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Test fixes
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+45
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‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java‎

Lines changed: 45 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,6 @@ abstract public static class AbstractPipelineTestCase extends Assert
216216

217217
protected Container _project;
218218
protected TestContext _context;
219-
protected File _pipelineRoot;
220219
protected File _sampleData;
221220

222221
protected Boolean _isExternalPipelineEnabled = null;
@@ -269,9 +268,7 @@ public void setUp() throws Exception
269268
{
270269
_context = TestContext.get();
271270
_sampleData = getSampleDataDir();
272-
273271
_project = ContainerManager.getForPath(getProjectName());
274-
_pipelineRoot = PipelineService.get().getPipelineRootSetting(_project).getRootPath();
275272

276273
String path = PipelineJobService.get().getConfigProperties().getSoftwarePackagePath(SequencePipelineService.SEQUENCE_TOOLS_PARAM);
277274
path = StringUtils.trimToNull(path);
@@ -396,14 +393,16 @@ protected void decompressAndCleanFastq(File input, File output)
396393
}
397394
}
398395

399-
protected void verifyFileInputs(File basedir, String[] fileNames, JSONObject config, String prefix)
396+
protected void verifyFileInputs(File basedir, String[] fileNames, JSONObject config, String prefix, Container jobContainer)
400397
{
398+
File pipelineRoot = PipelineService.get().findPipelineRoot(jobContainer).getRootPath();
399+
401400
String handling = config.getString("inputFileTreatment");
402401
if ("none".equals(handling))
403402
{
404403
for (String fn : fileNames)
405404
{
406-
File input = FileUtil.appendName(_pipelineRoot, prefix + fn);
405+
File input = FileUtil.appendName(pipelineRoot, prefix + fn);
407406
Assert.assertTrue("Input file missing: " + input.getPath(), input.exists());
408407
}
409408
}
@@ -413,7 +412,7 @@ else if ("compress".equals(handling))
413412

414413
for (String fn : fileNames)
415414
{
416-
File input = FileUtil.appendName(_pipelineRoot, prefix + fn);
415+
File input = FileUtil.appendName(pipelineRoot, prefix + fn);
417416
Assert.assertFalse("Input file still exists: " + input.getPath(), input.exists());
418417

419418
File compressed;
@@ -429,7 +428,7 @@ else if ("delete".equals(handling))
429428
{
430429
for (String fn : fileNames)
431430
{
432-
File input = FileUtil.appendName(_pipelineRoot, prefix + fn);
431+
File input = FileUtil.appendName(pipelineRoot, prefix + fn);
433432
Assert.assertFalse("Input file still present: " + input.getPath(), input.exists());
434433
}
435434
}
@@ -738,6 +737,11 @@ protected static void doCleanup(String projectName)
738737
ContainerManager.deleteAll(project, TestContext.get().getUser());
739738
}
740739
}
740+
741+
protected File getPipelineRoot(Container c)
742+
{
743+
return PipelineService.get().getPipelineRootSetting(c).getRootPath();
744+
}
741745
}
742746

743747
public static class SequenceImportPipelineTestCase extends AbstractPipelineTestCase
@@ -799,7 +803,7 @@ public void basicTest() throws Exception
799803
try
800804
{
801805
verifyFileOutputs(basedir, expectedOutputs);
802-
verifyFileInputs(basedir, fileNames, config, prefix);
806+
verifyFileInputs(basedir, fileNames, config, prefix, workbook);
803807
validateReadsets(jobs, config);
804808

805809
Assert.assertEquals("Incorrect read number", 3260L, FastqUtils.getSequenceCount(fq));
@@ -836,7 +840,7 @@ public void leaveInPlaceTest() throws Exception
836840
Set<File> expectedOutputs = new HashSet<>();
837841
File basedir = getBaseDir(jobs.iterator().next());
838842
Assert.assertFalse("Unexpected file found", FileUtil.appendName(basedir, prefix + PAIRED_FILENAME1).exists());
839-
File fq = FileUtil.appendName(_pipelineRoot, prefix + PAIRED_FILENAME1);
843+
File fq = FileUtil.appendName(getPipelineRoot(c), prefix + PAIRED_FILENAME1);
840844
Assert.assertTrue("File not found", fq.exists());
841845
expectedOutputs.add(FileUtil.appendName(basedir, "sequenceImport.json"));
842846
expectedOutputs.add(FileUtil.appendName(basedir, "sequenceSupport.json.gz"));
@@ -846,7 +850,7 @@ public void leaveInPlaceTest() throws Exception
846850
try
847851
{
848852
verifyFileOutputs(basedir, expectedOutputs);
849-
verifyFileInputs(basedir, fileNames, config, prefix);
853+
verifyFileInputs(basedir, fileNames, config, prefix, c);
850854
validateReadsets(jobs, config);
851855

