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
  16 from arvados_cwl.pathmapper import ArvPathMapper
  17
  18 def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
  19     pdh = "99999999999999999999999999999991+99"
  20     for c in files:
  21         c.fn = fnPattern % (pdh, os.path.basename(c.fn))
  22
  23 class TestPathmap(unittest.TestCase):
  24     def setUp(self):
  25         self.api = mock.MagicMock()
  26         self.api._rootDesc = arvados.api('v1')._rootDesc
  27
  28     def test_keepref(self):
  29         """Test direct keep references."""
  30
  31         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  32
  33         p = ArvPathMapper(arvrunner, [{
  34             "class": "File",
  35             "location": "keep:99999999999999999999999999999991+99/hw.py"
  36         }], "", "/test/%s", "/test/%s/%s")
  37
  38         self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  39                          p._pathmap)
  40
  41     @mock.patch("arvados.commands.run.uploadfiles")
  42     def test_upload(self, upl):
  43         """Test pathmapper uploading files."""
  44
  45         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  46
  47         upl.side_effect = upload_mock
  48
  49         p = ArvPathMapper(arvrunner, [{
  50             "class": "File",
  51             "location": "tests/hw.py"
  52         }], "", "/test/%s", "/test/%s/%s")
  53
  54         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  55                          p._pathmap)
  56
  57     @mock.patch("arvados.commands.run.uploadfiles")
  58     def test_prev_uploaded(self, upl):
  59         """Test pathmapper handling previously uploaded files."""
  60
  61         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  62         arvrunner.add_uploaded('tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File'))
  63
  64         upl.side_effect = upload_mock
  65
  66         p = ArvPathMapper(arvrunner, [{
  67             "class": "File",
  68             "location": "tests/hw.py"
  69         }], "", "/test/%s", "/test/%s/%s")
  70
  71         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  72                          p._pathmap)
  73
  74     @mock.patch("arvados.commands.run.uploadfiles")
  75     @mock.patch("arvados.commands.run.statfile")
  76     def test_statfile(self, statfile, upl):
  77         """Test pathmapper handling ArvFile references."""
  78         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
  79
  80         # An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
  81         # keep mount, so we can construct a direct reference directly without upload.
  82         def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
  83             st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
  84             return st
  85
  86         upl.side_effect = upload_mock
  87         statfile.side_effect = statfile_mock
  88
  89         p = ArvPathMapper(arvrunner, [{
  90             "class": "File",
  91             "location": "tests/hw.py"
  92         }], "", "/test/%s", "/test/%s/%s")
  93
  94         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  95                          p._pathmap)