[ARVADOS] updated: b9f912472b42ffffb26da11eaf9b19a825acec47

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py |  1 +
 sdk/cwl/tests/test_container.py | 17 +++++++++++++----
 sdk/cwl/tests/test_job.py       | 15 ++++++++-------
 3 files changed, 22 insertions(+), 11 deletions(-)

       via  b9f912472b42ffffb26da11eaf9b19a825acec47 (commit)
      from  c5ac66520889330a417b1dbc03da2fbc5ef5cfd0 (commit)

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commit b9f912472b42ffffb26da11eaf9b19a825acec47
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Aug 11 18:18:13 2016 -0400

    Fix failing tests. refs #9776

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index abe916f..27af075 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -150,6 +150,7 @@ class ArvCwlRunner(object):
             kwargs["outdir"] = "/var/spool/cwl"
             kwargs["docker_outdir"] = "/var/spool/cwl"
             kwargs["tmpdir"] = "/tmp"
+            kwargs["docker_tmpdir"] = "/tmp"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
             kwargs["docker_outdir"] = "$(task.outdir)"
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index a65c02e..e060037 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -3,6 +3,7 @@ import logging
 import mock
 import unittest
 import os
+import functools
 import cwltool.process
 
 if not os.getenv('ARVADOS_DEBUG'):
@@ -32,13 +33,17 @@ class TestContainer(unittest.TestCase):
             "baseCommand": "ls",
             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names, basedir="")
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
+                                                 basedir="", make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run"):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run",
+                             make_fs_access=make_fs_access, tmpdir="/tmp"):
             j.run()
             runner.api.container_requests().create.assert_called_with(
                 body={
                     'environment': {
+                        'HOME': '/var/spool/cwl',
                         'TMPDIR': '/tmp'
                     },
                     'name': 'test_run',
@@ -81,14 +86,18 @@ class TestContainer(unittest.TestCase):
             }],
             "baseCommand": "ls"
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
+                                                 avsc_names=avsc_names, make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements"):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
+                             make_fs_access=make_fs_access, tmpdir="/tmp"):
             j.run()
 
         runner.api.container_requests().create.assert_called_with(
             body={
                 'environment': {
+                    'HOME': '/var/spool/cwl',
                     'TMPDIR': '/tmp'
                 },
                 'name': 'test_resource_requirements',
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 46d2048..21b72d1 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -27,10 +27,10 @@ class TestJob(unittest.TestCase):
             "baseCommand": "ls",
             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="", make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir="",
-        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
@@ -38,7 +38,7 @@ class TestJob(unittest.TestCase):
                     'runtime_constraints': {},
                     'script_parameters': {
                         'tasks': [{
-                            'task.env': {'TMPDIR': '$(task.tmpdir)'},
+                            'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
                             'command': ['ls', '$(task.outdir)']
                         }],
                     },
@@ -79,9 +79,10 @@ class TestJob(unittest.TestCase):
             }],
             "baseCommand": "ls"
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
         runner.api.jobs().create.assert_called_with(
             body={
@@ -89,7 +90,7 @@ class TestJob(unittest.TestCase):
                 'runtime_constraints': {},
                 'script_parameters': {
                     'tasks': [{
-                        'task.env': {'TMPDIR': '$(task.tmpdir)'},
+                        'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
                         'command': ['ls']
                     }]
             },

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