X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/233e184eaf40febfbc9b083bdfdd45a438cc350f..35658af99f09f2f6768583d65246429f789fc5a2:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 6aa9a34067..aa3388d00b 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -123,6 +123,8 @@ class ArvadosContainer(JobBase):
                 "kind": "collection",
                 "portable_data_hash": pdh
             }
+            if pdh in self.pathmapper.pdh_to_uuid:
+                mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
             if len(sp) == 2:
                 if tp == "Directory":
                     path = sp[1]
@@ -153,7 +155,7 @@ class ArvadosContainer(JobBase):
                                 vwd.mkdirs(p.target)
                             else:
                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
-                                vwd.copy(path, p.target, source_collection=source)
+                                vwd.copy(path or ".", p.target, source_collection=source)
                         elif p.type == "CreateFile":
                             if self.arvrunner.secret_store.has_secret(p.resolved):
                                 secret_mounts["%s/%s" % (self.outdir, p.target)] = {
@@ -223,6 +225,10 @@ class ArvadosContainer(JobBase):
                                                                     runtimeContext.pull_image,
                                                                     runtimeContext.project_uuid)
 
+        network_req, _ = self.get_requirement("NetworkAccess")
+        if network_req:
+            runtime_constraints["API"] = network_req["networkAccess"]
+
         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
         if api_req:
             runtime_constraints["API"] = True
@@ -254,7 +260,7 @@ class ArvadosContainer(JobBase):
         if self.output_ttl < 0:
             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 
-        if self.timelimit is not None:
+        if self.timelimit is not None and self.timelimit > 0:
             scheduling_parameters["max_run_time"] = self.timelimit
 
         extra_submit_params = {}
@@ -270,6 +276,9 @@ class ArvadosContainer(JobBase):
 
         enable_reuse = runtimeContext.enable_reuse
         if enable_reuse:
+            reuse_req, _ = self.get_requirement("WorkReuse")
+            if reuse_req:
+                enable_reuse = reuse_req["enableReuse"]
             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
             if reuse_req:
                 enable_reuse = reuse_req["enableReuse"]
@@ -483,6 +492,9 @@ class RunnerContainer(Runner):
         if self.arvrunner.project_uuid:
             command.append("--project-uuid="+self.arvrunner.project_uuid)
 
+        if self.enable_dev:
+            command.append("--enable-dev")
+
         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 
         container_req["command"] = command
@@ -525,6 +537,7 @@ class RunnerContainer(Runner):
             container = self.arvrunner.api.containers().get(
                 uuid=record["container_uuid"]
             ).execute(num_retries=self.arvrunner.num_retries)
+            container["log"] = record["log_uuid"]
         except Exception:
             logger.exception("%s while getting runner container", self.arvrunner.label(self))
             self.arvrunner.output_callback({}, "permanentFail")