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test_samples_fillout_index_batch_workflow_cwl.py
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test_samples_fillout_index_batch_workflow_cwl.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Test case for the samples_fillout_index_batch_workflow cwl
example commands:
run all tests in parallel;
$ CWL_ENGINE=Toil PRINT_COMMAND=T KEEP_TMP=T pytest -n 8 -s tests/test_samples_fillout_index_batch_workflow_cwl.py
run just one set of tests, pwd is tests/ dir;
$ CWL_ENGINE=Toil KEEP_TMP=T PRINT_COMMAND=T PYTHONPATH=../pluto nice pytest -s test_samples_fillout_workflow_cwl.py -k TestSamplesFilloutMixedGroup1
the same as above but from parent dir;
$ CWL_ENGINE=Toil KEEP_TMP=T PRINT_COMMAND=T nice pytest -s tests/test_samples_fillout_workflow_cwl.py -k TestSamplesFilloutMixedGroup1
"""
import os
import sys
from typing import Dict, Tuple
from datasets import (
DATA_SETS,
)
from pluto import (
CWLFile,
PlutoTestCase,
PlutoPreRunTestCase,
OFile
)
sample1_maf = os.path.join(DATA_SETS['Fillout01']['MAF_DIR'], 'Sample1.FillOutUnitTest01.muts.maf')
sample2_maf = os.path.join(DATA_SETS['Fillout01']['MAF_DIR'], 'Sample2.FillOutUnitTest01.muts.maf')
sample3_maf = os.path.join(DATA_SETS['Fillout01']['MAF_DIR'], 'Sample3.FillOutUnitTest01.muts.maf')
sample4_maf = os.path.join(DATA_SETS['Fillout01']['MAF_DIR'], 'Sample4.FillOutUnitTest01.muts.maf')
sample5_maf = os.path.join(DATA_SETS['Fillout01']['MAF_DIR'], 'Sample5.FillOutUnitTest01.muts.maf')
sample1_bam = os.path.join(DATA_SETS['Fillout01']['BAM_DIR'], 'Sample1.UnitTest01.bam')
sample2_bam = os.path.join(DATA_SETS['Fillout01']['BAM_DIR'], 'Sample2.UnitTest01.bam')
sample3_bam = os.path.join(DATA_SETS['Fillout01']['BAM_DIR'], 'Sample3.UnitTest01.bam')
sample4_bam = os.path.join(DATA_SETS['Fillout01']['BAM_DIR'], 'Sample4.UnitTest01.bam')
sample5_bam = os.path.join(DATA_SETS['Fillout01']['BAM_DIR'], 'Sample5.UnitTest01.bam')
class TestSamplesFilloutIndexBatch(PlutoPreRunTestCase):
"""
Three sample groups,
One group has a singleton,
Some samples are clinical,
Some samples lack maf
"""
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
# research + clinical sample group
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample1_maf },
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
},
]
# research + clinical sample group; no maf
sample_group2 = [
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
{
"sample_id": "Sample4",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
# "maf_file": { "class": "File", "path": sample4_maf },
"bam_file": { "class": "File", "path": sample4_bam }
}
]
# singleton sample group
sample_group3 = [
{
"sample_id": "Sample5",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample5_maf },
"bam_file": { "class": "File", "path": sample5_bam }
},
]
self.input = {
"sample_groups": [sample_group1, sample_group2, sample_group3],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 118)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "828804208213b258565ca5612a4bc5e0")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 118)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "53de1a8800f5e86979512bbc8baf88b0")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 105)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "95fb5bc50730548f8005b1db71a22b65")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 13)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "559aedb3b03d0eb5a637cb789e80f635")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3", "Sample4", "Sample5"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])
class TestSamplesFilloutIndexBatch2Group0(PlutoPreRunTestCase):
"""
Test case for two sample groups,
one sample missing a maf file,
one sample group has only one singleton
"""
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
# "maf_file": { "class": "File", "path": sample1_maf }, # this one is missing a maf file
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
}]
sample_group2 = [
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
]
self.input = {
"sample_groups": [sample_group1, sample_group2],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 68)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "7adbbd22006179fe407128b0a2fcbfae")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 68)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "7adbbd22006179fe407128b0a2fcbfae")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 68)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "da306fe0cad18b307105f6a330fc2545")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 0)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "d751713988987e9331980363e24189ce")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])
