def test_parse_submit_succeeds_if_second_input_blob_missing_for_bam(self):
argv = create_valid_args_output_for_submission()
i, j = argv.index("--input-blob-name-1"), argv.index("--input-blob-name-2")
argv[i+1] = "i.bam"
argv = argv[:j] + argv[j+2:]
result = malibuargs.parse(argv, None, None, None, None, None)
self.assertIsNotNone(result)
def test_parse_empty_bools_keeps_defaults(self):
argv = "cancel -u https://url -k key -w 123".split()
args = malibuargs.parse(argv + ["-pl", ""], None, None, None, None, None)
args_output = malibuargs.ArgsOutput()
args_output.fill(args)
self.assertEquals(args_output.command, "CANCEL")
self.assertEquals(args_output.api_url_base, "https://url")
self.assertEquals(args_output.access_key, "key")
self.assertEquals(args_output.workflow_id, "123")
self.assertEquals(args_output.poll, False)
def test_parse_runs_successfully_with_unmatching_fastq_names(self):
argv = "submit -f tests/unittestconfig.txt".split()
using_key = False
with open("tests/unittestconfig.txt", 'r') as file:
for line in file:
if "input_storage_account_key" in line.lower():
using_key = True
break
if using_key:
args = malibuargs.parse(argv + ["-b2", "file1.fq"], None, None,
None, None, None)
blobs1 = args.input_blob_name_1
blobs2 = args.input_blob_name_2
blobs1_parsed = []
blobs2_parsed = []
for blob in blobs1:
if "?" in blob:
blob = blob.split("?")[0]
blobs1_parsed.append(blob)
for blob in blobs2:
if "?" in blob:
blob = blob.split("?")[0]
blobs2_parsed.append(blob)
self.assertListEqual(blobs1_parsed, ["chr21-10k_1.fq.gz"])
self.assertListEqual(blobs2_parsed, ["file1.fq"])
else:
args = malibuargs.parse(argv + ["-b2", "file1.fq?sas"], None, None,
None, None, None)
blobs1 = args.input_blob_name_1
blobs2 = args.input_blob_name_2
blobs1_parsed = []
blobs2_parsed = []
for blob in blobs1:
if "?" in blob:
blob = blob.split("?")[0]
blobs1_parsed.append(blob)
for blob in blobs2:
if "?" in blob:
blob = blob.split("?")[0]
blobs2_parsed.append(blob)
self.assertListEqual(blobs1_parsed, ["chr21-10k_1.fq.gz"])
self.assertListEqual(blobs2_parsed, ["file1.fq"])
def test_parse_submit_fails_if_one_io_arg_missing(self):
argv = create_valid_args_output_for_submission()
missing = [
"--process-args", "--input-storage-account-container",
"--input-storage-account-key", "--input-storage-account-name",
"--output-storage-account-container",
"--output-storage-account-key", "--output-storage-account-name"
]
for arg in missing:
i = argv.index(arg)
argv[i + 1] = ""
with self.assertRaises(SystemExit):
result = malibuargs.parse(argv, None, None, None, None, None)
def test_parse_runs_successfully_with_uneven_bam(self):
argv = "submit -f tests/unittestconfig.txt".split()
using_key = False
with open("tests/unittestconfig.txt", 'r') as file:
for line in file:
if "input_storage_account_key" in line.lower():
using_key = True
break
if using_key:
args = malibuargs.parse(
argv + ["-b2", "file1.bam", "-b1", "file1.sam", "file2.sam"],
None, None, None, None, None)
self.assertListEqual(args.input_blob_name_1,
["file1.sam", "file2.sam"])
self.assertListEqual(args.input_blob_name_2, ["file1.bam"])
else:
args = malibuargs.parse(
argv + [
"-b2", "file1.bam?sas", "-b1", "file1.sam?sas",
"file2.sam?sas"
], None, None, None, None, None)
self.assertListEqual(args.input_blob_name_1,
["file1.sam?sas", "file2.sam?sas"])
self.assertListEqual(args.input_blob_name_2, ["file1.bam?sas"])
def test_parse_runs_successfully_with_options_from_config(self):
argv = "status -f tests/unittestconfig.txt -w 123".split()
args = malibuargs.parse(argv, None, None, None, None, None)
