Crunch script doesn't fail in file/directory literals that don't have a 'location...

[arvados.git] / sdk / cwl / arvados_cwl / arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 28107b491ca45f760813c03cefa63bb9c693b331..657d5927d0328025eb948f6e8ee62ba215486769 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -7,16 +7,16 @@ import ruamel.yaml as yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
 from cwltool.utils import aslist
 
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
 from . import done
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location
 from .fsaccess import CollectionFetcher
-from .pathmapper import NoFollowPathMapper
+from .pathmapper import NoFollowPathMapper, trim_listing
 from .perf import Perf
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -48,37 +48,39 @@ class ArvadosContainer(object):
         mounts = {
             self.outdir: {
                 "kind": "tmp"
+            },
+            self.tmpdir: {
+                "kind": "tmp"
             }
         }
         scheduling_parameters = {}
 
-        dirs = set()
-        for f in self.pathmapper.files():
-            pdh, p, tp = self.pathmapper.mapper(f)
-            if tp == "Directory" and '/' not in pdh:
-                mounts[p] = {
-                    "kind": "collection",
-                    "portable_data_hash": pdh[5:]
-                }
-                dirs.add(pdh)
-
-        for f in self.pathmapper.files():
-            res, p, tp = self.pathmapper.mapper(f)
-            if res.startswith("keep:"):
-                res = res[5:]
-            elif res.startswith("/keep/"):
-                res = res[6:]
-            else:
+        rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
+        rf.sort(key=lambda k: k.resolved)
+        prevdir = None
+        for resolved, target, tp, stg in rf:
+            if not stg:
                 continue
-            sp = res.split("/", 1)
-            pdh = sp[0]
-            if pdh not in dirs:
-                mounts[p] = {
-                    "kind": "collection",
-                    "portable_data_hash": pdh
-                }
-                if len(sp) == 2:
-                    mounts[p]["path"] = urllib.unquote(sp[1])
+            if prevdir and target.startswith(prevdir):
+                continue
+            if tp == "Directory":
+                targetdir = target
+            else:
+                targetdir = os.path.dirname(target)
+            sp = resolved.split("/", 1)
+            pdh = sp[0][5:]   # remove "keep:"
+            mounts[targetdir] = {
+                "kind": "collection",
+                "portable_data_hash": pdh
+            }
+            if len(sp) == 2:
+                if tp == "Directory":
+                    path = sp[1]
+                else:
+                    path = os.path.dirname(sp[1])
+                if path and path != "/":
+                    mounts[targetdir]["path"] = path
+            prevdir = targetdir + "/"
 
         with Perf(metrics, "generatefiles %s" % self.name):
             if self.generatefiles["listing"]:
@@ -115,10 +117,14 @@ class ArvadosContainer(object):
             container_request["environment"].update(self.environment)
 
         if self.stdin:
-            raise UnsupportedRequirement("Stdin redirection currently not suppported")
+            sp = self.stdin[6:].split("/", 1)
+            mounts["stdin"] = {"kind": "collection",
+                                "portable_data_hash": sp[0],
+                                "path": sp[1]}
 
         if self.stderr:
-            raise UnsupportedRequirement("Stderr redirection currently not suppported")
+            mounts["stderr"] = {"kind": "file",
+                                "path": "%s/%s" % (self.outdir, self.stderr)}
 
         if self.stdout:
             mounts["stdout"] = {"kind": "file",
@@ -234,6 +240,8 @@ class RunnerContainer(Runner):
         """
 
         adjustDirObjs(self.job_order, trim_listing)
+        adjustFileObjs(self.job_order, trim_anonymous_location)
+        adjustDirObjs(self.job_order, trim_anonymous_location)
 
         container_req = {
             "owner_uuid": self.arvrunner.project_uuid,