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 bb15e60f1f31faebd7f901f34d0cd264822d5aed..21b72d17db40853c89ab397a8b00ba893f1a4f01 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,6 +1,15 @@
-import unittest
-import mock
 import arvados_cwl
+import logging
+import mock
+import unittest
+import os
+import functools
+import cwltool.process
+
+if not os.getenv('ARVADOS_DEBUG'):
+    logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
+    logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+
 
 class TestJob(unittest.TestCase):
 
@@ -10,15 +19,18 @@ class TestJob(unittest.TestCase):
         runner = mock.MagicMock()
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
 
         tool = {
             "inputs": [],
             "outputs": [],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="", make_fs_access=make_fs_access)
         arvtool.formatgraph = None
-        for j in arvtool.job({}, "", mock.MagicMock()):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
@@ -26,11 +38,11 @@ class TestJob(unittest.TestCase):
                     'runtime_constraints': {},
                     'script_parameters': {
                         'tasks': [{
-                            'task.env': {'TMPDIR': '$(task.tmpdir)'},
-                            'command': ['ls']
-                        }]
-            },
-            'script_version': 'master',
+                            'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+                            'command': ['ls', '$(task.outdir)']
+                        }],
+                    },
+                    'script_version': 'master',
                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
                     'repository': 'arvados',
                     'script': 'crunchrunner',
@@ -40,8 +52,8 @@ class TestJob(unittest.TestCase):
                         'min_ram_mb_per_node': 1024,
                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
                     }
-        },
-                                                    find_or_create=True,
+                },
+                find_or_create=True,
                 filters=[['repository', '=', 'arvados'],
                          ['script', '=', 'crunchrunner'],
                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
@@ -54,6 +66,7 @@ class TestJob(unittest.TestCase):
         runner = mock.MagicMock()
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
 
         tool = {
             "inputs": [],
@@ -66,9 +79,10 @@ class TestJob(unittest.TestCase):
             }],
             "baseCommand": "ls"
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
+        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()):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
         runner.api.jobs().create.assert_called_with(
             body={
@@ -76,7 +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']
                     }]
             },
@@ -90,7 +104,7 @@ class TestJob(unittest.TestCase):
                     'min_ram_mb_per_node': 3000,
                     'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
                 }
-        },
+            },
             find_or_create=True,
             filters=[['repository', '=', 'arvados'],
                      ['script', '=', 'crunchrunner'],