def test_study_prep_get_req(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {'18S': [{
'id': 1,
'status': 'private',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'}]}}
self.assertEqual(obs, exp)
# Add a new prep template
pt = npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.prep_template.PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'private',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'}],
'16S': [{'id': pt.id,
'status': 'sandbox',
'name': 'PREP %d NAME' % pt.id,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None}]}}
self.assertEqual(obs, exp)
obs = study_prep_get_req(1, '*****@*****.**')
self.assertEqual(obs, exp)
qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'public',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'}]}}
self.assertEqual(obs, exp)
def test_study_prep_get_req_no_access(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
def test_study_prep_get_req_failed_EBI(self):
temp_dir = mkdtemp()
self._clean_up_files.append(temp_dir)
user_email = '*****@*****.**'
# creating a (A) new study, (B) sample info, (C) prep without EBI
# values
# (A)
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 3,
"number_samples_promised": 3,
"study_alias": "Test EBI",
"study_description": "Study for testing EBI",
"study_abstract": "Study for testing EBI",
"emp_person_id": qdb.study.StudyPerson(2),
"principal_investigator_id": qdb.study.StudyPerson(3),
"lab_person_id": qdb.study.StudyPerson(1)
}
study = qdb.study.Study.create(qdb.user.User(user_email),
"Test EBI study", info)
# (B)
metadata_dict = {
'Sample1': {
'collection_timestamp': datetime(2015, 6, 1, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 1'
},
'Sample2': {
'collection_timestamp': datetime(2015, 6, 2, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 2'
},
'Sample3': {
'collection_timestamp': datetime(2015, 6, 3, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 3'
}
}
metadata = pd.DataFrame.from_dict(metadata_dict,
orient='index',
dtype=str)
npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.sample_template.SampleTemplate.create,
metadata, study)
# (C)
metadata_dict = {
'Sample1': {
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTC',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 1"
},
'Sample2': {
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTA',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 2"
},
'Sample3': {
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTT',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 3"
},
}
metadata = pd.DataFrame.from_dict(metadata_dict,
orient='index',
dtype=str)
pt = qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, study, "16S", 'Metagenomics')
# making sure that the EBI values are empty
exp = {
('%d.Sample3' % study.id): None,
('%d.Sample2' % study.id): None,
('%d.Sample1' % study.id): None
}
self.assertEqual(pt.ebi_experiment_accessions, exp)
# actual test
obs = study_prep_get_req(study.id, user_email)
exp = {
'info': {
'16S': [{
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact': None,
'youngest_artifact': None,
'ebi_experiment': False,
'id': pt.id,
'start_artifact_id': None
}]
},
'message': '',
'status': 'success'
}
self.assertEqual(obs, exp)
qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
def test_study_prep_get_req(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27
}, {
'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27,
'start_artifact_id': 7
}]
}
}
self.assertEqual(obs, exp)
# Add a new prep template
pt = npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.prep_template.PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27
}, {
'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact_id': 7,
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27
}],
'16S': [{
'id': pt.id,
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None,
'ebi_experiment': 0
}]
}
}
self.assertEqual(obs, exp)
obs = study_prep_get_req(1, '*****@*****.**')
self.assertEqual(obs, exp)
qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'public',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27
}]
}
}
self.assertEqual(obs, exp)
# Reset visibility of the artifacts
for i in range(4, 0, -1):
qdb.artifact.Artifact(i).visibility = "private"
qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
def test_study_prep_get_req(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'
}]
}
}
self.assertEqual(obs, exp)
# Add a new prep template
pt = npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.prep_template.PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'
}],
'16S': [{
'id': pt.id,
'status': 'sandbox',
'name': 'PREP %d NAME' % pt.id,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None
}]
}
}
self.assertEqual(obs, exp)
obs = study_prep_get_req(1, '*****@*****.**')
self.assertEqual(obs, exp)
qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'public',
'name': 'PREP 1 NAME',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM'
}]
}
}
self.assertEqual(obs, exp)
def test_study_prep_get_req_no_access(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
def test_study_prep_get_req_failed_EBI(self):
temp_dir = mkdtemp()
self._clean_up_files.append(temp_dir)
user_email = '*****@*****.**'
# creating a (A) new study, (B) sample info, (C) prep without EBI
# values
# (A)
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 3,
"number_samples_promised": 3,
"study_alias": "Test EBI",
"study_description": "Study for testing EBI",
"study_abstract": "Study for testing EBI",
"emp_person_id": qdb.study.StudyPerson(2),
"principal_investigator_id": qdb.study.StudyPerson(3),
"lab_person_id": qdb.study.StudyPerson(1)
}
study = qdb.study.Study.create(
qdb.user.User(user_email), "Test EBI study", info)
# (B)
metadata_dict = {
'Sample1': {'collection_timestamp': datetime(2015, 6, 1, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 1'},
'Sample2': {'collection_timestamp': datetime(2015, 6, 2, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 2'},
'Sample3': {'collection_timestamp': datetime(2015, 6, 3, 7, 0, 0),
'physical_specimen_location': 'location1',
'taxon_id': 9606,
'scientific_name': 'h**o sapiens',
'Description': 'Test Sample 3'}
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
dtype=str)
npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.sample_template.SampleTemplate.create,
metadata, study)
# (C)
metadata_dict = {
'Sample1': {'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTC',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 1"},
'Sample2': {'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTA',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 2"},
'Sample3': {'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'CGTAGAGCTCTT',
'center_name': 'KnightLab',
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'Protocol ABC',
'experiment_design_description': "Random value 3"},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
dtype=str)
pt = qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, study, "16S", 'Metagenomics')
# making sure that the EBI values are empty
exp = {('%d.Sample3' % study.id): None,
('%d.Sample2' % study.id): None,
('%d.Sample1' % study.id): None}
self.assertEqual(pt.ebi_experiment_accessions, exp)
# actual test
obs = study_prep_get_req(study.id, user_email)
exp = {
'info': {
'16S': [
{'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact': None, 'youngest_artifact': None,
'ebi_experiment': False, 'id': pt.id,
'start_artifact_id': None}]
},
'message': '',
'status': 'success'}
self.assertEqual(obs, exp)
qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
def test_study_prep_get_req(self):
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}, {
'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27,
'start_artifact_id': 7}]}}
self.assertEqual(obs, exp)
# Add a new prep template
pt = npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.prep_template.PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27},
{'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact_id': 7,
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}],
'16S': [{'id': pt.id,
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None,
'ebi_experiment': 0}]}}
self.assertEqual(obs, exp)
obs = study_prep_get_req(1, '*****@*****.**')
self.assertEqual(obs, exp)
qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, '*****@*****.**')
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'public',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}]}}
self.assertEqual(obs, exp)
# Reset visibility of the artifacts
for i in range(4, 0, -1):
qdb.artifact.Artifact(i).visibility = "private"
qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
def test_study_prep_get_req(self):
obs = study_prep_get_req(1, '*****@*****.**')
obs_info = obs['info']['18S']
temp_info = defaultdict(list)
temp_info['18S'] = [{
'id':
1,
'status':
'private',
'name':
'Prep information 1',
'start_artifact_id':
1,
'start_artifact':
'FASTQ',
'youngest_artifact':
'BIOM - BIOM',
'youngest_artifact_name':
'BIOM',
'youngest_artifact_type':
'BIOM',
'num_artifact_children':
2,
'total_samples':
27,
'ebi_experiment':
27,
'modification_timestamp':
obs_info[0]['modification_timestamp'],
'creation_timestamp':
obs_info[0]['creation_timestamp']
}, {
'id':
2,
'status':
'private',
'name':
'Prep information 2',
'start_artifact':
'BIOM',
'youngest_artifact':
'BIOM - BIOM',
'youngest_artifact_name':
'BIOM',
'youngest_artifact_type':
'BIOM',
'total_samples':
27,
'num_artifact_children':
0,
'ebi_experiment':
27,
'start_artifact_id':
7,
'modification_timestamp':
obs_info[1]['modification_timestamp'],
'creation_timestamp':
obs_info[1]['creation_timestamp']
}]
exp = {'status': 'success', 'message': '', 'info': temp_info}
self.assertEqual(obs, exp)
# Add a new prep template
pt = npt.assert_warns(
qdb.exceptions.QiitaDBWarning,
qdb.metadata_template.prep_template.PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, '*****@*****.**')
temp_info['16S'] = [{
'id': pt.id,
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'creation_timestamp': pt.creation_timestamp,
'modification_timestamp': pt.modification_timestamp,
'total_samples': 1,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None,
'num_artifact_children': 0,
'youngest_artifact_name': None,
'youngest_artifact_type': None,
'ebi_experiment': 0
}]
exp = {'status': 'success', 'message': '', 'info': temp_info}
self.assertEqual(obs, exp)
obs = study_prep_get_req(1, '*****@*****.**')
self.assertEqual(obs, exp)
qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, '*****@*****.**')
temp_info = defaultdict(list)
temp_info['18S'] = [{
'id':
1,
'status':
'public',
'name':
'Prep information 1',
'start_artifact_id':
1,
'start_artifact':
'FASTQ',
'youngest_artifact':
'BIOM - BIOM',
'youngest_artifact_name':
'BIOM',
'youngest_artifact_type':
'BIOM',
'num_artifact_children':
2,
'total_samples':
27,
'ebi_experiment':
27,
'modification_timestamp':
obs_info[0]['modification_timestamp'],
'creation_timestamp':
obs_info[0]['creation_timestamp']
}]
temp_info['16S'] = []
exp = {'status': 'success', 'message': '', 'info': temp_info}
self.assertEqual(obs, exp)
# Reset visibility of the artifacts
for i in range(4, 0, -1):
qdb.artifact.Artifact(i).visibility = "private"
qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