852856
Assert.assertEquals("Incorrect read number", 211L, FastqUtils.getSequenceCount(fq));
@@ -950,7 +954,7 @@ private void runMergePipelineJob(String jobName, boolean deleteIntermediates, St
950954
expectedOutputs.add(FileUtil.appendName(basedir, prefix + PAIRED_FILENAME2_L1b));
951955
}
952956

953-
verifyJob(basedir, jobName, expectedOutputs, new String[]{PAIRED_FILENAME_L1a, PAIRED_FILENAME2_L1a, PAIRED_FILENAME_L1b, PAIRED_FILENAME2_L1b, PAIRED_FILENAME_L2, PAIRED_FILENAME2_L2}, prefix, config);
957+
verifyJob(basedir, jobName, expectedOutputs, new String[]{PAIRED_FILENAME_L1a, PAIRED_FILENAME2_L1a, PAIRED_FILENAME_L1b, PAIRED_FILENAME2_L1b, PAIRED_FILENAME_L2, PAIRED_FILENAME2_L2}, prefix, config, _project);
954958

955959
Assert.assertEquals("Incorrect read number", 422L, FastqUtils.getSequenceCount(merge1));
956960
Assert.assertEquals("Incorrect read number", 422L, FastqUtils.getSequenceCount(merge2));
@@ -967,7 +971,7 @@ private void runMergePipelineJob(String jobName, boolean deleteIntermediates, St
967971
expectedOutputs.add(FileUtil.appendName(basedir, prefix + FileUtil.getBaseName(FileUtil.getBaseName(PAIRED_FILENAME2)) + "_fastqc.html.gz"));
968972
expectedOutputs.add(FileUtil.appendName(basedir, prefix + FileUtil.getBaseName(FileUtil.getBaseName(PAIRED_FILENAME2)) + "_fastqc.zip"));
969973

970-
verifyJob(basedir, jobName, expectedOutputs, new String[]{PAIRED_FILENAME1, PAIRED_FILENAME2}, prefix, config);
974+
verifyJob(basedir, jobName, expectedOutputs, new String[]{PAIRED_FILENAME1, PAIRED_FILENAME2}, prefix, config, _project);
971975

972976
//job3: g3
973977
expectedOutputs = new HashSet<>();
@@ -976,11 +980,11 @@ private void runMergePipelineJob(String jobName, boolean deleteIntermediates, St
976980
expectedOutputs.add(FileUtil.appendName(basedir, prefix + FileUtil.getBaseName(FileUtil.getBaseName(UNPAIRED_FILENAME)) + "_fastqc.html.gz"));
977981
expectedOutputs.add(FileUtil.appendName(basedir, prefix + FileUtil.getBaseName(FileUtil.getBaseName(UNPAIRED_FILENAME)) + "_fastqc.zip"));
978982

979-
verifyJob(basedir, jobName, expectedOutputs, new String[]{UNPAIRED_FILENAME}, prefix, config);
983+
verifyJob(basedir, jobName, expectedOutputs, new String[]{UNPAIRED_FILENAME}, prefix, config, _project);
980984
validateReadsets(jobs, config, 1); //we expect one per job, total of 3
981985
}
982986

