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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyHistories.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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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 from . import GalaxyTestBase, test_util
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9
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10
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11 class TestGalaxyHistories(GalaxyTestBase.GalaxyTestBase):
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12
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13 def setUp(self):
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14 super().setUp()
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15 self.default_history_name = "buildbot - automated test"
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16 self.history = self.gi.histories.create_history(name=self.default_history_name)
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17
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18 def test_create_history(self):
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19 history_name = "another buildbot - automated test"
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20 new_history = self.gi.histories.create_history(name=history_name)
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21 self.assertIsNotNone(new_history['id'])
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22 self.assertEqual(new_history['name'], history_name)
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23 self.assertIsNotNone(new_history['url'])
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24
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25 def test_update_history(self):
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26 new_name = 'buildbot - automated test renamed'
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27 new_annotation = 'Annotation for %s' % new_name
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28 new_tags = ['tag1', 'tag2']
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29 updated_hist = self.gi.histories.update_history(self.history['id'], name=new_name, annotation=new_annotation, tags=new_tags)
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30 if 'id' not in updated_hist:
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31 updated_hist = self.gi.histories.show_history(self.history['id'])
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32 self.assertEqual(self.history['id'], updated_hist['id'])
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33 self.assertEqual(updated_hist['name'], new_name)
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34 self.assertEqual(updated_hist['annotation'], new_annotation)
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35 self.assertEqual(updated_hist['tags'], new_tags)
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36 updated_hist = self.gi.histories.update_history(self.history['id'], published=True)
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37 if 'id' not in updated_hist:
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38 updated_hist = self.gi.histories.show_history(self.history['id'])
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39 self.assertEqual(self.history['id'], updated_hist['id'])
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40 self.assertTrue(updated_hist['published'])
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41
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42 def test_get_histories(self):
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43 # Make sure there's at least one value - the one we created
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44 all_histories = self.gi.histories.get_histories()
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45 self.assertGreater(len(all_histories), 0)
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46
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47 # Check whether name is correct, when searched by id
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48 new_history = self.gi.histories.get_histories(history_id=self.history['id'])[0]
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49 self.assertEqual(new_history['name'], self.default_history_name)
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50
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51 # Check whether id is present, when searched by name
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52 new_history = self.gi.histories.get_histories(name=self.default_history_name)
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53 self.assertTrue(any(d['id'] == self.history['id'] for d in new_history))
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54
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55 # TODO: check whether deleted history is returned correctly
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56 # At the moment, get_histories() returns only not-deleted histories
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57 # and get_histories(deleted=True) returns only deleted histories,
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58 # so they are not comparable.
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59 # In the future, according to https://trello.com/c/MoilsmVv/1673-api-incoherent-and-buggy-indexing-of-deleted-entities ,
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60 # get_histories() will return both not-deleted and deleted histories
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61 # and we can uncomment the following test.
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62 # deleted_history = self.gi.histories.get_histories(deleted=True)
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63 # self.assertGreaterEqual(len(all_histories), len(deleted_history))
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64
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65 def test_show_history(self):
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66 history_data = self.gi.histories.show_history(self.history['id'])
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67 self.assertEqual(self.history['id'], history_data['id'])
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68 self.assertEqual(self.history['name'], history_data['name'])
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69 self.assertEqual('new', history_data['state'])
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70
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71 def test_show_history_with_contents(self):
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72 history_id = self.history["id"]
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73 contents = self.gi.histories.show_history(history_id, contents=True)
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74 # Empty history has no datasets, content length should be 0
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75 self.assertEqual(len(contents), 0)
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76 self._test_dataset(history_id)
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77 contents = self.gi.histories.show_history(history_id, contents=True)
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78 # history has 1 dataset, content length should be 1
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79 self.assertEqual(len(contents), 1)
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80 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset'])
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81 # filtering for dataset, content length should still be 1
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82 self.assertEqual(len(contents), 1)
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83 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset_collection'])
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84 # filtering for dataset collection but there's no collection in the history
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85 self.assertEqual(len(contents), 0)
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86 contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset', 'dataset_collection'])
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87 self.assertEqual(len(contents), 1)
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88
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89 def test_create_history_tag(self):
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90 new_tag = 'tag1'
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91 self.gi.histories.create_history_tag(self.history['id'], new_tag)
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92 updated_hist = self.gi.histories.show_history(self.history['id'])
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93 self.assertEqual(self.history['id'], updated_hist['id'])
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94 self.assertIn(new_tag, updated_hist['tags'])
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95
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96 def test_show_dataset(self):
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97 history_id = self.history["id"]
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98 dataset1_id = self._test_dataset(history_id)
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99 dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
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100 for key in ["name", "hid", "id", "deleted", "history_id", "visible"]:
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101 self.assertIn(key, dataset)
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102 self.assertEqual(dataset["history_id"], history_id)
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103 self.assertEqual(dataset["hid"], 1)
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104 self.assertEqual(dataset["id"], dataset1_id)
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105 self.assertEqual(dataset["deleted"], False)
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106 self.assertEqual(dataset["visible"], True)
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107
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108 def test_show_dataset_provenance(self):
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109 history_id = self.history["id"]
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110 dataset1_id = self._test_dataset(history_id)
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111 prov = self.gi.histories.show_dataset_provenance(history_id, dataset1_id)
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112 for key in ["id", "job_id", "parameters", "stderr", "stdout", "tool_id"]:
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113 self.assertIn(key, prov)
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114
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115 def test_delete_dataset(self):
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116 history_id = self.history["id"]
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117 dataset1_id = self._test_dataset(history_id)
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118 self.gi.histories.delete_dataset(history_id, dataset1_id)
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119 dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
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120 self.assertTrue(dataset["deleted"])
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121 self.assertFalse(dataset['purged'])
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122
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123 def test_purge_dataset(self):
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124 history_id = self.history["id"]
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125 dataset1_id = self._test_dataset(history_id)
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126 self.gi.histories.delete_dataset(history_id, dataset1_id, purge=True)
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127 dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
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128 self.assertTrue(dataset["deleted"])
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129 self.assertTrue(dataset['purged'])
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130
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131 def test_update_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 updated_dataset = self.gi.histories.update_dataset(history_id, dataset1_id, visible=False)
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135 if 'id' not in updated_dataset:
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136 updated_dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
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137 self.assertFalse(updated_dataset["visible"])
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138
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139 def test_upload_dataset_from_library(self):
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140 pass
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141
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142 # download_dataset() is already tested in TestGalaxyDatasets
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143
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144 def test_delete_history(self):
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145 result = self.gi.histories.delete_history(self.history['id'])
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146 self.assertTrue(result['deleted'])
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147
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148 all_histories = self.gi.histories.get_histories()
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149 self.assertTrue(not any(d['id'] == self.history['id'] for d in all_histories))
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150
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151 def test_undelete_history(self):
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152 self.gi.histories.delete_history(self.history['id'])
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153 self.gi.histories.undelete_history(self.history['id'])
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154 all_histories = self.gi.histories.get_histories()
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155 self.assertTrue(any(d['id'] == self.history['id'] for d in all_histories))
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156
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157 def test_get_status(self):
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158 state = self.gi.histories.get_status(self.history['id'])
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159 self.assertEqual('new', state['state'])
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160
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161 def test_get_most_recently_used_history(self):
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162 most_recently_used_history = self.gi.histories.get_most_recently_used_history()
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163 # if the user has been created via the API, it does not have
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164 # a session, therefore no history
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165 if most_recently_used_history is not None:
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166 self.assertIsNotNone(most_recently_used_history['id'])
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167 self.assertIsNotNone(most_recently_used_history['name'])
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168 self.assertIsNotNone(most_recently_used_history['state'])
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169
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170 def test_download_history(self):
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171 jeha_id = self.gi.histories.export_history(
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172 self.history['id'], wait=True, maxwait=60)
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173 self.assertTrue(jeha_id)
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174 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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175 temp_fn = os.path.join(tempdir, 'export.tar.gz')
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176 try:
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177 with open(temp_fn, 'wb') as fo:
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178 self.gi.histories.download_history(self.history['id'], jeha_id,
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179 fo)
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180 self.assertTrue(tarfile.is_tarfile(temp_fn))
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181 finally:
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182 shutil.rmtree(tempdir)
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183
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184 def test_import_history(self):
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185 path = test_util.get_abspath(os.path.join('data', 'Galaxy-History-test.tar.gz'))
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186 self.gi.histories.import_history(file_path=path)
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187
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188 def test_copy_dataset(self):
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189 history_id = self.history["id"]
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190 contents = "1\t2\t3"
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191 dataset1_id = self._test_dataset(history_id, contents=contents)
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192 self.history_id2 = self.gi.histories.create_history('TestCopyDataset')['id']
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193 copied_dataset = self.gi.histories.copy_dataset(self.history_id2, dataset1_id)
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194 expected_contents = ("\n".join(contents.splitlines()) + "\n").encode()
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195 self._wait_and_verify_dataset(copied_dataset['id'], expected_contents)
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196 self.gi.histories.delete_history(self.history_id2, purge=True)
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197
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198 def tearDown(self):
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199 self.gi.histories.delete_history(self.history['id'], purge=True)