16306: Merge branch 'master'

[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 2b55ce9df5afa6b4a5e7d98ded954be50ae40aa0..72ef14f6731baf83de87df28534a5c76b5a7dc42 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -21,8 +21,7 @@ import ruamel.yaml as yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.utils import aslist
+from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
 from cwltool.job import JobBase
 
 import arvados.collection
@@ -150,21 +149,28 @@ 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):
@@ -191,10 +197,14 @@ 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 + "/"
@@ -224,7 +234,9 @@ class ArvadosContainer(JobBase):
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
                                                                     runtimeContext.pull_image,
-                                                                    runtimeContext.project_uuid)
+                                                                    runtimeContext.project_uuid,
+                                                                    runtimeContext.force_docker_pull,
+                                                                    runtimeContext.tmp_outdir_prefix)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -314,8 +326,9 @@ class ArvadosContainer(JobBase):
                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
             else:
                 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))
+        except Exception as e:
+            logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
+            logger.debug("Container request was %s", container_request)
             self.output_callback({}, "permanentFail")
 
     def done(self, record):
@@ -463,6 +476,7 @@ class RunnerContainer(Runner):
                    "--api=containers",
                    "--no-log-timestamps",
                    "--disable-validate",
+                   "--disable-color",
                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
                    "--thread-count=%s" % self.arvrunner.thread_count,
                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
@@ -533,6 +547,17 @@ class RunnerContainer(Runner):
 
         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 
+        workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
+        workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
+        url = ""
+        if workbench2:
+            url = "{}processes/{}".format(workbench2, response["uuid"])
+        elif workbench1:
+            url = "{}container_requests/{}".format(workbench1, response["uuid"])
+        if url:
+            logger.info("Monitor workflow progress at %s", url)
+
+
     def done(self, record):
         try:
             container = self.arvrunner.api.containers().get(