def test_delete_sample_or_column(self): st = SampleTemplate(1) # Delete a sample template column job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'season_environment' }) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('season_environment', st.categories()) # Delete a sample template sample - need to add one # sample that we will remove npt.assert_warns( QiitaDBWarning, st.extend, pd.DataFrame.from_dict({'Sample1': { 'taxon_id': '9606' }}, orient='index', dtype=str)) self.assertIn('1.Sample1', st.keys()) job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'samples', 'name': '1.Sample1' }) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('1.Sample1', st.keys()) # Delete a prep template column pt = PrepTemplate(1) job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'PrepTemplate', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'target_subfragment' }) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('target_subfragment', pt.categories()) # Delete a prep template sample metadata = pd.DataFrame.from_dict( { '1.SKB8.640193': { 'barcode': 'GTCCGCAAGTTA', 'primer': 'GTGCCAGCMGCCGCGGTAA' }, '1.SKD8.640184': { 'barcode': 'CGTAGAGCTCTC', 'primer': 'GTGCCAGCMGCCGCGGTAA' } }, orient='index', dtype=str) pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata, Study(1), "16S") job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'PrepTemplate', 'obj_id': pt.id, 'sample_or_col': 'samples', 'name': '1.SKD8.640184' }) private_task(job.id) self.assertNotIn('1.SKD8.640184', pt.keys()) # Test exceptions job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'UnknownClass', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'column' }) private_task(job.id) self.assertEqual(job.status, 'error') self.assertIn( 'Unknown value "UnknownClass". Choose between ' '"SampleTemplate" and "PrepTemplate"', job.log.msg) job = self._create_job( 'delete_sample_or_column', { 'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'unknown', 'name': 'column' }) private_task(job.id) self.assertEqual(job.status, 'error') self.assertIn( 'Unknown value "unknown". Choose between "samples" ' 'and "columns"', job.log.msg)
def test_delete_sample_or_column(self): st = SampleTemplate(1) # Delete a sample template column obs = delete_sample_or_column(SampleTemplate, 1, "columns", "season_environment") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('season_environment', st.categories()) # Delete a sample template sample - need to add one sample that we # will remove npt.assert_warns( QiitaDBWarning, st.extend, pd.DataFrame.from_dict({'Sample1': { 'taxon_id': '9606' }}, orient='index', dtype=str)) self.assertIn('1.Sample1', st.keys()) obs = delete_sample_or_column(SampleTemplate, 1, "samples", "1.Sample1") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('1.Sample1', st.keys()) # Delete a prep template column pt = PrepTemplate(2) obs = delete_sample_or_column(PrepTemplate, 2, "columns", "target_subfragment") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('target_subfragment', pt.categories()) # Delte a prep template sample metadata = pd.DataFrame.from_dict( { '1.SKB8.640193': { 'barcode': 'GTCCGCAAGTTA', 'primer': 'GTGCCAGCMGCCGCGGTAA' }, '1.SKD8.640184': { 'barcode': 'CGTAGAGCTCTC', 'primer': 'GTGCCAGCMGCCGCGGTAA' } }, orient='index', dtype=str) pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata, Study(1), "16S") obs = delete_sample_or_column(PrepTemplate, pt.id, "samples", '1.SKD8.640184') exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('1.SKD8.640184', pt.categories()) # Exception obs = delete_sample_or_column(PrepTemplate, 2, "samples", "1.SKM9.640192") exp = { 'status': "danger", 'message': "Prep info file '2' has files attached, you cannot " "delete samples." } self.assertEqual(obs, exp) # No "samples" or "columns" obs = delete_sample_or_column(PrepTemplate, 2, "not_samples", "NOP") exp = { 'status': 'danger', 'message': 'Unknown value "not_samples". Choose between ' '"samples" and "columns"' } self.assertEqual(obs, exp)
