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

Example 51 with Entity

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

the class CsvIteratorTest method testIteratorFromCsvFile.

@Test
public void testIteratorFromCsvFile() throws IOException {
    File csvFile = createTmpFileForResource("testdata.csv");
    CsvIterator it = new CsvIterator(csvFile, "testdata", null, null, entityType);
    assertEquals(it.getColNamesMap().keySet(), Sets.newLinkedHashSet(Arrays.asList("col1", "col2")));
    assertEquals(Iterators.size(it), 5);
    it = new CsvIterator(csvFile, "testdata", null, null, entityType);
    Entity entity = it.next();
    assertEquals(entity.get("col1"), "val1");
    assertEquals(entity.get("col2"), "val2");
}

Example 52 with Entity

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

the class CsvIteratorTest method testIteratorFromCsvFileWithBom.

@Test
public void testIteratorFromCsvFileWithBom() throws IOException {
    File csvFile = createTmpFileForResource("testDataWithBom.csv");
    CsvIterator it = new CsvIterator(csvFile, "testdata", null, null, entityType);
    assertEquals(it.getColNamesMap().keySet(), Sets.newLinkedHashSet(Arrays.asList("col1", "col2")));
    assertEquals(Iterators.size(it), 5);
    it = new CsvIterator(csvFile, "testdata", null, null, entityType);
    Entity entity = it.next();
    assertEquals(entity.get("col1"), "val1");
    assertEquals(entity.get("col2"), "val2");
}

Example 53 with Entity

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

the class CsvRepositoryTest method addCellProcessor_header.

@Test
public void addCellProcessor_header() throws IOException {
    CellProcessor processor = when(mock(CellProcessor.class).processHeader()).thenReturn(true).getMock();
    when(processor.process("col1")).thenReturn("col1");
    when(processor.process("col2")).thenReturn("col2");
    try (CsvRepository csvRepository = new CsvRepository(test, entityTypeFactory, attrMetaFactory, null)) {
        csvRepository.addCellProcessor(processor);
        for (@SuppressWarnings("unused") Entity entity : csvRepository) {
        }
        verify(processor).process("col1");
        verify(processor).process("col2");
    }
}

Example 54 with Entity

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

the class CsvRepositoryTest method iterator_emptylines.

@Test
public void iterator_emptylines() throws IOException {
    try (CsvRepository csvRepository = new CsvRepository(emptylines, entityTypeFactory, attrMetaFactory, null)) {
        Iterator<Entity> it = csvRepository.iterator();
        Entity entity = it.next();
        assertEquals(entity.get("col1"), "val1");
        assertEquals(entity.get("col2"), "val2");
        assertFalse(it.hasNext());
    }
}

Example 55 with Entity

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

the class SortaCsvRepository method iterator.

@Override
public Iterator<Entity> iterator() {
    final AtomicInteger count = new AtomicInteger(0);
    final Iterator<Entity> iterator = csvRepository.iterator();
    return new Iterator<Entity>() {

        @Override
        public boolean hasNext() {
            return iterator.hasNext();
        }

        @Override
        public Entity next() {
            Entity entity = iterator.next();
            if (isEmpty(entity.getString(ALLOWED_IDENTIFIER))) {
                DynamicEntity dynamicEntity = new DynamicEntity(getEntityType());
                dynamicEntity.set(entity);
                entity = dynamicEntity;
                entity.set(ALLOWED_IDENTIFIER, String.valueOf(count.incrementAndGet()));
            }
            return entity;
        }
    };
}