self.assertEquals(args.command, "status")
self.assertEquals(args.workflow_id, "123")
def test_parse_submit_arguments_on_full_set(self):
argv = create_valid_args_output_for_submission()
result = malibuargs.parse(argv, None, None, None, None, None)
self.assertIsNotNone(result)
def test_parse_skips_missing_config(self):
argv = "list -u https://url -k key -f imaginary.config".split()
args = malibuargs.parse(argv, None, None, None, None, None)
self.assertEquals(args.command, "list")
self.assertEquals(args.api_url_base, "https://url")
self.assertEquals(args.access_key, "key")
def test_parse_fails_with_uneven_fastq(self):
argv = "submit -f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(argv + ["-b2", ""], None, None, None, None,
None)
def test_parse_fails_without_inputs(self):
argv = "submit -f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
malibuargs.parse(argv + ["-b1", "", "-b2", ""], None, None, None, None, None)
def test_parse_submit_succeeds_if_bz_valid(self):
argv = create_valid_args_output_for_submission()
argv.extend(["--bgzip-output", "true"])
result = malibuargs.parse(argv, None, None, None, None, None)
self.assertIsNotNone(result)
def test_parse_submit_fails_if_bz_not_supported(self):
argv = create_valid_args_output_for_submission()
argv.extend(["--bgzip-output", "Invalid"])
with self.assertRaises(SystemExit):
malibuargs.parse(argv, None, None, None, None, None)
def test_parse_submit_succeeds_if_erc_valid(self):
argv = create_valid_args_output_for_submission()
argv.extend(["--emit-ref-confidence", "gvcf"])
result = malibuargs.parse(argv, None, None, None, None, None)
self.assertIsNotNone(result)
def test_parse_submit_fails_if_erc_not_supported(self):
argv = create_valid_args_output_for_submission()
argv.extend(["--emit-ref-confidence", "vcf"])
with self.assertRaises(SystemExit):
malibuargs.parse(argv, None, None, None, None, None)
def test_parse_submit_fails_if_both_input_blobs_missing(self):
argv = create_valid_args_output_for_submission()
i, j = argv.index("--input-blob-name-1"), argv.index("--input-blob-name-2")
argv = argv[:i] + argv[j+2:]
with self.assertRaises(SystemExit):
malibuargs.parse(argv, None, None, None, None, None)
def test_parse_fails_without_required_options(self):
argv = "submit -u https://url --access-key key -b1 blob1".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(argv, None, None, None, None, None)
def test_parse_fails_with_mixed_bam_fastq(self):
argv = "submit -f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(argv + ["-b1", "file1.bam"], None, None,
None, None, None)
def test_parse_fails_when_command_missing(self):
argv = "-f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(argv, None, None, None, None, None)
def test_parse_fails_with_no_known_files(self):
argv = "submit -f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(
argv + ["-b2", "file.txt", "-b1", "file.jpg"], None, None,
None, None, None)
def test_parse_fails_on_wrong_command(self):
argv = "do -f tests/unittestconfig.txt".split()
with self.assertRaises(SystemExit):
args = malibuargs.parse(argv, None, None, None, None, None)
def test_parse_handles_negative_range_value(self):
argv = "list -u https://url -k key -r -5:-1".split()
args = malibuargs.parse(argv, None, None, None, None, None)
self.assertIsNotNone(args.in_range)
def get_test_args():
"""Creates an instance of ArgsOutput for unit testing purposes """
args = malibuargs.parse("submit -f tests/unittestconfig.txt".split(), None, None, None, None, None)
args_output = malibuargs.ArgsOutput()
args_output.fill(args)
return args_output