983-
private void verifyJob(File basedir, String jobName, Set<File> expectedOutputs, String[] fileNames, String prefix, JSONObject config) throws Exception
987+
private void verifyJob(File basedir, String jobName, Set<File> expectedOutputs, String[] fileNames, String prefix, JSONObject config, Container c) throws Exception
984988
{
985989
expectedOutputs.add(FileUtil.appendName(basedir, basedir.getName() + ".pipe.xar.xml"));
986990
expectedOutputs.add(FileUtil.appendName(basedir, "sequenceImport.json"));
@@ -991,7 +995,7 @@ private void verifyJob(File basedir, String jobName, Set<File> expectedOutputs,
991995
try
992996
{
993997
verifyFileOutputs(basedir, expectedOutputs);
994-
verifyFileInputs(basedir, fileNames, config, prefix);
998+
verifyFileInputs(basedir, fileNames, config, prefix, c);
995999
}
9961000
catch (Exception e)
9971001
{
@@ -1129,7 +1133,7 @@ public void barcodeTest() throws Exception
11291133
try
11301134
{
11311135
verifyFileOutputs(basedir, expectedOutputs);
1132-
verifyFileInputs(basedir, fileNames, config, prefix);
1136+
verifyFileInputs(basedir, fileNames, config, prefix, workbook);
11331137
validateReadsets(jobs, config, 4);
11341138
validateBarcodeFastqs(expectedOutputs);
11351139
}
@@ -1175,7 +1179,7 @@ public void barcodeTestDeletingIntermediates() throws Exception
11751179
try
11761180
{
11771181
verifyFileOutputs(basedir, expectedOutputs);
1178-
verifyFileInputs(basedir, fileNames, config, prefix);
1182+
verifyFileInputs(basedir, fileNames, config, prefix, _project);
11791183
validateReadsets(jobs, config, 4);
11801184
validateBarcodeFastqs(expectedOutputs);
11811185
}
@@ -1245,7 +1249,7 @@ public void pairedEndTest() throws Exception
12451249
try
12461250
{
12471251
verifyFileOutputs(basedir, expectedOutputs);
1248-
verifyFileInputs(basedir, fileNames, config, prefix);
1252+
verifyFileInputs(basedir, fileNames, config, prefix, c);
12491253
validateReadsets(jobs, config);
12501254
}
12511255
catch (Exception e)
@@ -1303,7 +1307,7 @@ public void pairedEndTestMovingInputs() throws Exception
13031307
try
13041308
{
13051309
verifyFileOutputs(basedir, expectedOutputs);
1306-
verifyFileInputs(basedir, fileNames, config, prefix);
1310+
verifyFileInputs(basedir, fileNames, config, prefix, _project);
13071311
validateReadsets(jobs, config);
13081312
}
13091313
catch (Exception e)
@@ -1361,7 +1365,7 @@ public void pairedEndTestDeletingInputs() throws Exception
13611365
try
13621366
{
13631367
verifyFileOutputs(basedir, expectedOutputs);
1364-
verifyFileInputs(basedir, fileNames, config, prefix);
1368+
verifyFileInputs(basedir, fileNames, config, prefix, workbook);
13651369
validateReadsets(jobs, config);
13661370
}
13671371
catch (Exception e)
@@ -1508,7 +1512,7 @@ protected void validateAlignmentJob(Set<PipelineJob> jobs, Collection<String> ad
15081512

15091513
for (String fn : additionalFiles)
15101514
{
1511-
expectedOutputs.add(FileUtil.appendName(basedir, fn));
1515+
expectedOutputs.add(FileUtil.appendPath(basedir, Path.parse(fn)));
15121516
}
15131517

15141518
File bam = FileUtil.appendPath(basedir, Path.parse(outDir + "/Alignment/" + rs.getName() + ".bam"));
@@ -1572,21 +1576,22 @@ public void setUp() throws Exception
15721576

15731577
protected void copyInputFiles() throws Exception
15741578
{
1575-
File file3 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME1);
1579+
File pipelineRoot = getPipelineRoot(_project);
1580+
File file3 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME1);
15761581
if (!file3.exists())
15771582
FileUtils.copyFile(FileUtil.appendName(_sampleData, PAIRED_FILENAME1), file3);
15781583

1579-
File file4 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME2);
1584+
File file4 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME2);
15801585
if (!file4.exists())
15811586
FileUtils.copyFile(FileUtil.appendName(_sampleData, PAIRED_FILENAME2), file4);
15821587

1583-
File file5 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
1588+
File file5 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
15841589
if (!file5.exists())
15851590
{
15861591
decompressAndCleanFastq(FileUtil.appendName(_sampleData, PAIRED_FILENAME1), file5);
15871592
}
15881593

