Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyObjects.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 # pylint: disable=C0103,E1101
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2 import json
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3 import os
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4 import shutil
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5 import socket
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6 import sys
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7 import tarfile
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8 import tempfile
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9 import uuid
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10 from ssl import SSLError
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11
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12 import six
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13 from six.moves.urllib.error import URLError
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14 from six.moves.urllib.request import urlopen
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15
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16 import bioblend
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17 import bioblend.galaxy.objects.galaxy_instance as galaxy_instance
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18 import bioblend.galaxy.objects.wrappers as wrappers
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19 from bioblend import ConnectionError
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20 from bioblend.galaxy import dataset_collections
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21 from . import test_util
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22 from .test_util import unittest
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23
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24 bioblend.set_stream_logger('test', level='INFO')
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25 socket.setdefaulttimeout(10.0)
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26 SAMPLE_FN = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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27 SAMPLE_WF_COLL_FN = test_util.get_abspath(os.path.join('data', 'paste_columns_collections.ga'))
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28 FOO_DATA = 'foo\nbar\n'
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29 FOO_DATA_2 = 'foo2\nbar2\n'
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30 SAMPLE_WF_DICT = {
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31 'deleted': False,
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32 'id': '9005c5112febe774',
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33 'inputs': {
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34 '571': {'label': 'Input Dataset', 'value': ''},
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35 '572': {'label': 'Input Dataset', 'value': ''},
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36 },
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37 'model_class': 'StoredWorkflow',
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38 'name': 'paste_columns',
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39 'published': False,
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40 'steps': {
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41 '571': {
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42 'id': 571,
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43 'input_steps': {},
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44 'tool_id': None,
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45 'tool_inputs': {'name': 'Input Dataset'},
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46 'tool_version': None,
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47 'type': 'data_input',
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48 },
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49 '572': {
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50 'id': 572,
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51 'input_steps': {},
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52 'tool_id': None,
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53 'tool_inputs': {'name': 'Input Dataset'},
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54 'tool_version': None,
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55 'type': 'data_input',
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56 },
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57 '573': {
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58 'id': 573,
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59 'input_steps': {
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60 'input1': {'source_step': 571, 'step_output': 'output'},
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61 'input2': {'source_step': 572, 'step_output': 'output'},
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62 },
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63 'tool_id': 'Paste1',
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64 'tool_inputs': {
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65 'delimiter': '"T"',
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66 'input1': 'null',
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67 'input2': 'null',
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68 },
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69 'tool_version': '1.0.0',
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70 'type': 'tool',
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71 }
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72 },
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73 'tags': [],
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74 'url': '/api/workflows/9005c5112febe774',
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75 }
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76
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77
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78 def is_reachable(url):
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79 res = None
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80 try:
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81 res = urlopen(url, timeout=5)
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82 except (SSLError, URLError, socket.timeout):
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83 return False
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84 if res is not None:
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85 res.close()
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86 return True
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87
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88
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89 def upload_from_fs(lib, bnames, **kwargs):
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90 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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91 try:
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92 fnames = [os.path.join(tempdir, _) for _ in bnames]
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93 for fn in fnames:
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94 with open(fn, 'w') as f:
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95 f.write(FOO_DATA)
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96 dss = lib.upload_from_galaxy_fs(fnames, **kwargs)
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97 finally:
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98 shutil.rmtree(tempdir)
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99 return dss, fnames
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100
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101
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102 class MockWrapper(wrappers.Wrapper):
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103 BASE_ATTRS = frozenset(['a', 'b'])
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104
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105 def __init__(self, *args, **kwargs):
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106 super(MockWrapper, self).__init__(*args, **kwargs)
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107
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108 @property
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109 def gi_module(self):
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110 return super(MockWrapper, self).gi_module()
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111
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112
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113 class TestWrapper(unittest.TestCase):
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114
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115 def setUp(self):
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116 self.d = {'a': 1, 'b': [2, 3], 'c': {'x': 4}}
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117 self.assertRaises(TypeError, wrappers.Wrapper, self.d)
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118 self.w = MockWrapper(self.d)
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119
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120 def test_initialize(self):
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121 for k in MockWrapper.BASE_ATTRS:
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122 self.assertEqual(getattr(self.w, k), self.d[k])
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123 self.w.a = 222
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124 self.w.b[0] = 222
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125 self.assertEqual(self.w.a, 222)
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126 self.assertEqual(self.w.b[0], 222)
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127 self.assertEqual(self.d['a'], 1)
