def test_twoinvalid_check_existing_file_status():
'''
Test to make sure both invalid statues get passed back
'''
validation_statusdf = pd.DataFrame({
'id': ['syn1234', 'syn2345'],
'status': ['INVALID', 'INVALID'],
'md5': ['3333', '44444'],
'name': ['first.txt', 'second.txt']
})
error_trackerdf = pd.DataFrame({
'id': ['syn1234', 'syn2345'],
'errors': ['Invalid file format', 'Invalid formatting issues']
})
first_entity = synapseclient.Entity(name='first.txt',
id='syn1234',
md5='3333')
second_entity = synapseclient.Entity(name='second.txt',
id='syn2345',
md5='44444')
entities = [first_entity, second_entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(error_trackerdf), entities)
assert not file_status['to_validate']
assert file_status['status_list'] == ['INVALID', 'INVALID']
assert file_status['error_list'] == [
'Invalid file format', 'Invalid formatting issues'
]
def test__find_by_obj_or_create__create():
"""Tests creation"""
entity = synapseclient.Entity(name=str(uuid.uuid1()))
returned = synapseclient.Entity(name=str(uuid.uuid1()))
with patch.object(SYN, "store", return_value=returned) as patch_syn_store:
created_ent = CREATE_CLS._find_by_obj_or_create(entity)
patch_syn_store.assert_called_once_with(entity,
createOrUpdate=False)
assert created_ent == returned
def test_create_new_fileformat_table():
fileformat = str(uuid.uuid1())
db_synid = "syn1111111"
database_mappingdf = pd.DataFrame({
'Database': [fileformat, "foo"],
"Id": [db_synid, "bar"]
})
db_mapping_info = {'synid': 'syn666', 'df': database_mappingdf}
table_ent = synapseclient.Entity(parentId="syn123",
name="foo",
primaryKey=['annot'],
id='syn12345')
project_id = "syn234"
archived_project_id = "syn23333"
new_table_name = str(uuid.uuid1())
new_table_ent = synapseclient.Entity(parentId="syn123323",
name="foofoo",
id='syn23231')
update_return = Mock()
move_entity_return = Mock()
with patch.object(process_functions, "get_dbmapping",
return_value=db_mapping_info) as patch_getdb,\
patch.object(syn, "get",
return_value=table_ent) as patch_syn_get,\
patch.object(syn, "getTableColumns",
return_value=['foo', 'ddooo']) as patch_get_table_cols,\
patch.object(process_functions, "_create_schema",
return_value=new_table_ent) as patch_create_schema,\
patch.object(process_functions,
"_update_database_mapping",
return_value=update_return) as patch_update,\
patch.object(process_functions, "_move_entity",
return_value=move_entity_return) as patch_move,\
patch.object(process_functions.time, "time", return_value=2):
new_table = process_functions.create_new_fileformat_table(
syn, fileformat, new_table_name, project_id, archived_project_id)
patch_getdb.assert_called_once_with(syn, project_id)
patch_syn_get.assert_called_once_with(db_synid)
patch_get_table_cols.assert_called_once_with(db_synid)
patch_create_schema.assert_called_once_with(
syn,
table_name=new_table_name,
columns=['foo', 'ddooo'],
parentid=project_id,
annotations=table_ent.annotations)
patch_update.assert_called_once_with(syn, database_mappingdf, 'syn666',
fileformat, new_table_ent.id)
patch_move.assert_called_once_with(syn,
table_ent,
archived_project_id,
name="ARCHIVED 2-foo")
assert new_table == {
"newdb_ent": new_table_ent,
"newdb_mappingdf": update_return,
"moved_ent": move_entity_return
}
def test__find_by_obj_or_create__wrongcode_raise():
"""Tests correct error is raised when not 409 code"""
entity = synapseclient.Entity(name=str(uuid.uuid1()))
returned = synapseclient.Entity(name=str(uuid.uuid1()))
# Mock SynapseHTTPError with 404 response
mocked_404 = SynapseHTTPError("Not Found", response=Mock(status_code=404))
with patch.object(SYN, "store",
side_effect=mocked_404) as patch_syn_store,\
pytest.raises(SynapseHTTPError, match="Not Found"):
CREATE_CLS._find_by_obj_or_create(entity)
patch_syn_store.assert_called_once_with(entity, createOrUpdate=False)
