import arvados import arvados.keep import arvados.collection import arvados_cwl import copy import cStringIO import functools import hashlib import mock import sys import unittest from .matcher import JsonDiffMatcher def stubs(func): @functools.wraps(func) @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.KeepClient") @mock.patch("arvados.events.subscribe") def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs): class Stubs: pass stubs = Stubs() stubs.events = events stubs.KeepClient = KeepClient stubs.keepdocker = keepdocker def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) stubs.KeepClient().put.side_effect = putstub stubs.keepdocker.return_value = True stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" stubs.api = mock.MagicMock() stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, } stubs.api.collections().list().execute.return_value = {"items": []} stubs.api.collections().create().execute.side_effect = ({ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1", "portable_data_hash": "99999999999999999999999999999991+99", }, { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", "portable_data_hash": "99999999999999999999999999999992+99", }) stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" stubs.api.jobs().create().execute.return_value = { "uuid": stubs.expect_job_uuid, "state": "Queued", } stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" stubs.api.pipeline_templates().create().execute.return_value = { "uuid": stubs.expect_pipeline_template_uuid, } stubs.expect_job_spec = { 'runtime_constraints': { 'docker_image': 'arvados/jobs' }, 'script_parameters': { 'x': { 'path': '99999999999999999999999999999992+99/blorp.txt', 'class': 'File' }, 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl' }, 'repository': 'arvados', 'script_version': 'master', 'script': 'cwl-runner' } return func(self, stubs, *args, **kwargs) return wrapped class TestSubmit(unittest.TestCase): @stubs def test_submit(self, stubs): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.api.collections().create.assert_has_calls([ mock.call(), mock.call(body={ 'manifest_text': './tool 84ec4df683711de31b782505389a8843+429 ' '0:16:blub.txt 16:413:submit_tool.cwl\n./wf ' '81d977a245a41b8e79859fbe00623fd0+344 0:344:submit_wf.cwl\n', 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', 'name': 'submit_wf.cwl', }, ensure_unique_name=True), mock.call().execute(), mock.call(body={ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) expect_job = copy.deepcopy(stubs.expect_job_spec) expect_job["owner_uuid"] = stubs.fake_user_uuid stubs.api.jobs().create.assert_called_with( body=expect_job, find_or_create=True) self.assertEqual(capture_stdout.getvalue(), stubs.expect_job_uuid + '\n') @stubs def test_submit_with_project_uuid(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' exited = arvados_cwl.main( ["--submit", "--no-wait", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], sys.stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_body = copy.deepcopy(stubs.expect_job_spec) expect_body["owner_uuid"] = project_uuid stubs.api.jobs().create.assert_called_with( body=expect_body, find_or_create=True) class TestCreateTemplate(unittest.TestCase): @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--create-template", "--no-wait", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.api.pipeline_instances().create.refute_called() stubs.api.jobs().create.refute_called() expect_component = copy.deepcopy(stubs.expect_job_spec) expect_component['script_parameters']['x'] = { 'dataclass': 'File', 'required': True, 'type': 'File', 'value': '99999999999999999999999999999992+99/blorp.txt', } expect_template = { "components": { "submit_wf.cwl": expect_component, }, "name": "submit_wf.cwl", "owner_uuid": project_uuid, } stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_template_uuid + '\n') class TestTemplateInputs(unittest.TestCase): expect_template = { "components": { "inputs_test.cwl": { 'runtime_constraints': { 'docker_image': 'arvados/jobs', }, 'script_parameters': { 'cwl:tool': '99999999999999999999999999999991+99/' 'wf/inputs_test.cwl', 'optionalFloatInput': None, 'fileInput': { 'type': 'File', 'dataclass': 'File', 'required': True, 'title': "It's a file; we expect to find some characters in it.", 'description': 'If there were anything further to say, it would be said here,\nor here.' }, 'floatInput': { 'type': 'float', 'dataclass': 'number', 'required': True, 'title': 'Floats like a duck', 'default': 0.1, 'value': 0.1, }, 'optionalFloatInput': { 'type': ['null', 'float'], 'dataclass': 'number', 'required': False, }, 'boolInput': { 'type': 'boolean', 'dataclass': 'boolean', 'required': True, 'title': 'True or false?', }, }, 'repository': 'arvados', 'script_version': 'master', 'script': 'cwl-runner', }, }, "name": "inputs_test.cwl", } @stubs def test_inputs_empty(self, stubs): exited = arvados_cwl.main( ["--create-template", "--no-wait", "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"], cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_template = copy.deepcopy(self.expect_template) expect_template["owner_uuid"] = stubs.fake_user_uuid stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template)) @stubs def test_inputs(self, stubs): exited = arvados_cwl.main( ["--create-template", "--no-wait", "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"], cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) self.expect_template["owner_uuid"] = stubs.fake_user_uuid expect_template = copy.deepcopy(self.expect_template) expect_template["owner_uuid"] = stubs.fake_user_uuid params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt' params["floatInput"]["value"] = 1.234 params["boolInput"]["value"] = True stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template))