Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyHistories.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 """ |
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3 import os |
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4 import shutil |
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5 import tarfile |
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6 import tempfile |
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7 |
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8 import bioblend.galaxy |
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9 from . import GalaxyTestBase, test_util |
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10 |
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11 |
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12 class TestGalaxyHistories(GalaxyTestBase.GalaxyTestBase): |
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13 |
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14 def setUp(self): |
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15 super().setUp() |
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16 self.default_history_name = "buildbot - automated test" |
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17 self.history = self.gi.histories.create_history(name=self.default_history_name) |
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18 |
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19 def test_create_history(self): |
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20 history_name = "another buildbot - automated test" |
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21 new_history = self.gi.histories.create_history(name=history_name) |
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22 self.assertIsNotNone(new_history['id']) |
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23 self.assertEqual(new_history['name'], history_name) |
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24 self.assertIsNotNone(new_history['url']) |
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25 |
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26 def test_update_history(self): |
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27 new_name = 'buildbot - automated test renamed' |
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28 new_annotation = 'Annotation for %s' % new_name |
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29 new_tags = ['tag1', 'tag2'] |
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30 updated_hist = self.gi.histories.update_history(self.history['id'], name=new_name, annotation=new_annotation, tags=new_tags) |
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31 if 'id' not in updated_hist: |
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32 updated_hist = self.gi.histories.show_history(self.history['id']) |
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33 self.assertEqual(self.history['id'], updated_hist['id']) |
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34 self.assertEqual(updated_hist['name'], new_name) |
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35 self.assertEqual(updated_hist['annotation'], new_annotation) |
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36 self.assertEqual(updated_hist['tags'], new_tags) |
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37 |
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38 def test_publish_history(self): |
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39 # Verify that searching for published histories does not return the test history |
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40 published_histories = self.gi.histories.get_histories(published=True) |
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41 self.assertFalse(any(h['id'] == self.history['id'] for h in published_histories)) |
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42 updated_hist = self.gi.histories.update_history(self.history['id'], published=True) |
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43 if 'id' not in updated_hist: |
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44 updated_hist = self.gi.histories.show_history(self.history['id']) |
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45 self.assertEqual(self.history['id'], updated_hist['id']) |
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46 self.assertTrue(updated_hist['published']) |
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47 # Verify that searching for published histories now returns the test history |
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48 published_histories = self.gi.histories.get_histories(published=True) |
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49 self.assertTrue(any(h['id'] == self.history['id'] for h in published_histories)) |
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50 # Verify that get_published_histories as an anonymous user also returns the test history |
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51 anonymous_gi = bioblend.galaxy.GalaxyInstance(url=self.gi.base_url, key=None) |
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52 published_histories = anonymous_gi.histories.get_published_histories() |
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53 self.assertTrue(any(h['id'] == self.history['id'] for h in published_histories)) |
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54 history_from_slug = anonymous_gi.histories.get_published_histories(slug=updated_hist['slug']) |
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55 self.assertTrue(len(history_from_slug) == 1) |
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56 self.assertEqual(self.history['id'], history_from_slug[0]['id']) |
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57 |
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58 def test_get_histories(self): |
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59 # Make sure there's at least one value - the one we created |
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60 all_histories = self.gi.histories.get_histories() |
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61 self.assertGreater(len(all_histories), 0) |
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62 |
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63 # Check whether name is correct, when searched by id |
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64 new_history = self.gi.histories.get_histories(history_id=self.history['id'])[0] |
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65 self.assertEqual(new_history['name'], self.default_history_name) |
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66 |
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67 # Check whether id is present, when searched by name |
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68 histories = self.gi.histories.get_histories(name=self.default_history_name) |
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69 self.assertTrue(any(h['id'] == self.history['id'] for h in histories)) |
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70 |
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71 # TODO: check whether deleted history is returned correctly |
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72 # At the moment, get_histories() returns only not-deleted histories |
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73 # and get_histories(deleted=True) returns only deleted histories, |
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74 # so they are not comparable. |
