def setUpClass(cls):
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({'token': token,
'user_id': user_id,
'provenance': [
{'service': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.pca_util = PCAUtil(cls.cfg)
suffix = int(time.time() * 1000)
cls.wsName = "test_pca_util_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.wsId = ret[0]
def setUpClass(cls):
cls.token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(cls.token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
cls.token,
'user_id':
user_id,
'provenance': [{
'service': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.shockURL = cls.cfg['shock-url']
cls.dfu = DataFileUtil(cls.callback_url)
cls.sample_uploader = sample_uploader(cls.callback_url,
service_ver="dev")
cls.sample_url = cls.cfg.get('kbase-endpoint') + '/sampleservice'
cls.sample_ser = SampleService(cls.sample_url)
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
suffix = int(time.time() * 1000)
cls.wsName = "test_GenericsAPI_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.wsId = ret[0]
small_file = os.path.join(cls.scratch, 'test.txt')
with open(small_file, "w") as f:
f.write("empty content")
cls.test_shock = cls.dfu.file_to_shock({
'file_path': small_file,
'make_handle': True
})
cls.handles_to_delete = []
cls.nodes_to_delete = []
cls.handles_to_delete.append(cls.test_shock['handle']['hid'])
cls.nodes_to_delete.append(cls.test_shock['shock_id'])
cls.prepare_data()
def setUpClass(cls):
cls.maxDiff = 70000
cls.token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(cls.token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({'token': cls.token,
'user_id': user_id,
'provenance': [
{'service': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.serviceUtils = AttributesUtil(cls.cfg)
cls.shockURL = cls.cfg['shock-url']
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
suffix = int(time.time() * 1000)
cls.wsName = "test_CompoundSetUtils_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.wsId = ret[0]
cls.attribute_mapping = json.load(open('data/AM1.json'))
info = cls.dfu.save_objects({
"id": cls.wsId,
"objects": [{
"type": "KBaseExperiments.AttributeMapping",
"data": cls.attribute_mapping,
"name": "test_cond_set"
}]
})[0]
cls.attribute_mapping_ref = "%s/%s/%s" % (info[6], info[0], info[4])
cls.attribute_mapping_2 = json.load(open('data/AM2.json'))
small_file = os.path.join(cls.scratch, 'test.txt')
with open(small_file, "w") as f:
f.write("empty content")
cls.test_shock = cls.dfu.file_to_shock({'file_path': small_file, 'make_handle': True})
cls.handles_to_delete = []
cls.nodes_to_delete = []
cls.handles_to_delete.append(cls.test_shock['handle']['hid'])
cls.nodes_to_delete.append(cls.test_shock['shock_id'])
def setUpClass(cls):
cls.maxDiff = 70000
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({'token': token,
'user_id': user_id,
'provenance': [
{'service': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.serviceUtils = AttributesUtil(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
suffix = int(time.time() * 1000)
#cls.wsName = "test_CompoundSetUtils_" + str(suffix)
cls.wsName = "man4ish_gupta:narrative_1568644342277"
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
#exit(cls.wsId)
#cls.wsId = ret[0]
cls.wsid = 44071
cls.attribute_mapping = json.load(open('data/AM1.json'))
info = cls.dfu.save_objects({
"id": cls.wsId,
"objects": [{
"type": "KBaseExperiments.AttributeMapping",
"data": cls.attribute_mapping,
"name": "test_cond_set"
}]
})[0]
cls.attribute_mapping_ref = "%s/%s/%s" % (info[6], info[0], info[4])
cls.attribute_mapping_2 = json.load(open('data/AM2.json'))
def __init__(self):
submod = get_service_name() or 'GenericsAPI'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_GenericsAPI.fetch_data,
name='GenericsAPI.fetch_data',
types=[dict])
self.method_authentication[
'GenericsAPI.fetch_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_matrix,
name='GenericsAPI.export_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.export_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.validate_data,
name='GenericsAPI.validate_data',
types=[dict])
self.method_authentication[
'GenericsAPI.validate_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.import_matrix_from_excel,
name='GenericsAPI.import_matrix_from_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.import_matrix_from_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.import_matrix_from_biom,
name='GenericsAPI.import_matrix_from_biom',
types=[dict])
self.method_authentication[
'GenericsAPI.import_matrix_from_biom'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.save_object,
name='GenericsAPI.save_object',
types=[dict])
self.method_authentication[
'GenericsAPI.save_object'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.search_matrix,
