Examples with DataRequest org.molgenis.dataexplorer.controller.DataRequest used on opensource projects

Example 1 with DataRequest

use of org.molgenis.dataexplorer.controller.DataRequest in project molgenis by molgenis.

the class DataExplorerDownloadHandlerTest method testWriteToExcelTooManyCells.

@Test(expectedExceptions = MolgenisDataException.class, expectedExceptionsMessageRegExp = "Total number of cells for this download exceeds the maximum of 500000 for .xlsx downloads, please use .csv instead")
public void testWriteToExcelTooManyCells() throws Exception {
    when(dataService.count("sys_set_thousandgenomes", query)).thenReturn(2500001L);
    when(dataService.getEntityType("sys_set_thousandgenomes")).thenReturn(entityType);
    when(entityType.getAtomicAttributes()).thenReturn(asList(attribute1, attribute2, attribute3));
    when(attribute1.getName()).thenReturn("attr1");
    when(attribute2.getName()).thenReturn("attr2");
    when(attribute3.getName()).thenReturn("attr3");
    DataRequest dataRequest = new DataRequest();
    dataRequest.setEntityName("sys_set_thousandgenomes");
    dataRequest.setQuery(query);
    dataRequest.setAttributeNames(asList("attr1", "attr2"));
    dataRequest.setColNames(DataRequest.ColNames.ATTRIBUTE_NAMES);
    dataRequest.setEntityValues(DataRequest.EntityValues.ENTITY_LABELS);
    dataExplorerDownloadHandler.writeToExcel(dataRequest, mock(OutputStream.class));
}

Example 2 with DataRequest

use of org.molgenis.dataexplorer.controller.DataRequest in project molgenis by molgenis.

the class DataExplorerDownloadHandlerTest method testWriteToCSV.

@Test(dataProvider = "writeToExcelDataProvider")
public void testWriteToCSV(DataRequest.ColNames colNames, DataRequest.EntityValues entityValues, Map<String, List<List<String>>> expected) throws Exception {
    String entityTypeId = "sys_set_thousandgenomes";
    when(dataService.getEntityType(entityTypeId)).thenReturn(entityType);
    when(entityType.getAtomicAttributes()).thenReturn(asList(attribute1, attribute2, attribute3));
    if (colNames == DataRequest.ColNames.ATTRIBUTE_LABELS) {
        when(attribute1.getLabel()).thenReturn("attr1Label");
        when(attribute2.getLabel()).thenReturn("attr2Label");
    }
    when(attribute1.getName()).thenReturn("attr1");
    when(attribute2.getName()).thenReturn("attr2");
    when(attribute3.getName()).thenReturn("attr3");
    DataRequest dataRequest = new DataRequest();
    dataRequest.setEntityName(entityTypeId);
    dataRequest.setQuery(query);
    dataRequest.setAttributeNames(asList("attr1", "attr2"));
    dataRequest.setColNames(colNames);
    dataRequest.setEntityValues(entityValues);
    when(dataService.findAll(entityTypeId, query)).thenReturn(Stream.of(entity1, entity2));
    doReturn("entity1attr1").when(entity1).get("attr1");
    doReturn(refEntity1).when(entity1).get("attr2");
    doReturn("entity2attr1").when(entity2).get("attr1");
    doReturn(refEntity2).when(entity2).get("attr2");
    if (entityValues == DataRequest.EntityValues.ENTITY_LABELS) {
        when(refEntity1.getLabelValue()).thenReturn("refEntity1Label");
        when(refEntity2.getLabelValue()).thenReturn("refEntity2Label");
    } else {
        when(refEntity1.getIdValue()).thenReturn("refEntity1Id");
        when(refEntity2.getIdValue()).thenReturn("refEntity2Id");
    }
    File tmpFile = File.createTempFile("download", ".csv");
    FileOutputStream fos = new FileOutputStream(tmpFile);
    dataExplorerDownloadHandler.writeToCsv(dataRequest, fos, ',');
    assertEquals(readCsv(tmpFile), expected.get(entityTypeId), "entities should get exported");
    assertTrue(tmpFile.delete());
    verifyNoMoreInteractions(refEntity1, refEntity2, attribute1, attribute2);
}

Example 3 with DataRequest

use of org.molgenis.dataexplorer.controller.DataRequest in project molgenis by molgenis.

the class DataExplorerDownloadHandler method filterAttributes.

private List<Attribute> filterAttributes(DataRequest dataRequest) {
    EntityType entityType = dataService.getEntityType(dataRequest.getEntityName());
    final Set<String> attributeNames = newHashSet(dataRequest.getAttributeNames());
    return Streams.stream(entityType.getAtomicAttributes()).filter(attribute -> attributeNames.contains(attribute.getName())).collect(toList());
}

Example 4 with DataRequest

use of org.molgenis.dataexplorer.controller.DataRequest in project molgenis by molgenis.

the class DataExplorerDownloadHandlerTest method testWriteToExcel.

@Test(dataProvider = "writeToExcelDataProvider")
public void testWriteToExcel(DataRequest.ColNames colNames, DataRequest.EntityValues entityValues, Map<String, List<List<String>>> expected) throws Exception {
    String entityTypeId = "sys_set_thousandgenomes";
    when(dataService.count(entityTypeId, query)).thenReturn(2L);
    when(dataService.getEntityType(entityTypeId)).thenReturn(entityType);
    when(entityType.getAtomicAttributes()).thenReturn(asList(attribute1, attribute2, attribute3));
    if (colNames == DataRequest.ColNames.ATTRIBUTE_LABELS) {
        when(attribute1.getLabel()).thenReturn("attr1Label");
        when(attribute2.getLabel()).thenReturn("attr2Label");
    }
    when(attribute1.getName()).thenReturn("attr1");
    when(attribute2.getName()).thenReturn("attr2");
    when(attribute3.getName()).thenReturn("attr3");
    DataRequest dataRequest = new DataRequest();
    dataRequest.setEntityName(entityTypeId);
    dataRequest.setQuery(query);
    dataRequest.setAttributeNames(asList("attr1", "attr2"));
    dataRequest.setColNames(colNames);
    dataRequest.setEntityValues(entityValues);
    when(dataService.findAll(entityTypeId, query)).thenReturn(Stream.of(entity1, entity2));
    doReturn("entity1attr1").when(entity1).get("attr1");
    doReturn(refEntity1).when(entity1).get("attr2");
    doReturn("entity2attr1").when(entity2).get("attr1");
    doReturn(refEntity2).when(entity2).get("attr2");
    if (entityValues == DataRequest.EntityValues.ENTITY_LABELS) {
        when(refEntity1.getLabelValue()).thenReturn("refEntity1Label");
        when(refEntity2.getLabelValue()).thenReturn("refEntity2Label");
    } else {
        when(refEntity1.getIdValue()).thenReturn("refEntity1Id");
        when(refEntity2.getIdValue()).thenReturn("refEntity2Id");
    }
    File tmpFile = File.createTempFile("download", ".xlsx");
    FileOutputStream fos = new FileOutputStream(tmpFile);
    dataExplorerDownloadHandler.writeToExcel(dataRequest, fos);
    assertEquals(readExcel(tmpFile), expected, "entities should get exported");
    assertTrue(tmpFile.delete());
    verifyNoMoreInteractions(refEntity1, refEntity2, attribute1, attribute2);
}