def setUpClass(cls):
print('Setting up class')
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
config = configparser.ConfigParser()
config.read(config_file)
cls.cfg = {n[0]: n[1] for n in config.items('GenomeAnnotationAPI')}
authServiceUrl = cls.cfg.get('auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
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': 'GenomeAnnotationAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.ws = Workspace(cls.cfg['workspace-url'], token=token)
cls.impl = GenomeAnnotationAPI(cls.cfg)
# Second user
test_cfg_file = '/kb/module/work/test.cfg'
test_cfg_text = "[test]\n"
with open(test_cfg_file, "r") as f:
test_cfg_text += f.read()
config = configparser.ConfigParser()
config.read_file(io.StringIO(test_cfg_text))
test_cfg_dict = dict(config.items("test"))
if ('test_token2' not in test_cfg_dict):
raise ValueError("Configuration in <module>/test_local/test.cfg file should " +
"include second user credentials ('test_token2')")
token2 = test_cfg_dict['test_token2']
user2 = auth_client.get_user(token2)
cls.ctx2 = MethodContext(None)
cls.ctx2.update({'token': token2,
'user_id': user2,
'provenance': [
{'service': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
# create one WS for all tests
suffix = int(time.time() * 1000)
wsName = "test_GenomeAnnotationAPI_" + str(suffix)
ret = cls.ws.create_workspace({'workspace': wsName})
cls.wsName = wsName
# preload with reference data
with open ('data/rhodobacter.json', 'r') as file:
data_str=file.read()
data = json.loads(data_str)
# save old genome
info = cls.impl.save_one_genome_v1(cls.ctx, {
'workspace': wsName,
'name': "rhodobacter",
'data': data,
})[0]['info']
cls.rhodobacter_ref = str(info[6]) +'/' + str(info[0]) + '/' + str(info[4])
print('created rhodobacter test genome: ' + cls.rhodobacter_ref)
assembly_file_path = os.path.join(cls.cfg['scratch'],
'e_coli_assembly.fasta')
shutil.copy('data/e_coli_assembly.fasta', assembly_file_path)
au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'])
assembly_ref = au.save_assembly_from_fasta({
'workspace_name': cls.wsName,
'assembly_name': 'ecoli.assembly',
'file': {'path': assembly_file_path}
})
data = json.load(open('data/new_ecoli_genome.json'))
data['assembly_ref'] = assembly_ref
# save new genome
save_info = {
'workspace': wsName,
'objects': [{
'type': 'KBaseGenomes.Genome',
'data': data,
'name': 'new_ecoli'
}]
}
info = cls.ws.save_objects(save_info)[0]
cls.new_genome_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(
info[4])
print('created new test genome')
def __init__(self):
submod = get_service_name() or 'GenomeAnnotationAPI'
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_GenomeAnnotationAPI.get_taxon,
name='GenomeAnnotationAPI.get_taxon',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_taxon'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_assembly,
name='GenomeAnnotationAPI.get_assembly',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_assembly'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_types,
name='GenomeAnnotationAPI.get_feature_types',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_types'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_type_descriptions,
name='GenomeAnnotationAPI.get_feature_type_descriptions',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_type_descriptions'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_type_counts,
name='GenomeAnnotationAPI.get_feature_type_counts',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_type_counts'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_proteins,
name='GenomeAnnotationAPI.get_proteins',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_proteins'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_locations,
name='GenomeAnnotationAPI.get_feature_locations',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_locations'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_dna,
name='GenomeAnnotationAPI.get_feature_dna',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_dna'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_functions,
name='GenomeAnnotationAPI.get_feature_functions',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_functions'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_aliases,
name='GenomeAnnotationAPI.get_feature_aliases',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_feature_aliases'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_genome_v1,
