use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSinglePairSuccess.
/**
* Tests out successfully preparing paired and single workflow input files
* for execution.
*
* @throws InterruptedException
* @throws ExecutionManagerException
* @throws IOException
* @throws IridaWorkflowException
*/
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSinglePairSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
History history = new History();
history.setName("testPrepareAnalysisFilesPairSuccess");
HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
History createdHistory = historiesClient.create(history);
IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSinglePaired);
Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSinglePairSubmissionInDatabaseDifferentSample(1L, 2L, pairSequenceFiles1A, pairSequenceFiles2A, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
PreparedWorkflowGalaxy preparedWorkflow = analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
assertEquals("the response history id should match the input history id", createdHistory.getId(), preparedWorkflow.getRemoteAnalysisId());
WorkflowInputsGalaxy workflowInputsGalaxy = preparedWorkflow.getWorkflowInputs();
assertNotNull("the returned workflow inputs should not be null", workflowInputsGalaxy);
// verify correct files have been uploaded
List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
assertEquals("the created history has an invalid number of elements", 6, historyContents.size());
Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
assertTrue("the created history should contain the file " + sequenceFilePath2A.toFile().getName(), contentsMap.containsKey(sequenceFilePath2A.toFile().getName()));
assertTrue("the created history should contain the file " + sequenceFilePath3.toFile().getName(), contentsMap.containsKey(sequenceFilePath3.toFile().getName()));
assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
assertTrue("the created history should contain a dataset collection with the name " + INPUTS_SINGLE_NAME, contentsMap.containsKey(INPUTS_SINGLE_NAME));
assertTrue("the created history should contain a dataset collection with the name " + INPUTS_PAIRED_NAME, contentsMap.containsKey(INPUTS_PAIRED_NAME));
// make sure workflow inputs contains correct information
Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
assertEquals("the created workflow inputs has an invalid number of elements", 3, workflowInputsMap.size());
}
use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxyTest method testPrepareAnalysisFilesSingleSuccess.
/**
* Tests out successfully to preparing an analysis with single files.
*
* @throws ExecutionManagerException
* @throws IridaWorkflowException
*/
@SuppressWarnings("unchecked")
@Test
public void testPrepareAnalysisFilesSingleSuccess() throws ExecutionManagerException, IridaWorkflowException {
Set<SingleEndSequenceFile> singleFiles = Sets.newHashSet(sampleSingleSequenceFileMap.values());
submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(Sets.newHashSet(singleFiles)).referenceFile(referenceFile).build();
submission.setRemoteAnalysisId(HISTORY_ID);
submission.setRemoteWorkflowId(WORKFLOW_ID);
when(sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SingleEndSequenceFile.class)).thenReturn(singleFiles);
when(iridaWorkflowsService.getIridaWorkflow(workflowId)).thenReturn(iridaWorkflowSingle);
when(galaxyHistoriesService.findById(HISTORY_ID)).thenReturn(workflowHistory);
when(galaxyLibrariesService.buildEmptyLibrary(any(GalaxyProjectName.class))).thenReturn(workflowLibrary);
when(sequencingObjectService.getUniqueSamplesForSequencingObjects(singleFiles)).thenReturn(sampleSingleSequenceFileMap);
when(galaxyHistoriesService.fileToHistory(refFile, InputFileType.FASTA, workflowHistory)).thenReturn(refDataset);
when(galaxyWorkflowService.getWorkflowDetails(WORKFLOW_ID)).thenReturn(workflowDetails);
when(analysisParameterServiceGalaxy.prepareAnalysisParameters(any(Map.class), any(IridaWorkflow.class))).thenReturn(new WorkflowInputsGalaxy(new WorkflowInputs()));
when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, SEQUENCE_FILE_SINGLE_LABEL)).thenReturn(SEQUENCE_FILE_SINGLE_ID);
when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, REFERENCE_FILE_LABEL)).thenReturn(REFERENCE_FILE_ID);
when(analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(any(Map.class), eq(workflowHistory), eq(workflowLibrary))).thenReturn(collectionResponseSingle);
PreparedWorkflowGalaxy preparedWorkflow = workflowPreparation.prepareAnalysisFiles(submission);
assertEquals("preparedWorflow history id not equal to " + HISTORY_ID, HISTORY_ID, preparedWorkflow.getRemoteAnalysisId());
assertEquals("preparedWorkflow library is invalid", LIBRARY_ID, preparedWorkflow.getRemoteDataId());
assertNotNull("workflowInputs in preparedWorkflow is null", preparedWorkflow.getWorkflowInputs());
Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
assertEquals("workflow inputs has invalid size", 2, workflowInputsMap.size());
assertTrue("workflow inputs should contain reference file entry", workflowInputsMap.containsKey(REFERENCE_FILE_ID));
assertTrue("workflow inputs should contain sequence file single entry", workflowInputsMap.containsKey(SEQUENCE_FILE_SINGLE_ID));
verify(analysisCollectionServiceGalaxy).uploadSequenceFilesSingleEnd(any(Map.class), any(History.class), any(Library.class));
verify(analysisCollectionServiceGalaxy, never()).uploadSequenceFilesPaired(any(Map.class), any(History.class), any(Library.class));
}
use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesPairSuccess.