def test__find_by_obj_or_create__onlycreate_raise():
"""Tests only create flag raises error when entity exists"""
entity = synapseclient.Entity(name=str(uuid.uuid1()))
returned = synapseclient.Entity(name=str(uuid.uuid1()))
# Mock SynapseHTTPError with 409 response
mocked_409 = SynapseHTTPError("foo", response=Mock(status_code=409))
with patch.object(SYN, "store",
side_effect=mocked_409) as patch_syn_store,\
pytest.raises(ValueError, match="foo. To use existing entities, "
"set only_get to True."):
CREATE_CLS._find_by_obj_or_create(entity)
patch_syn_store.assert_called_once_with(entity, createOrUpdate=False)
def test_invalid__get_status_and_error_list():
'''
Tests the correct status and error lists received
when file is invalid.
'''
modified_on = 1561143558000
modified_on_string = "2019-06-21T18:59:18.456Z"
entity = synapseclient.Entity(id='syn1234',
md5='44444',
path='/path/to/foobar.txt',
name='data_clinical_supp_SAGE.txt')
entity.properties.versionNumber = '1'
entity.properties.modifiedOn = modified_on_string
entities = [entity]
filetype = "clinical"
# This valid variable control the validation status
valid = False
errors = 'invalid file content'
input_status_list, invalid_errors_list = \
input_to_database._get_status_and_error_list(
valid, errors, entities)
assert input_status_list == [{'entity': entity, 'status': 'INVALID'}]
assert invalid_errors_list == [{'entity': entity, 'errors': errors}]
def test_dups_email_duplication_error():
'''
Test duplicated email sent
'''
duplicated_filesdf = pd.DataFrame({
'id': ['syn1234'],
'name': ['first.cbs']
})
entity = synapseclient.Entity(id='syn1234')
entity.modifiedBy = '333'
entity.createdBy = '333'
error_email = (
"Dear {},\n\n"
"Your files ({}) are duplicated! FILES SHOULD BE UPLOADED AS "
"NEW VERSIONS AND THE ENTIRE DATASET SHOULD BE "
"UPLOADED EVERYTIME".format("trial", "first.cbs"))
with patch.object(syn, "get", return_value=entity) as patch_syn_get,\
patch.object(syn, "getUserProfile",
return_value={'userName':
'******'}) as patch_syn_profile,\
patch.object(syn, "sendMessage") as patch_send:
input_to_database.email_duplication_error(syn, duplicated_filesdf)
patch_syn_get.assert_called_once_with('syn1234')
patch_syn_profile.assert_called_once_with('333')
patch_send.assert_called_once_with(['333'], "GENIE Validation Error",
error_email)
def test_store_assay_info_files():
"""Tests storing of assay information file"""
assay_infodf = pd.DataFrame({'library_strategy': ['WXS'],
'SEQ_ASSAY_ID': ['A']})
clinicaldf = pd.DataFrame({'SEQ_ASSAY_ID': ['A']})
database_to_staging.GENIE_RELEASE_DIR = "./"
path = os.path.join(database_to_staging.GENIE_RELEASE_DIR,
"assay_information_vTEST.txt")
with patch.object(SYN, "create_snapshot_version",
return_value=2) as patch_create_version,\
patch.object(process_functions, "get_syntabledf",
return_value=assay_infodf) as patch_table_query,\
patch.object(database_to_staging, "store_file",
return_value=synapseclient.Entity()) as patch_storefile:
wes_ids = database_to_staging.store_assay_info_files(SYN,
GENIE_VERSION,
FILEVIEW_SYNID,
clinicaldf,
CONSORTIUM_SYNID)
patch_create_version.assert_called_once_with(FILEVIEW_SYNID,
comment=GENIE_VERSION)
patch_table_query.assert_called_once_with(
SYN,
f"select * from {FILEVIEW_SYNID} where SEQ_ASSAY_ID in ('A')"
)
patch_storefile.assert_called_once_with(SYN, path,
parent=CONSORTIUM_SYNID,
genieVersion=GENIE_VERSION,
name="assay_information.txt",
used=f"{FILEVIEW_SYNID}.2")
assert wes_ids == ['A']
def test_wrong_permission_level():
with pytest.raises(ValueError,
match=r'permission_level must be one of these:.*'):
challengeutils.permissions._set_permissions(syn,
synapseclient.Entity(),
principalid="3",
permission_level="foo")
def test_valid__get_status_and_error_list():
'''
Tests the correct status and error lists received
when file is valid.
