9701: Merge branch 'master' into 9701-collection-pack-small-files-alt

[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 19516d5b4416cbfe608b4e0ea0d88a37c6790022..a3220f97b7c7c1faa73b5df8898c25499ebbcb1c 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -5,6 +5,7 @@ import os
 from cwltool.errors import WorkflowException
 from cwltool.process import get_feature, UnsupportedRequirement, shortname
 from cwltool.pathmapper import adjustFiles
+from cwltool.utils import aslist
 
 import arvados.collection
 
@@ -42,17 +43,27 @@ class ArvadosContainer(object):
             }
         }
 
+        dirs = set()
         for f in self.pathmapper.files():
-            _, p, _ = self.pathmapper.mapper(f)
-            mounts[p] = {
-                "kind": "collection",
-                "portable_data_hash": p[6:]
-            }
+            _, p, tp = self.pathmapper.mapper(f)
+            if tp == "Directory" and '/' not in p[6:]:
+                mounts[p] = {
+                    "kind": "collection",
+                    "portable_data_hash": p[6:]
+                }
+                dirs.add(p[6:])
+        for f in self.pathmapper.files():
+            _, p, tp = self.pathmapper.mapper(f)
+            if p[6:].split("/")[0] not in dirs:
+                mounts[p] = {
+                    "kind": "collection",
+                    "portable_data_hash": p[6:]
+                }
 
         if self.generatefiles["listing"]:
             raise UnsupportedRequirement("Generate files not supported")
 
-        container_request["environment"] = {"TMPDIR": "/tmp"}
+        container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
             container_request["environment"].update(self.environment)
 
@@ -80,6 +91,18 @@ class ArvadosContainer(object):
             runtime_constraints["vcpus"] = resources.get("cores", 1)
             runtime_constraints["ram"] = resources.get("ram") * 2**20
 
+        api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
+        if api_req:
+            runtime_constraints["API"] = True
+
+        runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
+        if runtime_req:
+            logger.warn("RuntimeConstraints not yet supported by container API")
+
+        partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
+        if partition_req:
+            runtime_constraints["partition"] = aslist(partition_req["partition"])
+
         container_request["mounts"] = mounts
         container_request["runtime_constraints"] = runtime_constraints
 
@@ -90,7 +113,7 @@ class ArvadosContainer(object):
 
             self.arvrunner.processes[response["container_uuid"]] = self
 
-            logger.info("Container %s (%s) request state is %s", self.name, response["container_uuid"], response["state"])
+            logger.info("Container %s (%s) request state is %s", self.name, response["uuid"], response["state"])
 
             if response["state"] == "Final":
                 self.done(response)
@@ -143,7 +166,9 @@ class RunnerContainer(Runner):
 
         workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
 
-        with arvados.collection.Collection(api_client=self.arvrunner.api) as jobobj:
+        with arvados.collection.Collection(api_client=self.arvrunner.api,
+                                           keep_client=self.arvrunner.keep_client,
+                                           num_retries=self.arvrunner.num_retries) as jobobj:
             with jobobj.open("cwl.input.json", "w") as f:
                 json.dump(self.job_order, f, sort_keys=True, indent=4)
             jobobj.save_new(owner_uuid=self.arvrunner.project_uuid)
@@ -159,8 +184,13 @@ class RunnerContainer(Runner):
                                                pull_image,
                                                self.arvrunner.project_uuid)
 
+        command = ["arvados-cwl-runner", "--local", "--api=containers"]
+        if self.output_name:
+            command.append("--output-name=" + self.output_name)
+        command.extend([workflowpath, jobpath])
+
         return {
-            "command": ["arvados-cwl-runner", "--local", "--api=containers", workflowpath, jobpath],
+            "command": command,
             "owner_uuid": self.arvrunner.project_uuid,
             "name": self.name,
             "output_path": "/var/spool/cwl",