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128 self.assertEqual(self.d['b'][0], 2)
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129 self.assertRaises(AttributeError, getattr, self.w, 'foo')
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130 self.assertRaises(AttributeError, setattr, self.w, 'foo', 0)
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131
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132 def test_taint(self):
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133 self.assertFalse(self.w.is_modified)
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134 self.w.a = 111 # pylint: disable=W0201
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135 self.assertTrue(self.w.is_modified)
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136
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137 def test_serialize(self):
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138 w = MockWrapper.from_json(self.w.to_json())
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139 self.assertEqual(w.wrapped, self.w.wrapped)
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140
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141 def test_clone(self):
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142 w = self.w.clone()
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143 self.assertEqual(w.wrapped, self.w.wrapped)
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144 w.b[0] = 111
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145 self.assertEqual(self.w.b[0], 2)
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146
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147 def test_kwargs(self):
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148 parent = MockWrapper({'a': 10})
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149 w = MockWrapper(self.d, parent=parent)
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150 self.assertIs(w.parent, parent)
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151 self.assertRaises(AttributeError, setattr, w, 'parent', 0)
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152
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153
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154 class TestWorkflow(unittest.TestCase):
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155
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156 def setUp(self):
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157 self.wf = wrappers.Workflow(SAMPLE_WF_DICT)
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158
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159 def test_initialize(self):
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160 self.assertEqual(self.wf.id, '9005c5112febe774')
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161 self.assertEqual(self.wf.name, 'paste_columns')
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162 self.assertEqual(self.wf.deleted, False)
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163 self.assertEqual(self.wf.published, False)
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164 self.assertEqual(self.wf.tags, [])
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165 self.assertEqual(
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166 self.wf.input_labels_to_ids, {'Input Dataset': set(['571', '572'])})
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167 self.assertEqual(self.wf.tool_labels_to_ids, {'Paste1': set(['573'])})
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168 self.assertEqual(self.wf.data_input_ids, set(['571', '572']))
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169 self.assertEqual(self.wf.source_ids, set(['571', '572']))
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170 self.assertEqual(self.wf.sink_ids, set(['573']))
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171
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172 def test_dag(self):
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173 inv_dag = {}
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174 for h, tails in six.iteritems(self.wf.dag):
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175 for t in tails:
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176 inv_dag.setdefault(str(t), set()).add(h)
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177 self.assertEqual(self.wf.inv_dag, inv_dag)
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178 heads = set(self.wf.dag)
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179 self.assertEqual(heads, set.union(*self.wf.inv_dag.values()))
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180 tails = set(self.wf.inv_dag)
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181 self.assertEqual(tails, set.union(*self.wf.dag.values()))
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182 ids = self.wf.sorted_step_ids()
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183 self.assertEqual(set(ids), heads | tails)
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184 for h, tails in six.iteritems(self.wf.dag):
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185 for t in tails:
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186 self.assertLess(ids.index(h), ids.index(t))
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187
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188 def test_steps(self):
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189 steps = SAMPLE_WF_DICT['steps']
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190 for sid, s in six.iteritems(self.wf.steps):
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191 self.assertIsInstance(s, wrappers.Step)
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192 self.assertEqual(s.id, sid)
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193 self.assertIn(sid, steps)
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194 self.assertIs(s.parent, self.wf)
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195 self.assertEqual(self.wf.data_input_ids, set(['571', '572']))
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196 self.assertEqual(self.wf.tool_ids, set(['573']))
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197
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198 def test_taint(self):
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199 self.assertFalse(self.wf.is_modified)
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200 self.wf.steps['571'].tool_id = 'foo'
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201 self.assertTrue(self.wf.is_modified)
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202
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203 def test_input_map(self):
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204 class DummyLD(object):
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205 SRC = 'ld'
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206
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207 def __init__(self, id_):
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208 self.id = id_
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209
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210 label = 'Input Dataset'
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211 self.assertEqual(self.wf.input_labels, set([label]))
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212 input_map = self.wf.convert_input_map(
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213 {label: [DummyLD('a'), DummyLD('b')]})
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214 # {'571': {'id': 'a', 'src': 'ld'}, '572': {'id': 'b', 'src': 'ld'}}
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215 # OR
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216 # {'571': {'id': 'b', 'src': 'ld'}, '572': {'id': 'a', 'src': 'ld'}}
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217 self.assertEqual(set(input_map), set(['571', '572']))
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218 for d in six.itervalues(input_map):
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219 self.assertEqual(set(d), set(['id', 'src']))
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220 self.assertEqual(d['src'], 'ld')
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221 self.assertIn(d['id'], 'ab')
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222
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223
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224 @test_util.skip_unless_galaxy()
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225 class GalaxyObjectsTestBase(unittest.TestCase):
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226
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227 def setUp(self):
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228 galaxy_key = os.environ['BIOBLEND_GALAXY_API_KEY']
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229 galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
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230 self.gi = galaxy_instance.GalaxyInstance(galaxy_url, galaxy_key)
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231
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232
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233 class TestGalaxyInstance(GalaxyObjectsTestBase):
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234
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235 def test_library(self):
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236 name = 'test_%s' % uuid.uuid4().hex
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237 description, synopsis = 'D', 'S'
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238 lib = self.gi.libraries.create(
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239 name, description=description, synopsis=synopsis)
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240 self.assertEqual(lib.name, name)
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241 self.assertEqual(lib.description, description)
