def run(service_host, kbase_host):
pid = os.getpid()
ws = Workspace(url=get_workspace_url(kbase_host), token=token)
for name in workspace_names:
while 1:
print('[{:d}] List objects'.format(pid))
try:
annotations = ws.list_objects({"workspaces": [name], "type": "KBaseGenomeAnnotations.GenomeAnnotation"})
break
except Exception as err:
print('Retry on timeout: {}'.format(str(err)))
print('[{:d}] Got {:d} objects'.format(pid, len(annotations)))
for obj_num, obj in enumerate(annotations):
ref = obj[7] + "/" + obj[1]
print('[{:d}] Fetch {:d}/{:d}: {}'.format(pid, obj_num +1, len(annotations), ref))
ga = GenomeAnnotationClientAPI(get_genome_annotation_url(service_host),token,ref)
#taxon = TaxonClientAPI(services["taxon_service_url"],token,ga.get_taxon())
assembly = AssemblyClientAPI(get_assembly_url(service_host), token, ga.get_assembly())
while 1:
try:
fids = ga.get_feature_ids()
fdata = ga.get_features()
cids = assembly.get_contig_ids()
contigs = assembly.get_contigs()
except doekbase.data_api.exceptions.ServiceError as err:
print('[{:d}] Error: {}'.format(pid, err))
time.sleep(0.5)
print('[{:d}] Retrying'.format(pid))
def run(service_host, kbase_host):
pid = os.getpid()
ws = Workspace(url=get_workspace_url(kbase_host), token=token)
for name in workspace_names:
while 1:
print('[{:d}] List objects'.format(pid))
try:
annotations = ws.list_objects({
"workspaces": [name],
"type":
"KBaseGenomeAnnotations.GenomeAnnotation"
})
break
except Exception as err:
print('Retry on timeout: {}'.format(str(err)))
print('[{:d}] Got {:d} objects'.format(pid, len(annotations)))
for obj_num, obj in enumerate(annotations):
ref = obj[7] + "/" + obj[1]
print('[{:d}] Fetch {:d}/{:d}: {}'.format(pid, obj_num + 1,
len(annotations), ref))
ga = GenomeAnnotationClientAPI(
get_genome_annotation_url(service_host), token, ref)
#taxon = TaxonClientAPI(services["taxon_service_url"],token,ga.get_taxon())
assembly = AssemblyClientAPI(get_assembly_url(service_host), token,
ga.get_assembly())
while 1:
try:
fids = ga.get_feature_ids()
fdata = ga.get_features()
cids = assembly.get_contig_ids()
contigs = assembly.get_contigs()
except doekbase.data_api.exceptions.ServiceError as err:
print('[{:d}] Error: {}'.format(pid, err))
time.sleep(0.5)
print('[{:d}] Retrying'.format(pid))
"handle_service_url": "https://kbase.us/services/handle_service/"
}
token = os.environ["KB_AUTH_TOKEN"]
ws = Workspace(url=services["workspace_service_url"], token=token)
hc = handleClient(url=services["handle_service_url"], token=token)
fix_workspace = "ReferenceEnsemblPlantGenomeAnnotations"
count = 0
limit = 10000
skip = 0
done = False
while not done:
results = ws.list_objects({"workspaces": [fix_workspace],
"type": "KBaseGenomeAnnotations.Assembly",
"skip": skip,
"limit": limit})
if len(results) == 0:
done = True
for x in results:
count += 1
ac = AssemblyAPI(services, token, ref="{}/{}".format(fix_workspace, x[1]))
handle_ref = ac.get_data()["fasta_handle_ref"]
shock_node_id = None
try:
handle = hc.hids_to_handles([handle_ref])[0]
shock_node_id = handle["id"]
except Exception, e:
}
token = os.environ["KB_AUTH_TOKEN"]
ws = Workspace(url=services["workspace_service_url"], token=token)
hc = handleClient(url=services["handle_service_url"], token=token)
fix_workspace = "ReferenceEnsemblPlantGenomeAnnotations"
count = 0
limit = 10000
skip = 0
done = False
while not done:
results = ws.list_objects({
"workspaces": [fix_workspace],
"type": "KBaseGenomeAnnotations.Assembly",
"skip": skip,
"limit": limit
})
if len(results) == 0:
done = True
for x in results:
count += 1
ac = AssemblyAPI(services,
token,
ref="{}/{}".format(fix_workspace, x[1]))
handle_ref = ac.get_data()["fasta_handle_ref"]
shock_node_id = None
try:
