Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyLibraries.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyLibraries.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,104 @@ +import os +import shutil +import tempfile + +from . import GalaxyTestBase, test_util + +FOO_DATA = 'foo\nbar\n' + + +class TestGalaxyLibraries(GalaxyTestBase.GalaxyTestBase): + + def setUp(self): + super(TestGalaxyLibraries, self).setUp() + self.name = 'automated test library' + self.library = self.gi.libraries.create_library(self.name, description='automated test', synopsis='automated test synopsis') + + def tearDown(self): + self.gi.libraries.delete_library(self.library['id']) + + def test_create_library(self): + self.assertEqual(self.library['name'], self.name) + self.assertIsNotNone(self.library['id']) + + def test_get_libraries(self): + library_data = self.gi.libraries.get_libraries(library_id=self.library['id'])[0] + self.assertTrue(library_data['name'] == self.name) + deleted_name = 'deleted test library' + deleted_library = self.gi.libraries.create_library(deleted_name, description='a deleted library', synopsis='automated test synopsis') + self.gi.libraries.delete_library(deleted_library['id']) + deleted_library_data = self.gi.libraries.get_libraries(library_id=deleted_library['id'], deleted=True)[0] + self.assertTrue(deleted_library_data['name'] == deleted_name) + all_non_deleted_libraries = self.gi.libraries.get_libraries(deleted=False) + self.assertTrue(any(l['id'] == self.library['id'] for l in all_non_deleted_libraries)) + self.assertFalse(any(l['id'] == deleted_library['id'] for l in all_non_deleted_libraries)) + all_deleted_libraries = self.gi.libraries.get_libraries(deleted=True) + self.assertFalse(any(l['id'] == self.library['id'] for l in all_deleted_libraries)) + self.assertTrue(any(l['id'] == deleted_library['id'] for l in all_deleted_libraries)) + all_libraries = self.gi.libraries.get_libraries(deleted=None) + self.assertTrue(any(l['id'] == self.library['id'] for l in all_libraries)) + self.assertTrue(any(l['id'] == deleted_library['id'] for l in all_libraries)) + + def test_show_library(self): + library_data = self.gi.libraries.show_library(self.library['id']) + self.assertEqual(self.library['id'], library_data['id']) + self.assertEqual(self.library['name'], library_data['name']) + + def test_upload_file_from_url(self): + pass + + def test_upload_file_contents(self): + self.gi.libraries.upload_file_contents(self.library['id'], FOO_DATA) + + def test_upload_file_from_local_path(self): + with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f: + f.write(FOO_DATA) + f.flush() + self.gi.libraries.upload_file_from_local_path(self.library['id'], f.name) + + def test_upload_file_from_server(self): + pass + + def test_upload_from_galaxy_filesystem(self): + bnames = ['f%d.txt' % i for i in range(2)] + tempdir = tempfile.mkdtemp(prefix='bioblend_test_') + try: + fnames = [os.path.join(tempdir, _) for _ in bnames] + for fn in fnames: + with open(fn, 'w') as f: + f.write(FOO_DATA) + filesystem_paths = '\n'.join(fnames) + ret = self.gi.libraries.upload_from_galaxy_filesystem(self.library['id'], filesystem_paths) + for dataset_dict in ret: + dataset = self.gi.libraries.wait_for_dataset(self.library['id'], dataset_dict['id']) + self.assertEqual(dataset['state'], 'ok') + ret = self.gi.libraries.upload_from_galaxy_filesystem(self.library['id'], filesystem_paths, link_data_only='link_to_files') + for dataset_dict in ret: + dataset = self.gi.libraries.wait_for_dataset(self.library['id'], dataset_dict['id']) + self.assertEqual(dataset['state'], 'ok') + finally: + shutil.rmtree(tempdir) + + def test_copy_from_dataset(self): + history = self.gi.histories.create_history() + dataset_id = self._test_dataset(history['id']) + self.gi.libraries.copy_from_dataset(self.library['id'], dataset_id, message='Copied from dataset') + + @test_util.skip_unless_galaxy('release_17.09') + def test_update_dataset(self): + library_id = self.library["id"] + dataset1 = self.gi.libraries.upload_file_contents(library_id, FOO_DATA) + updated_dataset = self.gi.libraries.update_library_dataset(dataset1[0]['id'], name='Modified name', misc_info='Modified the name succesfully') + self.assertEqual(updated_dataset["name"], 'Modified name') + self.assertEqual(updated_dataset["misc_info"], 'Modified the name succesfully') + + @test_util.skip_unless_galaxy('release_14.10') + def test_library_permissions(self): + current_user = self.gi.users.get_current_user() + user_id_list_new = [current_user['id']] + 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) + ret = self.gi.libraries.get_library_permissions(self.library['id']) + self.assertEqual(set(_[1] for _ in ret['access_library_role_list']), set(user_id_list_new)) + self.assertEqual(set(_[1] for _ in ret['modify_library_role_list']), set(user_id_list_new)) + self.assertEqual(set(_[1] for _ in ret['add_library_item_role_list']), set(user_id_list_new)) + self.assertEqual(set(_[1] for _ in ret['manage_library_role_list']), set(user_id_list_new))