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242 self.assertEqual(lib.synopsis, synopsis)
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243 self.assertEqual(len(lib.content_infos), 1) # root folder
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244 self.assertEqual(len(lib.folder_ids), 1)
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245 self.assertEqual(len(lib.dataset_ids), 0)
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246 self.assertIn(lib.id, [_.id for _ in self.gi.libraries.list()])
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247 lib.delete()
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248 self.assertFalse(lib.is_mapped)
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249
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250 def test_workflow_from_str(self):
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251 with open(SAMPLE_FN) as f:
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252 wf = self.gi.workflows.import_new(f.read())
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253 self._check_and_del_workflow(wf)
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254
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255 def test_workflow_collections_from_str(self):
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256 with open(SAMPLE_WF_COLL_FN) as f:
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257 wf = self.gi.workflows.import_new(f.read())
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258 self._check_and_del_workflow(wf)
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259
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260 def test_workflow_from_dict(self):
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261 with open(SAMPLE_FN) as f:
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262 wf = self.gi.workflows.import_new(json.load(f))
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263 self._check_and_del_workflow(wf)
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264
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265 def test_workflow_publish_from_dict(self):
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266 with open(SAMPLE_FN) as f:
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267 wf = self.gi.workflows.import_new(json.load(f), publish=True)
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268 self._check_and_del_workflow(wf, check_is_public=True)
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269
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270 def test_workflow_missing_tools(self):
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271 with open(SAMPLE_FN) as f:
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272 wf_dump = json.load(f)
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273 wf_info = self.gi.gi.workflows.import_workflow_dict(wf_dump)
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274 wf_dict = self.gi.gi.workflows.show_workflow(wf_info['id'])
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275 for id_, step in six.iteritems(wf_dict['steps']):
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276 if step['type'] == 'tool':
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277 for k in 'tool_inputs', 'tool_version':
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278 wf_dict['steps'][id_][k] = None
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279 wf = wrappers.Workflow(wf_dict, gi=self.gi)
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280 self.assertFalse(wf.is_runnable)
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281 self.assertRaises(RuntimeError, wf.run)
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282 wf.delete()
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283
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284 def test_workflow_export(self):
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285 with open(SAMPLE_FN) as f:
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286 wf1 = self.gi.workflows.import_new(f.read())
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287 wf2 = self.gi.workflows.import_new(wf1.export())
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288 self.assertNotEqual(wf1.id, wf2.id)
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289 for wf in wf1, wf2:
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290 self._check_and_del_workflow(wf)
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291
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292 def _check_and_del_workflow(self, wf, check_is_public=False):
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293 # Galaxy appends additional text to imported workflow names
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294 self.assertTrue(wf.name.startswith('paste_columns'))
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295 self.assertEqual(len(wf.steps), 3)
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296 for step_id, step in six.iteritems(wf.steps):
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297 self.assertIsInstance(step, wrappers.Step)
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298 self.assertEqual(step_id, step.id)
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299 self.assertIsInstance(step.tool_inputs, dict)
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300 if step.type == 'tool':
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301 self.assertIsNotNone(step.tool_id)
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302 self.assertIsNotNone(step.tool_version)
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303 self.assertIsInstance(step.input_steps, dict)
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304 elif step.type in ('data_collection_input', 'data_input'):
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305 self.assertIsNone(step.tool_id)
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306 self.assertIsNone(step.tool_version)
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307 self.assertEqual(step.input_steps, {})
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308 wf_ids = set(_.id for _ in self.gi.workflows.list())
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309 self.assertIn(wf.id, wf_ids)
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310 if check_is_public:
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311 self.assertTrue(wf.published)
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312 wf.delete()
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313
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314 # not very accurate:
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315 # * we can't publish a wf from the API
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316 # * we can't directly get another user's wf
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317 def test_workflow_from_shared(self):
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318 all_prevs = dict(
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319 (_.id, _) for _ in self.gi.workflows.get_previews(published=True)
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320 )
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321 pub_only_ids = set(all_prevs).difference(
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322 _.id for _ in self.gi.workflows.get_previews())
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323 if pub_only_ids:
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324 wf_id = pub_only_ids.pop()
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325 imported = self.gi.workflows.import_shared(wf_id)
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326 self.assertIsInstance(imported, wrappers.Workflow)
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327 imported.delete()
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328 else:
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329 self.skipTest('no published workflows, manually publish a workflow to run this test')
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330
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331 def test_get_libraries(self):
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332 self._test_multi_get('library')
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333
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334 def test_get_histories(self):
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335 self._test_multi_get('history')
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336
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337 def test_get_workflows(self):
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338 self._test_multi_get('workflow')
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339
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340 def _normalized_functions(self, obj_type):
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341 if obj_type == 'library':
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342 create = self.gi.libraries.create
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343 get_objs = self.gi.libraries.list
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344 get_prevs = self.gi.libraries.get_previews
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345 del_kwargs = {}
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346 elif obj_type == 'history':
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347 create = self.gi.histories.create
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348 get_objs = self.gi.histories.list
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349 get_prevs = self.gi.histories.get_previews
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350 del_kwargs = {'purge': True}
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351 elif obj_type == 'workflow':
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352 def create(name):