'''
modified_on = 1561143558000
modified_on_string = "2019-06-21T18:59:18.456Z"
entity = synapseclient.Entity(id='syn1234',
md5='44444',
path='/path/to/foobar.txt',
name='data_clinical_supp_SAGE.txt')
entity.properties.modifiedOn = modified_on_string
entities = [entity]
valid = True
message = 'valid'
filetype = 'clinical'
input_status_list, invalid_errors_list = \
input_to_database._get_status_and_error_list(
valid, message, entities)
assert input_status_list == [{'entity': entity, 'status': 'VALIDATED'}]
assert not invalid_errors_list
def test_specifyloc_download_submission():
'''
Download submission json object with specified location
'''
entity = synapseclient.Entity(versionNumber=4,
concreteType='foo',
id='syn123')
submission_dict = {
'entity': entity,
'evaluationId': 12345,
'filePath': '/path/here'
}
expected_submission_dict = {
'docker_repository': None,
'docker_digest': None,
'entity_id': entity['id'],
'entity_version': entity.get('versionNumber'),
'entity_type': entity.get('concreteType'),
'evaluation_id': 12345,
'file_path': '/path/here'
}
with mock.patch.object(
syn, "getSubmission",
return_value=submission_dict) as patch_get_submission:
sub_dict = challengeutils.utils.download_submission(
syn, "12345", download_location=".")
patch_get_submission.assert_called_once_with("12345",
downloadLocation=".")
assert sub_dict == expected_submission_dict
def test_noname__move_entity():
"""Tests not changing entity name"""
ent = synapseclient.Entity(name="foo", parentId="syn2222")
new_parent = "syn1234"
with patch.object(syn, "store") as patch_syn_store:
process_functions._move_entity(syn, ent, new_parent)
ent.parentId = new_parent
patch_syn_store.assert_called_once_with(ent)
def test_wrong_permission_level():
"""Error raised if incorrect permission level is passed in"""
with pytest.raises(ValueError,
match=r'permission_level must be one of these:.*'):
permissions._set_permissions(SYN,
synapseclient.Entity(),
principalid="3",
permission_level="foo")
def test_valid_validatefile():
'''
Tests the behavior of a file that gets validated that becomes
valid
'''
validation_statusdf = pd.DataFrame()
error_trackerdf = pd.DataFrame()
entity = synapseclient.Entity(name="data_clinical_supp_SAGE.txt",
id='syn1234',
md5='44444',
path='/path/to/data_clinical_supp_SAGE.txt')
entity['modifiedOn'] = '2019-03-24T12:00:00.Z'
# This modifiedOn translates to: 1553428800000
entity.modifiedBy = '333'
entity.createdBy = '444'
entities = [entity]
threads = 0
valid = True
message = "Is valid"
filetype = "clinical"
# Only a list is returned as opposed a list of lists when there are
# invalid errors
status_error_list_results = ([{
'entity': entity,
'status': 'VALIDATED'
}], [])
expected_results = ([{
'entity': entity,
'status': 'VALIDATED',
'fileType': filetype,
'center': center
}], [], [])
with patch.object(GenieValidationHelper, "determine_filetype",
return_value=filetype) as patch_determine_filetype,\
patch.object(input_to_database, "check_existing_file_status",
return_value={'status_list': [],
'error_list': [],
'to_validate': True}) as patch_check, \
patch.object(GenieValidationHelper, "validate_single_file",
return_value=(valid, message)) as patch_validate,\
patch.object(input_to_database, "_get_status_and_error_list",
return_value=status_error_list_results) as patch_get_staterror_list,\
patch.object(input_to_database,
"_send_validation_error_email") as patch_send_email:
validate_results = input_to_database.validatefile(
