity19 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
    Mockito.when(dataService.findAll(sourceRefEntityType2.getId())).thenAnswer(invocation -> Stream.of(sourceEntity17, sourceEntity18, sourceEntity19));
    sourceEntityType = entityTypeFactory.create("source");
    sourceEntityType.addAttributes(Lists.newArrayList(sourceAttribute, sourceAttribute1, sourceAttribute2));
}