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353 with open(SAMPLE_FN) as f:
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354 d = json.load(f)
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355 d['name'] = name
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356 return self.gi.workflows.import_new(d)
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357
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358 get_objs = self.gi.workflows.list
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359 get_prevs = self.gi.workflows.get_previews
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360 del_kwargs = {}
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361 return create, get_objs, get_prevs, del_kwargs
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362
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363 def _test_multi_get(self, obj_type):
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364 create, get_objs, get_prevs, del_kwargs = self._normalized_functions(
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365 obj_type)
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366
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367 def ids(seq):
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368 return set(_.id for _ in seq)
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369
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370 names = ['test_%s' % uuid.uuid4().hex for _ in range(2)]
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371 objs = []
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372 try:
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373 objs = [create(_) for _ in names]
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374 self.assertLessEqual(ids(objs), ids(get_objs()))
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diff changeset
375 if obj_type != 'workflow':
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diff changeset
376 filtered = get_objs(name=names[0])
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377 self.assertEqual(len(filtered), 1)
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378 self.assertEqual(filtered[0].id, objs[0].id)
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379 del_id = objs[-1].id
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diff changeset
380 objs.pop().delete(**del_kwargs)
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diff changeset
381 self.assertIn(del_id, ids(get_prevs(deleted=True)))
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diff changeset
382 else:
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diff changeset
383 # Galaxy appends info strings to imported workflow names
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diff changeset
384 prev = get_prevs()[0]
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diff changeset
385 filtered = get_objs(name=prev.name)
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diff changeset
386 self.assertEqual(len(filtered), 1)
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387 self.assertEqual(filtered[0].id, prev.id)
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diff changeset
388 finally:
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389 for o in objs:
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390 o.delete(**del_kwargs)
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391
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392 def test_delete_libraries_by_name(self):
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393 self._test_delete_by_name('library')
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394
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395 def test_delete_histories_by_name(self):
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396 self._test_delete_by_name('history')
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397
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398 def test_delete_workflows_by_name(self):
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399 self._test_delete_by_name('workflow')
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400
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diff changeset
401 def _test_delete_by_name(self, obj_type):
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diff changeset
402 create, _, get_prevs, del_kwargs = self._normalized_functions(
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403 obj_type)
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404 name = 'test_%s' % uuid.uuid4().hex
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parents:
diff changeset
405 objs = [create(name) for _ in range(2)] # noqa: F812
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406 final_name = objs[0].name
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parents:
diff changeset
407 prevs = [_ for _ in get_prevs(name=final_name) if not _.deleted]
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parents:
diff changeset
408 self.assertEqual(len(prevs), len(objs))
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409 del_kwargs['name'] = final_name
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parents:
diff changeset
410 objs[0].gi_module.delete(**del_kwargs)
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parents:
diff changeset
411 prevs = [_ for _ in get_prevs(name=final_name) if not _.deleted]
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diff changeset
412 self.assertEqual(len(prevs), 0)
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413
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414
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diff changeset
415 class TestLibrary(GalaxyObjectsTestBase):
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diff changeset
416 # just something that can be expected to be always up
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417 DS_URL = 'https://tools.ietf.org/rfc/rfc1866.txt'
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418
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419 def setUp(self):
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420 super(TestLibrary, self).setUp()
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parents:
diff changeset
421 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex)
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diff changeset
422
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diff changeset
423 def tearDown(self):
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parents:
diff changeset
424 self.lib.delete()
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diff changeset
425
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diff changeset
426 def test_root_folder(self):
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parents:
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427 r = self.lib.root_folder
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diff changeset
428 self.assertIsNone(r.parent)
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429
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diff changeset
430 def test_folder(self):
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diff changeset
431 name, desc = 'test_%s' % uuid.uuid4().hex, 'D'
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diff changeset
432 folder = self.lib.create_folder(name, description=desc)
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parents:
diff changeset
433 self.assertEqual(folder.name, name)
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parents:
diff changeset
434 self.assertEqual(folder.description, desc)
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diff changeset
435 self.assertIs(folder.container, self.lib)
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parents:
diff changeset
436 self.assertEqual(folder.parent.id, self.lib.root_folder.id)
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parents:
diff changeset
437 self.assertEqual(len(self.lib.content_infos), 2)
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parents:
diff changeset
438 self.assertEqual(len(self.lib.folder_ids), 2)
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parents:
diff changeset
439 self.assertIn(folder.id, self.lib.folder_ids)
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parents:
diff changeset
440 retrieved = self.lib.get_folder(folder.id)
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parents:
diff changeset
441 self.assertEqual(folder.id, retrieved.id)
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diff changeset
442
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diff changeset
443 def _check_datasets(self, dss):
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parents:
diff changeset
444 self.assertEqual(len(dss), len(self.lib.dataset_ids))
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parents:
diff changeset
445 self.assertEqual(set(_.id for _ in dss), set(self.lib.dataset_ids))
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parents:
diff changeset
446 for ds in dss:
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parents:
diff changeset
447 self.assertIs(ds.container, self.lib)
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diff changeset
448
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parents:
diff changeset
449 def test_dataset(self):
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parents:
diff changeset
450 folder = self.lib.create_folder('test_%s' % uuid.uuid4().hex)
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parents:
diff changeset
451 ds = self.lib.upload_data(FOO_DATA, folder=folder)
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parents:
diff changeset
452 self.assertEqual(len(self.lib.content_infos), 3)
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parents:
diff changeset
453 self.assertEqual(len(self.lib.folder_ids), 2)
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parents:
diff changeset
454 self._check_datasets([ds])
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parents:
diff changeset
455
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parents:
diff changeset
456 def test_dataset_from_url(self):
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shellac
parents:
diff changeset
457 if is_reachable(self.DS_URL):
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parents:
diff changeset
458 ds = self.lib.upload_from_url(self.DS_URL)
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parents:
diff changeset
459 self._check_datasets([ds])
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parents:
diff changeset
460 else:
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parents:
diff changeset
461 self.skipTest('%s not reachable' % self.DS_URL)
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parents:
diff changeset
462
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parents:
diff changeset
463 def test_dataset_from_local(self):
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shellac
parents:
diff changeset
464 with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f:
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parents:
diff changeset
465 f.write(FOO_DATA)
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parents:
diff changeset
466 f.flush()
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parents:
diff changeset
467 ds = self.lib.upload_from_local(f.name)
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shellac
parents:
diff changeset
468 self._check_datasets([ds])
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parents:
diff changeset
469
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parents:
diff changeset
470 def test_datasets_from_fs(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
471 bnames = ['f%d.txt' % i for i in range(2)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
472 dss, fnames = upload_from_fs(self.lib, bnames)
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shellac
parents:
diff changeset
473 self._check_datasets(dss)
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shellac
parents:
diff changeset
474 dss, fnames = upload_from_fs(
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shellac
parents:
diff changeset
475 self.lib, bnames, link_data_only='link_to_files')
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shellac
parents:
diff changeset
476 for ds, fn in zip(dss, fnames):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
477 self.assertEqual(ds.file_name, fn)
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shellac
parents:
diff changeset
478
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
479 def test_copy_from_dataset(self):
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shellac
parents:
diff changeset
480 hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex)
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shellac
parents:
diff changeset
481 try:
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parents:
diff changeset
482 hda = hist.paste_content(FOO_DATA)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
483 ds = self.lib.copy_from_dataset(hda)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
484 finally:
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parents:
diff changeset
485 hist.delete(purge=True)
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shellac
parents:
diff changeset
486 self._check_datasets([ds])
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shellac
parents:
diff changeset
487
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
488 def test_get_dataset(self):
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shellac
parents:
diff changeset
489 ds = self.lib.upload_data(FOO_DATA)
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shellac
parents:
diff changeset
490 retrieved = self.lib.get_dataset(ds.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
491 self.assertEqual(ds.id, retrieved.id)
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shellac
parents:
diff changeset
492
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parents:
diff changeset
493 def test_get_datasets(self):
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shellac
parents:
diff changeset
494 bnames = ['f%d.txt' % _ for _ in range(2)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
495 dss, _ = upload_from_fs(self.lib, bnames)
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shellac
parents:
diff changeset
496 retrieved = self.lib.get_datasets()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
497 self.assertEqual(len(dss), len(retrieved))
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diff changeset
498 self.assertEqual(set(_.id for _ in dss), set(_.id for _ in retrieved))
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499 name = '/%s' % bnames[0]
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diff changeset
500 selected = self.lib.get_datasets(name=name)
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501 self.assertEqual(len(selected), 1)
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502 self.assertEqual(selected[0].name, bnames[0])
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503
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504
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505 class TestLDContents(GalaxyObjectsTestBase):
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506
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507 def setUp(self):
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508 super(TestLDContents, self).setUp()
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509 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex)
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510 self.ds = self.lib.upload_data(FOO_DATA)
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511 self.ds.wait()
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512
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513 def tearDown(self):
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514 self.lib.delete()
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515
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516 def test_dataset_get_stream(self):
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517 for idx, c in enumerate(self.ds.get_stream(chunk_size=1)):
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518 self.assertEqual(six.b(FOO_DATA[idx]), c)
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519
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520 def test_dataset_peek(self):
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521 fetched_data = self.ds.peek(chunk_size=4)
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522 self.assertEqual(six.b(FOO_DATA[0:4]), fetched_data)
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523
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524 def test_dataset_download(self):
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525 with tempfile.TemporaryFile() as f:
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526 self.ds.download(f)
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527 f.seek(0)
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528 self.assertEqual(six.b(FOO_DATA), f.read())
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529
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530 def test_dataset_get_contents(self):
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531 self.assertEqual(six.b(FOO_DATA), self.ds.get_contents())
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532
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533 def test_dataset_delete(self):
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534 self.ds.delete()
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diff changeset
535 # Cannot test this yet because the 'deleted' attribute is not exported
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diff changeset
536 # by the API at the moment
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diff changeset
537 # self.assertTrue(self.ds.deleted)
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538
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diff changeset
539 @test_util.skip_unless_galaxy('release_17.09')
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540 def test_dataset_update(self):
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diff changeset
541 new_name = 'test_%s' % uuid.uuid4().hex
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542 new_misc_info = 'Annotation for %s' % new_name
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543 new_genome_build = 'hg19'
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544 updated_ldda = self.ds.update(name=new_name, misc_info=new_misc_info, genome_build=new_genome_build)
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545 self.assertEqual(self.ds.id, updated_ldda.id)
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546 self.assertEqual(self.ds.name, new_name)
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547 self.assertEqual(self.ds.misc_info, new_misc_info)
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548 self.assertEqual(self.ds.genome_build, new_genome_build)
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549
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550
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551 class TestHistory(GalaxyObjectsTestBase):
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552
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553 def setUp(self):
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554 super(TestHistory, self).setUp()
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diff changeset
555 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex)
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parents:
diff changeset
556
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diff changeset
557 def tearDown(self):
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diff changeset
558 self.hist.delete(purge=True)