syn, None, entities, validation_statusdf, error_trackerdf, center,
threads, oncotree_link)
assert expected_results == validate_results
patch_validate.assert_called_once_with(oncotree_link=oncotree_link,
nosymbol_check=False)
patch_check.assert_called_once_with(validation_statusdf,
error_trackerdf, entities)
patch_determine_filetype.assert_called_once()
patch_get_staterror_list.assert_called_once_with(
valid, message, entities)
patch_send_email.assert_not_called()
def test_store_gene_panel_files():
data_gene_panel = pd.DataFrame({'mutations': ['PANEL1']})
gene_paneldf = pd.DataFrame({'id': ['syn3333']})
with mock.patch.object(
SYN, "tableQuery",
return_value=Tablequerydf(gene_paneldf)) as patch_syn_table_query,\
mock.patch.object(
database_to_staging, "store_file",
return_value=synapseclient.Entity()) as patch_storefile,\
mock.patch.object(
SYN, "get",
return_value=synapseclient.Entity(
path="/foo/bar/PANEL1.txt",
versionNumber=2)) as patch_syn_get,\
mock.patch.object(os, "rename") as patch_os_rename:
database_to_staging.store_gene_panel_files(SYN,
FILEVIEW_SYNID,
GENIE_VERSION,
data_gene_panel,
CONSORTIUM_SYNID,
["TEST"])
patch_syn_table_query.assert_called_once_with(
"select id from %s where cBioFileFormat = 'genePanel' "
"and fileStage = 'staging' and "
"name not in ('data_gene_panel_TEST.txt')" % FILEVIEW_SYNID)
patch_storefile.assert_called_once_with(
SYN,
os.path.join(database_to_staging.GENIE_RELEASE_DIR,
"PANEL1_vTEST.txt"),
parent=CONSORTIUM_SYNID,
genieVersion=GENIE_VERSION,
name="PANEL1.txt",
cBioFileFormat="genePanel",
used='syn3333.2')
patch_syn_get.assert_called_once_with('syn3333')
patch_os_rename.assert_called_once_with(
"/foo/bar/PANEL1.txt",
os.path.join(database_to_staging.GENIE_RELEASE_DIR,
"PANEL1_vTEST.txt"))
def test_name__move_entity():
"""Tests entity name is updated"""
ent = synapseclient.Entity(name="foo", parentId="syn2222")
new_parent = "syn1234"
new_name = "updated name"
with patch.object(syn, "store") as patch_syn_store:
process_functions._move_entity(syn, ent, new_parent, new_name)
ent.parentId = new_parent
ent.name = new_name
patch_syn_store.assert_called_once_with(ent)
def test__find_by_obj_or_create__get():
"""Tests getting of entity"""
concretetype = str(uuid.uuid1())
entity = synapseclient.Entity(name=str(uuid.uuid1()),
parentId=str(uuid.uuid1()),
concreteType=concretetype)
returned = synapseclient.Entity(name=str(uuid.uuid1()),
id=str(uuid.uuid1()),
parentId=str(uuid.uuid1()),
concreteType=concretetype)
mocked_409 = SynapseHTTPError("foo", response=Mock(status_code=409))
with patch.object(SYN, "store",
side_effect=mocked_409) as patch_syn_store,\
patch.object(GET_CLS, "_get_obj",
return_value=returned) as patch_cls_get:
get_ent = GET_CLS._find_by_obj_or_create(entity)
assert get_ent == returned
patch_syn_store.assert_called_once()
patch_cls_get.assert_called_once_with(entity)
def test_invalid_check_existing_file_status():
'''
Test the values returned by input that is invalid
'''
entity = synapseclient.Entity(name='second.txt', id='syn2345', md5='44444')
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(error_trackerdf), entities)
assert not file_status['to_validate']
assert file_status['status_list'] == ['INVALID']
assert file_status['error_list'] == ['Invalid file format']
def test_valid_check_existing_file_status():
'''
Test the values returned by input that is already valid
'''