/**
* Tests out successfully preparing paired workflow input files for
* execution.
*
* @throws InterruptedException
* @throws ExecutionManagerException
* @throws IOException
* @throws IridaWorkflowException
*/
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesPairSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
History history = new History();
history.setName("testPrepareAnalysisFilesPairSuccess");
HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
History createdHistory = historiesClient.create(history);
IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdPaired);
Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, validWorkflowIdPaired, false);
analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
PreparedWorkflowGalaxy preparedWorkflow = analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
assertEquals("the response history id should match the input history id", createdHistory.getId(), preparedWorkflow.getRemoteAnalysisId());
WorkflowInputsGalaxy workflowInputsGalaxy = preparedWorkflow.getWorkflowInputs();
assertNotNull("the returned workflow inputs should not be null", workflowInputsGalaxy);
assertNotNull("the returned library id should not be null", preparedWorkflow.getRemoteDataId());
// verify correct library is created
List<LibraryContent> libraryContents = librariesClient.getLibraryContents(preparedWorkflow.getRemoteDataId());
Map<String, List<LibraryContent>> libraryContentsMap = libraryContents.stream().collect(Collectors.groupingBy(LibraryContent::getName));
assertFalse("the returned library should exist in Galaxy", libraryContentsMap.isEmpty());
String sequenceFile1ALibraryName = "/" + sequenceFilePathA.getFileName().toString();
String sequenceFile2ALibraryName = "/" + sequenceFilePath2A.getFileName().toString();
assertEquals("the returned library does not contain the correct number of elements", 3, libraryContentsMap.size());
assertTrue("the returned library does not contain a root folder", libraryContentsMap.containsKey("/"));
assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFile1ALibraryName));
assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFile1ALibraryName).size());
assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFile2ALibraryName));
assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFile2ALibraryName).size());
// verify correct files have been uploaded
List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
assertEquals("the created history has an invalid number of elements", 4, historyContents.size());
Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
assertTrue("the created history should contain the file " + sequenceFilePath2A.toFile().getName(), contentsMap.containsKey(sequenceFilePath2A.toFile().getName()));
assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
assertTrue("the created history should contain the collection with name " + INPUTS_PAIRED_NAME, contentsMap.containsKey(INPUTS_PAIRED_NAME));
// make sure workflow inputs contains correct information
Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
assertEquals("the created workflow inputs has an invalid number of elements", 2, workflowInputsMap.size());
}
use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSingleSuccess.
/**
* Tests out successfully preparing single workflow input files for
* execution.
*
* @throws InterruptedException
* @throws ExecutionManagerException
* @throws IOException
* @throws IridaWorkflowException
*/
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSingleSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
History history = new History();
history.setName("testPrepareAnalysisFilesSingleSuccess");
HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
History createdHistory = historiesClient.create(history);
IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSingle);
Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingle, false);
analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
PreparedWorkflowGalaxy preparedWorkflow = analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
assertEquals("the response history id should match the input history id", createdHistory.getId(), preparedWorkflow.getRemoteAnalysisId());
assertNotNull("the returned workflow inputs should not be null", preparedWorkflow.getWorkflowInputs());
assertNotNull("the returned library id should not be null", preparedWorkflow.getRemoteDataId());
// verify correct library is created
List<LibraryContent> libraryContents = librariesClient.getLibraryContents(preparedWorkflow.getRemoteDataId());
Map<String, List<LibraryContent>> libraryContentsMap = libraryContents.stream().collect(Collectors.groupingBy(LibraryContent::getName));
assertFalse("the returned library should exist in Galaxy", libraryContentsMap.isEmpty());
String sequenceFileALibraryName = "/" + sequenceFilePathA.getFileName().toString();
assertEquals("the returned library does not contain the correct number of elements", 2, libraryContentsMap.size());
assertTrue("the returned library does not contain a root folder", libraryContentsMap.containsKey("/"));
assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFileALibraryName));
assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFileALibraryName).size());
// verify correct files have been uploaded
List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
assertEquals("the created history should contain 3 entries", 3, historyContents.size());
Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
assertTrue("the created history should contain the collection with name " + INPUTS_SINGLE_NAME, contentsMap.containsKey(INPUTS_SINGLE_NAME));
// make sure workflow inputs contains correct information
Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
assertEquals("the created workflow inputs has an invalid number of elements", 2, workflowInputsMap.size());
}
use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxyTest method testPrepareAnalysisFilesSinglePairedSuccess.