name='GenericsAPI.search_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.search_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.filter_matrix,
name='GenericsAPI.filter_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.filter_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.standardize_matrix,
name='GenericsAPI.standardize_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.standardize_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.file_to_attribute_mapping,
name='GenericsAPI.file_to_attribute_mapping',
types=[dict])
self.method_authentication[
'GenericsAPI.file_to_attribute_mapping'] = 'required' # noqa
self.rpc_service.add(
impl_GenericsAPI.update_matrix_attribute_mapping,
name='GenericsAPI.update_matrix_attribute_mapping',
types=[dict])
self.method_authentication[
'GenericsAPI.update_matrix_attribute_mapping'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.attribute_mapping_to_tsv_file,
name='GenericsAPI.attribute_mapping_to_tsv_file',
types=[dict])
self.method_authentication[
'GenericsAPI.attribute_mapping_to_tsv_file'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_tsv,
name='GenericsAPI.export_attribute_mapping_tsv',
types=[dict])
self.method_authentication[
'GenericsAPI.export_attribute_mapping_tsv'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_excel,
name='GenericsAPI.export_attribute_mapping_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_attribute_mapping_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_cluster_set_excel,
name='GenericsAPI.export_cluster_set_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_cluster_set_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_corr_matrix_excel,
name='GenericsAPI.export_corr_matrix_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_corr_matrix_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_pca_matrix_excel,
name='GenericsAPI.export_pca_matrix_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_pca_matrix_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_amplicon_set_tsv,
name='GenericsAPI.export_amplicon_set_tsv',
types=[dict])
self.method_authentication[
'GenericsAPI.export_amplicon_set_tsv'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.compute_correlation_matrix,
name='GenericsAPI.compute_correlation_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.compute_correlation_matrix'] = 'required' # noqa
self.rpc_service.add(
impl_GenericsAPI.compute_correlation_across_matrices,
name='GenericsAPI.compute_correlation_across_matrices',
types=[dict])
self.method_authentication[
'GenericsAPI.compute_correlation_across_matrices'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.build_network,
name='GenericsAPI.build_network',
types=[dict])
self.method_authentication[
'GenericsAPI.build_network'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.run_pca,
name='GenericsAPI.run_pca',
types=[dict])
self.method_authentication['GenericsAPI.run_pca'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.view_matrix,
name='GenericsAPI.view_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.view_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.status,
name='GenericsAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'GenericsAPI'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_GenericsAPI.fetch_data,
name='GenericsAPI.fetch_data',
types=[dict])
self.method_authentication[
'GenericsAPI.fetch_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.generate_matrix_html,
name='GenericsAPI.generate_matrix_html',
types=[dict])
self.method_authentication[
'GenericsAPI.generate_matrix_html'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_matrix,
name='GenericsAPI.export_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.export_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.validate_data,
name='GenericsAPI.validate_data',
types=[dict])
self.method_authentication[
'GenericsAPI.validate_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.import_matrix_from_excel,
name='GenericsAPI.import_matrix_from_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.import_matrix_from_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.save_object,
name='GenericsAPI.save_object',
types=[dict])
self.method_authentication[
'GenericsAPI.save_object'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.search_matrix,
name='GenericsAPI.search_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.search_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.filter_matrix,
name='GenericsAPI.filter_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.filter_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.status,
name='GenericsAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
