use of com.github.jmchilton.blend4j.galaxy.beans.JobDetails in project irida by phac-nml.
the class AnalysisProvenanceServiceGalaxyTest method testBuildSingleStepToolExecutionOneParameterOnePredecessor.
@Test
public void testBuildSingleStepToolExecutionOneParameterOnePredecessor() throws ExecutionManagerException {
final HistoryContents hc = new HistoryContents();
hc.setName(FILENAME);
hc.setId("historyContentsId");
final HistoryContentsProvenance hcpWithPredecessor = new HistoryContentsProvenance();
hcpWithPredecessor.setParameters(ImmutableMap.of("akey", (Object) ImmutableMap.of("id", "previousKey")));
final HistoryContentsProvenance hcpWithoutPredecessor = new HistoryContentsProvenance();
hcpWithoutPredecessor.setParameters(ImmutableMap.of("akey", (Object) "value"));
when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc));
when(galaxyHistoriesService.showProvenance(any(String.class), eq("historyContentsId"))).thenReturn(hcpWithPredecessor);
when(galaxyHistoriesService.showProvenance(any(String.class), eq("previousKey"))).thenReturn(hcpWithoutPredecessor);
when(jobsClient.showJob(any(String.class))).thenReturn(new JobDetails());
when(toolsClient.showTool(any(String.class))).thenReturn(new Tool());
final ToolExecution toolExecution = provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
assertFalse("tool execution should not have an ID parameter.", toolExecution.getExecutionTimeParameters().containsKey("akey"));
assertFalse("tool execution should not have an ID parameter.", toolExecution.getExecutionTimeParameters().containsKey("akey.id"));
assertFalse("Tool execution has one predecessor, not input step.", toolExecution.isInputTool());
final ToolExecution predecessor = toolExecution.getPreviousSteps().iterator().next();
assertTrue("predecessor step is input step.", predecessor.isInputTool());
}
use of com.github.jmchilton.blend4j.galaxy.beans.JobDetails 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());
}
use of com.github.jmchilton.blend4j.galaxy.beans.JobDetails 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());
}
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