10081: Fix RunInSingleContainer test

[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 e74e000b60afca6a7665814898e2ac3621c82fe2..e95589cf65a3a1e20b7067e454d873a673b6da68 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,8 +1,14 @@
-import arvados_cwl
+
 import logging
 import mock
 import unittest
 import os
+import functools
+import json
+
+import arvados_cwl
+import cwltool.process
+from schema_salad.ref_resolver import Loader
 
 if not os.getenv('ARVADOS_DEBUG'):
     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
@@ -17,15 +23,19 @@ 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": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
         arvtool.formatgraph = None
-        for j in arvtool.job({}, "", mock.MagicMock()):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
@@ -33,8 +43,8 @@ class TestJob(unittest.TestCase):
                     'runtime_constraints': {},
                     'script_parameters': {
                         'tasks': [{
-                            'task.env': {'TMPDIR': '$(task.tmpdir)'},
-                            'command': ['ls']
+                            'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+                            'command': ['ls', '$(task.outdir)']
                         }],
                     },
                     'script_version': 'master',
@@ -61,6 +71,7 @@ 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": [],
@@ -73,9 +84,11 @@ 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, loader=Loader({}))
         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={
@@ -83,7 +96,7 @@ class TestJob(unittest.TestCase):
                 'runtime_constraints': {},
                 'script_parameters': {
                     'tasks': [{
-                        'task.env': {'TMPDIR': '$(task.tmpdir)'},
+                        'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
                         'command': ['ls']
                     }]
             },
@@ -181,3 +194,56 @@ class TestJob(unittest.TestCase):
             mock.call().execute(num_retries=0)])
 
         self.assertFalse(api.collections().create.called)
+
+
+class TestWorkflow(unittest.TestCase):
+    # The test passes no builder.resources
+    # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+    def test_run(self):
+        arvados_cwl.add_arv_hints()
+
+        runner = arvados_cwl.ArvCwlRunner(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("v1.0")
+
+        tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+        metadata["cwlVersion"] = tool["cwlVersion"]
+
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
+                                              basedir="", make_fs_access=make_fs_access, loader=document_loader,
+                                              makeTool=runner.arv_make_tool, metadata=metadata)
+        arvtool.formatgraph = None
+        it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+        it.next().run()
+        it.next().run()
+
+        runner.api.jobs().create.assert_called_with(
+            body={
+                'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+                'repository': 'arvados',
+                'script_version': 'master',
+                'script': 'crunchrunner',
+                'script_parameters': {
+                    'tasks': [{'task.env': {
+                        'HOME': '$(task.outdir)',
+                        'TMPDIR': '$(task.tmpdir)'},
+                               'task.vwd': {
+                                   'workflow.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/workflow.json',
+                                   'cwl.input.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/cwl.input.json'
+                               },
+                    'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.json', u'cwl.input.json'],
+                    'task.stdout': 'cwl.output.json'}]},
+                'runtime_constraints': {
+                    'min_scratch_mb_per_node': 2048,
+                    'min_cores_per_node': 1,
+                    'docker_image': 'arvados/jobs',
+                    'min_ram_mb_per_node': 1024
+                },
+                'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+            filters=[['repository', '=', 'arvados'],
+                     ['script', '=', 'crunchrunner'],
+                     ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+                     ['docker_image_locator', 'in docker', 'arvados/jobs']],
+            find_or_create=True)