import copy import cStringIO import functools import hashlib import json import logging import mock import sys import unittest import arvados import arvados.collection import arvados_cwl import arvados_cwl.runner import arvados.keep from .matcher import JsonDiffMatcher from .mock_discovery import get_rootDesc _rootDesc = None def stubs(func): @functools.wraps(func) @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.KeepClient") @mock.patch("arvados.keep.KeepClient") @mock.patch("arvados.events.subscribe") def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): class Stubs: pass stubs = Stubs() stubs.events = events stubs.keepdocker = keepdocker def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) keep_client1().put.side_effect = putstub keep_client1.put.side_effect = putstub keep_client2().put.side_effect = putstub keep_client2.put.side_effect = putstub stubs.keep_client = keep_client2 stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" stubs.api = mock.MagicMock() stubs.api._rootDesc = get_rootDesc() 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", "manifest_text": "" }, { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", "portable_data_hash": "99999999999999999999999999999992+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt" }, { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4", "portable_data_hash": "99999999999999999999999999999994+99", "manifest_text": "" }, { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5", "portable_data_hash": "99999999999999999999999999999995+99", "manifest_text": "" }, { "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6", "portable_data_hash": "99999999999999999999999999999996+99", "manifest_text": "" } ) stubs.api.collections().get().execute.return_value = { "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"} stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" stubs.api.jobs().create().execute.return_value = { "uuid": stubs.expect_job_uuid, "state": "Queued", } stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" stubs.api.container_requests().create().execute.return_value = { "uuid": stubs.expect_container_request_uuid, "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", "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:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'x': { 'basename': 'blorp.txt', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt', 'class': 'File' }, 'y': { 'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory' }, 'z': { 'basename': 'anonymous', "listing": [{ "basename": "renamed.txt", "class": "File", "location": "keep:99999999999999999999999999999998+99/file1.txt" }], 'class': 'Directory' }, 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl' }, 'repository': 'arvados', 'script_version': 'master', 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner' } stubs.pipeline_component = stubs.expect_job_spec.copy() stubs.expect_pipeline_instance = { 'name': 'submit_wf.cwl', 'state': 'RunningOnServer', 'owner_uuid': None, "components": { "cwl-runner": { 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024}, 'script_parameters': { 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}}, 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}}, 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', 'listing': [ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} ]}}, 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl', 'arv:enable_reuse': True }, 'repository': 'arvados', 'script_version': 'master', 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} } } } stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance) stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create) stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = { "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", "state": "Queued" } stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job stubs.expect_container_spec = { 'priority': 1, 'mounts': { '/var/spool/cwl': { 'writable': True, 'kind': 'collection' }, '/var/lib/cwl/workflow': { 'portable_data_hash': '99999999999999999999999999999991+99', 'kind': 'collection' }, 'stdout': { 'path': '/var/spool/cwl/cwl.output.json', 'kind': 'file' }, '/var/lib/cwl/cwl.input.json': { 'kind': 'json', 'content': { 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}, 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'}, 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} ]} }, 'kind': 'json' } }, 'state': 'Committed', 'owner_uuid': None, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'output_path': '/var/spool/cwl', 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, 'ram': 1024*1024*1024 }, "properties": {} } stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" stubs.api.workflows().create().execute.return_value = { "uuid": stubs.expect_workflow_uuid, } def update_mock(**kwargs): stubs.updated_uuid = kwargs.get('uuid') return mock.DEFAULT stubs.api.workflows().update.side_effect = update_mock stubs.api.workflows().update().execute.side_effect = lambda **kwargs: { "uuid": stubs.updated_uuid, } return func(self, stubs, *args, **kwargs) return wrapped class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "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 d51232d96b6116d964a69bfb7e0c73bf+450 ' '0:16:blub.txt 16:434:submit_tool.cwl\n./wf ' 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n', 'owner_uuid': None, 'name': 'submit_wf.cwl', }, ensure_unique_name=True), mock.call().execute(), mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 ' '0:0:blub.txt 0:0:submit_tool.cwl\n', 'replication_desired': None, 'name': 'New collection' }, ensure_unique_name=True), mock.call().execute(num_retries=4), mock.call(body={ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'owner_uuid': None, 