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559
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diff changeset
560 def test_create_delete(self):
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diff changeset
561 name = 'test_%s' % uuid.uuid4().hex
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562 hist = self.gi.histories.create(name)
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563 self.assertEqual(hist.name, name)
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diff changeset
564 hist_id = hist.id
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diff changeset
565 self.assertIn(hist_id, [_.id for _ in self.gi.histories.list()])
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diff changeset
566 hist.delete(purge=True)
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diff changeset
567 self.assertFalse(hist.is_mapped)
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diff changeset
568 try:
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diff changeset
569 h = self.gi.histories.get(hist_id)
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diff changeset
570 self.assertTrue(h.deleted)
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diff changeset
571 except ConnectionError:
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diff changeset
572 # Galaxy up to release_2015.01.13 gives a ConnectionError
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parents:
diff changeset
573 pass
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diff changeset
574
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diff changeset
575 def _check_dataset(self, hda):
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diff changeset
576 self.assertIsInstance(hda, wrappers.HistoryDatasetAssociation)
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diff changeset
577 self.assertIs(hda.container, self.hist)
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diff changeset
578 self.assertEqual(len(self.hist.dataset_ids), 1)
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diff changeset
579 self.assertEqual(self.hist.dataset_ids[0], hda.id)
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diff changeset
580
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diff changeset
581 def test_import_dataset(self):
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parents:
diff changeset
582 lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex)
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parents:
diff changeset
583 lds = lib.upload_data(FOO_DATA)
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parents:
diff changeset
584 self.assertEqual(len(self.hist.dataset_ids), 0)
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parents:
diff changeset
585 hda = self.hist.import_dataset(lds)
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parents:
diff changeset
586 lib.delete()
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diff changeset
587 self._check_dataset(hda)
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diff changeset
588
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parents:
diff changeset
589 def test_upload_file(self):
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parents:
diff changeset
590 with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f:
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parents:
diff changeset
591 f.write(FOO_DATA)
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parents:
diff changeset
592 f.flush()
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parents:
diff changeset
593 hda = self.hist.upload_file(f.name)
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parents:
diff changeset
594 self._check_dataset(hda)
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diff changeset
595
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parents:
diff changeset
596 def test_paste_content(self):
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parents:
diff changeset
597 hda = self.hist.paste_content(FOO_DATA)
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parents:
diff changeset
598 self._check_dataset(hda)
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diff changeset
599
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parents:
diff changeset
600 def test_get_dataset(self):
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parents:
diff changeset
601 hda = self.hist.paste_content(FOO_DATA)
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shellac
parents:
diff changeset
602 retrieved = self.hist.get_dataset(hda.id)
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shellac
parents:
diff changeset
603 self.assertEqual(hda.id, retrieved.id)
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parents:
diff changeset
604
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parents:
diff changeset
605 def test_get_datasets(self):
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shellac
parents:
diff changeset
606 bnames = ['f%d.txt' % _ for _ in range(2)]
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shellac
parents:
diff changeset
607 lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 lds = upload_from_fs(lib, bnames)[0]
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shellac
parents:
diff changeset
609 hdas = [self.hist.import_dataset(_) for _ in lds]
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parents:
diff changeset
610 lib.delete()
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parents:
diff changeset
611 retrieved = self.hist.get_datasets()
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parents:
diff changeset
612 self.assertEqual(len(hdas), len(retrieved))
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parents:
diff changeset
613 self.assertEqual(set(_.id for _ in hdas), set(_.id for _ in retrieved))
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parents:
diff changeset
614 selected = self.hist.get_datasets(name=bnames[0])
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parents:
diff changeset
615 self.assertEqual(len(selected), 1)
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parents:
diff changeset
616 self.assertEqual(selected[0].name, bnames[0])
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parents:
diff changeset
617
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parents:
diff changeset
618 def test_export_and_download(self):
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shellac
parents:
diff changeset
619 jeha_id = self.hist.export(wait=True, maxwait=60)
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parents:
diff changeset
620 self.assertTrue(jeha_id)
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parents:
diff changeset
621 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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parents:
diff changeset
622 temp_fn = os.path.join(tempdir, 'export.tar.gz')
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parents:
diff changeset
623 try:
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diff changeset
624 with open(temp_fn, 'wb') as fo:
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diff changeset
625 self.hist.download(jeha_id, fo)
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parents:
diff changeset
626 self.assertTrue(tarfile.is_tarfile(temp_fn))
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parents:
diff changeset
627 finally:
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628 shutil.rmtree(tempdir)
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diff changeset
629
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parents:
diff changeset
630 def test_update(self):
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parents:
diff changeset
631 new_name = 'test_%s' % uuid.uuid4().hex
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parents:
diff changeset
632 new_annotation = 'Annotation for %s' % new_name
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parents:
diff changeset
633 new_tags = ['tag1', 'tag2']
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parents:
diff changeset
634 updated_hist = self.hist.update(name=new_name, annotation=new_annotation, tags=new_tags)
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parents:
diff changeset
635 self.assertEqual(self.hist.id, updated_hist.id)
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parents:
diff changeset
636 self.assertEqual(self.hist.name, new_name)
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parents:
diff changeset
637 self.assertEqual(self.hist.annotation, new_annotation)
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parents:
diff changeset
638 self.assertEqual(self.hist.tags, new_tags)
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parents:
diff changeset
639 updated_hist = self.hist.update(published=True)
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parents:
diff changeset
640 self.assertEqual(self.hist.id, updated_hist.id)
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diff changeset
641 self.assertTrue(self.hist.published)
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642
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diff changeset
643 def test_create_dataset_collection(self):
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644 self._create_collection_description()
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645 hdca = self.hist.create_dataset_collection(self.collection_description)
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parents:
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646 self.assertIsInstance(hdca, wrappers.HistoryDatasetCollectionAssociation)
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647 self.assertEqual(hdca.collection_type, 'list')
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648 self.assertIs(hdca.container, self.hist)
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649 self.assertEqual(len(hdca.elements), 2)
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650 self.assertEqual(self.dataset1.id, hdca.elements[0]['object']['id'])
