11100: Add test for --trash-intermediate. Add log message when intermediate

outputs are scheduled for trash.

diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index 7c75c1c453ad8bd4e70107d9c5866f6e10137b10..f62d9e3ce8b79e9aabc8091d2773be2bffcb3e43 100644 (file)
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -126,7 +126,7 @@ By default, the @arvados-cwl-runner@ is installed on Arvados shell nodes.  If yo
 
 h3. Check Docker access
 
-In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker.  You do not need Docker if the Docker images you intend to use are already available in Aravdos.
+In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker.  You do not need Docker if the Docker images you intend to use are already available in Arvados.
 
 You can determine if you have access to Docker by running @docker version@:
 

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index be1ec27820fd9fd8aa33789e1095983f3b8b898c..fbe91b9f399163917284cc224610704bca0653e0 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -346,10 +346,16 @@ class ArvCwlRunner(object):
                                                                  collection_cache=self.collection_cache)
         self.fs_access = make_fs_access(kwargs["basedir"])
 
-        self.intermediate_output_ttl = kwargs["intermediate_output_ttl"]
+
         self.trash_intermediate = kwargs["trash_intermediate"]
+        if self.trash_intermediate and self.work_api != "containers":
+            raise Exception("--trash-intermediate is only supported with --api=containers.")
+
+        self.intermediate_output_ttl = kwargs["intermediate_output_ttl"]
         if self.intermediate_output_ttl and self.work_api != "containers":
-            raise Exception("--intermediate-output-ttl is only supported when using the containers api.")
+            raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
+        if self.intermediate_output_ttl < 0:
+            raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
 
         if not kwargs.get("name"):
             kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index dc2d02f3ccc1f3b81af95606d6a1cd16d23ef036..b58a858c8d40775c227038ddb3fe43665b851b3c 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -2,6 +2,9 @@ import logging
 import json
 import os
 import urllib
+import time
+import datetime
+import ciso8601
 
 import ruamel.yaml as yaml
 
@@ -211,8 +214,6 @@ class ArvadosContainer(object):
     def done(self, record):
         outputs = {}
         try:
-            self.arvrunner.add_intermediate_output(record["output_uuid"])
-
             container = self.arvrunner.api.containers().get(
                 uuid=record["container_uuid"]
             ).execute(num_retries=self.arvrunner.num_retries)
@@ -238,6 +239,17 @@ class ArvadosContainer(object):
                                                            num_retries=self.arvrunner.num_retries)
                 done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
 
+            if record["output_uuid"]:
+                if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
+                    # Compute the trash time to avoid requesting the collection record.
+                    trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+                    aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
+                    orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
+                    oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
+                    logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
+                        self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
+                self.arvrunner.add_intermediate_output(record["output_uuid"])
+
             if container["output"]:
                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
         except WorkflowException as e:
@@ -338,6 +350,9 @@ class RunnerContainer(Runner):
         if self.intermediate_output_ttl:
             command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
 
+        if self.arvrunner.trash_intermediate:
+            command.append("--trash-intermediate")
+
         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 
         container_req["command"] = command

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 731b1d561f277b82c8a7a8a668393db146c6b4bb..112f432579d67ca6318f1fbfb19a278f92b0fad1 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -544,6 +544,29 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
+    @stubs
+    def test_submit_container_trash_intermediate(self, stubs):
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+                                       '--enable-reuse', '--on-error=continue',
+                                       "--trash-intermediate",
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
     @stubs
     def test_submit_container_output_tags(self, stubs):
         output_tags = "tag0,tag1,tag2"