def test_validate_per_sample_FASTQ(self):
prep_info = {
"1.SKB2.640194": {
"not_a_run_prefix": "prefix1"
},
"1.SKM4.640180": {
"not_a_run_prefix": "prefix1"
},
"1.SKB3.640195": {
"not_a_run_prefix": "prefix2"
}
}
files = {
'raw_forward_seqs': [
'/path/to/SKB2.640194_file.fastq',
'/path/to/SKM4.640180_file.fastq',
'/path/to/SKB3.640195_file.fastq'
]
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertTrue(obs_success)
filepaths = [('/path/to/SKB2.640194_file.fastq', 'raw_forward_seqs'),
('/path/to/SKM4.640180_file.fastq', 'raw_forward_seqs'),
('/path/to/SKB3.640195_file.fastq', 'raw_forward_seqs')]
exp = [ArtifactInfo(None, "per_sample_FASTQ", filepaths)]
self.assertEqual(obs_ainfo, exp)
self.assertEqual(obs_error, "")
def test_validate_per_sample_FASTQ(self):
prep_info = {"1.SKB2.640194": {"not_a_run_prefix": "prefix1"},
"1.SKM4.640180": {"not_a_run_prefix": "prefix1"},
"1.SKB3.640195": {"not_a_run_prefix": "prefix2"}}
files = {'raw_forward_seqs': ['/path/to/SKB2.640194_file.fastq',
'/path/to/SKM4.640180_file.fastq',
'/path/to/SKB3.640195_file.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertTrue(obs_success)
filepaths = [('/path/to/SKB2.640194_file.fastq', 'raw_forward_seqs'),
('/path/to/SKM4.640180_file.fastq', 'raw_forward_seqs'),
('/path/to/SKB3.640195_file.fastq', 'raw_forward_seqs')]
exp = [ArtifactInfo(None, "per_sample_FASTQ", filepaths)]
self.assertEqual(obs_ainfo, exp)
self.assertEqual(obs_error, "")
def test_validate_per_sample_FASTQ_error(self):
# Filepath type not supported
prep_info = {"1.SKB2.640194": {"run_prefix": "prefix1"},
"1.SKM4.640180": {"run_prefix": "prefix2"},
"1.SKB3.640195": {"run_prefix": "prefix3"}}
files = {'Unknown': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"Filepath type(s) Unknown not supported by artifact "
"type per_sample_FASTQ. Supported filepath types: "
"raw_forward_seqs, raw_reverse_seqs, "
"preprocessed_fastq")
# Missing raw_forward_seqs and preprocessed_fastq
files = {'raw_reverse_seqs': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"Missing required filepath type: raw_forward_seqs "
"or preprocessed_fastq")
# Raw forward seqs and preprocessed_fastq
files = {'raw_forward_seqs': ['/path/to/file1.fastq'],
'preprocessed_fastq': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"If raw_forward_seqs is provided, preprocessed_fastq "
"should not be provided")
# Preprocessed fastq and raw_reverse_seqs
files = {'raw_reverse_seqs': ['/path/to/file1.fastq'],
'preprocessed_fastq': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"If preprocessed_fastq is provided, raw_reverse_seqs "
"should not be provided")
# Count mismatch
files = {'raw_forward_seqs': ['/path/to/file1.fastq'],
'raw_reverse_seqs': ['/path/to/file1.fastq',
'/path/to/file1.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"The number of provided files doesn't match the "
"number of samples (3): 1 raw_forward_seqs, "
"2 raw_reverse_seqs (optional, 0 is ok)")
# preprocessed_fastq count mismatch
files = {'preprocessed_fastq': ['/path/to/file1_R1.fastq',
'/path/to/file1_R2.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"The number of provided files doesn't match the "
"number of samples (3): 2 raw_forward_seqs, "
"0 raw_reverse_seqs (optional, 0 is ok)")
# Run prefix mismatch
files = {'raw_forward_seqs': ['/path/to/prefix1_fwd.fastq',
'/path/to/prefix2_fwd.fastq',
'/path/to/Aprefix3_fwd.fastq']}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
'The provided files are not prefixed by sample id or '
'do not match the run prefix values in the prep '
'information. Offending files:\n raw_forward_seqs: '
'Aprefix3_fwd.fastq\nraw_reverse_seqs: ')
# Non-unique run-prefix values
prep_info = {"1.SKB2.640194": {"run_prefix": "prefix1"},
"1.SKM4.640180": {"run_prefix": "prefix1"},
"1.SKB3.640195": {"run_prefix": "prefix3"}}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