name='GenomeAnnotationAPI.get_genome_v1',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.get_genome_v1'] = 'optional' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.save_one_genome_v1,
name='GenomeAnnotationAPI.save_one_genome_v1',
types=[dict])
self.method_authentication['GenomeAnnotationAPI.save_one_genome_v1'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.status,
name='GenomeAnnotationAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
config = configparser.ConfigParser()
config.read(config_file)
cls.cfg = {n[0]: n[1] for n in config.items('GenomeAnnotationAPI')}
authServiceUrl = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
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': 'GenomeAnnotationAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.ws = Workspace(cls.cfg['workspace-url'], token=token)
cls.impl = GenomeAnnotationAPI(cls.cfg)
test_gbk_file = "/kb/module/test/data/kb_g.399.c.1.gbk"
temp_gbk_file = "/kb/module/work/tmp/kb_g.399.c.1.gbk"
shutil.copy(test_gbk_file, temp_gbk_file)
suffix = int(time.time() * 1000)
wsName = "test_GenomeAnnotationAPI_" + str(suffix)
cls.ws.create_workspace({'workspace': wsName})
cls.wsName = wsName
data = json.load(open('data/rhodobacter_contigs.json'))
# save to ws
save_info = {
'workspace':
wsName,
'objects': [{
'type': 'KBaseGenomes.ContigSet',
'data': data,
'name': 'rhodo_contigs'
}]
}
info = cls.ws.save_objects(save_info)[0]
contigset_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(info[4])
data = json.load(open('data/rhodobacter.json'))
data['contigset_ref'] = contigset_ref
# save to ws
info = cls.impl.save_one_genome_v1(cls.ctx, {
'workspace': wsName,
'name': "rhodobacter",
'data': data,
})[0]['info']
cls.old_genome_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(
info[4])
print('created old test genome')
assembly_file_path = os.path.join(cls.cfg['scratch'],
'e_coli_assembly.fasta')
shutil.copy('data/e_coli_assembly.fasta', assembly_file_path)
au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'])
assembly_ref = au.save_assembly_from_fasta({
'workspace_name': cls.wsName,
'assembly_name': 'ecoli.assembly',
'file': {
'path': assembly_file_path
}
})
data = json.load(open('data/new_ecoli_genome.json'))
data['assembly_ref'] = assembly_ref
# save to ws
save_info = {
'workspace':
wsName,
'objects': [{
'type': 'KBaseGenomes.Genome',
'data': data,
'name': 'new_ecoli'
}]
}
info = cls.ws.save_objects(save_info)[0]
cls.new_genome_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(
info[4])
print('created new test genome')
def setUpClass(cls):
print('Setting up class')
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
config = ConfigParser.ConfigParser()
config.read(config_file)
cls.cfg = {n[0]: n[1] for n in config.items('GenomeAnnotationAPI')}
authServiceUrl = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
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': 'GenomeAnnotationAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.ws = Workspace(cls.cfg['workspace-url'], token=token)
cls.impl = GenomeAnnotationAPI(cls.cfg)
# Second user
test_cfg_file = '/kb/module/work/test.cfg'
test_cfg_text = "[test]\n"
with open(test_cfg_file, "r") as f:
test_cfg_text += f.read()
config = ConfigParser.ConfigParser()
config.readfp(StringIO.StringIO(test_cfg_text))
test_cfg_dict = dict(config.items("test"))
if ('test_token2' not in test_cfg_dict):
raise ValueError(
"Configuration in <module>/test_local/test.cfg file should " +
"include second user credentials ('test_token2')")
token2 = test_cfg_dict['test_token2']
user2 = auth_client.get_user(token2)
cls.ctx2 = MethodContext(None)
cls.ctx2.update({
'token':
token2,
'user_id':
user2,
'provenance': [{
'service': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
# create one WS for all tests
suffix = int(time.time() * 1000)
wsName = "test_GenomeAnnotationAPI_" + str(suffix)
ret = cls.ws.create_workspace({'workspace': wsName})
cls.wsName = wsName
# preload with reference data
with open('data/rhodobacter.json', 'r') as file:
data_str = file.read()
data = json.loads(data_str)
data['cdss'] = [] # Support for new Genome type structure
data['mrnas'] = [] # Support for new Genome type structure
# save to ws
result = cls.ws.save_objects({
'workspace':
wsName,
'objects': [{
'type': 'KBaseGenomes.Genome',
'data': data,
'name': 'rhodobacter'
}]
})
info = result[0]
cls.rhodobacter_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(
info[4])
print('created rhodobacter test genome: ' + cls.rhodobacter_ref)
def __init__(self):
