#
# SPDX-License-Identifier: Apache-2.0
-from future import standard_library
-standard_library.install_aliases()
-from builtins import object
-from builtins import str
-from future.utils import viewvalues
-
import copy
import io
+import itertools
import functools
import hashlib
import json
import logging
-import mock
import sys
import unittest
import cwltool.process
import re
import os
-from io import BytesIO
-
-# StringIO.StringIO and io.StringIO have different behavior write() is
-# called with both python2 (byte) strings and unicode strings
-# (specifically there's some logging in cwltool that causes trouble).
-# This isn't a problem on python3 because all string are unicode.
-if sys.version_info[0] < 3:
- from StringIO import StringIO
-else:
- from io import StringIO
+from io import BytesIO, StringIO
+from unittest import mock
import arvados
import arvados.collection
return CollectionExecute(created_collections[uuid])
def collection_getstub(created_collections, uuid):
- for v in viewvalues(created_collections):
+ for v in created_collections.values():
if uuid in (v["uuid"], v["portable_data_hash"]):
return CollectionExecute(v)
api.return_value = mock.MagicMock()
arvrunner.api = api.return_value
arvrunner.runtimeContext.match_local_docker = False
- arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
- "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "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},
- {"items": [{"created_at": "",
- "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "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}
- )
+ arvrunner.api.links().list().execute.side_effect = itertools.cycle([
+ {"items": [{"created_at": "2023-08-25T12:34:56.123456Z",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "link_class": "docker_image_repo+tag",
+ "name": "arvados/jobs:"+arvados_cwl.__version__,
+ "owner_uuid": "",
+ "uuid": "zzzzz-o0j2j-arvadosjobsrepo",
+ "properties": {"image_timestamp": ""}}]},
+ {"items": []},
+ {"items": []},
+ {"items": [{"created_at": "2023-08-25T12:34:57.234567Z",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "uuid": "zzzzz-o0j2j-arvadosjobshash",
+ "properties": {"image_timestamp": ""}}]},
+ {"items": []},
+ {"items": []},
+ ])
find_one_image_hash.return_value = "123456"
- arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "owner_uuid": "",
- "manifest_text": "",
- "properties": ""
- }], "items_available": 1, "offset": 0},
- {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "owner_uuid": "",
- "manifest_text": "",
- "properties": ""
- }], "items_available": 1, "offset": 0})
+ arvrunner.api.collections().list().execute.side_effect = itertools.cycle([
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "owner_uuid": "",
+ "manifest_text": "",
+ "created_at": "2023-08-25T12:34:55.012345Z",
+ "properties": {}}]},
+ {"items": []},
+ {"items": []},
+ ])
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"portable_data_hash": "9999999999999999999999999999999b+99"}
"out": [
{"id": "#main/step/out"}
],
- "run": "keep:7628e49da34b93de9f4baf08a6212817+247/secret_wf.cwl"
+ "run": "keep:991302581d01db470345a131480e623b+247/secret_wf.cwl"
}
]
}
self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_create_map(self, stubs):
+ # test uploading a document that uses objects instead of arrays
+ # for certain fields like inputs and requirements.
+
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "--disable-git",
+ "tests/wf/submit_wf_map.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ expect_workflow = StripYAMLComments(
+ open("tests/wf/expect_upload_wrapper_map.cwl").read().rstrip())
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "submit_wf_map.cwl",
+ "description": "",
+ "definition": expect_workflow,
+ }
+ }
+ stubs.api.workflows().create.assert_called_with(
+ body=JsonDiffMatcher(body))
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+
+class TestPrintKeepDeps(unittest.TestCase):
+ @stubs()
+ def test_print_keep_deps(self, stubs):
+ # test --print-keep-deps which is used by arv-copy
+
+ exited = arvados_cwl.main(
+ ["--print-keep-deps", "--debug",
+ "tests/wf/submit_wf_map.cwl"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ '["5d373e7629203ce39e7c22af98a0f881+52", "999999999999999999999999999999d4+99"]' + '\n')
+ self.assertEqual(exited, 0)
projects / arvados.git / blobdiff