1589-
File file6 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
1594+
File file6 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
15901595
if (!file6.exists())
15911596
{
15921597
decompressAndCleanFastq(FileUtil.appendName(_sampleData, PAIRED_FILENAME2), file6);
@@ -1596,16 +1601,16 @@ protected void copyInputFiles() throws Exception
15961601
protected List<SequenceReadsetImpl> createReadsets() throws Exception
15971602
{
15981603
List<SequenceReadsetImpl> models = new ArrayList<>();
1599-
1600-
File file1 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME1);
1601-
File file2 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME2);
1604+
File pipelineRoot = getPipelineRoot(_project);
1605+
File file1 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME1);
1606+
File file2 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME2);
16021607
models.add(createReadset("TestReadset1", List.of(Pair.of(file1, file2)), false));
16031608

16041609

1605-
File file3 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
1610+
File file3 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
16061611
models.add(createReadset("TestReadset2", List.of(Pair.of(file3, null)), true));
16071612

1608-
File file4 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
1613+
File file4 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
16091614
models.add(createReadset("TestReadset3", List.of(Pair.of(file4, null)), true));
16101615

16111616
return models;
@@ -1677,17 +1682,17 @@ protected void appendSamplesForAlignment(JSONObject config, List<SequenceReadset
16771682
protected void validateInputs()
16781683
{
16791684
//all files have 204 reads
1680-
1681-
File file1 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME1);
1685+
File pipelineRoot = getPipelineRoot(_project);
1686+
File file1 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME1);
16821687
Assert.assertTrue("Unable to find input: " + file1.getPath(), file1.exists());
16831688

1684-
File file2 = FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME2);
1689+
File file2 = FileUtil.appendName(pipelineRoot, PAIRED_FILENAME2);
16851690
Assert.assertTrue("Unable to find input: " + file2.getPath(), file2.exists());
16861691

1687-
File file3 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
1692+
File file3 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME1);
16881693
Assert.assertTrue("Unable to find input: " + file3.getPath(), file3.exists());
16891694

1690-
File file4 = FileUtil.appendName(_pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
1695+
File file4 = FileUtil.appendName(pipelineRoot, UNZIPPED_PAIRED_FILENAME2);
16911696
Assert.assertTrue("Unable to find input: " + file4.getPath(), file4.exists());
16921697
}
16931698

@@ -2654,25 +2659,26 @@ public void testMergedAlignments() throws Exception
26542659
JSONObject config = substituteParams(FileUtil.appendName(_sampleData, ALIGNMENT_JOB), jobName);
26552660
config.put("alignment", "BWA-Mem");
26562661

2662+
File pipelineRoot = getPipelineRoot(_project);
26572663
for (String fn : Arrays.asList(PAIRED_FILENAME_L1a, PAIRED_FILENAME_L2))
26582664
{
2659-
File file3 = FileUtil.appendName(_pipelineRoot, fn);
2665+
File file3 = FileUtil.appendName(pipelineRoot, fn);
26602666
if (!file3.exists())
26612667
FileUtils.copyFile(FileUtil.appendName(_sampleData, PAIRED_FILENAME1), file3);
26622668
}
26632669

26642670
for (String fn : Arrays.asList(PAIRED_FILENAME2_L1a, PAIRED_FILENAME2_L2))
26652671
{
2666-
File file4 = FileUtil.appendName(_pipelineRoot, fn);
2672+
File file4 = FileUtil.appendName(pipelineRoot, fn);
26672673
if (!file4.exists())
26682674
FileUtils.copyFile(FileUtil.appendName(_sampleData, PAIRED_FILENAME2), file4);
26692675
}
26702676

26712677
List<SequenceReadsetImpl> models = new ArrayList<>();
26722678

26732679
models.add(createReadset("TestMergedReadset", Arrays.asList(
2674-
Pair.of(FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME_L1a), FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME2_L1a)),
2675-
Pair.of(FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME_L2), FileUtil.appendName(_pipelineRoot, PAIRED_FILENAME2_L2))
2680+
Pair.of(FileUtil.appendName(pipelineRoot, PAIRED_FILENAME_L1a), FileUtil.appendName(pipelineRoot, PAIRED_FILENAME2_L1a)),
2681+
Pair.of(FileUtil.appendName(pipelineRoot, PAIRED_FILENAME_L2), FileUtil.appendName(pipelineRoot, PAIRED_FILENAME2_L2))
26762682
), true));
26772683

26782684
appendSamplesForAlignment(config, models);

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