[ARVADOS] created: 7f9839be2facf7e5bf3106dab0859da5d971f31e

[Git user]

        at  7f9839be2facf7e5bf3106dab0859da5d971f31e (commit)


commit 7f9839be2facf7e5bf3106dab0859da5d971f31e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue May 2 23:06:28 2017 -0400

    11369: Containers API:  Add capacity to tmp and output mounts. Also support {outputDirType: keep_output_dir} of RuntimeConstraints.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 657d592..0b302b6 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -45,12 +45,20 @@ class ArvadosContainer(object):
             "properties": {}
         }
         runtime_constraints = {}
+
+        resources = self.builder.resources
+        if resources is not None:
+            runtime_constraints["vcpus"] = resources.get("cores", 1)
+            runtime_constraints["ram"] = resources.get("ram") * 2**20
+
         mounts = {
             self.outdir: {
-                "kind": "tmp"
+                "kind": "tmp",
+                "capacity": resources.get("outdirSize", 0) * 2**20
             },
             self.tmpdir: {
-                "kind": "tmp"
+                "kind": "tmp",
+                "capacity": resources.get("tmpdirSize", 0) * 2**20
             }
         }
         scheduling_parameters = {}
@@ -139,11 +147,6 @@ class ArvadosContainer(object):
                                                                      pull_image,
                                                                      self.arvrunner.project_uuid)
 
-        resources = self.builder.resources
-        if resources is not None:
-            runtime_constraints["vcpus"] = resources.get("cores", 1)
-            runtime_constraints["ram"] = resources.get("ram") * 2**20
-
         api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
         if api_req:
             runtime_constraints["API"] = True
@@ -152,6 +155,15 @@ class ArvadosContainer(object):
         if runtime_req:
             if "keep_cache" in runtime_req:
                 runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
+            if "outputDirType" in runtime_req:
+                if runtime_req["outputDirType"] == "local_output_dir":
+                    # Currently the default behavior.
+                    pass
+                elif runtime_req["outputDirType"] == "keep_output_dir":
+                    mounts[self.outdir]= {
+                        "kind": "collection",
+                        "writable": True
+                    }
 
         partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
         if partition_req:
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index b06eae8..af05773 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -63,8 +63,11 @@ class TestContainer(unittest.TestCase):
                         'use_existing': enable_reuse,
                         'priority': 1,
                         'mounts': {
-                            '/tmp': {'kind': 'tmp'},
-                            '/var/spool/cwl': {'kind': 'tmp'}
+                            '/tmp': {'kind': 'tmp',
+                                     "capacity": 1073741824
+                                 },
+                            '/var/spool/cwl': {'kind': 'tmp',
+                                               "capacity": 1073741824 }
                         },
                         'state': 'Committed',
                         'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
@@ -97,7 +100,8 @@ class TestContainer(unittest.TestCase):
                 "class": "ResourceRequirement",
                 "coresMin": 3,
                 "ramMin": 3000,
-                "tmpdirMin": 4000
+                "tmpdirMin": 4000,
+                "outdirMin": 5000
             }, {
                 "class": "http://arvados.org/cwl#RuntimeConstraints",
                 "keep_cache": 512
@@ -136,8 +140,10 @@ class TestContainer(unittest.TestCase):
                 'use_existing': True,
                 'priority': 1,
                 'mounts': {
-                    '/tmp': {'kind': 'tmp'},
-                    '/var/spool/cwl': {'kind': 'tmp'}
+                    '/tmp': {'kind': 'tmp',
+                             "capacity": 4194304000 },
+                    '/var/spool/cwl': {'kind': 'tmp',
+                                       "capacity": 5242880000 }
                 },
                 'state': 'Committed',
                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
@@ -242,8 +248,10 @@ class TestContainer(unittest.TestCase):
                 'use_existing': True,
                 'priority': 1,
                 'mounts': {
-                    '/tmp': {'kind': 'tmp'},
-                    '/var/spool/cwl': {'kind': 'tmp'},
+                    '/tmp': {'kind': 'tmp',
+                             "capacity": 1073741824 },
+                    '/var/spool/cwl': {'kind': 'tmp',
+                                       "capacity": 1073741824 },
                     '/var/spool/cwl/foo': {
                         'kind': 'collection',
                         'path': 'foo',
@@ -328,8 +336,10 @@ class TestContainer(unittest.TestCase):
                     'use_existing': True,
                     'priority': 1,
                     'mounts': {
-                        '/tmp': {'kind': 'tmp'},
-                        '/var/spool/cwl': {'kind': 'tmp'},
+                        '/tmp': {'kind': 'tmp',
+                                 "capacity": 1073741824 },
+                        '/var/spool/cwl': {'kind': 'tmp',
+                                           "capacity": 1073741824 },
                         "stderr": {
                             "kind": "file",
                             "path": "/var/spool/cwl/stderr.txt"
@@ -460,8 +470,10 @@ class TestContainer(unittest.TestCase):
                             "kind": "collection",
                             "portable_data_hash": "99999999999999999999999999999994+44"
                         },
-                        '/tmp': {'kind': 'tmp'},
-                        '/var/spool/cwl': {'kind': 'tmp'}
+                        '/tmp': {'kind': 'tmp',
+                                 "capacity": 1073741824 },
+                        '/var/spool/cwl': {'kind': 'tmp',
+                                           "capacity": 1073741824 }
                     },
                     'state': 'Committed',
                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',

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hooks/post-receive
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