X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7cd03709ba594237b9cf88afac76d39f28011b35..523dadebfbee9a73a21c3f78c7b4af329930d393:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 384b03b6d9..413435db23 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -3,7 +3,8 @@ import json
 import os
 
 from cwltool.errors import WorkflowException
-from cwltool.process import get_feature, adjustFiles, UnsupportedRequirement, shortname
+from cwltool.process import get_feature, UnsupportedRequirement, shortname
+from cwltool.pathmapper import adjustFiles
 
 import arvados.collection
 
@@ -14,11 +15,12 @@ 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
         self.running = False
+        self.uuid = None
 
     def update_pipeline_component(self, r):
         pass
@@ -28,52 +30,51 @@ 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"
             }
         }
 
+        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:
+        if self.generatefiles["listing"]:
             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"}
+        container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
             container_request["environment"].update(self.environment)
 
         if self.stdin:
             raise UnsupportedRequirement("Stdin redirection currently not suppported")
 
+        if self.stderr:
+            raise UnsupportedRequirement("Stderr redirection currently not suppported")
+
         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:
@@ -88,7 +89,6 @@ 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
@@ -100,7 +100,7 @@ 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)
@@ -128,7 +128,7 @@ 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"
@@ -145,11 +145,10 @@ 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)