entity = synapseclient.Entity(name='first.txt', id='syn1234', md5='3333')
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(error_trackerdf), entities)
assert not file_status['to_validate']
assert file_status['status_list'] == ['VALID']
assert file_status['error_list'] == []
def test_diffnametovalidate_check_existing_file_status():
'''
If name is different from stored name, must re-validate file
'''
entity = synapseclient.Entity(name='second.txt', id='syn1234', md5='3333')
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(emptydf), entities)
assert file_status['to_validate']
assert file_status['status_list'] == ['VALID']
assert file_status['error_list'] == []
def test_nostorederrors_check_existing_file_status():
'''
If there is no error uploaded, must re-validate file
'''
entity = synapseclient.Entity(name='second.txt', id='syn2345', md5='44444')
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(emptydf), entities)
assert file_status['to_validate']
assert file_status['status_list'] == ['INVALID']
assert file_status['error_list'] == []
def test_diffmd5validate_check_existing_file_status():
'''
If md5 is different from stored md5, must re-validate file
'''
entity = synapseclient.Entity(name='first.txt', id='syn1234', md5='44444')
entity.properties.versionNumber = '1'
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(validation_statusdf),
mock_csv_query_result(emptydf), entities)
assert file_status['to_validate']
assert file_status['status_list'] == ['VALID']
assert file_status['error_list'] == []
def test_unvalidatedinput_check_existing_file_status():
'''
Test the values returned by input that hasn't be validated
'''
entity = synapseclient.Entity(id='syn1234')
entities = [entity]
file_status = input_to_database.check_existing_file_status(
mock_csv_query_result(emptydf), mock_csv_query_result(emptydf),
entities)
assert file_status['to_validate']
assert file_status['status_list'] == []
assert file_status['error_list'] == []
def test_create_and_archive_maf_database():
'''
Test the creation and archive of the maf database
'''
table_ent = synapseclient.Entity(parentId="syn123",
name="foo",
primaryKey=['annot'],
id='syn12345')
new_maf_ent = synapseclient.Entity(id="syn2222")
database_synid_mappingdf = pd.DataFrame({
'Database': ['vcf2maf', 'main'],
'Id': ['syn12345', 'syn23455']
})
with patch.object(syn, "store",
return_value=new_maf_ent) as patch_syn_store,\
patch.object(syn, "setPermissions",
return_value=None) as patch_syn_set_permissions,\
patch.object(syn, "get",
return_value=table_ent) as patch_syn_get,\
patch.object(syn, "getTableColumns",
return_value=['foo', 'ddooo']) as patch_syn_get_table_columns:
database_mappingdf = input_to_database.create_and_archive_maf_database(
syn, database_synid_mappingdf)
assert database_mappingdf['Id'][
database_mappingdf['Database'] == 'vcf2maf'].values[0] \
== new_maf_ent.id
assert database_mappingdf['Id'][database_mappingdf['Database'] ==
'main'].values[0] == 'syn23455'
patch_syn_get_table_columns.assert_called_once_with('syn12345')
patch_syn_get.assert_called_once_with('syn12345')
assert patch_syn_store.call_count == 3
patch_syn_set_permissions.assert_called_once_with(
new_maf_ent.id, 3326313, [])
from mock import patch
import pytest
import challengeutils
import synapseclient
syn = synapseclient.Synapse()
SET_PERMS = {"set"}
@pytest.fixture(params=[
# tuple with (input, expectedOutput)
(synapseclient.Project(), None, "view",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['view']),