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651 self.assertEqual(self.dataset2.id, hdca.elements[1]['object']['id'])
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652
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653 def test_delete_dataset_collection(self):
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654 self._create_collection_description()
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655 hdca = self.hist.create_dataset_collection(self.collection_description)
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parents:
diff changeset
656 hdca.delete()
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diff changeset
657 self.assertTrue(hdca.deleted)
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diff changeset
658
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diff changeset
659 def _create_collection_description(self):
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parents:
diff changeset
660 self.dataset1 = self.hist.paste_content(FOO_DATA)
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parents:
diff changeset
661 self.dataset2 = self.hist.paste_content(FOO_DATA_2)
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parents:
diff changeset
662 self.collection_description = dataset_collections.CollectionDescription(
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parents:
diff changeset
663 name="MyDatasetList",
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parents:
diff changeset
664 elements=[
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parents:
diff changeset
665 dataset_collections.HistoryDatasetElement(name="sample1", id=self.dataset1.id),
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parents:
diff changeset
666 dataset_collections.HistoryDatasetElement(name="sample2", id=self.dataset2.id),
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parents:
diff changeset
667 ]
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parents:
diff changeset
668 )
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parents:
diff changeset
669
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parents:
diff changeset
670
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diff changeset
671 class TestHDAContents(GalaxyObjectsTestBase):
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672
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673 def setUp(self):
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parents:
diff changeset
674 super(TestHDAContents, self).setUp()
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parents:
diff changeset
675 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex)
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parents:
diff changeset
676 self.ds = self.hist.paste_content(FOO_DATA)
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parents:
diff changeset
677 self.ds.wait()
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diff changeset
678
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diff changeset
679 def tearDown(self):
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diff changeset
680 self.hist.delete(purge=True)
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parents:
diff changeset
681
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parents:
diff changeset
682 def test_dataset_get_stream(self):
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parents:
diff changeset
683 for idx, c in enumerate(self.ds.get_stream(chunk_size=1)):
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parents:
diff changeset
684 self.assertEqual(six.b(FOO_DATA[idx]), c)
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parents:
diff changeset
685
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parents:
diff changeset
686 def test_dataset_peek(self):
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parents:
diff changeset
687 fetched_data = self.ds.peek(chunk_size=4)
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parents:
diff changeset
688 self.assertEqual(six.b(FOO_DATA[0:4]), fetched_data)
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parents:
diff changeset
689
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parents:
diff changeset
690 def test_dataset_download(self):
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parents:
diff changeset
691 with tempfile.TemporaryFile() as f:
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parents:
diff changeset
692 self.ds.download(f)
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parents:
diff changeset
693 f.seek(0)
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parents:
diff changeset
694 self.assertEqual(six.b(FOO_DATA), f.read())
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parents:
diff changeset
695
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parents:
diff changeset
696 def test_dataset_get_contents(self):
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parents:
diff changeset
697 self.assertEqual(six.b(FOO_DATA), self.ds.get_contents())
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parents:
diff changeset
698
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parents:
diff changeset
699 def test_dataset_update(self):
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parents:
diff changeset
700 new_name = 'test_%s' % uuid.uuid4().hex
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parents:
diff changeset
701 new_annotation = 'Annotation for %s' % new_name
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parents:
diff changeset
702 new_genome_build = 'hg19'
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shellac
parents:
diff changeset
703 updated_hda = self.ds.update(name=new_name, annotation=new_annotation, genome_build=new_genome_build)
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parents:
diff changeset
704 self.assertEqual(self.ds.id, updated_hda.id)
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shellac
parents:
diff changeset
705 self.assertEqual(self.ds.name, new_name)
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parents:
diff changeset
706 self.assertEqual(self.ds.annotation, new_annotation)
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parents:
diff changeset
707 self.assertEqual(self.ds.genome_build, new_genome_build)
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parents:
diff changeset
708
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parents:
diff changeset
709 def test_dataset_delete(self):
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shellac
parents:
diff changeset
710 self.ds.delete()
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parents:
diff changeset
711 self.assertTrue(self.ds.deleted)
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shellac
parents:
diff changeset
712 self.assertFalse(self.ds.purged)
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shellac
parents:
diff changeset
713
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shellac
parents:
diff changeset
714 @test_util.skip_unless_galaxy("release_17.05")
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shellac
parents:
diff changeset
715 def test_dataset_purge(self):
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shellac
parents:
diff changeset
716 self.ds.delete(purge=True)
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shellac
parents:
diff changeset
717 # Galaxy from release_15.03 to release_17.01 wrongly reports ds.deleted as False, see https://github.com/galaxyproject/galaxy/issues/3548
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shellac
parents:
diff changeset
718 self.assertTrue(self.ds.deleted)
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shellac
parents:
diff changeset
719 self.assertTrue(self.ds.purged)
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shellac
parents:
diff changeset
720
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shellac
parents:
diff changeset
721
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shellac
parents:
diff changeset
722 class TestRunWorkflow(GalaxyObjectsTestBase):
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shellac
parents:
diff changeset
723
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 def setUp(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725 super(TestRunWorkflow, self).setUp()
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shellac
parents:
diff changeset
726 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 with open(SAMPLE_FN) as f:
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shellac
parents:
diff changeset
728 self.wf = self.gi.workflows.import_new(f.read())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 self.contents = ['one\ntwo\n', '1\n2\n']
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shellac
parents:
diff changeset
730 self.inputs = [self.lib.upload_data(_) for _ in self.contents]
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shellac
parents:
diff changeset
731
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shellac
parents:
diff changeset
732 def tearDown(self):
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shellac
parents:
diff changeset
733 self.wf.delete()
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shellac
parents:
diff changeset
734 self.lib.delete()
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parents:
diff changeset
735
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shellac
parents:
diff changeset
736 def _test(self, existing_hist=False, params=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 hist_name = 'test_%s' % uuid.uuid4().hex
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shellac
parents:
diff changeset
738 if existing_hist:
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shellac
parents:
diff changeset
739 hist = self.gi.histories.create(hist_name)
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shellac
parents:
diff changeset
740 else:
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shellac
parents:
