Fix failing tests. refs #9776

[arvados.git] / sdk / cwl / tests / test_job.py

diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index dba65b0f8a884c207c29656d9f5d0107479f0b7a..21b72d17db40853c89ab397a8b00ba893f1a4f01 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -3,6 +3,7 @@ import logging
 import mock
 import unittest
 import os
+import functools
 import cwltool.process
 
 if not os.getenv('ARVADOS_DEBUG'):
@@ -23,11 +24,13 @@ class TestJob(unittest.TestCase):
         tool = {
             "inputs": [],
             "outputs": [],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, avsc_names=avsc_names, basedir="")
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="", make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
@@ -35,8 +38,8 @@ class TestJob(unittest.TestCase):
                     'runtime_constraints': {},
                     'script_parameters': {
                         'tasks': [{
-                            'task.env': {'TMPDIR': '$(task.tmpdir)'},
-                            'command': ['ls']
+                            'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+                            'command': ['ls', '$(task.outdir)']
                         }],
                     },
                     'script_version': 'master',
@@ -76,9 +79,10 @@ class TestJob(unittest.TestCase):
             }],
             "baseCommand": "ls"
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, avsc_names=avsc_names)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
         runner.api.jobs().create.assert_called_with(
             body={
@@ -86,7 +90,7 @@ class TestJob(unittest.TestCase):
                 'runtime_constraints': {},
                 'script_parameters': {
                     'tasks': [{
-                        'task.env': {'TMPDIR': '$(task.tmpdir)'},
+                        'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
                         'command': ['ls']
                     }]
             },