9706: If "foo.service" exists in the source dir for a Go program, package it so it...

[arvados.git] / crunch_scripts / cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 3142fab5939c2d4cbb74aa6b0787fefa2861eccc..fe4e8009aca1af0b04fb483983a09fd59de25390 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -1,38 +1,109 @@
 #!/usr/bin/env python
 
+# Crunch script integration for running arvados-cwl-runner (importing
+# arvados_cwl module) inside a crunch job.
+#
+# 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_cwl
 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 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)
 
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
 
-    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+    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:])
 
-    outputObj = runner.arvExecutor(t, job_order_object, "", None)
+    adjustFileObjs(outputObj, makeRelative)
 
-    c = arvados.collection.Collection()
-    with c.open("cwl.output.json") as f:
-        json.dump(f, indent=4)
+    with final.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),
+                                             'output': final.save_new(create_collection_record=False),
                                              '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,