+import arvados.collection
+import arvados.util
+from cwltool.process import shortname
+import cwltool.main
+import logging
+import os
+import json
+import argparse
+import re
+from arvados.api import OrderedJsonModel
+from cwltool.process import adjustFileObjs, adjustDirObjs
+from cwltool.load_tool import load_tool
+
+# Print package versions
+logging.info(cwltool.main.versionstring())
+
+api = arvados.api("v1")
+
+try:
+ job_order_object = arvados.current_job()['script_parameters']
+
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
+ def keeppath(v):
+ if pdh_path.match(v):
+ return "keep:%s" % v
+ else:
+ return v
+
+ def keeppathObj(v):
+ v["location"] = keeppath(v["location"])
+
+ job_order_object["cwl:tool"] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
+
+ for k,v in job_order_object.items():
+ if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
+ job_order_object[k] = {
+ "class": "File",
+ "location": "keep:%s" % v
+ }
+
+ adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
+
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+
+ t = load_tool(job_order_object, runner.arvMakeTool)
+
+ args = argparse.Namespace()
+ args.project_uuid = arvados.current_job()["owner_uuid"]
+ args.enable_reuse = True
+ args.submit = False
+ args.debug = True
+ args.quiet = False
+ args.ignore_docker_for_reuse = False
+ args.basedir = os.getcwd()
+ args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
+ outputObj = runner.arvExecutor(t, job_order_object, **vars(args))
+
+ files = {}
+ def capture(fileobj):
+ path = fileobj["location"]
+ sp = path.split("/")
+ col = sp[0][5:]
+ if col not in files:
+ files[col] = set()
+ files[col].add("/".join(sp[1:]))
+ fileobj["location"] = path
+
+ adjustFileObjs(outputObj, capture)
+
+ final = arvados.collection.Collection()
+
+ for k,v in files.iteritems():
+ with arvados.collection.Collection(k) as c:
+ for f in c:
+ final.copy(f, f, c, True)
+
+ def makeRelative(fileobj):
+ fileobj["location"] = "/".join(fileobj["location"].split("/")[1:])
+
+ adjustFileObjs(outputObj, makeRelative)
+
+ with final.open("cwl.output.json", "w") as f:
+ json.dump(outputObj, f, indent=4)