Merge branch '9511-cwl-type-checking' closes #9511

[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 2fb2c33b39088b031ed39ab5f66518e6316c4389..9bf93e7c5661420727ff01ad3da9e16aaec40271 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -14,7 +14,7 @@ from .runner import Runner
 logger = logging.getLogger('arvados.cwl-runner')
 
 class ArvadosContainer(object):
-    """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
+    """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
 
     def __init__(self, runner):
         self.arvrunner = runner
@@ -29,14 +29,14 @@ class ArvadosContainer(object):
             "command": self.command_line,
             "owner_uuid": self.arvrunner.project_uuid,
             "name": self.name,
-            "output_path": "/var/spool/cwl",
-            "cwd": "/var/spool/cwl",
+            "output_path": self.outdir,
+            "cwd": self.outdir,
             "priority": 1,
             "state": "Committed"
         }
         runtime_constraints = {}
         mounts = {
-            "/var/spool/cwl": {
+            self.outdir: {
                 "kind": "tmp"
             }
         }
@@ -51,20 +51,6 @@ class ArvadosContainer(object):
         if self.generatefiles:
             raise UnsupportedRequirement("Generate files not supported")
 
-            vwd = arvados.collection.Collection(api_client=self.arvrunner.api_client)
-            container_request["task.vwd"] = {}
-            for t in self.generatefiles:
-                if isinstance(self.generatefiles[t], dict):
-                    src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:"))
-                    vwd.copy(rest, t, source_collection=src)
-                else:
-                    with vwd.open(t, "w") as f:
-                        f.write(self.generatefiles[t])
-            vwd.save_new()
-            # TODO
-            # for t in self.generatefiles:
-            #     container_request["task.vwd"][t] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), t)
-
         container_request["environment"] = {"TMPDIR": "/tmp"}
         if self.environment:
             container_request["environment"].update(self.environment)
@@ -74,7 +60,7 @@ class ArvadosContainer(object):
 
         if self.stdout:
             mounts["stdout"] = {"kind": "file",
-                                "path": "/var/spool/cwl/%s" % (self.stdout)}
+                                "path": "%s/%s" % (self.outdir, self.stdout)}
 
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
         if not docker_req:
@@ -89,7 +75,6 @@ class ArvadosContainer(object):
         if resources is not None:
             runtime_constraints["vcpus"] = resources.get("cores", 1)
             runtime_constraints["ram"] = resources.get("ram") * 2**20
-            #runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
 
         container_request["mounts"] = mounts
         container_request["runtime_constraints"] = runtime_constraints
@@ -129,7 +114,7 @@ class ArvadosContainer(object):
             try:
                 outputs = {}
                 if record["output"]:
-                    outputs = done.done(self, record, "/tmp", "/var/spool/cwl", "/keep")
+                    outputs = done.done(self, record, "/tmp", self.outdir, "/keep")
             except WorkflowException as e:
                 logger.error("Error while collecting container outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
                 processStatus = "permanentFail"
@@ -146,11 +131,10 @@ class RunnerContainer(Runner):
     """Submit and manage a container that runs arvados-cwl-runner."""
 
     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
-        """Create an Arvados job specification for this workflow.
+        """Create an Arvados container request for this workflow.
 
-        The returned dict can be used to create a job (i.e., passed as
-        the +body+ argument to jobs().create()), or as a component in
-        a pipeline template or pipeline instance.
+        The returned dict can be used to create a container passed as
+        the +body+ argument to container_requests().create().
         """
 
         workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)