(synapseclient.Folder(parentId="syn123"), None, "download",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['download']),
(synapseclient.Entity(), None, "edit",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['edit']),
(synapseclient.Schema(parentId="syn123"), None, "edit_and_delete",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['edit_and_delete']),
(synapseclient.File(parentId="syn123"), None, "admin",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['admin']),
(synapseclient.Entity(), None, "remove",
challengeutils.permissions.ENTITY_PERMS_MAPPINGS['remove']),
(synapseclient.Evaluation(contentSource="syn123"), None, "view",
challengeutils.permissions.EVALUATION_PERMS_MAPPINGS['view']),
(synapseclient.Evaluation(contentSource="syn123"), None, "submit",
challengeutils.permissions.EVALUATION_PERMS_MAPPINGS['submit']),
(synapseclient.Evaluation(contentSource="syn123"), None, "score",
challengeutils.permissions.EVALUATION_PERMS_MAPPINGS['score']),
(synapseclient.Evaluation(contentSource="syn123"), None, "admin",
challengeutils.permissions.EVALUATION_PERMS_MAPPINGS['admin']),
(synapseclient.Evaluation(contentSource="syn123"), None, "remove",
from challengeutils import permissions
SYN = create_autospec(synapseclient.Synapse)
SET_PERMS = {"set"}
@pytest.mark.parametrize(
"entity,principalid,permission_level,mapped",
[
# tuple with (input, expectedOutput)
(synapseclient.Project(), None, "view",
permissions.ENTITY_PERMS_MAPPINGS['view']),
(synapseclient.Folder(parentId="syn123"), None, "download",
permissions.ENTITY_PERMS_MAPPINGS['download']),
(synapseclient.Entity(), None, "edit",
permissions.ENTITY_PERMS_MAPPINGS['edit']),
(synapseclient.Schema(parentId="syn123"), None, "edit_and_delete",
permissions.ENTITY_PERMS_MAPPINGS['edit_and_delete']),
(synapseclient.File(parentId="syn123"), None, "admin",
permissions.ENTITY_PERMS_MAPPINGS['admin']),
(synapseclient.Entity(), None, "remove",
permissions.ENTITY_PERMS_MAPPINGS['remove']),
(synapseclient.Evaluation(contentSource="syn123"), None, "view",
permissions.EVALUATION_PERMS_MAPPINGS['view']),
(synapseclient.Evaluation(contentSource="syn123"), None, "submit",
permissions.EVALUATION_PERMS_MAPPINGS['submit']),
(synapseclient.Evaluation(contentSource="syn123"), None, "score",
permissions.EVALUATION_PERMS_MAPPINGS['score']),
(synapseclient.Evaluation(contentSource="syn123"), None, "admin",
permissions.EVALUATION_PERMS_MAPPINGS['admin']),
def test_invalid_validatefile():
'''
Tests the behavior of a file that gets validated that becomes
invalid
'''
validation_statusdf = pd.DataFrame()
error_trackerdf = pd.DataFrame(columns=['id'], dtype=str)
entity = synapseclient.Entity(name="data_clinical_supp_SAGE.txt",
id='syn1234',
md5='44444',
path='/path/to/data_clinical_supp_SAGE.txt')
entity['modifiedOn'] = '2019-03-24T12:00:00.Z'
# This modifiedOn translates to: 1553428800000
entity.modifiedBy = '333'
entity.createdBy = '444'
entities = [entity]
threads = 0
valid = False
message = "Is invalid"
filetype = "clinical"
status_error_list_results = ([{
'entity': entity,
'status': 'INVALID'
}], [{
'entity': entity,
'errors': message
}])
expected_results = ([{
'entity': entity,
'status': 'INVALID',
'fileType': filetype,
'center': center
}], [{
'entity': entity,
'errors': message,
'fileType': filetype,
'center': center
}], [(['data_clinical_supp_SAGE.txt'], 'Is invalid', ['333', '444'])])