diff changeset
741 hist = hist_name
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shellac
parents:
diff changeset
742 if params:
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shellac
parents:
diff changeset
743 params = {'Paste1': {'delimiter': 'U'}}
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shellac
parents:
diff changeset
744 sep = '_' # 'U' maps to '_' in the paste tool
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745 else:
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746 params = None
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747 sep = '\t' # default
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748 input_map = {'Input 1': self.inputs[0], 'Input 2': self.inputs[1]}
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749 sys.stderr.write(os.linesep)
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750 outputs, out_hist = self.wf.run(
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751 input_map, hist, params=params, wait=True, polling_interval=1)
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752 self.assertEqual(len(outputs), 1)
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753 out_ds = outputs[0]
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754 self.assertIn(out_ds.id, out_hist.dataset_ids)
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755 res = out_ds.get_contents()
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parents:
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756 exp_rows = zip(*(_.splitlines() for _ in self.contents))
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757 exp_res = six.b("\n".join(sep.join(t) for t in exp_rows) + "\n")
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758 self.assertEqual(res, exp_res)
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759 if existing_hist:
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760 self.assertEqual(out_hist.id, hist.id)
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761 out_hist.delete(purge=True)
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762
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763 def test_existing_history(self):
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764 self._test(existing_hist=True)
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765
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766 def test_new_history(self):
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767 self._test(existing_hist=False)
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768
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769 def test_params(self):
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770 self._test(params=True)
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771
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772
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773 class TestRunDatasetCollectionWorkflow(GalaxyObjectsTestBase):
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774
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775 def setUp(self):
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776 super(TestRunDatasetCollectionWorkflow, self).setUp()
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777 with open(SAMPLE_WF_COLL_FN) as f:
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778 self.wf = self.gi.workflows.import_new(f.read())
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779 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex)
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780
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781 def tearDown(self):
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782 self.wf.delete()
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783 self.hist.delete(purge=True)
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784
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785 def test_run_workflow_with_dataset_collection(self):
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parents:
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786 dataset1 = self.hist.paste_content(FOO_DATA)
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parents:
diff changeset
787 dataset2 = self.hist.paste_content(FOO_DATA_2)
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parents:
diff changeset
788 collection_description = dataset_collections.CollectionDescription(
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parents:
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789 name="MyDatasetList",
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790 elements=[
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791 dataset_collections.HistoryDatasetElement(name="sample1", id=dataset1.id),
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792 dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2.id),
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793 ]
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794 )
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795 dataset_collection = self.hist.create_dataset_collection(collection_description)
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796 input_map = {"Input Dataset Collection": dataset_collection,
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797 "Input 2": dataset1}
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798 outputs, out_hist = self.wf.run(input_map, self.hist, wait=True)
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799 self.assertEqual(len(outputs), 1)
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800 out_hdca = outputs[0]
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801 self.assertIsInstance(out_hdca, wrappers.HistoryDatasetCollectionAssociation)
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802 self.assertEqual(out_hdca.collection_type, 'list')
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803 self.assertEqual(len(out_hdca.elements), 2)
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804 self.assertEqual(out_hist.id, self.hist.id)
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diff changeset
805
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806
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807 class TestJob(GalaxyObjectsTestBase):
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808
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809 def setUp(self):
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diff changeset
810 super(TestJob, self).setUp()
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diff changeset
811
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812 def test_get(self):
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parents:
diff changeset
813 job_prevs = self.gi.jobs.get_previews()
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parents:
diff changeset
814 if len(job_prevs) > 0:
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parents:
diff changeset
815 job_prev = job_prevs[0]
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parents:
diff changeset
816 self.assertIsInstance(job_prev, wrappers.JobPreview)
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parents:
diff changeset
817 job = self.gi.jobs.get(job_prev.id)
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parents:
diff changeset
818 self.assertIsInstance(job, wrappers.Job)
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parents:
diff changeset
819 self.assertEqual(job.id, job_prev.id)
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parents:
diff changeset
820 for job in self.gi.jobs.list():
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parents:
diff changeset
821 self.assertIsInstance(job, wrappers.Job)
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parents:
diff changeset
822
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parents:
diff changeset
823
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parents:
diff changeset
824 def suite():
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parents:
diff changeset
825 loader = unittest.TestLoader()
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parents:
diff changeset
826 s = unittest.TestSuite()
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parents:
diff changeset
827 s.addTests([loader.loadTestsFromTestCase(c) for c in (
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parents:
diff changeset
828 TestWrapper,
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parents:
diff changeset
829 TestWorkflow,
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parents:
diff changeset
830 TestGalaxyInstance,
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diff changeset
831 TestLibrary,
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parents:
diff changeset
832 TestLDContents,
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parents:
diff changeset
833 TestHistory,
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diff changeset
834 TestHDAContents,
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parents:
diff changeset
835 TestRunWorkflow,
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diff changeset
836 )])
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parents:
diff changeset
837 return s
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838
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diff changeset
839
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840 if __name__ == '__main__':
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diff changeset
841 # By default, run all tests. To run specific tests, do the following:
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parents:
diff changeset
842 # python -m unittest <module>.<class>.<test_method>
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diff changeset
843 tests = suite()
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parents:
diff changeset
844 RUNNER = unittest.TextTestRunner(verbosity=2)
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parents:
diff changeset
845 RUNNER.run(tests)