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 import functools
   6 import json
   7 import logging
   8 import mock
   9 import os
  10 import StringIO
  11 import unittest
  12
  13 import arvados
  14 import arvados_cwl
  15 from .mock_discovery import get_rootDesc
  16
  17 class TestMakeOutput(unittest.TestCase):
  18     def setUp(self):
  19         self.api = mock.MagicMock()
  20         self.api._rootDesc = get_rootDesc()
  21
  22     @mock.patch("arvados.collection.Collection")
  23     @mock.patch("arvados.collection.CollectionReader")
  24     def test_make_output_collection(self, reader, col):
  25         keep_client = mock.MagicMock()
  26         runner = arvados_cwl.ArvCwlRunner(self.api, keep_client=keep_client)
  27         runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
  28
  29         final = mock.MagicMock()
  30         col.return_value = final
  31         readermock = mock.MagicMock()
  32         reader.return_value = readermock
  33
  34         final_uuid = final.manifest_locator()
  35         num_retries = runner.num_retries
  36
  37         cwlout = StringIO.StringIO()
  38         openmock = mock.MagicMock()
  39         final.open.return_value = openmock
  40         openmock.__enter__.return_value = cwlout
  41
  42         _, runner.final_output_collection = runner.make_output_collection("Test output", "tag0,tag1,tag2", {
  43             "foo": {
  44                 "class": "File",
  45                 "location": "keep:99999999999999999999999999999991+99/foo.txt",
  46                 "size": 3,
  47                 "basename": "foo.txt"
  48             },
  49             "bar": {
  50                 "class": "File",
  51                 "location": "keep:99999999999999999999999999999992+99/bar.txt",
  52                 "basename": "baz.txt",
  53                 "size": 4
  54             }
  55         })
  56
  57         final.copy.assert_has_calls([mock.call('bar.txt', 'baz.txt', overwrite=False, source_collection=readermock)])
  58         final.copy.assert_has_calls([mock.call('foo.txt', 'foo.txt', overwrite=False, source_collection=readermock)])
  59         final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz')])
  60         self.assertEqual("""{
  61     "bar": {
  62         "class": "File",
  63         "location": "baz.txt",
  64         "size": 4
  65     },
  66     "foo": {
  67         "class": "File",
  68         "location": "foo.txt",
  69         "size": 3
  70     }
  71 }""", cwlout.getvalue())
  72
  73         self.assertIs(final, runner.final_output_collection)
  74         self.assertIs(final_uuid, runner.final_output_collection.manifest_locator())
  75         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)])
  76         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)])
  77         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)])