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add generic plugin tests, fix and refactor (#1980)
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| Original file line number | Diff line number | Diff line change |
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| """Plugin tests for the the generic assay plugin""" | ||
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| import os | ||
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| from copy import deepcopy | ||
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| from samplesheets.assayapps.generic.plugins import ( | ||
| DATA_COMMENT_PREFIX, | ||
| DATA_LINK_COMMENT, | ||
| MISC_FILES_COMMENT, | ||
| RESULTS_COMMENT, | ||
| ) | ||
| from samplesheets.assayapps.tests.base import AssayPluginTestBase | ||
| from samplesheets.models import ISA_META_ASSAY_PLUGIN | ||
| from samplesheets.rendering import SIMPLE_LINK_TEMPLATE | ||
| from samplesheets.views import MISC_FILES_COLL, RESULTS_COLL | ||
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| # Local constants | ||
| PLUGIN_NAME = 'samplesheets_assay_generic' | ||
| NONEXISTENT_COL = 'XXXNOTEXISTINGXXX' | ||
| FILE_NAME = 'file.txt' | ||
| FOLDER_COL = 'folder name' | ||
| FOLDER_VAL = 'alpha' | ||
| STRAT_COL = 'library strategy' | ||
| STRAT_VAL = 'RNA-seq' | ||
| CUSTOM_COLL = 'custom_coll' | ||
| RAW_DATA_COL = 'raw data file' | ||
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| class TestGenericAssayPlugin(AssayPluginTestBase): | ||
| """Tests for generic assay plugin""" | ||
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| plugin_name = PLUGIN_NAME | ||
| template_name = 'generic' | ||
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| def _get_row_path(self): | ||
| """Shortcut for plugin get_row_path() call with first assay row""" | ||
| return self.plugin.get_row_path( | ||
| self.assay_table['table_data'][0], | ||
| self.assay_table, | ||
| self.assay, | ||
| self.assay_path, | ||
| ) | ||
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| def _update_row(self): | ||
| """Shortcut for plugin update_row() with first assay row""" | ||
| return self.plugin.update_row( | ||
| self.assay_table['table_data'][0], self.assay_table, self.assay, 0 | ||
| ) | ||
|
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| def setUp(self): | ||
| super().setUp() | ||
| # Override plugin | ||
| self.assay.comments[ISA_META_ASSAY_PLUGIN] = PLUGIN_NAME | ||
| self.assay.save() | ||
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| def test_get_row_path(self): | ||
| """Test get_row_path() with no assay comments""" | ||
| row_path = self._get_row_path() | ||
| self.assertIsNone(row_path) | ||
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| def test_get_row_path_set(self): | ||
| """Test get_row_path() with column set""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = FOLDER_COL | ||
| self.assertEqual( | ||
| self.assay_table['table_data'][0][47]['value'], FOLDER_VAL | ||
| ) | ||
| row_path = self._get_row_path() | ||
| self.assertEqual(row_path, os.path.join(self.assay_path, FOLDER_VAL)) | ||
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| def test_get_row_path_empty_value(self): | ||
| """Test get_row_path() with empty column value""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = FOLDER_COL | ||
| self.assay_table['table_data'][0][47]['value'] = '' | ||
| row_path = self._get_row_path() | ||
| self.assertIsNone(row_path) | ||
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| def test_get_row_path_set_nonexistent(self): | ||
| """Test get_row_path() with nonexistent column""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = NONEXISTENT_COL | ||
| row_path = self._get_row_path() | ||
| self.assertIsNone(row_path) | ||
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| def test_get_row_path_set_multiple(self): | ||
| """Test get_row_path() with multiple columns""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '1'] = STRAT_COL | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '2'] = FOLDER_COL | ||
| self.assertEqual( | ||
| self.assay_table['table_data'][0][34]['value'], STRAT_VAL | ||
| ) | ||
| self.assertEqual( | ||
| self.assay_table['table_data'][0][47]['value'], FOLDER_VAL | ||
| ) | ||
| row_path = self._get_row_path() | ||
| self.assertEqual( | ||
| row_path, os.path.join(self.assay_path, STRAT_VAL, FOLDER_VAL) | ||
| ) | ||
|
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| def test_get_row_path_set_multiple_nonexistent(self): | ||
| """Test get_row_path() with multiple columns and nonexistent column""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '1'] = FOLDER_COL | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '2'] = NONEXISTENT_COL | ||
| row_path = self._get_row_path() | ||
| self.assertEqual(row_path, os.path.join(self.assay_path, FOLDER_VAL)) | ||
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| def test_get_row_path_set_multiple_empty_value(self): | ||
| """Test get_row_path() with multiple columns and empty value""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '1'] = FOLDER_COL | ||
| self.assay.comments[DATA_COMMENT_PREFIX + '2'] = STRAT_COL | ||
| self.assay_table['table_data'][0][47]['value'] = '' | ||
| row_path = self._get_row_path() | ||
| self.assertEqual(row_path, os.path.join(self.assay_path, STRAT_VAL)) | ||
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| def test_get_row_path_duplicate_column_names(self): | ||
| """Test get_row_path() with duplicate column names""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = 'perform date' | ||
