X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1dee1aad0573bf3a54d536c8dd3693a352cf0cbe..e8d1a643cdbc3a5f4c0e5c745da58d9f7e1248d8:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 52ab2ca4bb..fb23c2ccf7 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -33,6 +33,7 @@ from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_
 from .fsaccess import CollectionFetcher
 from .pathmapper import NoFollowPathMapper, trim_listing
 from .perf import Perf
+from ._version import __version__
 
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
@@ -149,21 +150,28 @@ class ArvadosContainer(JobBase):
                 with Perf(metrics, "createfiles %s" % self.name):
                     for f, p in sorteditems:
                         if not p.target:
-                            pass
-                        elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
+                            continue
+
+                        if p.target.startswith("/"):
+                            dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
+                        else:
+                            dst = p.target
+
+                        if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
                             if p.resolved.startswith("_:"):
-                                vwd.mkdirs(p.target)
+                                vwd.mkdirs(dst)
                             else:
                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
-                                vwd.copy(path or ".", p.target, source_collection=source)
+                                vwd.copy(path or ".", dst, source_collection=source)
                         elif p.type == "CreateFile":
                             if self.arvrunner.secret_store.has_secret(p.resolved):
-                                secret_mounts["%s/%s" % (self.outdir, p.target)] = {
+                                mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
+                                secret_mounts[mountpoint] = {
                                     "kind": "text",
                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
                                 }
                             else:
-                                with vwd.open(p.target, "w") as n:
+                                with vwd.open(dst, "w") as n:
                                     n.write(p.resolved)
 
                 def keepemptydirs(p):
@@ -190,10 +198,14 @@ class ArvadosContainer(JobBase):
                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
                         (prev is not None and p.target.startswith(prev))):
                         continue
-                    mountpoint = "%s/%s" % (self.outdir, p.target)
+                    if p.target.startswith("/"):
+                        dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
+                    else:
+                        dst = p.target
+                    mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
                     mounts[mountpoint] = {"kind": "collection",
                                           "portable_data_hash": vwd.portable_data_hash(),
-                                          "path": p.target}
+                                          "path": dst}
                     if p.type.startswith("Writable"):
                         mounts[mountpoint]["writable"] = True
                     prev = p.target + "/"
@@ -218,7 +230,7 @@ class ArvadosContainer(JobBase):
 
         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
         if not docker_req:
-            docker_req = {"dockerImageId": "arvados/jobs"}
+            docker_req = {"dockerImageId": "arvados/jobs:"+__version__}
 
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
@@ -315,6 +327,7 @@ class ArvadosContainer(JobBase):
                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
         except Exception:
             logger.exception("%s got an error", self.arvrunner.label(self))
+            logger.debug("Container request was %s", container_request)
             self.output_callback({}, "permanentFail")
 
     def done(self, record):