#!/usr/bin/env python

import arvados
import arvados_cwl
import arvados.collection
import arvados.util
from cwltool.process import shortname
import cwltool.main
import logging
import os
import json
from arvados.api import OrderedJsonModel

api = arvados.api("v1")

try:
    job_order_object = arvados.current_job()['script_parameters']

    print job_order_object

    for k,v in job_order_object.items():
        if arvados.util.keep_locator_pattern.match(v):
            job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)

    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))

    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)

    outputObj = runner.arvExecutor(t, job_order_object, "", None)

    c = arvados.collection.Collection()
    with c.open("cwl.output.json", "w") as f:
        json.dump(outputObj, f, indent=4)

    api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                         body={
                                             'output': c.save_new(create_collection_record=False),
                                             'success': True,
                                             'progress':1.0
                                         }).execute()
except Exception as e:
    logging.exception("Unhandled exception")
    api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                         body={
                                             'output': None,
                                             'success': False,
                                             'progress':1.0
                                         }).execute()