X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0278f7f56ed5ce972803079bdeb4ba031676a171..81d1a618e724c6e9f20f4efa47acbcef4bba5f15:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 5734821562..0ff9da927a 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,106 +1,470 @@ -import arvados -import arvados.keep -import arvados.collection -import arvados_cwl +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.keep + +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): + def wrapped(self, events, keep_client, keepdocker, *args, **kwargs): class Stubs: pass stubs = Stubs() stubs.events = events - stubs.KeepClient = KeepClient stubs.keepdocker = keepdocker + stubs.keep_client = keep_client def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) - stubs.KeepClient().put.side_effect = putstub + stubs.keep_client().put.side_effect = putstub + stubs.keep_client.put.side_effect = putstub - stubs.keepdocker.return_value = True + stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] 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._rootDesc = arvados.api('v1')._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": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", + "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 = { - 'owner_uuid': stubs.fake_user_uuid, 'runtime_constraints': { 'docker_image': 'arvados/jobs' }, 'script_parameters': { 'x': { - 'path': '99999999999999999999999999999992+99/blorp.txt', + 'basename': 'blorp.txt', + 'location': 'keep:99999999999999999999999999999994+99/blorp.txt', 'class': 'File' }, - 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl' + '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', 'script': 'cwl-runner' } + stubs.pipeline_component = stubs.expect_job_spec.copy() + stubs.expect_pipeline_instance = { + 'name': 'submit_wf.cwl', + 'state': 'RunningOnServer', + "components": { + "cwl-runner": { + 'runtime_constraints': {'docker_image': 'arvados/jobs'}, + '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' + }, + 'repository': 'arvados', + 'script_version': 'master', + 'script': 'cwl-runner' + } + } + } + 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/job/cwl.input.json': { + 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json', + 'kind': 'collection' + } + }, + 'state': 'Committed', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'], + 'name': 'submit_wf.cwl', + 'container_image': '99999999999999999999999999999993+99', + 'output_path': '/var/spool/cwl', + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + 'ram': 268435456 + } + } + + stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" + stubs.api.workflows().create().execute.return_value = { + "uuid": stubs.expect_workflow_uuid, + } + return func(self, stubs, *args, **kwargs) return wrapped class TestSubmit(unittest.TestCase): + @mock.patch("time.sleep") @stubs - def test_submit(self, stubs): - arvados_cwl.main( - ["--debug", "--submit", "--no-wait", + 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"], - sys.stdout, sys.stderr, api_client=stubs.api) + 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', + '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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', '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', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + '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', + 'manifest_text': + '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) - stubs.api.jobs().create.assert_called_with( - body=stubs.expect_job_spec, - find_or_create=True) + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + expect_pipeline["owner_uuid"] = stubs.fake_user_uuid + 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_with_project_uuid(self, stubs): + def test_submit_with_project_uuid(self, stubs, tm): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - arvados_cwl.main( - ["--debug", "--submit", "--no-wait", + 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=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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + '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', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + '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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'name': '#', + }, ensure_unique_name=True), + mock.call().execute()]) + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["owner_uuid"] = stubs.fake_user_uuid + stubs.api.container_requests().create.assert_called_with( + body=expect_container) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + +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", "--debug", + "--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': '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', + } + 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') + + +class TestCreateWorkflow(unittest.TestCase): + @stubs + def test_create(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--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() + + with open("tests/wf/expect_packed.cwl") as f: + expect_workflow = f.read() + + body = { + "workflow": { + "owner_uuid": project_uuid, + "name": "submit_wf.cwl", + "description": "", + "definition": expect_workflow + } + } + stubs.api.workflows().create.assert_called_with( + body=JsonDiffMatcher(body)) + + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_workflow_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), ensure_unique_name=True) + + @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"] = '99999999999999999999999999999994+99/blorp.txt' + params["floatInput"]["value"] = 1.234 + params["boolInput"]["value"] = True - expect_body = stubs.expect_job_spec.copy() - expect_body["owner_uuid"] = project_uuid - stubs.api.jobs().create.assert_called_with( - body=expect_body, - find_or_create=True) + stubs.api.pipeline_templates().create.assert_called_with( + body=JsonDiffMatcher(expect_template), ensure_unique_name=True)