Merge branch '9766-register-workflow' closes #9766

[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 94a7579f202a62d88f7a69481e4f2fe65dfa0f7b..413435db2392e38aa22ba0d5222fef333080dbde 100644 (file)
--- 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
 
@@ -29,38 +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")
 
-        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:
@@ -86,7 +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)
@@ -114,7 +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"