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=expect_pipeline) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_no_reuse(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--disable-reuse", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_runner_ram(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_invalid_runner_ram(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 1) @mock.patch("time.sleep") @stubs def test_submit_output_name(self, stubs, tm): output_name = "test_output_name" capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_pipeline_name(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--name=hello job 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.expect_pipeline_instance["name"] = "hello job 123" expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=expect_pipeline) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_output_tags(self, stubs, tm): output_tags = "tag0,tag1,tag2" capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_with_project_uuid(self, stubs, tm): 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_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) expect_pipeline["owner_uuid"] = project_uuid stubs.api.pipeline_instances().create.assert_called_with( body=JsonDiffMatcher(expect_pipeline)) @stubs def test_submit_container(self, stubs): capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.api.collections().create.assert_has_calls([ mock.call(), mock.call(body={ 'manifest_text': './tool d51232d96b6116d964a69bfb7e0c73bf+450 ' '0:16:blub.txt 16:434:submit_tool.cwl\n./wf ' 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n', 'owner_uuid': None, 'name': 'submit_wf.cwl', }, ensure_unique_name=True), mock.call().execute(), mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 ' '0:0:blub.txt 0:0:submit_tool.cwl\n', 'name': 'New collection', 'replication_desired': None, }, ensure_unique_name=True), mock.call().execute(num_retries=4), mock.call(body={ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'owner_uuid': None, 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_no_reuse(self, stubs): capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_output_name(self, stubs): output_name = "test_output_name" capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_output_tags(self, stubs): output_tags = "tag0,tag1,tag2" capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_runner_ram(self, stubs): capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024 expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_keepref_wf.cwl"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") @stubs def test_submit_keepref(self, stubs, tm, reader): capture_stdout = cStringIO.StringIO() with open("tests/wf/expect_arvworkflow.cwl") as f: reader().open().__enter__().read.return_value = f.read() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_container = { 'priority': 1, 'mounts': { '/var/spool/cwl': { 'writable': True, 'kind': 'collection' }, 'stdout': { 'path': '/var/spool/cwl/cwl.output.json', 'kind': 'file' }, '/var/lib/cwl/workflow': { 'portable_data_hash': '99999999999999999999999999999994+99', 'kind': 'collection' }, '/var/lib/cwl/cwl.input.json': { 'content': { 'x': 'XxX' }, 'kind': 'json' } }, 'state': 'Committed', 'owner_uuid': None, 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, 'ram': 1073741824 }, "properties": {} } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @mock.patch("time.sleep") @stubs def test_submit_arvworkflow(self, stubs, tm): capture_stdout = cStringIO.StringIO() with open("tests/wf/expect_arvworkflow.cwl") as f: stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_container = { 'priority': 1, 'mounts': { '/var/spool/cwl': { 'writable': True, 'kind': 'collection' }, 'stdout': { 'path': '/var/spool/cwl/cwl.output.json', 'kind': 'file' }, '/var/lib/cwl/workflow.json': { 'kind': 'json', 'json': { 'cwlVersion': 'v1.0', '$graph': [ { 'inputs': [ { 'inputBinding': {'position': 1}, 'type': 'string', 'id': '#submit_tool.cwl/x'} ], 'requirements': [ {'dockerPull': 'debian:8', 'class': 'DockerRequirement'} ], 'id': '#submit_tool.cwl', 'outputs': [], 'baseCommand': 'cat', 'class': 'CommandLineTool' }, { 'id': '#main', 'inputs': [ {'type': 'string', 'id': '#main/x'} ], 'steps': [ {'in': [{'source': '#main/x', 'id': '#main/step1/x'}], 'run': '#submit_tool.cwl', 'id': '#main/step1', 'out': []} ], 'class': 'Workflow', 'outputs': [] } ] } }, '/var/lib/cwl/cwl.input.json': { 'content': { 'x': 'XxX' }, 'kind': 'json' } }, 'state': 'Committed', 'owner_uuid': None, 'output_path': '/var/spool/cwl', 'name': 'a test workflow', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, 'ram': 1073741824 }, "properties": { "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" } } stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @stubs def test_submit_container_name(self, stubs): capture_stdout = cStringIO.StringIO() try: exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 0) except: logging.exception("") stubs.expect_container_spec["name"] = "hello container 123" expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( body=expect_container) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @mock.patch("arvados.commands.keepdocker.find_one_image_hash") @mock.patch("cwltool.docker.get_image") @mock.patch("arvados.api") def test_arvados_jobs_image(self, api, get_image, find_one_image_hash): arvrunner = mock.MagicMock() arvrunner.project_uuid = "" api.return_value = mock.MagicMock() arvrunner.api = api.return_value arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, {"items": [], "items_available": 0, "offset": 0}, {"items": [], "items_available": 0, "offset": 0}, {"items": [{"created_at": "", "head_uuid": "", "link_class": "docker_image_hash", "name": "123456", "owner_uuid": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, {"items": [], "items_available": 0, "offset": 0}, {"items": [{"created_at": "", "head_uuid": "", "link_class": "docker_image_repo+tag", "name": "arvados/jobs:"+arvados_cwl.