From 001e1ecfddb4f1d0cc26cdb415395ff47cde4914 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Tue, 27 Oct 2015 16:26:10 -0400
Subject: [PATCH] 7593: References to files in keep must have keep: URI scheme.
  Improve error handling.  Support configuring which git repo has
 crunchrunner.

---
 sdk/cwl/arvados_cwl/__init__.py | 41 +++++++++++++++++++--------------
 1 file changed, 24 insertions(+), 17 deletions(-)

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d1e53faeb9..0fdf75340f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -73,7 +73,7 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
     def glob(self, pattern):
         collection, rest = self.get_collection(pattern)
         patternsegments = rest.split("/")
-        return self._match(collection, patternsegments, collection.manifest_locator())
+        return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
 
     def open(self, fn, mode):
         collection, rest = self.get_collection(fn)
@@ -128,20 +128,25 @@ class ArvadosJob(object):
         if docker_req and kwargs.get("use_container") is not False:
             runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image)
 
-        response = self.arvrunner.api.jobs().create(body={
-            "script": "crunchrunner",
-            "repository": "peteramstutz/cr",
-            "script_version": "master",
-            "script_parameters": {"tasks": [script_parameters]},
-            "runtime_constraints": runtime_constraints
-        }, find_or_create=kwargs.get("enable_reuse", True)).execute()
+        try:
+            response = self.arvrunner.api.jobs().create(body={
+                "script": "crunchrunner",
+                "repository": kwargs["repository"],
+                "script_version": "master",
+                "script_parameters": {"tasks": [script_parameters]},
+                "runtime_constraints": runtime_constraints
+            }, find_or_create=kwargs.get("enable_reuse", True)).execute()
+
+            self.arvrunner.jobs[response["uuid"]] = self
 
-        self.arvrunner.jobs[response["uuid"]] = self
+            logger.info("Job %s is %s", response["uuid"], response["state"])
 
-        logger.info("Job %s is %s", response["uuid"], response["state"])
+            if response["state"] in ("Complete", "Failed", "Cancelled"):
+                self.done(response)
+        except Exception as e:
+            logger.error("Got error %s" % str(e))
+            self.output_callback({}, "permanentFail")
 
-        if response["state"] in ("Complete", "Failed", "Cancelled"):
-            self.done(response)
 
     def done(self, record):
         try:
@@ -161,19 +166,18 @@ class ArvadosJob(object):
         finally:
             del self.arvrunner.jobs[record["uuid"]]
 
+
 class ArvPathMapper(cwltool.pathmapper.PathMapper):
     def __init__(self, arvrunner, referenced_files, basedir, **kwargs):
         self._pathmap = copy.copy(arvrunner.uploaded)
         uploadfiles = []
 
-        pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+/.+')
+        pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+')
 
         for src in referenced_files:
             if isinstance(src, basestring) and pdh_path.match(src):
-                self._pathmap[src] = (src, "$(task.keep)/%s" % src)
-            if src in self._pathmap:
-                pass
-            else:
+                self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
+            if src not in self._pathmap:
                 ab = cwltool.pathmapper.abspath(src, basedir)
                 st = arvados.commands.run.statfile("", ab)
                 if kwargs.get("conformance_test"):
@@ -255,6 +259,7 @@ class ArvCwlRunner(object):
 
         kwargs["fs_access"] = self.fs_access
         kwargs["enable_reuse"] = args.enable_reuse
+        kwargs["repository"] = args.repository
 
         if kwargs.get("conformance_test"):
             return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
@@ -306,4 +311,6 @@ def main(args, stdout, stderr, api_client=None):
                         default=False, dest="enable_reuse",
                         help="")
 
+    parser.add_argument('--repository', type=str, default="crunchrunner", help="Repository containing the 'crunchrunner' program.")
+
     return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)
-- 
2.30.2