# These are old test cases that we dont need to run with the test suite but we should hold on to them for a bit
class DontRun____TestSamplesFilloutIndexBatch1Group(PlutoPreRunTestCase):
"""
One sample group,
Dont need to run this test case right now but keep the code here for reference
"""
# dont run this test
# https://docs.pytest.org/en/7.1.x/example/pythoncollection.html#customizing-test-collection
__test__ = False
# # # # # # # # # # #
# # # # # # # # # # #
# Test setup
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
"""
Run the workflow and return the results; output accessible under self.res.output in downstream 'test_' methods
"""
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample1_maf },
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
},
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
]
self.input = {
"sample_groups": [sample_group1],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
"""
Return the expected CWL workflow output with the tmpdir output dir path included
Accessible in downstream 'test_' methods under self.res.expected
"""
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 147)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "4732e626d2859e4c2e8a7d4eeca0e0f4")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 96)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "f934e6bd6f1767372b9737d3865e9f0b")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 70)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "10f4469d0128b6e0bf9e1ef315feb08c")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 26)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "f996e92adc6d1fecb946533a9f23ae99")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])
class DontRun____TestSamplesFilloutIndexBatch2Group2(PlutoPreRunTestCase):
"""
Two sample groups
Skip running this test since its covered by the other tests but leave the code here for now
"""
__test__ = False
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample1_maf },
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
},
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
]
sample_group2 = [
{
"sample_id": "Sample4",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample4_maf },
"bam_file": { "class": "File", "path": sample4_bam }
},
{
"sample_id": "Sample5",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample5_maf },
"bam_file": { "class": "File", "path": sample5_bam }
},
]
self.input = {
"sample_groups": [sample_group1, sample_group2],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 235)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "4e4c91ef129a853a35b86f7fa6f1268a")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 150)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "8397a12302977db14e798a1b2e3ba151")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 120)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "dc0941e362f97df67508cd70d2d8a76e")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 30)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "3b78a67aaa0429cc577578910faf5c10")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3", "Sample4", "Sample5"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])
class DontRun____TestSamplesFilloutIndexBatch3Group(PlutoPreRunTestCase):
"""
Three sample groups,
one group contains a singleton
"""
__test__ = False
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample1_maf },
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
},
]
sample_group2 = [
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
{
"sample_id": "Sample4",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample4_maf },
"bam_file": { "class": "File", "path": sample4_bam }
}
]
# Singleton sample; no DMP clinical matches
sample_group3 = [
{
"sample_id": "Sample5",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample5_maf },
"bam_file": { "class": "File", "path": sample5_bam }
},
]
self.input = {
"sample_groups": [sample_group1, sample_group2, sample_group3],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 144)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "85abef967b1d43112da6a026e80f5cea")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 144)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "6614e73fc609a8cfaba4d0a99f9773ea")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 126)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "683a9892a9727960da82532328b43ae9")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 18)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "7405745e675ea524d8e16e09b9bb749d")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3", "Sample4", "Sample5"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])
