sdk/cwl/tests/test_make_output.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from future import standard_library
   6 standard_library.install_aliases()
   7
   8 import functools
   9 import json
  10 import logging
  11 import mock
  12 import os
  13 import io
  14 import unittest
  15
  16 import arvados
  17 import arvados_cwl
  18 import arvados_cwl.executor
  19 from .mock_discovery import get_rootDesc
  20
  21 class TestMakeOutput(unittest.TestCase):
  22     def setUp(self):
  23         self.api = mock.MagicMock()
  24         self.api._rootDesc = get_rootDesc()
  25
  26     def tearDown(self):
  27         root_logger = logging.getLogger('')
  28
  29         # Remove existing RuntimeStatusLoggingHandlers if they exist
  30         handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
  31         root_logger.handlers = handlers
  32
  33     @mock.patch("arvados.collection.Collection")
  34     @mock.patch("arvados.collection.CollectionReader")
  35     def test_make_output_collection(self, reader, col):
  36         keep_client = mock.MagicMock()
  37         runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client)
  38         runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
  39
  40         final = mock.MagicMock()
  41         col.return_value = final
  42         readermock = mock.MagicMock()
  43         reader.return_value = readermock
  44
  45         final_uuid = final.manifest_locator()
  46         num_retries = runner.num_retries
  47
  48         cwlout = io.StringIO()
  49         openmock = mock.MagicMock()
  50         final.open.return_value = openmock
  51         openmock.__enter__.return_value = cwlout
  52
  53         _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "tag0,tag1,tag2", {}, {
  54             "foo": {
  55                 "class": "File",
  56                 "location": "keep:99999999999999999999999999999991+99/foo.txt",
  57                 "size": 3,
  58                 "basename": "foo.txt"
  59             },
  60             "bar": {
  61                 "class": "File",
  62                 "location": "keep:99999999999999999999999999999992+99/bar.txt",
  63                 "basename": "baz.txt",
  64                 "size": 4
  65             }
  66         })
  67
  68         final.copy.assert_has_calls([mock.call('bar.txt', 'baz.txt', overwrite=False, source_collection=readermock)])
  69         final.copy.assert_has_calls([mock.call('foo.txt', 'foo.txt', overwrite=False, source_collection=readermock)])
  70         final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz', properties={}, storage_classes=['foo'])])
  71         self.assertEqual("""{
  72     "bar": {
  73         "basename": "baz.txt",
  74         "class": "File",
  75         "location": "baz.txt",
  76         "size": 4
  77     },
  78     "foo": {
  79         "basename": "foo.txt",
  80         "class": "File",
  81         "location": "foo.txt",
  82         "size": 3
  83     }
  84 }""", cwlout.getvalue())
  85
  86         self.assertIs(final, runner.final_output_collection)
  87         self.assertIs(final_uuid, runner.final_output_collection.manifest_locator())
  88         self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag0"}), mock.call().execute(num_retries=num_retries)])
  89         self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag1"}), mock.call().execute(num_retries=num_retries)])
  90         self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag2"}), mock.call().execute(num_retries=num_retries)])
  91
  92     @mock.patch("arvados.collection.Collection")
  93     @mock.patch("arvados.collection.CollectionReader")
  94     def test_make_output_for_multiple_file_targets(self, reader, col):
  95         keep_client = mock.MagicMock()
  96         runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client)
  97         runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
  98
  99         final = mock.MagicMock()
 100         col.return_value = final
 101         readermock = mock.MagicMock()
 102         reader.return_value = readermock
 103
 104         # This output describes a single file listed in 2 different directories
 105         _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "", {}, { 'out': [
 106         {
 107             'basename': 'testdir1',
 108             'listing': [
 109                 {
 110                     'basename': 'test.txt',
 111                     'nameroot': 'test',
 112                     'nameext': '.txt',
 113                     'location': 'keep:99999999999999999999999999999991+99/test.txt',
 114                     'class': 'File',
 115                     'size': 16
 116                 }
 117             ],
 118             'location': '_:99999999999999999999999999999992+99',
 119             'class': 'Directory'
 120         },
 121         {
 122             'basename': 'testdir2',
 123             'listing': [
 124                 {
 125                     'basename': 'test.txt',
 126                     'nameroot': 'test',
 127                     'nameext': '.txt',
 128                     'location': 'keep:99999999999999999999999999999991+99/test.txt',
 129                     'class':
 130                     'File',
 131                     'size': 16
 132                 }
 133             ],
 134             'location': '_:99999999999999999999999999999993+99',
 135             'class': 'Directory'
 136         }]})
 137
 138         # Check that copy is called on the collection for both locations
 139         final.copy.assert_any_call("test.txt", "testdir1/test.txt", source_collection=mock.ANY, overwrite=mock.ANY)
 140         final.copy.assert_any_call("test.txt", "testdir2/test.txt", source_collection=mock.ANY, overwrite=mock.ANY)
 141
 142     @mock.patch("arvados.collection.Collection")
 143     @mock.patch("arvados.collection.CollectionReader")
 144     def test_make_output_for_literal_name_conflicts(self, reader, col):
 145         keep_client = mock.MagicMock()
 146         runner = arvados_cwl.executor.ArvCwlExecutor(self.api, keep_client=keep_client)
 147         runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
 148
 149         final = mock.MagicMock()
 150         col.return_value = final
 151         readermock = mock.MagicMock()
 152         reader.return_value = readermock
 153
 154         # This output describes two literals with the same basename
 155         _, runner.final_output_collection = runner.make_output_collection("Test output", ["foo"], "",  {}, [
 156         {
 157             'lit':
 158             {
 159                 'basename': 'a_file',
 160                 'nameext': '',
 161                 'nameroot': 'a_file',
 162                 'location': '_:f168fc0c-4291-40aa-a04e-366d57390560',
 163                 'class': 'File',
 164                 'contents': 'Hello file literal.'
 165             }
 166         },
 167         {
 168             'lit':
 169             {
 170                 'basename': 'a_file',
 171                 'nameext': '',
 172                 'nameroot': 'a_file',
 173                 'location': '_:1728da8f-c64e-4a3e-b2e2-1ee356be7bc8',
 174                 'class': 'File',
 175                 'contents': 'Hello file literal.'
 176             }
 177         }])
 178
 179         # Check that the file name conflict is resolved and open is called for both
 180         final.open.assert_any_call("a_file", "wb")
 181         final.open.assert_any_call("a_file_2", "wb")