- tool = {
- "inputs": [],
- "outputs": [],
- "baseCommand": "ls",
- "arguments": [{"valueFrom": "$(runtime.outdir)"}]
- }
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
- basedir="", make_fs_access=make_fs_access, loader=Loader({}))
- arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run()
- runner.api.jobs().create.assert_called_with(
- body={
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls', '$(task.outdir)']
- }],
- },
- 'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script': 'crunchrunner',
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs',
- 'min_cores_per_node': 1,
- 'min_ram_mb_per_node': 1024,
- 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
- }
- },
- find_or_create=True,
- filters=[['repository', '=', 'arvados'],
- ['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs']]
- )
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ loadingContext = arvados_cwl.context.ArvLoadingContext(
+ {"avsc_names": avsc_names,
+ "basedir": "",
+ "make_fs_access": make_fs_access,
+ "loader": Loader({}),
+ "metadata": {"cwlVersion": "v1.0"},
+ "makeTool": runner.arv_make_tool})
+ runtimeContext = arvados_cwl.context.ArvRuntimeContext(
+ {"work_api": "jobs",
+ "basedir": "",
+ "name": "test_run_job_"+str(enable_reuse),
+ "make_fs_access": make_fs_access,
+ "enable_reuse": enable_reuse,
+ "priority": 500})
+
+ return loadingContext, runtimeContext
+
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
+ def test_run(self, list_images_in_arv):
+ for enable_reuse in (True, False):
+ runner = mock.MagicMock()
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+
+ list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
+ runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ # Simulate reused job from another project so that we can check is a can_read
+ # link is added.
+ runner.api.jobs().create().execute.return_value = {
+ 'state': 'Complete' if enable_reuse else 'Queued',
+ 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
+ 'output': None,
+ }
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+ "id": "#",
+ "class": "CommandLineTool"
+ })
+
+ loadingContext, runtimeContext = self.helper(runner, enable_reuse)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool.formatgraph = None
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.jobs().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls', '$(task.outdir)']
+ }],
+ },
+ 'script_version': 'master',
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
+ 'repository': 'arvados',
+ 'script': 'crunchrunner',
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ 'min_cores_per_node': 1,
+ 'min_ram_mb_per_node': 1024,
+ 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
+ }
+ }),
+ find_or_create=enable_reuse,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
+ )
+ if enable_reuse:
+ runner.api.links().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'link_class': 'permission',
+ 'name': 'can_read',
+ "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
+ })
+ )
+ # Simulate an API excepction when trying to create a
+ # sharing link on the job
+ runner.api.links().create.side_effect = ApiError(
+ mock.MagicMock(return_value={'status': 403}),
+ 'Permission denied')
+ j.run(runtimeContext)
+ else:
+ assert not runner.api.links().create.called