14360: Merge branch 'master' into 14360-dispatch-cloud

[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 4973c8a8c61bc2c9362d1b8fffba058af282cd15..9a03372d32de9375e9401fe4fc4099dce61f1181 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -14,9 +14,11 @@ from cwltool.command_line_tool import revmap_file, CommandLineTool
 from cwltool.load_tool import fetch_document
 from cwltool.builder import Builder
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
+from cwltool.job import JobBase
 
 from schema_salad.sourceline import SourceLine
 
+import arvados_cwl.util
 import ruamel.yaml as yaml
 
 import arvados.collection
@@ -28,6 +30,7 @@ from .pathmapper import VwdPathMapper, trim_listing
 from .perf import Perf
 from . import done
 from ._version import __version__
+from .util import get_intermediate_collection_info
 
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
@@ -36,10 +39,18 @@ crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)
 
 crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
 
-class ArvadosJob(object):
+class ArvadosJob(JobBase):
     """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
 
-    def __init__(self, runner):
+    def __init__(self, runner,
+                 builder,   # type: Builder
+                 joborder,  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
+                 make_path_mapper,  # type: Callable[..., PathMapper]
+                 requirements,      # type: List[Dict[Text, Text]]
+                 hints,     # type: List[Dict[Text, Text]]
+                 name       # type: Text
+    ):
+        super(ArvadosJob, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
         self.arvrunner = runner
         self.running = False
         self.uuid = None
@@ -67,7 +78,12 @@ class ArvadosJob(object):
 
                 if vwd:
                     with Perf(metrics, "generatefiles.save_new %s" % self.name):
-                        vwd.save_new()
+                        info = get_intermediate_collection_info(self.name, None, runtimeContext.intermediate_output_ttl)
+                        vwd.save_new(name=info["name"],
+                                     owner_uuid=self.arvrunner.project_uuid,
+                                     ensure_unique_name=True,
+                                     trash_at=info["trash_at"],
+                                     properties=info["properties"])
 
                 for f, p in generatemapper.items():
                     if p.type == "File":
@@ -97,11 +113,14 @@ class ArvadosJob(object):
 
         with Perf(metrics, "arv_docker_get_image %s" % self.name):
             (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
-            if docker_req and runtimeContextuse_container is not False:
+            if docker_req and runtimeContext.use_container is not False:
                 if docker_req.get("dockerOutputDirectory"):
                     raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                         "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
-                runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+                runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api,
+                                                                           docker_req,
+                                                                           runtimeContext.pull_image,
+                                                                           self.arvrunner.project_uuid)
             else:
                 runtime_constraints["docker_image"] = "arvados/jobs"
 
@@ -243,7 +262,7 @@ class ArvadosJob(object):
                                 dirs[g.group(1)] = g.group(2)
 
                     if processStatus == "permanentFail":
-                        done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+                        done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 
                     with Perf(metrics, "output collection %s" % self.name):
                         outputs = done.done(self, record, dirs["tmpdir"],
@@ -269,7 +288,7 @@ class ArvadosJob(object):
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 
-    def arvados_job_spec(self, runtimeContext):
+    def arvados_job_spec(self, debug=False):
         """Create an Arvados job specification for this workflow.
 
         The returned dict can be used to create a job (i.e., passed as
@@ -299,7 +318,7 @@ class RunnerJob(Runner):
         if self.on_error:
             self.job_order["arv:on_error"] = self.on_error
 
-        if runtimeContext.debug:
+        if debug:
             self.job_order["arv:debug"] = True
 
         return {
@@ -315,7 +334,7 @@ class RunnerJob(Runner):
         }
 
     def run(self, runtimeContext):
-        job_spec = self.arvados_job_spec(runtimeContext)
+        job_spec = self.arvados_job_spec(runtimeContext.debug)
 
         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)