"The values for the column 'run_prefix' are not "
"unique for each sample. Repeated values: prefix1 "
"(2)")
# Sample id mismatch
prep_info = {"1.SKB2.640194": {"not_a_run_prefix": "prefix1"},
"1.SKM4.640180": {"not_a_run_prefix": "prefix1"},
"1.SKB3.640195": {"not_a_run_prefix": "prefix3"}}
job_id = self._create_template_and_job(
prep_info, files, "per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(obs_error,
'The provided files are not prefixed by sample id. '
'Offending files:\n raw_forward_seqs: '
'prefix1_fwd.fastq, prefix2_fwd.fastq, '
'Aprefix3_fwd.fastq\nraw_reverse_seqs: ')
def test_validate_per_sample_FASTQ_error(self):
# Filepath type not supported
prep_info = {
"1.SKB2.640194": {
"run_prefix": "prefix1"
},
"1.SKM4.640180": {
"run_prefix": "prefix2"
},
"1.SKB3.640195": {
"run_prefix": "prefix3"
}
}
files = {'Unknown': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "Filepath type(s) Unknown not supported by artifact "
"type per_sample_FASTQ. Supported filepath types: "
"raw_forward_seqs, raw_reverse_seqs, "
"preprocessed_fastq")
# Missing raw_forward_seqs and preprocessed_fastq
files = {'raw_reverse_seqs': ['/path/to/file1.fastq']}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "Missing required filepath type: raw_forward_seqs "
"or preprocessed_fastq")
# Raw forward seqs and preprocessed_fastq
files = {
'raw_forward_seqs': ['/path/to/file1.fastq'],
'preprocessed_fastq': ['/path/to/file1.fastq']
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "If raw_forward_seqs is provided, preprocessed_fastq "
"should not be provided")
# Preprocessed fastq and raw_reverse_seqs
files = {
'raw_reverse_seqs': ['/path/to/file1.fastq'],
'preprocessed_fastq': ['/path/to/file1.fastq']
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "If preprocessed_fastq is provided, raw_reverse_seqs "
"should not be provided")
# Count mismatch
files = {
'raw_forward_seqs': ['/path/to/file1.fastq'],
'raw_reverse_seqs':
['/path/to/file1.fastq', '/path/to/file1.fastq']
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "The number of provided files doesn't match the "
"number of samples (3): 1 raw_forward_seqs, "
"2 raw_reverse_seqs (optional, 0 is ok)")
# preprocessed_fastq count mismatch
files = {
'preprocessed_fastq':
['/path/to/file1_R1.fastq', '/path/to/file1_R2.fastq']
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "The number of provided files doesn't match the "
"number of samples (3): 2 raw_forward_seqs, "
"0 raw_reverse_seqs (optional, 0 is ok)")
# Run prefix mismatch
files = {
'raw_forward_seqs': [
'/path/to/prefix1_fwd.fastq', '/path/to/prefix2_fwd.fastq',
'/path/to/Aprefix3_fwd.fastq'
]
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "The provided files do not match the run prefix "
"values in the prep information. Offending files: "
"raw_forward_seqs: Aprefix3_fwd.fastq, "
"raw_reverse_seqs: ")
# Non-unique run-prefix values
prep_info = {
"1.SKB2.640194": {
"run_prefix": "prefix1"
},
"1.SKM4.640180": {
"run_prefix": "prefix1"
},
"1.SKB3.640195": {
"run_prefix": "prefix3"
}
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "The values for the column 'run_prefix' are not "
"unique for each sample. Repeated values: prefix1 "
"(2)")
# Sample id mismatch
prep_info = {
"1.SKB2.640194": {
"not_a_run_prefix": "prefix1"
},
"1.SKM4.640180": {
"not_a_run_prefix": "prefix1"
},
"1.SKB3.640195": {
"not_a_run_prefix": "prefix3"
}
}
job_id = self._create_template_and_job(prep_info, files,
"per_sample_FASTQ")
obs_success, obs_ainfo, obs_error = _validate_per_sample_FASTQ(
self.qclient, job_id, prep_info, files)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error, "The provided files are not prefixed by sample id. "
"Please provide the 'run_prefix' column in your prep "
"information. Offending files: raw_forward_seqs: "
"prefix1_fwd.fastq, prefix2_fwd.fastq, "
"Aprefix3_fwd.fastq, raw_reverse_seqs: ")
