sdk/cwl/tests/test_make_output.py

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