class DontRun____TestSamplesFilloutIndexBatch4Group(PlutoPreRunTestCase):
"""
Four sample groups,
Two groups have singletons,
One singleton is clinical sample
"""
__test__ = False
cwl_file = CWLFile('samples_fillout_index_batch_workflow.cwl')
def setUp(self):
super().setUp()
self.runner_args['use_cache'] = False # do not use cache for samples fillout workflow it breaks on split_vcf_to_mafs
def setUpRun(self):
sample_group1 = [
{
"sample_id": "Sample1",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample1_maf },
"bam_file": { "class": "File", "path": sample1_bam }
},
{
"sample_id": "Sample2",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample2_maf },
"bam_file": { "class": "File", "path": sample2_bam }
},
]
sample_group2 = [
{
"sample_id": "Sample3",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample3_maf },
"bam_file": { "class": "File", "path": sample3_bam }
},
]
sample_group3 = [
{
"sample_id": "Sample5",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "research",
"prefilter": True,
"maf_file": { "class": "File", "path": sample5_maf },
"bam_file": { "class": "File", "path": sample5_bam }
},
]
sample_group4 = [
{
"sample_id": "Sample4",
"normal_id": "FROZENPOOLEDNORMAL_IMPACT505_V2",
"sample_type": "clinical",
"prefilter": False,
"maf_file": { "class": "File", "path": sample4_maf },
"bam_file": { "class": "File", "path": sample4_bam }
}
]
self.input = {
"sample_groups": [sample_group1, sample_group2, sample_group3, sample_group4],
"fillout_output_fname": 'output.maf',
"ref_fasta": {"class": "File", "path": DATA_SETS['Proj_08390_G']['REF_FASTA']},
}
output_json, output_dir = self.run_cwl()
return(output_json, output_dir)
def getExpected(self, output_dir):
return({
'output_file': OFile(name = 'output.maf', dir = output_dir),
'filtered_file': OFile(name = 'output.filtered.maf', dir = output_dir),
'portal_file': OFile(name = 'data_mutations_extended.txt', dir = output_dir),
'uncalled_file': OFile(name = 'data_mutations_uncalled.txt', dir = output_dir),
})
# # # # # # # # # # #
# # # # # # # # # # #
def test_CWLDictEqual(self):
"""
Test case for running the fillout workflow on a number of samples, each with a bam and maf
"""
# file contents are inconsistent so strip some keys from the output dict
strip_related_keys = [
('basename', 'output.maf', ['size', 'checksum']),
('basename', 'output.filtered.maf', ['size', 'checksum']),
('basename', 'data_mutations_extended.txt', ['size', 'checksum']),
('basename', 'data_mutations_uncalled.txt', ['size', 'checksum'])
]
self.assertCWLDictEqual(
self.res.output,
self.res.expected,
related_keys = strip_related_keys)
def test_output_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['output_file']).path, 222)
def test_output_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['output_file']).path, "610d91b05a37b371a6b1b1615042dcc3")
def test_filtered_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['filtered_file']).path, 222)
def test_filtered_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['filtered_file']).path, "ead4f5ba539e87e64eac2c5f3e02aba7")
def test_portal_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['portal_file']).path, 113)
def test_portal_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['portal_file']).path, "143f4d2e2eb0f09e9505e08c11baff03")
def test_uncalled_file_num_muts(self):
self.assertNumMutations(OFile.init_dict(self.res.output['uncalled_file']).path, 109)
def test_uncalled_file_muts_hash(self):
self.assertMutationsHash(OFile.init_dict(self.res.output['uncalled_file']).path, "788fe2049c3cb23d0232f046fcb98ba3")
def test_portal_output_path_num_muts(self):
self.assertEqualNumMutations([
OFile.init_dict(self.res.output['portal_file']).path,
OFile.init_dict(self.res.output['uncalled_file']).path,
],
OFile.init_dict(self.res.output['filtered_file']).path)
def test_output_file_fields(self):
self.assertMutFieldContains(
OFile.init_dict(self.res.output['output_file']).path,
"Tumor_Sample_Barcode", ["Sample1", "Sample2", "Sample3", "Sample4", "Sample5"], containsAll = True)
def test_portal_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['portal_file']).path,
"Amino_Acid_Change", [""])
def test_uncalled_output_path_fields(self):
self.assertMutFieldDoesntContain(
OFile.init_dict(self.res.output['uncalled_file']).path,
"Amino_Acid_Change", [""])