sdk/cwl/tests/test_pathmapper.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import functools
   6 import mock
   7 import sys
   8 import unittest
   9 import json
  10 import logging
  11 import os
  12 import datetime
  13
  14 import arvados
  15 import arvados.keep
  16 import arvados.collection
  17 import arvados_cwl
  18
  19 from cwltool.pathmapper import MapperEnt
  20 from .mock_discovery import get_rootDesc
  21
  22 from arvados_cwl.pathmapper import ArvPathMapper
  23
  24 def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None, collection=None, packed=None):
  25     pdh = "99999999999999999999999999999991+99"
  26     for c in files:
  27         c.keepref = "%s/%s" % (pdh, os.path.basename(c.fn))
  28         c.fn = fnPattern % (pdh, os.path.basename(c.fn))
  29
  30 class MockDateTime(datetime.datetime):
  31     @classmethod
  32     def now(cls):
  33         return datetime.datetime(2018, 1, 1, 0, 0, 0, 0)
  34
  35 datetime.datetime = MockDateTime
  36
  37 class TestPathmap(unittest.TestCase):
  38     def setUp(self):
  39         self.api = mock.MagicMock()
  40         self.api._rootDesc = get_rootDesc()
  41
  42     def test_keepref(self):
  43         """Test direct keep references."""
  44
  45         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  46
  47         p = ArvPathMapper(arvrunner, [{
  48             "class": "File",
  49             "location": "keep:99999999999999999999999999999991+99/hw.py"
  50         }], "", "/test/%s", "/test/%s/%s")
  51
  52         self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  53                          p._pathmap)
  54
  55     @mock.patch("arvados.commands.run.uploadfiles")
  56     @mock.patch("arvados.commands.run.statfile")
  57     def test_upload(self, statfile, upl):
  58         """Test pathmapper uploading files."""
  59
  60         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  61
  62         def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
  63             st = arvados.commands.run.UploadFile("", "tests/hw.py")
  64             return st
  65
  66         upl.side_effect = upload_mock
  67         statfile.side_effect = statfile_mock
  68
  69         p = ArvPathMapper(arvrunner, [{
  70             "class": "File",
  71             "location": "file:tests/hw.py"
  72         }], "", "/test/%s", "/test/%s/%s")
  73
  74         self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  75                          p._pathmap)
  76
  77     @mock.patch("arvados.commands.run.uploadfiles")
  78     @mock.patch("arvados.commands.run.statfile")
  79     def test_statfile(self, statfile, upl):
  80         """Test pathmapper handling ArvFile references."""
  81         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  82
  83         # An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
  84         # keep mount, so we can construct a direct reference directly without upload.
  85         def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
  86             st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
  87             return st
  88
  89         upl.side_effect = upload_mock
  90         statfile.side_effect = statfile_mock
  91
  92         p = ArvPathMapper(arvrunner, [{
  93             "class": "File",
  94             "location": "file:tests/hw.py"
  95         }], "", "/test/%s", "/test/%s/%s")
  96
  97         self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  98                          p._pathmap)
  99
 100     @mock.patch("os.stat")
 101     def test_missing_file(self, stat):
 102         """Test pathmapper handling missing references."""
 103         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
 104
 105         stat.side_effect = OSError(2, "No such file or directory")
 106
 107         with self.assertRaises(OSError):
 108             p = ArvPathMapper(arvrunner, [{
 109                 "class": "File",
 110                 "location": "file:tests/hw.py"
 111             }], "", "/test/%s", "/test/%s/%s")
 112
 113     def test_get_intermediate_collection_info(self):
 114         self.api.containers().current().execute.return_value = {"uuid" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"}
 115         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
 116         arvrunner.intermediate_output_ttl = 60
 117
 118         path_mapper = ArvPathMapper(arvrunner, [{
 119             "class": "File",
 120             "location": "keep:99999999999999999999999999999991+99/hw.py"
 121         }], "", "/test/%s", "/test/%s/%s")
 122
 123         info = path_mapper._get_intermediate_collection_info()
 124
 125         self.assertEqual(info["name"], "Intermediate collection")
 126         self.assertEqual(info["trash_at"], datetime.datetime(2018, 1, 1, 0, 1))
 127         self.assertEqual(info["properties"], {"type" : "Intermediate", "container" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"})