10081: Rename cwl.input.json to cwl.input.yml, fix 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 abaf1614f1601d5296b1718af474513e0794ebcb..fdb4520018fef3906826519ad3db929bd9b2b0e2 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,9 +1,13 @@
-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)
@@ -23,11 +27,14 @@ class TestJob(unittest.TestCase):
         tool = {
             "inputs": [],
             "outputs": [],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}]
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
@@ -35,8 +42,8 @@ class TestJob(unittest.TestCase):
                     'runtime_constraints': {},
                     'script_parameters': {
                         'tasks': [{
-                            'task.env': {'TMPDIR': '$(task.tmpdir)'},
-                            'command': ['ls']
+                            'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+                            'command': ['ls', '$(task.outdir)']
                         }],
                     },
                     'script_version': 'master',
@@ -76,9 +83,11 @@ class TestJob(unittest.TestCase):
             }],
             "baseCommand": "ls"
         }
-        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names)
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
+                                                 make_fs_access=make_fs_access, loader=Loader({}))
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run()
         runner.api.jobs().create.assert_called_with(
             body={
@@ -86,7 +95,7 @@ class TestJob(unittest.TestCase):
                 'runtime_constraints': {},
                 'script_parameters': {
                     'tasks': [{
-                        'task.env': {'TMPDIR': '$(task.tmpdir)'},
+                        'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
                         'command': ['ls']
                     }]
             },
@@ -184,3 +193,65 @@ 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}
+    @mock.patch("arvados.collection.Collection")
+    def test_run(self, mockcollection):
+        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"]
+
+        mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+
+        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()
+
+        with open("tests/wf/scatter2_subwf.cwl") as f:
+            subwf = f.read()
+
+        mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
+        mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+
+        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.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
+                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+                               },
+                    'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.cwl#main', u'cwl.input.yml'],
+                    '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)