def prep_template_ajax_get_req(user_id, prep_id): """Returns the prep tempalte information needed for the AJAX handler Parameters ---------- user_id : str The user id prep_id : int The prep template id Returns ------- dict of {str: object} A dictionary with the following keys: - status: str, whether the request is successful or not - message: str, if the request is unsuccessful, a human readable error - name: str, the name of the prep template - files: list of str, the files available to update the prep template - download_prep: int, the filepath_id of the prep file - download_qiime, int, the filepath_id of the qiime mapping file - num_samples: int, the number of samples present in the template - num_columns: int, the number of columns present in the template - investigation_type: str, the investigation type of the template - ontology: str, dict of {str, list of str} containing the information of the ENA ontology - artifact_attached: bool, whether the template has an artifact attached - study_id: int, the study id of the template """ # Currently there is no name attribute, but it will be soon name = "Prep information %d" % prep_id pt = PrepTemplate(prep_id) job_info = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_id) if job_info: job_info = loads(job_info) job_id = job_info['job_id'] if job_id: redis_info = loads(r_client.get(job_id)) processing = redis_info['status_msg'] == 'Running' if processing: alert_type = 'info' alert_msg = 'This prep template is currently being updated' elif redis_info['status_msg'] == 'Success': alert_type = redis_info['return']['status'] alert_msg = redis_info['return']['message'].replace('\n', '</br>') payload = {'job_id': None, 'status': alert_type, 'message': alert_msg} r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id, dumps(payload)) else: alert_type = redis_info['return']['status'] alert_msg = redis_info['return']['message'].replace('\n', '</br>') else: processing = False alert_type = job_info['status'] alert_msg = job_info['message'].replace('\n', '</br>') else: processing = False alert_type = '' alert_msg = '' artifact_attached = pt.artifact is not None study_id = pt.study_id files = [f for _, f in get_files_from_uploads_folders(study_id) if f.endswith(('.txt', '.tsv'))] # The call to list is needed because keys is an iterator num_samples = len(list(pt.keys())) num_columns = len(pt.categories()) investigation_type = pt.investigation_type # Retrieve the information to download the prep template and QIIME # mapping file. See issue https://github.com/biocore/qiita/issues/1675 download_prep = [] download_qiime = [] for fp_id, fp in pt.get_filepaths(): if 'qiime' in basename(fp): download_qiime.append(fp_id) else: download_prep.append(fp_id) download_prep = download_prep[0] download_qiime = download_qiime[0] ontology = _get_ENA_ontology() editable = Study(study_id).can_edit(User(user_id)) and not processing return {'status': 'success', 'message': '', 'name': name, 'files': files, 'download_prep': download_prep, 'download_qiime': download_qiime, 'num_samples': num_samples, 'num_columns': num_columns, 'investigation_type': investigation_type, 'ontology': ontology, 'artifact_attached': artifact_attached, 'study_id': study_id, 'editable': editable, 'data_type': pt.data_type(), 'alert_type': alert_type, 'is_submitted_to_ebi': pt.is_submitted_to_ebi, 'alert_message': alert_msg}
def prep_template_ajax_get_req(user_id, prep_id): """Returns the prep tempalte information needed for the AJAX handler Parameters ---------- user_id : str The user id prep_id : int The prep template id Returns ------- dict of {str: object} A dictionary with the following keys: - status: str, whether the request is successful or not - message: str, if the request is unsuccessful, a human readable error - name: str, the name of the prep template - files: list of str, the files available to update the prep template - download_prep: int, the filepath_id of the prep file - download_qiime, int, the filepath_id of the qiime mapping file - num_samples: int, the number of samples present in the template - num_columns: int, the number of columns present in the template - investigation_type: str, the investigation type of the template - ontology: str, dict of {str, list of str} containing the information of the ENA ontology - artifact_attached: bool, whether the template has an artifact attached - study_id: int, the study id of the template """ pt = PrepTemplate(prep_id) name = pt.name # Initialize variables here processing = False alert_type = '' alert_msg = '' job_info = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_id) if job_info: job_info = defaultdict(lambda: '', loads(job_info)) job_id = job_info['job_id'] job = ProcessingJob(job_id) job_status = job.status processing = job_status not in ('success', 'error') if processing: alert_type = 'info' alert_msg = 'This prep template is currently being updated' elif job_status == 'error': alert_type = 'danger' alert_msg = job.log.msg.replace('\n', '</br>') else: alert_type = job_info['alert_type'] alert_msg = job_info['alert_msg'].replace('\n', '</br>') artifact_attached = pt.artifact is not None study_id = pt.study_id files = [f for _, f, _ in get_files_from_uploads_folders(study_id) if f.endswith(('.txt', '.tsv'))] # The call to list is needed