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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyDatasetCollections.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 from bioblend.galaxy import dataset_collections
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2 from . import GalaxyTestBase
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3
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4
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5 class TestGalaxyDatasetCollections(GalaxyTestBase.GalaxyTestBase):
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6
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7 def test_create_list_in_history(self):
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8 history_id = self.gi.histories.create_history(name="TestDSListCreate")["id"]
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9 dataset1_id = self._test_dataset(history_id)
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10 dataset2_id = self._test_dataset(history_id)
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11 dataset3_id = self._test_dataset(history_id)
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12 collection_response = self.gi.histories.create_dataset_collection(
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13 history_id=history_id,
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14 collection_description=dataset_collections.CollectionDescription(
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15 name="MyDatasetList",
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16 elements=[
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17 dataset_collections.HistoryDatasetElement(name="sample1", id=dataset1_id),
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18 dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2_id),
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19 dataset_collections.HistoryDatasetElement(name="sample3", id=dataset3_id),
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20 ]
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21 )
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22 )
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23 self.assertEqual(collection_response["name"], "MyDatasetList")
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24 self.assertEqual(collection_response["collection_type"], "list")
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25 elements = collection_response["elements"]
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26 self.assertEqual(len(elements), 3)
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27 self.assertEqual(elements[0]["element_index"], 0)
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28 self.assertEqual(elements[0]["object"]["id"], dataset1_id)
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29 self.assertEqual(elements[1]["object"]["id"], dataset2_id)
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30 self.assertEqual(elements[2]["object"]["id"], dataset3_id)
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31 self.assertEqual(elements[2]["element_identifier"], "sample3")
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32
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33 def test_create_list_of_paired_datasets_in_history(self):
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34 history_id = self.gi.histories.create_history(name="TestDSListCreate")["id"]
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35 dataset1_id = self._test_dataset(history_id)
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36 dataset2_id = self._test_dataset(history_id)
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37 dataset3_id = self._test_dataset(history_id)
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38 dataset4_id = self._test_dataset(history_id)
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39 collection_response = self.gi.histories.create_dataset_collection(
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40 history_id=history_id,
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41 collection_description=dataset_collections.CollectionDescription(
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42 name="MyListOfPairedDatasets",
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43 type="list:paired",
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44 elements=[
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45 dataset_collections.CollectionElement(
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46 name="sample1",
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47 type="paired",
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48 elements=[
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49 dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
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50 dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
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51 ]
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52 ),
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53 dataset_collections.CollectionElement(
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54 name="sample2",
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55 type="paired",
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56 elements=[
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57 dataset_collections.HistoryDatasetElement(name="forward", id=dataset3_id),
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58 dataset_collections.HistoryDatasetElement(name="reverse", id=dataset4_id),
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59 ]
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60 ),
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61 ]
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62 )
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63 )
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64 self.assertEqual(collection_response["name"], "MyListOfPairedDatasets")
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65 self.assertEqual(collection_response["collection_type"], "list:paired")
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66 elements = collection_response["elements"]
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67 self.assertEqual(len(elements), 2)
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68 self.assertEqual(elements[0]["element_index"], 0)
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69 created_pair1 = elements[0]["object"]
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70 self.assertEqual(created_pair1["collection_type"], "paired")
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71 self.assertEqual(len(created_pair1["elements"]), 2)
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72 forward_element1 = created_pair1["elements"][0]
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73 self.assertEqual(forward_element1["element_identifier"], "forward")
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74 self.assertEqual(forward_element1["element_index"], 0)
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75 forward_dataset1 = forward_element1["object"]
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76 self.assertEqual(forward_dataset1["id"], dataset1_id)
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77
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78 self.assertEqual(elements[1]["element_index"], 1)
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79 created_pair2 = elements[1]["object"]
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80 self.assertEqual(created_pair2["collection_type"], "paired")
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81 self.assertEqual(len(created_pair2["elements"]), 2)
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82 reverse_element2 = created_pair2["elements"][1]
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83 reverse_dataset2 = reverse_element2["object"]
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84
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85 self.assertEqual(reverse_element2["element_identifier"], "reverse")
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86 self.assertEqual(reverse_element2["element_index"], 1)
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87 self.assertEqual(reverse_dataset2["id"], dataset4_id)
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88
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89 def test_collections_in_history_index(self):
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90 history_id = self.gi.histories.create_history(name="TestHistoryDSIndex")["id"]
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91 history_dataset_collection = self._create_pair_in_history(history_id)
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92 contents = self.gi.histories.show_history(history_id, contents=True)
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93 self.assertEqual(len(contents), 3)
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94 self.assertEqual(contents[2]["id"], history_dataset_collection["id"])
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95 self.assertEqual(contents[2]["name"], "MyTestPair")
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96 self.assertEqual(contents[2]["collection_type"], "paired")
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97
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98 def test_show_history_dataset_collection(self):
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99 history_id = self.gi.histories.create_history(name="TestHistoryDSIndexShow")["id"]
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100 history_dataset_collection = self._create_pair_in_history(history_id)
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101 show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
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102 for key in ["collection_type", "elements", "name", "deleted", "visible"]:
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103 self.assertIn(key, show_response)
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104 self.assertFalse(show_response["deleted"])
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105 self.assertTrue(show_response["visible"])
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106
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107 def test_delete_history_dataset_collection(self):
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108 history_id = self.gi.histories.create_history(name="TestHistoryDSDelete")["id"]
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109 history_dataset_collection = self._create_pair_in_history(history_id)
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110 self.gi.histories.delete_dataset_collection(history_id, history_dataset_collection["id"])
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111 show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
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112 self.assertTrue(show_response["deleted"])
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113
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114 def test_update_history_dataset_collection(self):
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115 history_id = self.gi.histories.create_history(name="TestHistoryDSDelete")["id"]
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116 history_dataset_collection = self._create_pair_in_history(history_id)
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117 self.gi.histories.update_dataset_collection(history_id, history_dataset_collection["id"], visible=False)
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118 show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
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119 self.assertFalse(show_response["visible"])
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120
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121 def _create_pair_in_history(self, history_id):
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122 dataset1_id = self._test_dataset(history_id)
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123 dataset2_id = self._test_dataset(history_id)
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124 collection_response = self.gi.histories.create_dataset_collection(
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125 history_id=history_id,
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126 collection_description=dataset_collections.CollectionDescription(
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127 name="MyTestPair",
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128 type="paired",
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129 elements=[
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130 dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
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131 dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
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132 ]
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133 )
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134 )
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135 return collection_response