Merge branch 'master' into 9835-container-api-doc

[arvados.git] / sdk / cwl / arvados_cwl / arvjob.py

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 5d253cab742b0990c46d2f08d9319b08078a08c2..a688469634bf31a20b6cf8cff5ede456277a21c4 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -7,12 +7,12 @@ 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 PathMapper
 
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
 from .runner import Runner
+from .pathmapper import InitialWorkDirPathMapper
 from . import done
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -38,8 +38,8 @@ class ArvadosJob(object):
         if self.generatefiles["listing"]:
             vwd = arvados.collection.Collection()
             script_parameters["task.vwd"] = {}
-            generatemapper = PathMapper([self.generatefiles], self.outdir,
-                                        ".", separateDirs=False)
+            generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+                                        separateDirs=False)
             for f, p in generatemapper.items():
                 if p.type == "CreateFile":
                     with vwd.open(p.target, "w") as n:
@@ -47,23 +47,11 @@ class ArvadosJob(object):
             vwd.save_new()
             for f, p in generatemapper.items():
                 if p.type == "File":
-                    script_parameters["task.vwd"][p.target] = self.pathmapper.mapper(f).target
+                    script_parameters["task.vwd"][p.target] = p.resolved
                 if p.type == "CreateFile":
                     script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
 
-        # if self.generatefiles:
-        #     for t in self.generatefiles:
-        #         if isinstance(self.generatefiles[t], dict):
-        #             src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:"))
-        #             vwd.copy(rest, t, source_collection=src)
-        #         else:
-        #             with vwd.open(t, "w") as f:
-        #                 f.write(t.encode('utf-8'))
-        #     vwd.save_new()
-        #     for t in self.generatefiles:
-        #         script_parameters["task.vwd"][t] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), t)
-
-        script_parameters["task.env"] = {"TMPDIR": "$(task.tmpdir)"}
+        script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
             script_parameters["task.env"].update(self.environment)
 
@@ -76,6 +64,13 @@ class ArvadosJob(object):
         if self.stderr:
             script_parameters["task.stderr"] = self.stderr
 
+        if self.successCodes:
+            script_parameters["task.successCodes"] = self.successCodes
+        if self.temporaryFailCodes:
+            script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
+        if self.permanentFailCodes:
+            script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
+
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
         if docker_req and kwargs.get("use_container") is not False:
             runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
@@ -100,7 +95,7 @@ class ArvadosJob(object):
                     "owner_uuid": self.arvrunner.project_uuid,
                     "script": "crunchrunner",
                     "repository": "arvados",
-                    "script_version": "9570-cwl-v1.0",
+                    "script_version": "master",
                     "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
                     "script_parameters": {"tasks": [script_parameters]},
                     "runtime_constraints": runtime_constraints
@@ -232,7 +227,7 @@ class RunnerJob(Runner):
         logger.info("Submitted job %s", response["uuid"])
 
         if kwargs.get("submit"):
-            self.pipeline = self.arvrunner.api.pipeline_instances().create(
+            self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
                 body={
                     "owner_uuid": self.arvrunner.project_uuid,
                     "name": shortname(self.tool.tool["id"]),
@@ -302,7 +297,7 @@ class RunnerTemplate(object):
 
             # Title and description...
             title = param.pop('label', '')
-            descr = param.pop('description', '').rstrip('\n')
+            descr = param.pop('doc', '').rstrip('\n')
             if title:
                 param['title'] = title
             if descr:
@@ -315,8 +310,8 @@ class RunnerTemplate(object):
                 pass
             elif not isinstance(value, dict):
                 param['value'] = value
-            elif param.get('dataclass') == 'File' and value.get('path'):
-                param['value'] = value['path']
+            elif param.get('dataclass') == 'File' and value.get('location'):
+                param['value'] = value['location']
 
             spec['script_parameters'][param_id] = param
         spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']