__version__, "owner_uuid": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, {"items": [{"created_at": "", "head_uuid": "", "link_class": "docker_image_hash", "name": "123456", "owner_uuid": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} , ) find_one_image_hash.return_value = "123456" arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, {"items": [{"uuid": "", "owner_uuid": "", "manifest_text": "", "properties": "" }], "items_available": 1, "offset": 0}, {"items": [{"uuid": ""}], "items_available": 1, "offset": 0}) arvrunner.api.collections().create().execute.return_value = {"uuid": ""} self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner)) class TestCreateTemplate(unittest.TestCase): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" def _adjust_script_params(self, expect_component): expect_component['script_parameters']['x'] = { 'dataclass': 'File', 'required': True, 'type': 'File', 'value': '99999999999999999999999999999994+99/blorp.txt', } expect_component['script_parameters']['y'] = { 'dataclass': 'Collection', 'required': True, 'type': 'Directory', 'value': '99999999999999999999999999999998+99', } expect_component['script_parameters']['z'] = { 'dataclass': 'Collection', 'required': True, 'type': 'Directory', } @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=jobs", "--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) self._adjust_script_params(expect_component) 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), ensure_unique_name=True) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_template_uuid + '\n') @stubs def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", "--project-uuid", project_uuid, "--api=jobs", "--name", "testing 123", "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) self._adjust_script_params(expect_component) expect_template = { "components": { "testing 123": expect_component, }, "name": "testing 123", "owner_uuid": project_uuid, } stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template), ensure_unique_name=True) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_template_uuid + '\n') @stubs def test_update_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_template_uuid, "--debug", "--project-uuid", project_uuid, "--api=jobs", "--name", "testing 123", "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) self._adjust_script_params(expect_component) expect_template = { "components": { "testing 123": expect_component, }, "name": "testing 123", "owner_uuid": project_uuid, } stubs.api.pipeline_templates().create.refute_called() stubs.api.pipeline_templates().update.assert_called_with( body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid) self.assertEqual(capture_stdout.getvalue(), self.existing_template_uuid + '\n') class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" expect_workflow = open("tests/wf/expect_packed.cwl").read() @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--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_templates().create.refute_called() stubs.api.container_requests().create.refute_called() body = { "workflow": { "owner_uuid": project_uuid, "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') @stubs def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, "--name", "testing 123", "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_templates().create.refute_called() stubs.api.container_requests().create.refute_called() body = { "workflow": { "owner_uuid": project_uuid, "name": "testing 123", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') @stubs def test_incompatible_api(self, stubs): capture_stderr = cStringIO.StringIO() logging.getLogger('arvados.cwl-runner').addHandler( logging.StreamHandler(capture_stderr)) exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--api=jobs", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], sys.stderr, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 1) self.assertRegexpMatches( capture_stderr.getvalue(), "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) @stubs def test_update(self, stubs): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) body = { "workflow": { "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().update.assert_called_with( uuid=self.existing_workflow_uuid, body=JsonDiffMatcher(body)) self.assertEqual(capture_stdout.getvalue(), self.existing_workflow_uuid + '\n') @stubs def test_update_name(self, stubs): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "--name", "testing 123", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) body = { "workflow": { "name": "testing 123", "description": "", "definition": self.expect_workflow, } } stubs.api.workflows().update.assert_called_with( uuid=self.existing_workflow_uuid, body=JsonDiffMatcher(body)) self.assertEqual(capture_stdout.getvalue(), self.existing_workflow_uuid + '\n') class TestTemplateInputs(unittest.TestCase): expect_template = { "components": { "inputs_test.cwl": { 'runtime_constraints': { 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024 }, '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', 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', }, }, "name": "inputs_test.cwl", } @stubs def test_inputs_empty(self, stubs): exited = arvados_cwl.main( ["--create-template", "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"], cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True) @stubs def test_inputs(self, stubs): exited = arvados_cwl.main( ["--create-template", "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"], cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) expect_template = copy.deepcopy(self.expect_template) params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt' params["floatInput"]["value"] = 1.234 params["boolInput"]["value"] = True stubs.api.pipeline_templates().create.assert_called_with( body=JsonDiffMatcher(expect_template), ensure_unique_name=True)