with patch.object(ValidationHelper, "determine_filetype",
return_value=filetype) as patch_determine_filetype,\
patch.object(input_to_database, "check_existing_file_status",
return_value={'status_list': [],
'error_list': [],
'to_validate': True}) as patch_check, \
patch.object(ValidationHelper, "validate_single_file",
return_value=(valid, message)) as patch_validate,\
patch.object(input_to_database, "_get_status_and_error_list",
return_value=status_error_list_results) as patch_get_staterror_list:
validate_results = input_to_database.validatefile(
syn,
None,
entities,
validation_statusdf,
error_trackerdf,
center,
threads,
validator_cls=ValidationHelper)
assert expected_results == validate_results
patch_validate.assert_called_once_with()
patch_check.assert_called_once_with(validation_statusdf,
error_trackerdf, entities)
patch_determine_filetype.assert_called_once()
patch_get_staterror_list.assert_called_once_with(
valid, message, entities)
def test_validation(self):
"""Test validation steps"""
modified_on = 1561143558000
process = "main"
databaseToSynIdMapping = {
'Database': ["clinical", 'validationStatus', 'errorTracker'],
'Id': ['syn222', 'syn333', 'syn444']
}
databaseToSynIdMappingDf = pd.DataFrame(databaseToSynIdMapping)
entity = synapseclient.Entity(id='syn1234',
md5='44444',
path='/path/to/foobar.txt',
name='data_clinical_supp_SAGE.txt')
entities = [entity]
filetype = "clinical"
input_status_list = [[
entity.id, entity.path, entity.md5, 'VALIDATED', entity.name,
modified_on, filetype, center
]]
invalid_errors_list = []
messages = []
new_tables = {
'validation_statusdf': self.validation_statusdf,
'error_trackingdf': self.errors_df,
'duplicated_filesdf': self.empty_dup
}
validationstatus_mock = emptytable_mock()
errortracking_mock = emptytable_mock()
valiate_cls = Mock()
with patch.object(syn, "tableQuery",
side_effect=[validationstatus_mock,
errortracking_mock]) as patch_query,\
patch.object(input_to_database, "validatefile",
return_value=(input_status_list,
invalid_errors_list,
messages)) as patch_validatefile,\
patch.object(input_to_database, "build_validation_status_table",
return_value=self.validation_statusdf),\
patch.object(input_to_database, "build_error_tracking_table",
return_value=self.errors_df),\
patch.object(input_to_database, "_update_tables_content",
return_value=new_tables),\
patch.object(input_to_database, "update_status_and_error_tables"):
valid_filedf = input_to_database.validation(
syn,
"syn123",
center,
process,
entities,
databaseToSynIdMappingDf,
oncotree_link,
format_registry={"test": valiate_cls})
assert patch_query.call_count == 2
patch_validatefile.assert_called_once_with(
syn,
"syn123",
entity,
validationstatus_mock,
errortracking_mock,
center='SAGE',
threads=1,
oncotree_link=oncotree_link,
format_registry={"test": valiate_cls})
assert valid_filedf.equals(
self.validation_statusdf[['id', 'path', 'fileType', 'name']])
def test_already_validated_validatefile():
'''
Test already validated files
'''
validation_statusdf = pd.DataFrame()
error_trackerdf = pd.DataFrame()
entity = synapseclient.Entity(name="data_clinical_supp_SAGE.txt",
id='syn1234',
md5='44444',
path='/path/to/data_clinical_supp_SAGE.txt')
entity['modifiedOn'] = '2019-03-24T12:00:00.Z'
# This modifiedOn translates to: 1553428800000
entity.modifiedBy = '333'
entity.createdBy = '444'
entities = [entity]
threads = 0
valid = False
errors = "Invalid file"
filetype = "markdown"
status = "INVALID"
