X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8f46e1564dd7c4f42fdccc6e5c8222ce8955405e..de3633d7652a8b9fb372345e437dcaa226b8b896:/crunch_scripts/cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 7fb14abd96..0c79844d5f 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -1,71 +1,109 @@
 #!/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 adjustFiles
+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']
 
-    print job_order_object
+    pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
 
     def keeppath(v):
-        if arvados.util.keep_locator_pattern.match(v):
-            return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
-
-    job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
-
-    adjustFiles(job_order_object, keeppath)
-
-    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
-
-    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
-
-    np = argparse.Namespace()
-    np.project_uuid = arvados.current_job()["owner_uuid"]
-    np.enable_reuse = True
-    outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
-
-    files = {}
-    def capture(path):
-        sp = path.split("/")
-        col = sp[0][5:]
-        if col not in files:
-            files[col] = set()
-        files[col].add("/".join(sp[1:]))
-        return path
-
-    adjustFiles(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(path):
-        return "/".join(path.split("/")[1:])
-
-    adjustFiles(outputObj, makeRelative)
-
-    with final.open("cwl.output.json", "w") as f:
-        json.dump(outputObj, f, indent=4)
+        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)
+    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()),
+                                      output_name=output_name)
+
+    t = load_tool(job_order_object, runner.arv_make_tool)
+
+    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))
+
+    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': final.save_new(create_collection_record=False),
+                                             'output': outputCollection,
                                              'success': True,
                                              'progress':1.0
                                          }).execute()