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 test_keepref(self):
  25         """Test direct keep references."""
  26
  27         arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
  28
  29         p = ArvPathMapper(arvrunner, [{
  30             "class": "File",
  31             "location": "keep:99999999999999999999999999999991+99/hw.py"
  32         }], "", "/test/%s", "/test/%s/%s")
  33
  34         self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  35                          p._pathmap)
  36
  37     @mock.patch("arvados.commands.run.uploadfiles")
  38     def test_upload(self, upl):
  39         """Test pathmapper uploading files."""
  40
  41         arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
  42
  43         upl.side_effect = upload_mock
  44
  45         p = ArvPathMapper(arvrunner, [{
  46             "class": "File",
  47             "location": "tests/hw.py"
  48         }], "", "/test/%s", "/test/%s/%s")
  49
  50         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  51                          p._pathmap)
  52
  53     @mock.patch("arvados.commands.run.uploadfiles")
  54     def test_prev_uploaded(self, upl):
  55         """Test pathmapper handling previously uploaded files."""
  56
  57         arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
  58         arvrunner.add_uploaded('tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File'))
  59
  60         upl.side_effect = upload_mock
  61
  62         p = ArvPathMapper(arvrunner, [{
  63             "class": "File",
  64             "location": "tests/hw.py"
  65         }], "", "/test/%s", "/test/%s/%s")
  66
  67         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  68                          p._pathmap)
  69
  70     @mock.patch("arvados.commands.run.uploadfiles")
  71     @mock.patch("arvados.commands.run.statfile")
  72     def test_statfile(self, statfile, upl):
  73         """Test pathmapper handling ArvFile references."""
  74         arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
  75
  76         # An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
  77         # keep mount, so we can construct a direct reference directly without upload.
  78         def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
  79             st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
  80             return st
  81
  82         upl.side_effect = upload_mock
  83         statfile.side_effect = statfile_mock
  84
  85         p = ArvPathMapper(arvrunner, [{
  86             "class": "File",
  87             "location": "tests/hw.py"
  88         }], "", "/test/%s", "/test/%s/%s")
  89
  90         self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
  91                          p._pathmap)