X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/30443c31bf020b6f558c4b7d954599b24c1a98ce..9777970b61c21a55565b09e0a918ed64f59b0b22:/crunch_scripts/cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index a5e8ac7832..0c79844d5f 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -1,38 +1,114 @@
 #!/usr/bin/env python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# Crunch script integration for running arvados-cwl-runner inside a crunch job.
 
-import arvados
 import arvados_cwl
+import sys
+
+try:
+    # Use the crunch script defined in the arvados_cwl package.  This helps
+    # prevent the crunch script from going out of sync with the rest of the
+    # arvados_cwl package.
+    import arvados_cwl.crunch_script
+    arvados_cwl.crunch_script.run()
+    sys.exit()
+except ImportError:
+    pass
+
+# When running against an older arvados-cwl-runner package without
+# arvados_cwl.crunch_script, fall back to the old code.
+
+
+# This gets the job record, transforms the script parameters into a valid CWL
+# input object, then executes the CWL runner to run the underlying workflow or
+# tool.  When the workflow completes, record the output object in an output
+# collection for this runner job.
+
+import arvados
 import arvados.collection
 import arvados.util
-from cwltool.process import shortname
 import cwltool.main
+import logging
+import os
+import json
+import argparse
+import re
+import functools
+
+from arvados.api import OrderedJsonModel
+from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+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 arvados.util.keep_locator_pattern.match(v):
-            job_order_object[k] = "%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+        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)
+    normalizeFilesDirs(job_order_object)
+    adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
+
+    output_name = None
+    if "arv:output_name" in job_order_object:
+        output_name = job_order_object["arv:output_name"]
+        del job_order_object["arv:output_name"]
 
-    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
+                                      output_name=output_name)
 
-    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+    t = load_tool(job_order_object, runner.arv_make_tool)
 
-    outputObj = runner.arvExecutor(t, job_order_object, "", None)
+    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.arv_executor(t, job_order_object, **vars(args))
 
-    c = arvados.collection.Collection():
-    with c.open("cwl.output.json") as f:
-        json.dump(f, indent=4)
+    if runner.final_output_collection:
+        outputCollection = runner.final_output_collection.portable_data_hash()
+    else:
+        outputCollection = None
 
     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                          body={
-                                             'output': c.save_new(create_collection_record=False),
+                                             'output': outputCollection,
                                              'success': True,
                                              'progress':1.0
                                          }).execute()
-except:
+except Exception as e:
+    logging.exception("Unhandled exception")
     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                          body={
                                              'output': None,