/**
* Tests out successfully to preparing an analysis with both single and
* paired files
*
* @throws ExecutionManagerException
* @throws IridaWorkflowException
*/
@SuppressWarnings("unchecked")
@Test
public void testPrepareAnalysisFilesSinglePairedSuccess() throws ExecutionManagerException, IridaWorkflowException {
Set<SingleEndSequenceFile> singleFiles = Sets.newHashSet(sampleSingleSequenceFileMap.values());
Set<SequenceFilePair> pairedFiles = Sets.newHashSet(sampleSequenceFilePairMap.values());
Set<SequencingObject> joinedInput = Sets.newHashSet(singleFiles);
joinedInput.addAll(pairedFiles);
submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(joinedInput).referenceFile(referenceFile).build();
submission.setRemoteAnalysisId(HISTORY_ID);
submission.setRemoteWorkflowId(WORKFLOW_ID);
when(sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SingleEndSequenceFile.class)).thenReturn(singleFiles);
when(sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SequenceFilePair.class)).thenReturn(pairedFiles);
when(iridaWorkflowsService.getIridaWorkflow(workflowId)).thenReturn(iridaWorkflowSinglePaired);
when(galaxyHistoriesService.findById(HISTORY_ID)).thenReturn(workflowHistory);
when(galaxyLibrariesService.buildEmptyLibrary(any(GalaxyProjectName.class))).thenReturn(workflowLibrary);
when(sequencingObjectService.getUniqueSamplesForSequencingObjects(singleFiles)).thenReturn(sampleSingleSequenceFileMap);
when(sequencingObjectService.getUniqueSamplesForSequencingObjects(pairedFiles)).thenReturn(sampleSequenceFilePairMap);
when(galaxyHistoriesService.fileToHistory(refFile, InputFileType.FASTA, workflowHistory)).thenReturn(refDataset);
when(galaxyWorkflowService.getWorkflowDetails(WORKFLOW_ID)).thenReturn(workflowDetails);
when(analysisParameterServiceGalaxy.prepareAnalysisParameters(any(Map.class), any(IridaWorkflow.class))).thenReturn(new WorkflowInputsGalaxy(new WorkflowInputs()));
when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, SEQUENCE_FILE_SINGLE_LABEL)).thenReturn(SEQUENCE_FILE_SINGLE_ID);
when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, SEQUENCE_FILE_PAIRED_LABEL)).thenReturn(SEQUENCE_FILE_PAIRED_ID);
when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, REFERENCE_FILE_LABEL)).thenReturn(REFERENCE_FILE_ID);
when(analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(any(Map.class), eq(workflowHistory), eq(workflowLibrary))).thenReturn(collectionResponseSingle);
when(analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(any(Map.class), eq(workflowHistory), eq(workflowLibrary))).thenReturn(collectionResponsePaired);
PreparedWorkflowGalaxy preparedWorkflow = workflowPreparation.prepareAnalysisFiles(submission);
assertEquals("preparedWorflow history id not equal to " + HISTORY_ID, HISTORY_ID, preparedWorkflow.getRemoteAnalysisId());
assertEquals("preparedWorkflow library is invalid", LIBRARY_ID, preparedWorkflow.getRemoteDataId());
assertNotNull("workflowInputs in preparedWorkflow is null", preparedWorkflow.getWorkflowInputs());
Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
assertEquals("invalid number of workflow inputs", 3, workflowInputsMap.size());
assertTrue("workflow inputs should contain reference entry", workflowInputsMap.containsKey(REFERENCE_FILE_ID));
assertTrue("workflow inputs should contain sequence file single entry", workflowInputsMap.containsKey(SEQUENCE_FILE_SINGLE_ID));
assertTrue("workflow inputs should contain sequence file paired entry", workflowInputsMap.containsKey(SEQUENCE_FILE_PAIRED_ID));
verify(analysisCollectionServiceGalaxy).uploadSequenceFilesSingleEnd(any(Map.class), any(History.class), any(Library.class));
verify(analysisCollectionServiceGalaxy).uploadSequenceFilesPaired(any(Map.class), any(History.class), any(Library.class));
}
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