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75 # In the future, according to https://trello.com/c/MoilsmVv/1673-api-incoherent-and-buggy-indexing-of-deleted-entities , |
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76 # get_histories() will return both not-deleted and deleted histories |
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77 # and we can uncomment the following test. |
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78 # deleted_history = self.gi.histories.get_histories(deleted=True) |
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79 # self.assertGreaterEqual(len(all_histories), len(deleted_history)) |
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80 |
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81 def test_show_history(self): |
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82 history_data = self.gi.histories.show_history(self.history['id']) |
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83 self.assertEqual(self.history['id'], history_data['id']) |
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84 self.assertEqual(self.history['name'], history_data['name']) |
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85 self.assertEqual('new', history_data['state']) |
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86 |
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87 def test_show_history_with_contents(self): |
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88 history_id = self.history["id"] |
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89 contents = self.gi.histories.show_history(history_id, contents=True) |
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90 # Empty history has no datasets, content length should be 0 |
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91 self.assertEqual(len(contents), 0) |
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92 self._test_dataset(history_id) |
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93 contents = self.gi.histories.show_history(history_id, contents=True) |
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94 # history has 1 dataset, content length should be 1 |
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95 self.assertEqual(len(contents), 1) |
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96 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset']) |
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97 # filtering for dataset, content length should still be 1 |
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98 self.assertEqual(len(contents), 1) |
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99 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset_collection']) |
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100 # filtering for dataset collection but there's no collection in the history |
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101 self.assertEqual(len(contents), 0) |
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102 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset', 'dataset_collection']) |
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103 self.assertEqual(len(contents), 1) |
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104 |
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105 def test_create_history_tag(self): |
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106 new_tag = 'tag1' |
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107 self.gi.histories.create_history_tag(self.history['id'], new_tag) |
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108 updated_hist = self.gi.histories.show_history(self.history['id']) |
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109 self.assertEqual(self.history['id'], updated_hist['id']) |
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110 self.assertIn(new_tag, updated_hist['tags']) |
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111 |
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112 def test_show_dataset(self): |
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113 history_id = self.history["id"] |
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114 dataset1_id = self._test_dataset(history_id) |
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115 dataset = self.gi.histories.show_dataset(history_id, dataset1_id) |
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116 for key in ["name", "hid", "id", "deleted", "history_id", "visible"]: |
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117 self.assertIn(key, dataset) |
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118 self.assertEqual(dataset["history_id"], history_id) |
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119 self.assertEqual(dataset["hid"], 1) |
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120 self.assertEqual(dataset["id"], dataset1_id) |
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121 self.assertEqual(dataset["deleted"], False) |
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122 self.assertEqual(dataset["visible"], True) |
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123 |
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124 def test_show_dataset_provenance(self): |
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125 history_id = self.history["id"] |
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126 dataset1_id = self._test_dataset(history_id) |
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127 prov = self.gi.histories.show_dataset_provenance(history_id, dataset1_id) |
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128 for key in ["id", "job_id", "parameters", "stderr", "stdout", "tool_id"]: |
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129 self.assertIn(key, prov) |
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130 |
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131 def test_delete_dataset(self): |
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132 history_id = self.history["id"] |
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133 dataset1_id = self._test_dataset(history_id) |
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134 self.gi.histories.delete_dataset(history_id, dataset1_id) |
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135 dataset = self.gi.histories.show_dataset(history_id, dataset1_id) |
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136 self.assertTrue(dataset["deleted"]) |
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137 self.assertFalse(dataset['purged']) |
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138 |
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139 def test_purge_dataset(self): |
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140 history_id = self.history["id"] |
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141 dataset1_id = self._test_dataset(history_id) |
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142 self.gi.histories.delete_dataset(history_id, dataset1_id, purge=True) |
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143 dataset = self.gi.histories.show_dataset(history_id, dataset1_id) |
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144 self.assertTrue(dataset["deleted"]) |
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145 self.assertTrue(dataset['purged']) |
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146 |
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147 def test_update_dataset(self): |
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148 history_id = self.history["id"] |
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149 dataset1_id = self._test_dataset(history_id) |
