def __init__(self):
submod = get_service_name() or 'kb_hisat2'
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_kb_hisat2.run_hisat2,
name='kb_hisat2.run_hisat2',
types=[dict])
self.method_authentication['kb_hisat2.run_hisat2'] = 'required' # noqa
self.rpc_service.add(impl_kb_hisat2.status,
name='kb_hisat2.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(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('kb_hisat2'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
auth_url = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(auth_url)
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': 'kb_hisat2',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.ws_client = Workspace(cls.wsURL)
cls.serviceImpl = kb_hisat2(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.srv_wiz_url = cls.cfg['srv-wiz-url']
# set up the test workspace
cls.ws_name = "test_kb_hisat2_{}".format(int(time.time() * 1000))
cls.ws_client.create_workspace({"workspace": cls.ws_name})
cls.dfu = DataFileUtil(cls.callback_url)
# Upload test genome
gbk_file = os.path.join(cls.scratch, os.path.basename(TEST_GBK_FILE))
shutil.copy(TEST_GBK_FILE, gbk_file)
cls.genome_ref = load_genbank_file(cls.callback_url, cls.ws_name,
gbk_file, "my_test_genome")
# Upload test reads - SingleEnd
reads_file = os.path.join(cls.scratch,
os.path.basename(TEST_READS_WT_1_FILE))
shutil.copy(TEST_READS_WT_1_FILE, reads_file)
cls.single_end_ref_wt_1 = load_reads(cls.callback_url, cls.ws_name,
"Illumina", reads_file, None,
"reads_wt_1")
reads_file = os.path.join(cls.scratch,
os.path.basename(TEST_READS_WT_2_FILE))
shutil.copy(TEST_READS_WT_2_FILE, reads_file)
cls.single_end_ref_wt_2 = load_reads(cls.callback_url, cls.ws_name,
"Illumina", reads_file, None,
"reads_wt_2")
# reads_file = os.path.join(cls.scratch, os.path.basename(TEST_READS_HY5_1_FILE))
# shutil.copy(TEST_READS_HY5_1_FILE, reads_file)
# cls.single_end_ref_hy5_1 = load_reads(
# cls.callback_url, cls.ws_name, "Illumina", reads_file, None, "reads_hy5_1"
# )
# reads_file = os.path.join(cls.scratch, os.path.basename(TEST_READS_HY5_2_FILE))
# shutil.copy(TEST_READS_HY5_2_FILE, reads_file)
# cls.single_end_ref_hy5_2 = load_reads(
# cls.callback_url, cls.ws_name, "Illumina", reads_file, None, "reads_hy5_2"
# )
# Upload test reads - PairedEnd
# Upload test ReadsSet of single end reads
reads_set = [{
"ref": cls.single_end_ref_wt_1,
"label": "rs_wt1"
}, {
"ref": cls.single_end_ref_wt_2,
"label": "rs_wt2"
}]
cls.single_end_reads_set = load_reads_set(cls.srv_wiz_url, cls.ws_name,
reads_set, "se_reads_set")
# Upload test SampleSet of single end reads
cls.reads_refs = [cls.single_end_ref_wt_1, cls.single_end_ref_wt_2]
conditions = ["ss_wt1", "ss_wt2"]
cls.single_end_sampleset = load_sample_set(cls.wsURL, cls.ws_name,
cls.reads_refs, conditions,
"SingleEnd", "se_sampleset")
genome_obj_info = cls.ws_client.get_objects2({
'objects': [{
'ref': cls.genome_ref
}],
'no_data':
1
})
# get the list of genome refs from the returned info.
# if there are no refs (or something funky with the return), this will be an empty list.
# this WILL fail if data is an empty list. But it shouldn't be, and we know because
# we have a real genome reference, or get_objects2 would fail.
genome_obj_refs = genome_obj_info.get('data', [{}])[0].get('refs', [])
# see which of those are of an appropriate type (ContigSet or Assembly), if any.
assembly_ref = list()
ref_params = [{'ref': x} for x in genome_obj_refs]
ref_info = cls.ws_client.get_object_info3({'objects': ref_params})
for idx, info in enumerate(ref_info.get('infos')):
if "KBaseGenomeAnnotations.Assembly" in info[
2] or "KBaseGenomes.ContigSet" in info[2]:
assembly_ref.append(";".join(ref_info.get('paths')[idx]))
cls.assembly_ref = assembly_ref[0]
def setUpClass(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('kb_hisat2'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
auth_url = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(auth_url)
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': 'kb_hisat2',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.ws_client = workspaceService(cls.wsURL)
cls.serviceImpl = kb_hisat2(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.srv_wiz_url = cls.cfg['srv-wiz-url']
# set up the test workspace
cls.ws_name = "test_kb_hisat2_{}".format(int(time.time() * 1000))
cls.ws_client.create_workspace({"workspace": cls.ws_name})
cls.dfu = DataFileUtil(cls.callback_url)
# Upload test genome
gbk_file = os.path.join(cls.scratch, os.path.basename(TEST_GBK_FILE))
shutil.copy(TEST_GBK_FILE, gbk_file)
cls.genome_ref = load_genbank_file(cls.callback_url, cls.ws_name,
gbk_file, "my_test_genome")
# Upload test reads - SingleEnd
reads_file = os.path.join(cls.scratch,
os.path.basename(TEST_READS_WT_1_FILE))
shutil.copy(TEST_READS_WT_1_FILE, reads_file)
cls.single_end_ref_wt_1 = load_reads(cls.callback_url, cls.ws_name,
"Illumina", reads_file, None,
"reads_wt_1")
reads_file = os.path.join(cls.scratch,
os.path.basename(TEST_READS_WT_2_FILE))
shutil.copy(TEST_READS_WT_2_FILE, reads_file)
cls.single_end_ref_wt_2 = load_reads(cls.callback_url, cls.ws_name,
"Illumina", reads_file, None,
"reads_wt_2")
# reads_file = os.path.join(cls.scratch, os.path.basename(TEST_READS_HY5_1_FILE))
# shutil.copy(TEST_READS_HY5_1_FILE, reads_file)
# cls.single_end_ref_hy5_1 = load_reads(
# cls.callback_url, cls.ws_name, "Illumina", reads_file, None, "reads_hy5_1"
# )
# reads_file = os.path.join(cls.scratch, os.path.basename(TEST_READS_HY5_2_FILE))
# shutil.copy(TEST_READS_HY5_2_FILE, reads_file)
# cls.single_end_ref_hy5_2 = load_reads(
# cls.callback_url, cls.ws_name, "Illumina", reads_file, None, "reads_hy5_2"
# )
# Upload test reads - PairedEnd
# Upload test ReadsSet of single end reads
reads_set = [{
"ref": cls.single_end_ref_wt_1,
"label": "rs_wt1"
}, {
"ref": cls.single_end_ref_wt_2,
"label": "rs_wt2"
}]
cls.single_end_reads_set = load_reads_set(cls.srv_wiz_url, cls.ws_name,
reads_set, "se_reads_set")
# Upload test SampleSet of single end reads
cls.reads_refs = [cls.single_end_ref_wt_1, cls.single_end_ref_wt_2]
conditions = ["ss_wt1", "ss_wt2"]
cls.single_end_sampleset = load_sample_set(cls.wsURL, cls.ws_name,
cls.reads_refs, conditions,
"SingleEnd", "se_sampleset")