| self.assay_table['table_data'][0][20]['value'] = '2024-10-01' | ||
| self.assay_table['table_data'][0][45]['value'] = '2024-10-02' | ||
| self.assay_table['table_data'][0][56]['value'] = '2024-10-03' | ||
| row_path = self._get_row_path() | ||
| # NOTE: The last one gets returned, is this correct? | ||
| self.assertEqual(row_path, os.path.join(self.assay_path, '2024-10-03')) | ||
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| def test_update_row(self): | ||
| """Test update_row() with no comments set""" | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_results(self): | ||
| """Test update_row() with results comment""" | ||
| self.assay.comments[RESULTS_COMMENT] = FOLDER_COL | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[47]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=FOLDER_VAL, | ||
| url=self.base_url + os.path.join('/', RESULTS_COLL, FOLDER_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_results_multiple(self): | ||
| """Test update_row() with multiple results comments""" | ||
| self.assay.comments[RESULTS_COMMENT] = ';'.join([FOLDER_COL, STRAT_COL]) | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[34]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=STRAT_VAL, | ||
| url=self.base_url + os.path.join('/', RESULTS_COLL, STRAT_VAL), | ||
| ) | ||
| row_ex[47]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=FOLDER_VAL, | ||
| url=self.base_url + os.path.join('/', RESULTS_COLL, FOLDER_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_misc(self): | ||
| """Test update_row() with misc files comment""" | ||
| self.assay.comments[MISC_FILES_COMMENT] = FOLDER_COL | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[47]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=FOLDER_VAL, | ||
| url=self.base_url + os.path.join('/', MISC_FILES_COLL, FOLDER_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_misc_multiple(self): | ||
| """Test update_row() with multiple misc files comments""" | ||
| self.assay.comments[MISC_FILES_COMMENT] = ';'.join( | ||
| [FOLDER_COL, STRAT_COL] | ||
| ) | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[34]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=STRAT_VAL, | ||
| url=self.base_url + os.path.join('/', MISC_FILES_COLL, STRAT_VAL), | ||
| ) | ||
| row_ex[47]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=FOLDER_VAL, | ||
| url=self.base_url + os.path.join('/', MISC_FILES_COLL, FOLDER_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_data_link_row_data(self): | ||
| """Test update_row() with data link comment and row data column""" | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = FOLDER_COL | ||
| self.assay.comments[DATA_LINK_COMMENT] = STRAT_COL | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[34]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=STRAT_VAL, | ||
| url=self.base_url + os.path.join('/', FOLDER_VAL, STRAT_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
|
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| def test_update_row_data_link_irods_paths(self): | ||
| """Test update_row() with data link comment and irods path""" | ||
| # NOTE: We'll still set the row data column to ensure it is not picked | ||
| self.assay.comments[DATA_COMMENT_PREFIX] = FOLDER_COL | ||
| self.assay.comments[DATA_LINK_COMMENT] = STRAT_COL | ||
| coll_path = os.path.join(self.assay_path, CUSTOM_COLL) | ||
| self.assay_table['irods_paths'] = [{'path': coll_path}] | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[34]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=STRAT_VAL, | ||
| url=self.base_url + os.path.join('/', CUSTOM_COLL, STRAT_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
|
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| def test_update_row_multiple_on_same_col(self): | ||
| """Test update_row() with multiple comments on same column""" | ||
| self.assay.comments[RESULTS_COMMENT] = FOLDER_COL | ||
| self.assay.comments[MISC_FILES_COMMENT] = FOLDER_COL | ||
| self.assay.comments[DATA_LINK_COMMENT] = FOLDER_COL | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| # First one should be picked | ||
| row_ex[47]['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=FOLDER_VAL, | ||
| url=self.base_url + os.path.join('/', RESULTS_COLL, FOLDER_VAL), | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_results_file(self): | ||
| """Test update_row() with results comment set on file column""" | ||
| self.assay.comments[RESULTS_COMMENT] = RAW_DATA_COL | ||
| self.assay_table['table_data'][0][57]['value'] = FILE_NAME | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row_ex[57]['link'] = self.base_url + os.path.join( | ||
| '/', RESULTS_COLL, FILE_NAME | ||
| ) | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_results_file_unset(self): | ||
| """Test update_row() with results comment set on unset file column""" | ||
| self.assay.comments[RESULTS_COMMENT] = RAW_DATA_COL | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| row = self._update_row() | ||
| # Row should not be changed | ||
| self.assertEqual(row, row_ex) | ||
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| def test_update_row_results_file_existing_link(self): | ||
| """Test update_row() with existing link value""" | ||
| self.assay.comments[RESULTS_COMMENT] = RAW_DATA_COL | ||
| self.assay_table['table_data'][0][57]['value'] = ( | ||
| SIMPLE_LINK_TEMPLATE.format(label=FILE_NAME, url='https://foo.bar/') | ||
| ) | ||
| row_ex = deepcopy(self.assay_table['table_data'][0]) | ||
| # Row should not be changed | ||
| row = self._update_row() | ||
| self.assertEqual(row, row_ex) |
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