Merge branch 'master' of git.curoverse.com:arvados into 13330-cwl-intermediate-collec...

[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 70c2173db9fa2f7ff5054ff4be7252bd64156b67..2d112c87a7c5affa2b6d490e526ae1e2d2aea28b 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -6,6 +6,7 @@ import logging
 import re
 import copy
 import json
+import datetime
 import time
 
 from cwltool.process import shortname, UnsupportedRequirement
@@ -76,7 +77,11 @@ class ArvadosJob(JobBase):
 
                 if vwd:
                     with Perf(metrics, "generatefiles.save_new %s" % self.name):
-                        vwd.save_new()
+                        info = self._get_intermediate_collection_info()
+                        vwd.save_new(name=info["name"],
+                                     ensure_unique_name=True,
+                                     trash_at=info["trash_at"],
+                                     properties=info["properties"])
 
                 for f, p in generatemapper.items():
                     if p.type == "File":
@@ -277,6 +282,26 @@ class ArvadosJob(JobBase):
         finally:
             self.output_callback(outputs, processStatus)
 
+    def _get_intermediate_collection_info(self):
+            trash_time = None
+            if self.arvrunner.intermediate_output_ttl > 0:
+                trash_time = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+
+            current_container_uuid = None
+            try:
+                current_container = self.arvrunner.api.containers().current().execute(num_retries=self.arvrunner.num_retries)
+                current_container_uuid = current_container['uuid']
+            except ApiError as e:
+                # Status code 404 just means we're not running in a container.
+                if e.resp.status != 404:
+                    logger.info("Getting current container: %s", e)
+            props = {"type": "Intermediate",
+                          "container": current_container_uuid}
+
+            return {"name" : "Intermediate collection",
+                    "trash_at" : trash_time,
+                    "properties" : props}
+
 
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""