Examples with Tool com.github.jmchilton.blend4j.galaxy.beans.Tool used on opensource projects

Example 6 with Tool

use of com.github.jmchilton.blend4j.galaxy.beans.Tool in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testBuildSingleStepToolExecutionComplexParameters.

@Test
public void testBuildSingleStepToolExecutionComplexParameters() throws ExecutionManagerException {
    final HistoryContents hc = new HistoryContents();
    hc.setName(FILENAME);
    final HistoryContentsProvenance hcp = new HistoryContentsProvenance();
    final Map<String, Object> mapWithNullValue = new HashMap<>();
    mapWithNullValue.put("key", null);
    final ImmutableMap.Builder<String, Object> builder = ImmutableMap.builder();
    builder.put("akey", (Object) "avalue").put("anotherKey", (Object) "{\"key\": \"value\"}").put("thirdKey", (Object) ImmutableMap.of("key", "{\"key\":\"value\"}")).put("fourthKey", (Object) "[{\"key\":\"value\"}]").put("fifthKey", (Object) mapWithNullValue).put("abadkey", (Object) "[{\"key\":\"value\"]").put("listKey", (Object) ImmutableList.of(ImmutableMap.of("key", "value"))).put("k", (Object) "value-lower").put("K", (Object) "value-upper").put("\\\\keyWithBackslash", (Object) "value-backslash-lower").put("\\\\KeyWithBackslash", (Object) "value-backslash-upper").put("MULTIPLE_UPPER_case", (Object) "upper-case-values!");
    hcp.setParameters(builder.build());
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc));
    when(galaxyHistoriesService.showProvenance(any(String.class), any(String.class))).thenReturn(hcp);
    when(toolsClient.showTool(any(String.class))).thenReturn(new Tool());
    when(jobsClient.showJob(any(String.class))).thenReturn(new JobDetails());
    final ToolExecution toolExecution = provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
    final Map<String, String> params = toolExecution.getExecutionTimeParameters();
    assertTrue("tool execution should have the specified parameter.", params.containsKey("akey"));
    assertEquals("tool execution parameter should be specified value.", "avalue", params.get("akey"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("anotherKey.key"));
    assertEquals("tool execution parameter should be specified value.", "value", params.get("anotherKey.key"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("thirdKey.key.key"));
    assertEquals("tool execution parameter should be specified value.", "value", params.get("thirdKey.key.key"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("fourthKey.key"));
    assertEquals("tool execution parameter should be specified value.", "value", params.get("fourthKey.key"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("fifthKey.key"));
    assertEquals("tool execution parameter should be specified value.", AnalysisProvenanceServiceGalaxy.emptyValuePlaceholder(), params.get("fifthKey.key"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("abadkey"));
    assertEquals("tool execution parameter should be specified value.", "[{\"key\":\"value\"]", params.get("abadkey"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("listKey.key"));
    assertEquals("tool execution parameter should be specified value.", "value", params.get("listKey.key"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("k"));
    assertEquals("tool execution parameter should be specified value.", "value-lower", params.get("k"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("K"));
    assertEquals("tool execution parameter should be specified value.", "value-upper", params.get("K"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("\\\\keyWithBackslash"));
    assertEquals("tool execution parameter should be specified value.", "value-backslash-lower", params.get("\\\\keyWithBackslash"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("\\\\KeyWithBackslash"));
    assertEquals("tool execution parameter should be specified value.", "value-backslash-upper", params.get("\\\\KeyWithBackslash"));
    assertTrue("tool execution should have the specified parameter.", params.containsKey("MULTIPLE_UPPER_case"));
    assertEquals("tool execution parameter should be specified value.", "upper-case-values!", params.get("MULTIPLE_UPPER_case"));
    assertTrue("Tool execution should be considered input step, no predecessors.", toolExecution.isInputTool());
}

Example 7 with Tool

use of com.github.jmchilton.blend4j.galaxy.beans.Tool in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testBuildSingleStepToolExecutionOneParameter.

@Test
public void testBuildSingleStepToolExecutionOneParameter() throws ExecutionManagerException {
    final HistoryContents hc = new HistoryContents();
    hc.setName(FILENAME);
    final HistoryContentsProvenance hcp = new HistoryContentsProvenance();
    hcp.setParameters(ImmutableMap.of("akey", (Object) "avalue"));
    final JobDetails jd = new JobDetails();
    jd.setCommandLine("");
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc));
    when(galaxyHistoriesService.showProvenance(any(String.class), any(String.class))).thenReturn(hcp);
    when(toolsClient.showTool(any(String.class))).thenReturn(new Tool());
    when(jobsClient.showJob(any(String.class))).thenReturn(jd);
    final ToolExecution toolExecution = provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
    assertTrue("tool execution should have the specified parameter.", toolExecution.getExecutionTimeParameters().containsKey("akey"));
    assertEquals("tool execution parameter should be specified value.", "avalue", toolExecution.getExecutionTimeParameters().get("akey"));
    assertTrue("Tool execution should be considered input step, no predecessors.", toolExecution.isInputTool());
}

Example 8 with Tool

use of com.github.jmchilton.blend4j.galaxy.beans.Tool in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxy method buildToolExecutionForOutputFile.

/**
 * Build up a provenance report for a specific file that's attached to the
 * outputs of an analysis submission.
 *
 * @param remoteAnalysisId
 *            the identifier of the submission history that the output file
 *            is attached to on the execution manager (i.e., Galaxy's
 *            history id).
 * @param analysisOutputFilename
 *            the filename to build the report for. This should be the raw
 *            basename of the file (i.e., only the filename + extension
 *            part).
 * @return the complete report for the file.
 * @throws ExecutionManagerException
 *             if the history contents could not be shown for the specified
 *             file.
 */
public ToolExecution buildToolExecutionForOutputFile(final String remoteAnalysisId, final String analysisOutputFilename) throws ExecutionManagerException {
    final List<HistoryContents> historyContents = galaxyHistoriesService.showHistoryContents(remoteAnalysisId);
    // group the history contents by name. The names that we're interested
    // in starting from should match the filename of the output file.
    final Map<String, List<HistoryContents>> historyContentsByName = historyContents.stream().collect(Collectors.groupingBy(HistoryContents::getName));
    final List<HistoryContents> currentContents = historyContentsByName.get(analysisOutputFilename);
    if (currentContents == null || currentContents.isEmpty() || currentContents.size() > 1) {
        throw new ExecutionManagerException("Could not load a unique history contents for the specified filename [" + analysisOutputFilename + "] in history with id [" + remoteAnalysisId + "]");
    }
    final HistoryContentsProvenance currentProvenance = galaxyHistoriesService.showProvenance(remoteAnalysisId, currentContents.get(0).getId());
    try {
        final Tool toolDetails = toolsClient.showTool(currentProvenance.getToolId());
        return buildToolExecutionForHistoryStep(toolDetails, currentProvenance, remoteAnalysisId);
    } catch (final RuntimeException e) {
        throw new ExecutionManagerException("Failed to build tool execution provenance.", e);
    }
}