submod = get_service_name() or 'GenomeAnnotationAPI'
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_GenomeAnnotationAPI.get_taxon,
name='GenomeAnnotationAPI.get_taxon',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_taxon'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_assembly,
name='GenomeAnnotationAPI.get_assembly',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_assembly'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_types,
name='GenomeAnnotationAPI.get_feature_types',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_types'] = 'required' # noqa
self.rpc_service.add(
impl_GenomeAnnotationAPI.get_feature_type_descriptions,
name='GenomeAnnotationAPI.get_feature_type_descriptions',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_type_descriptions'] = 'required' # noqa
self.rpc_service.add(
impl_GenomeAnnotationAPI.get_feature_type_counts,
name='GenomeAnnotationAPI.get_feature_type_counts',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_type_counts'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_proteins,
name='GenomeAnnotationAPI.get_proteins',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_proteins'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_locations,
name='GenomeAnnotationAPI.get_feature_locations',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_locations'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_dna,
name='GenomeAnnotationAPI.get_feature_dna',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_dna'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_functions,
name='GenomeAnnotationAPI.get_feature_functions',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_functions'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_feature_aliases,
name='GenomeAnnotationAPI.get_feature_aliases',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_feature_aliases'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.get_genome_v1,
name='GenomeAnnotationAPI.get_genome_v1',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.get_genome_v1'] = 'optional' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.save_one_genome_v1,
name='GenomeAnnotationAPI.save_one_genome_v1',
types=[dict])
self.method_authentication[
'GenomeAnnotationAPI.save_one_genome_v1'] = 'required' # noqa
self.rpc_service.add(impl_GenomeAnnotationAPI.status,
name='GenomeAnnotationAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
config = configparser.ConfigParser()
config.read(config_file)
cls.cfg = {n[0]: n[1] for n in config.items('GenomeAnnotationAPI')}
authServiceUrl = cls.cfg.get('auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
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': 'GenomeAnnotationAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.ws = Workspace(cls.cfg['workspace-url'], token=token)
cls.impl = GenomeAnnotationAPI(cls.cfg)
test_gbk_file = "/kb/module/test/data/kb_g.399.c.1.gbk"
temp_gbk_file = "/kb/module/work/tmp/kb_g.399.c.1.gbk"
shutil.copy(test_gbk_file, temp_gbk_file)
suffix = int(time.time() * 1000)
wsName = "test_GenomeAnnotationAPI_" + str(suffix)
cls.ws.create_workspace({'workspace': wsName})
cls.wsName = wsName
data = json.load(open('data/rhodobacter_contigs.json'))
# save to ws
save_info = {
'workspace': wsName,
'objects': [{
'type': 'KBaseGenomes.ContigSet',
'data': data,
'name': 'rhodo_contigs'
}]
}
info = cls.ws.save_objects(save_info)[0]
contigset_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(info[4])
data = json.load(open('data/rhodobacter.json'))
data['contigset_ref'] = contigset_ref
# save to ws
info = cls.impl.save_one_genome_v1(cls.ctx, {
'workspace': wsName,
'name': "rhodobacter",
'data': data,
})[0]['info']
cls.old_genome_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(
info[4])
print('created old test genome')
assembly_file_path = os.path.join(cls.cfg['scratch'],
'e_coli_assembly.fasta')
shutil.copy('data/e_coli_assembly.fasta', assembly_file_path)
au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'])
assembly_ref = au.save_assembly_from_fasta({
'workspace_name': cls.wsName,
'assembly_name': 'ecoli.assembly',
'file': {'path': assembly_file_path}
})
data = json.load(open('data/new_ecoli_genome.json'))
data['assembly_ref'] = assembly_ref
# save to ws
save_info = {
'workspace': wsName,
'objects': [{
'type': 'KBaseGenomes.Genome',
'data': data,
'name': 'new_ecoli'
}]
}
info = cls.ws.save_objects(save_info)[0]
cls.new_genome_ref = str(info[6]) + '/' + str(info[0]) + '/' + str(info[4])
print('created new test genome')