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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyLibraries.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 import os
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2 import shutil
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3 import tempfile
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4
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5 from . import GalaxyTestBase, test_util
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6
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7 FOO_DATA = 'foo\nbar\n'
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8
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9
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10 class TestGalaxyLibraries(GalaxyTestBase.GalaxyTestBase):
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11
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12 def setUp(self):
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13 super().setUp()
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14 self.name = 'automated test library'
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15 self.library = self.gi.libraries.create_library(self.name, description='automated test', synopsis='automated test synopsis')
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16
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17 def tearDown(self):
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18 self.gi.libraries.delete_library(self.library['id'])
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19
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20 def test_create_library(self):
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21 self.assertEqual(self.library['name'], self.name)
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22 self.assertIsNotNone(self.library['id'])
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23
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24 def test_get_libraries(self):
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25 library_data = self.gi.libraries.get_libraries(library_id=self.library['id'])[0]
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26 self.assertTrue(library_data['name'] == self.name)
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27 deleted_name = 'deleted test library'
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28 deleted_library = self.gi.libraries.create_library(deleted_name, description='a deleted library', synopsis='automated test synopsis')
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29 self.gi.libraries.delete_library(deleted_library['id'])
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30 deleted_library_data = self.gi.libraries.get_libraries(library_id=deleted_library['id'], deleted=True)[0]
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31 self.assertTrue(deleted_library_data['name'] == deleted_name)
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32 all_non_deleted_libraries = self.gi.libraries.get_libraries(deleted=False)
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33 self.assertTrue(any(l['id'] == self.library['id'] for l in all_non_deleted_libraries))
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34 self.assertFalse(any(l['id'] == deleted_library['id'] for l in all_non_deleted_libraries))
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35 all_deleted_libraries = self.gi.libraries.get_libraries(deleted=True)
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36 self.assertFalse(any(l['id'] == self.library['id'] for l in all_deleted_libraries))
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37 self.assertTrue(any(l['id'] == deleted_library['id'] for l in all_deleted_libraries))
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38 all_libraries = self.gi.libraries.get_libraries(deleted=None)
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39 self.assertTrue(any(l['id'] == self.library['id'] for l in all_libraries))
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40 self.assertTrue(any(l['id'] == deleted_library['id'] for l in all_libraries))
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41
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42 def test_show_library(self):
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43 library_data = self.gi.libraries.show_library(self.library['id'])
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44 self.assertEqual(self.library['id'], library_data['id'])
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45 self.assertEqual(self.library['name'], library_data['name'])
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46
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47 def test_upload_file_from_url(self):
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48 self.gi.libraries.upload_file_from_url(self.library['id'], 'https://zenodo.org/record/582600/files/wildtype.fna?download=1')
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49
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50 def test_upload_file_contents(self):
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51 self.gi.libraries.upload_file_contents(self.library['id'], FOO_DATA)
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52
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53 def test_upload_file_from_local_path(self):
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54 with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f:
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55 f.write(FOO_DATA)
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56 f.flush()
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57 self.gi.libraries.upload_file_from_local_path(self.library['id'], f.name)
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58
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59 def test_upload_file_from_server(self):
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60 pass
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61
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62 def test_upload_from_galaxy_filesystem(self):
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63 bnames = ['f%d.txt' % i for i in range(2)]
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64 tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
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65 try:
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66 fnames = [os.path.join(tempdir, _) for _ in bnames]
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67 for fn in fnames:
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68 with open(fn, 'w') as f:
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69 f.write(FOO_DATA)
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70 filesystem_paths = '\n'.join(fnames)
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71 ret = self.gi.libraries.upload_from_galaxy_filesystem(self.library['id'], filesystem_paths)
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72 for dataset_dict in ret:
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73 dataset = self.gi.libraries.wait_for_dataset(self.library['id'], dataset_dict['id'])
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74 self.assertEqual(dataset['state'], 'ok')
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75 ret = self.gi.libraries.upload_from_galaxy_filesystem(self.library['id'], filesystem_paths, link_data_only='link_to_files')
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76 for dataset_dict in ret:
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77 dataset = self.gi.libraries.wait_for_dataset(self.library['id'], dataset_dict['id'])
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78 self.assertEqual(dataset['state'], 'ok')
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79 finally:
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80 shutil.rmtree(tempdir)
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81
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82 def test_copy_from_dataset(self):
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83 history = self.gi.histories.create_history()
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84 dataset_id = self._test_dataset(history['id'])
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85 self.gi.libraries.copy_from_dataset(self.library['id'], dataset_id, message='Copied from dataset')
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86
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87 def test_update_dataset(self):
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88 library_id = self.library["id"]
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89 dataset1 = self.gi.libraries.upload_file_contents(library_id, FOO_DATA)
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90 updated_dataset = self.gi.libraries.update_library_dataset(dataset1[0]['id'], name='Modified name', misc_info='Modified the name succesfully')
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91 self.assertEqual(updated_dataset["name"], 'Modified name')
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92 self.assertEqual(updated_dataset["misc_info"], 'Modified the name succesfully')
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93
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94 def test_library_permissions(self):
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95 current_user = self.gi.users.get_current_user()
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96 user_id_list_new = [current_user['id']]
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97 self.gi.libraries.set_library_permissions(self.library['id'], access_in=user_id_list_new, modify_in=user_id_list_new, add_in=user_id_list_new, manage_in=user_id_list_new)
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98 ret = self.gi.libraries.get_library_permissions(self.library['id'])
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99 self.assertEqual(set(_[1] for _ in ret['access_library_role_list']), set(user_id_list_new))
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100 self.assertEqual(set(_[1] for _ in ret['modify_library_role_list']), set(user_id_list_new))
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101 self.assertEqual(set(_[1] for _ in ret['add_library_item_role_list']), set(user_id_list_new))
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102 self.assertEqual(set(_[1] for _ in ret['manage_library_role_list']), set(user_id_list_new))
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103
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104 def test_dataset_permissions(self):
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105 current_user = self.gi.users.get_current_user()
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106 user_id_list_new = [current_user['id']]
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107 library_id = self.library["id"]
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108 dataset1 = self.gi.libraries.upload_file_contents(library_id, FOO_DATA)
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109 ret = self.gi.libraries.set_dataset_permissions(dataset1[0]['id'], access_in=user_id_list_new, modify_in=user_id_list_new, manage_in=user_id_list_new)
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110 self.assertEqual(set(_[1] for _ in ret['access_dataset_roles']), set(user_id_list_new))
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111 self.assertEqual(set(_[1] for _ in ret['modify_item_roles']), set(user_id_list_new))
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112 self.assertEqual(set(_[1] for _ in ret['manage_dataset_roles']), set(user_id_list_new))
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113 # test get_dataset_permissions
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114 ret_get = self.gi.libraries.get_dataset_permissions(dataset1[0]['id'])
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115 self.assertEqual(set(_[1] for _ in ret_get['access_dataset_roles']), set(user_id_list_new))
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116 self.assertEqual(set(_[1] for _ in ret_get['modify_item_roles']), set(user_id_list_new))
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117 self.assertEqual(set(_[1] for _ in ret_get['manage_dataset_roles']), set(user_id_list_new))
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118
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119 @test_util.skip_unless_galaxy('release_19.09')
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120 def test_upload_file_contents_with_tags(self):
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121 datasets = self.gi.libraries.upload_file_contents(self.library['id'], FOO_DATA, tags=["name:foobar", "barfoo"])
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122 dataset_show = self.gi.libraries.show_dataset(self.library['id'], datasets[0]['id'])
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123 self.assertEqual(dataset_show['tags'], 'name:foobar, barfoo')
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124
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125 @test_util.skip_unless_galaxy('release_19.09')
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126 def test_update_dataset_tags(self):
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127 datasets = self.gi.libraries.upload_file_contents(self.library['id'], FOO_DATA)
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128 dataset_show = self.gi.libraries.show_dataset(self.library['id'], datasets[0]['id'])
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129 self.assertEqual(dataset_show['tags'], "")
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130
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131 updated_dataset = self.gi.libraries.update_library_dataset(datasets[0]['id'], tags=["name:foobar", "barfoo"])
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132 dataset_show = self.gi.libraries.show_dataset(self.library['id'], updated_dataset['id'])
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133
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134 self.assertEqual(dataset_show['tags'], 'name:foobar, barfoo')