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150 updated_dataset = self.gi.histories.update_dataset(history_id, dataset1_id, visible=False) |
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151 if 'id' not in updated_dataset: |
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152 updated_dataset = self.gi.histories.show_dataset(history_id, dataset1_id) |
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153 self.assertFalse(updated_dataset["visible"]) |
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154 |
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155 def test_upload_dataset_from_library(self): |
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156 pass |
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157 |
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158 # download_dataset() is already tested in TestGalaxyDatasets |
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159 |
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160 def test_delete_history(self): |
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161 result = self.gi.histories.delete_history(self.history['id']) |
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162 self.assertTrue(result['deleted']) |
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163 |
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164 all_histories = self.gi.histories.get_histories() |
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165 self.assertTrue(not any(d['id'] == self.history['id'] for d in all_histories)) |
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166 |
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167 def test_undelete_history(self): |
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168 self.gi.histories.delete_history(self.history['id']) |
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169 self.gi.histories.undelete_history(self.history['id']) |
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170 all_histories = self.gi.histories.get_histories() |
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171 self.assertTrue(any(d['id'] == self.history['id'] for d in all_histories)) |
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172 |
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173 def test_get_status(self): |
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174 state = self.gi.histories.get_status(self.history['id']) |
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175 self.assertEqual('new', state['state']) |
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176 |
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177 def test_get_most_recently_used_history(self): |
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178 most_recently_used_history = self.gi.histories.get_most_recently_used_history() |
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179 # if the user has been created via the API, it does not have |
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180 # a session, therefore no history |
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181 if most_recently_used_history is not None: |
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182 self.assertIsNotNone(most_recently_used_history['id']) |
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183 self.assertIsNotNone(most_recently_used_history['name']) |
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184 self.assertIsNotNone(most_recently_used_history['state']) |
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185 |
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186 def test_download_history(self): |
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187 jeha_id = self.gi.histories.export_history( |
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188 self.history['id'], wait=True, maxwait=60) |
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189 self.assertTrue(jeha_id) |
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190 tempdir = tempfile.mkdtemp(prefix='bioblend_test_') |
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191 temp_fn = os.path.join(tempdir, 'export.tar.gz') |
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192 try: |
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193 with open(temp_fn, 'wb') as fo: |
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194 self.gi.histories.download_history(self.history['id'], jeha_id, |
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195 fo) |
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196 self.assertTrue(tarfile.is_tarfile(temp_fn)) |
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197 finally: |
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198 shutil.rmtree(tempdir) |
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199 |
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200 def test_import_history(self): |
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201 path = test_util.get_abspath(os.path.join('data', 'Galaxy-History-test.tar.gz')) |
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202 self.gi.histories.import_history(file_path=path) |
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203 |
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204 def test_copy_dataset(self): |
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205 history_id = self.history["id"] |
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206 contents = "1\t2\t3" |
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207 dataset1_id = self._test_dataset(history_id, contents=contents) |
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208 self.history_id2 = self.gi.histories.create_history('TestCopyDataset')['id'] |
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209 copied_dataset = self.gi.histories.copy_dataset(self.history_id2, dataset1_id) |
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210 expected_contents = ("\n".join(contents.splitlines()) + "\n").encode() |
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211 self._wait_and_verify_dataset(copied_dataset['id'], expected_contents) |
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212 self.gi.histories.delete_history(self.history_id2, purge=True) |
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213 |
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214 @test_util.skip_unless_galaxy('release_20.09') |
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215 def test_update_dataset_datatype(self): |
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216 history_id = self.history["id"] |
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217 dataset1_id = self._test_dataset(history_id) |
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218 self._wait_and_verify_dataset(dataset1_id, b'1\t2\t3\n') |
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219 original_hda = self.gi.datasets.show_dataset(dataset1_id) |
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220 assert original_hda['extension'] == 'bed' |
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221 self.gi.histories.update_dataset(history_id, dataset1_id, datatype='tabular') |
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222 updated_hda = self.gi.datasets.show_dataset(dataset1_id) |
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223 assert updated_hda['extension'] == 'tabular' |
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224 |
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225 def tearDown(self): |
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226 self.gi.histories.delete_history(self.history['id'], purge=True) |