def do_version(_):
from tabulate import tabulate
import importlib_metadata
from janis_assistant.__meta__ import __version__ as jr_version
from janis_core.__meta__ import __version__ as jc_version
import janis_core.toolbox.entrypoints as EP
fields = [["janis-core", jc_version], ["janis-assistant", jr_version]]
# eps = pkg_resources.iter_entry_points(group=EP.EXTENSIONS)
eps = importlib_metadata.entry_points().get(EP.EXTENSIONS, [])
skip_eps = {"assistant"}
for entrypoint in eps:
if entrypoint.name in skip_eps:
continue
try:
version = entrypoint.load().__version__
if version:
fields.append(["janis-" + entrypoint.name, version])
skip_eps.add(entrypoint.name)
except Exception as e:
Logger.log_ex(e)
print(tabulate(fields))
def wrapper(*args, **kwargs):
try:
return func(*args, **kwargs)
except TranslationError:
raise
except Exception as e:
components = ", ".join([
*[repr(a) for a in args],
*[
f"{k}={v}"
for k, v in kwargs.items() if k not in kwargstoignore
],
])
message = f"Couldn't translate {type or ''} with ({components})"
er = TranslationError(message, inner=e)
Logger.log_ex(er)
raise er
def create_task(self,
wid,
source,
inputs: list,
dependencies,
workflow_type=None):
# curl \
# -X POST "http://*****:*****@whole_genome_germline.cwl;type=" \
# -F "workflowInputs=@whole_genome_germline-local.yml;type=" \
# -F "[email protected];type=application/zip
from requests import post
url = self.url_create()
max_inputs = 5
if len(inputs) > max_inputs:
raise Exception(
"Too many inputs (yaml files). Proposed: automatic merge into one file."
)
files = {
"workflowSource":
source,
"labels":
json.dumps({"taskid": wid}),
"workflowOptions":
json.dumps({
"google_labels": {
"taskid": wid
},
"monitoring_image": "quay.io/dinvlad/cromwell-monitor",
"workflow_failure_mode": "ContinueWhilePossible",
}),
}
if dependencies:
files["workflowDependencies"] = dependencies
for i in range(len(inputs)):
k = "workflowInputs" + ("" if i == 0 else "_" + str(i + 1))
files[k] = inputs[i]
Logger.log("Posting to " + url)
r = post(url, files=files)
try:
res = r.json()
except Exception as e:
Logger.log_ex(e)
Logger.critical(r.text)
raise e
if not r.ok or r.status_code > 201 or res["status"] != "Submitted":
raise Exception(res)
task_id = res["id"]
return task_id