check_file_status_dict = {
'status_list': [status],
'error_list': [errors],
'to_validate': False
}
status_error_list_results = ([{
'entity': entity,
'status': status
}], [{
'entity': entity,
'errors': errors
}])
expected_results = ([{
'entity': entity,
'status': status,
'fileType': filetype,
'center': center
}], [{
'entity': entity,
'errors': errors,
'fileType': filetype,
'center': center
}], [])
with patch.object(GenieValidationHelper, "determine_filetype",
return_value=filetype) as patch_determine_filetype,\
patch.object(input_to_database, "check_existing_file_status",
return_value=check_file_status_dict) as patch_check, \
patch.object(GenieValidationHelper, "validate_single_file",
return_value=(valid, errors)) as patch_validate,\
patch.object(input_to_database, "_get_status_and_error_list",
return_value=status_error_list_results) as patch_get_staterror_list,\
patch.object(input_to_database,
"_send_validation_error_email") as patch_send_email:
validate_results = input_to_database.validatefile(
syn,
None,
entities,
validation_statusdf,
error_trackerdf,
center,
threads,
oncotree_link,
)
assert expected_results == validate_results
patch_validate.assert_not_called()
patch_check.assert_called_once_with(validation_statusdf,
error_trackerdf, entities)
patch_determine_filetype.assert_called_once()
patch_get_staterror_list.assert_not_called()
patch_send_email.assert_not_called()
def test_validation():
'''
Test validation steps
'''
validation_statusdf = pd.DataFrame({
'id': ['syn1234'],
'status': ['VALIDATED'],
'path': ["/path/to/file"],
'fileType': ['clinical']
})
thread = 2
testing = False
modified_on = 1561143558000
process = "main"
databaseToSynIdMapping = {
'Database': ["clinical", 'validationStatus', 'errorTracker'],
'Id': ['syn222', 'syn333', 'syn444']
}
databaseToSynIdMappingDf = pd.DataFrame(databaseToSynIdMapping)
entity = synapseclient.Entity(id='syn1234',
md5='44444',
path='/path/to/foobar.txt',
name='data_clinical_supp_SAGE.txt')
entities = [entity]
filetype = "clinical"
input_status_list = [[
entity.id, entity.path, entity.md5, 'VALIDATED', entity.name,
modified_on, filetype, center
]]
invalid_errors_list = []
messages = []
validationstatus_mock = emptytable_mock()
errortracking_mock = emptytable_mock()
with patch.object(input_to_database, "get_center_input_files",
return_value=entities) as patch_get_center,\
patch.object(syn, "tableQuery",
side_effect=[validationstatus_mock,
errortracking_mock]) as patch_tablequery,\
patch.object(input_to_database, "validatefile",
return_value=(input_status_list,
invalid_errors_list,
messages)) as patch_validatefile,\
patch.object(input_to_database, "update_status_and_error_tables",
return_value=validation_statusdf) as patch_update_status:
valid_filedf = input_to_database.validation(
syn, center, process, center_mapping_df, databaseToSynIdMappingDf,
thread, testing, oncotree_link, genie.config.PROCESS_FILES)
patch_get_center.assert_called_once_with(syn, center_input_synid,
center, process)
assert patch_tablequery.call_count == 2
patch_validatefile.assert_called_once_with(
syn,
entity,
validationstatus_mock,
errortracking_mock,
center='SAGE',
threads=1,
testing=False,
oncotree_link=oncotree_link,
format_registry=genie.config.PROCESS_FILES)
patch_update_status.assert_called_once_with(syn, input_status_list, [],
validationstatus_mock,
errortracking_mock)
assert valid_filedf.equals(
validation_statusdf[['id', 'path', 'fileType']])