X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/60d986b8908487c086eb4e402ac69669cb26108b..8de338d1178abb71addc344382657d3826d7f0bb:/sdk/cwl/arvados_cwl/arvjob.py

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index a4cd5cd3f8..e86f5055c5 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -4,20 +4,22 @@ import copy
 import json
 import time
 
-from cwltool.process import get_feature, shortname
+from cwltool.process import get_feature, shortname, UnsupportedRequirement
 from cwltool.errors import WorkflowException
 from cwltool.draft2tool import revmap_file, CommandLineTool
 from cwltool.load_tool import fetch_document
 from cwltool.builder import Builder
-from cwltool.pathmapper import adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+
+from schema_salad.sourceline import SourceLine
 
 import ruamel.yaml as yaml
 
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
-from .pathmapper import InitialWorkDirPathMapper
+from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location
+from .pathmapper import VwdPathMapper, trim_listing
 from .perf import Perf
 from . import done
 from ._version import __version__
@@ -49,8 +51,8 @@ class ArvadosJob(object):
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
                 script_parameters["task.vwd"] = {}
-                generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
-                                                          separateDirs=False)
+                generatemapper = VwdPathMapper([self.generatefiles], "", "",
+                                               separateDirs=False)
 
                 with Perf(metrics, "createfiles %s" % self.name):
                     for f, p in generatemapper.items():
@@ -58,8 +60,9 @@ class ArvadosJob(object):
                             with vwd.open(p.target, "w") as n:
                                 n.write(p.resolved.encode("utf-8"))
 
-                with Perf(metrics, "generatefiles.save_new %s" % self.name):
-                    vwd.save_new()
+                if vwd:
+                    with Perf(metrics, "generatefiles.save_new %s" % self.name):
+                        vwd.save_new()
 
                 for f, p in generatemapper.items():
                     if p.type == "File":
@@ -139,11 +142,12 @@ class ArvadosJob(object):
 
             self.update_pipeline_component(response)
 
-            logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-
-            if response["state"] in ("Complete", "Failed", "Cancelled"):
+            if response["state"] == "Complete":
+                logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
                 with Perf(metrics, "done %s" % self.name):
                     self.done(response)
+            else:
+                logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
         except Exception as e:
             logger.exception("%s error" % (self.arvrunner.label(self)))
             self.output_callback({}, "permanentFail")
@@ -234,28 +238,6 @@ class ArvadosJob(object):
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 
-    def upload_workflow_collection(self, packed):
-        collection = arvados.collection.Collection(api_client=self.arvrunner.api,
-                                                   keep_client=self.arvrunner.keep_client,
-                                                   num_retries=self.arvrunner.num_retries)
-        with collection.open("workflow.cwl", "w") as f:
-            f.write(yaml.round_trip_dump(packed))
-
-        exists = self.arvrunner.api.collections().list(filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
-                                                 ["portable_data_hash", "=", collection.portable_data_hash()],
-                                                 ["name", "like", self.name+"%"]]).execute(num_retries=self.arvrunner.num_retries)
-
-        if exists["items"]:
-            logger.info("Using collection %s", exists["items"][0]["uuid"])
-        else:
-            collection.save_new(name=self.name,
-                                owner_uuid=self.arvrunner.project_uuid,
-                                ensure_unique_name=True,
-                                num_retries=self.arvrunner.num_retries)
-            logger.info("Uploaded to %s", collection.manifest_locator())
-
-        return collection.portable_data_hash()
-
     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
         """Create an Arvados job specification for this workflow.
 
@@ -265,13 +247,15 @@ class RunnerJob(Runner):
         """
 
         if self.tool.tool["id"].startswith("keep:"):
-            pass
+            self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
         else:
             packed = packed_workflow(self.arvrunner, self.tool)
-            wf_pdh = self.upload_workflow_collection(packed)
-            self.job_order["cwl:tool"] = "%s/workflow.cwl" % wf_pdh
+            wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
+            self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 
         adjustDirObjs(self.job_order, trim_listing)
+        adjustFileObjs(self.job_order, trim_anonymous_location)
+        adjustDirObjs(self.job_order, trim_anonymous_location)
 
         if self.output_name:
             self.job_order["arv:output_name"] = self.output_name
@@ -385,10 +369,12 @@ class RunnerTemplate(object):
             if not isinstance(types, list):
                 types = [types]
             param['required'] = 'null' not in types
-            non_null_types = set(types) - set(['null'])
+            non_null_types = [t for t in types if t != "null"]
             if len(non_null_types) == 1:
                 the_type = [c for c in non_null_types][0]
-                dataclass = self.type_to_dataclass.get(the_type)
+                dataclass = None
+                if isinstance(the_type, basestring):
+                    dataclass = self.type_to_dataclass.get(the_type)
                 if dataclass:
                     param['dataclass'] = dataclass
             # Note: If we didn't figure out a single appropriate