sdk/cwl/tests/test_pathmapper.py

   1 import functools
   2 import mock
   3 import sys
   4 import unittest
   5 import json
   6 import logging
   7 import os
   8
   9 import arvados
  10 import arvados.keep
  11 import arvados.collection
  12 import arvados_cwl
  13
  14 from cwltool.pathmapper import MapperEnt
  15 from .mock_discovery import get_rootDesc
  16
  17 from arvados_cwl.pathmapper import ArvPathMapper
  18
  19 def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
  20     pdh = "99999999999999999999999999999991+99"
  21     for c in files:
  22         c.keepref = "%s/%s" % (pdh, os.path.basename(c.fn))
  23         c.fn = fnPattern % (pdh, os.path.basename(c.fn))
  24
  25 class TestPathmap(unittest.TestCase):
  26     def setUp(self):
  27         self.api = mock.MagicMock()
  28         self.api._rootDesc = get_rootDesc()
  29
  30     def test_keepref(self):
  31         """Test direct keep references."""
  32
  33         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  34
  35         p = ArvPathMapper(arvrunner, [{
  36             "class": "File",
  37             "location": "keep:99999999999999999999999999999991+99/hw.py"
  38         }], "", "/test/%s", "/test/%s/%s")
  39
  40         self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  41                          p._pathmap)
  42
  43     @mock.patch("arvados.commands.run.uploadfiles")
  44     def test_upload(self, upl):
  45         """Test pathmapper uploading files."""
  46
  47         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  48
  49         upl.side_effect = upload_mock
  50
  51         p = ArvPathMapper(arvrunner, [{
  52             "class": "File",
  53             "location": "tests/hw.py"
  54         }], "", "/test/%s", "/test/%s/%s")
  55
  56         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  57                          p._pathmap)
  58
  59     @mock.patch("arvados.commands.run.uploadfiles")
  60     def test_prev_uploaded(self, upl):
  61         """Test pathmapper handling previously uploaded files."""
  62
  63         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  64         arvrunner.add_uploaded('tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File', staged=True))
  65
  66         upl.side_effect = upload_mock
  67
  68         p = ArvPathMapper(arvrunner, [{
  69             "class": "File",
  70             "location": "tests/hw.py"
  71         }], "", "/test/%s", "/test/%s/%s")
  72
  73         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  74                          p._pathmap)
  75
  76     @mock.patch("arvados.commands.run.uploadfiles")
  77     @mock.patch("arvados.commands.run.statfile")
  78     def test_statfile(self, statfile, upl):
  79         """Test pathmapper handling ArvFile references."""
  80         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  81
  82         # An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
  83         # keep mount, so we can construct a direct reference directly without upload.
  84         def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
  85             st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
  86             return st
  87
  88         upl.side_effect = upload_mock
  89         statfile.side_effect = statfile_mock
  90
  91         p = ArvPathMapper(arvrunner, [{
  92             "class": "File",
  93             "location": "tests/hw.py"
  94         }], "", "/test/%s", "/test/%s/%s")
  95
  96         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
  97                          p._pathmap)