because keys is an iterator num_samples = len(list(pt.keys())) num_columns = len(pt.categories()) investigation_type = pt.investigation_type download_prep_id = None download_qiime_id = None other_filepaths = [] for fp_id, fp in pt.get_filepaths(): fp = basename(fp) if 'qiime' in fp: if download_qiime_id is None: download_qiime_id = fp_id else: if download_prep_id is None: download_prep_id = fp_id else: other_filepaths.append(fp) ontology = _get_ENA_ontology() editable = Study(study_id).can_edit(User(user_id)) and not processing return {'status': 'success', 'message': '', 'name': name, 'files': files, 'download_prep_id': download_prep_id, 'download_qiime_id': download_qiime_id, 'other_filepaths': other_filepaths, 'num_samples': num_samples, 'num_columns': num_columns, 'investigation_type': investigation_type, 'ontology': ontology, 'artifact_attached': artifact_attached, 'study_id': study_id, 'editable': editable, 'data_type': pt.data_type(), 'alert_type': alert_type, 'is_submitted_to_ebi': pt.is_submitted_to_ebi, 'alert_message': alert_msg}
def test_delete_sample_or_column(self): st = SampleTemplate(1) # Delete a sample template column job = self._create_job('delete_sample_or_column', {'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'season_environment'}) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('season_environment', st.categories()) # Delete a sample template sample - need to add one # sample that we will remove npt.assert_warns( QiitaDBWarning, st.extend, pd.DataFrame.from_dict({'Sample1': {'taxon_id': '9606'}}, orient='index', dtype=str)) self.assertIn('1.Sample1', st.keys()) job = self._create_job('delete_sample_or_column', {'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'samples', 'name': '1.Sample1'}) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('1.Sample1', st.keys()) # Delete a prep template column pt = PrepTemplate(1) job = self._create_job('delete_sample_or_column', {'obj_class': 'PrepTemplate', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'target_subfragment'}) private_task(job.id) self.assertEqual(job.status, 'success') self.assertNotIn('target_subfragment', pt.categories()) # Delete a prep template sample metadata = pd.DataFrame.from_dict( {'1.SKB8.640193': {'barcode': 'GTCCGCAAGTTA', 'primer': 'GTGCCAGCMGCCGCGGTAA'}, '1.SKD8.640184': {'barcode': 'CGTAGAGCTCTC', 'primer': 'GTGCCAGCMGCCGCGGTAA'}}, orient='index', dtype=str) pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata, Study(1), "16S") job = self._create_job('delete_sample_or_column', {'obj_class': 'PrepTemplate', 'obj_id': pt.id, 'sample_or_col': 'samples', 'name': '1.SKD8.640184'}) private_task(job.id) self.assertNotIn('1.SKD8.640184', pt.keys()) # Test exceptions job = self._create_job('delete_sample_or_column', {'obj_class': 'UnknownClass', 'obj_id': 1, 'sample_or_col': 'columns', 'name': 'column'}) private_task(job.id) self.assertEqual(job.status, 'error') self.assertIn('Unknown value "UnknownClass". Choose between ' '"SampleTemplate" and "PrepTemplate"', job.log.msg) job = self._create_job('delete_sample_or_column', {'obj_class': 'SampleTemplate', 'obj_id': 1, 'sample_or_col': 'unknown', 'name': 'column'}) private_task(job.id) self.assertEqual(job.status, 'error') self.assertIn('Unknown value "unknown". Choose between "samples" ' 'and "columns"', job.log.msg)
def prep_template_ajax_get_req(user_id, prep_id): """Returns the prep tempalte information needed for the AJAX handler Parameters ---------- user_id : str The user id prep_id : int The prep template id Returns ------- dict of {str: object} A dictionary with the following keys: - status: str, whether the request is successful or not - message: str, if the request is unsuccessful, a human readable error - name: str, the name of the prep template - files: list of str, the files available to update the prep template - download_prep: int, the filepath_id of the prep file - download_qiime, int, the filepath_id of the qiime mapping file - num_samples: int, the number of samples present in the template - num_columns: int, the number of columns present in the template - investigation_type: str, the investigation type of the template - ontology: str, dict of {str, list of str} containing the information of the ENA ontology - artifact_attached: bool, whether the template has an artifact attached - study_id: int, the study id of the template """ # Currently there is no name attribute, but it will be soon name = "Prep information %d" % prep_id pt = PrepTemplate(prep_id) artifact_attached = pt.artifact is not None study_id = pt.study_id files = [f for _, f in get_files_from_uploads_folders(study_id) if f.endswith(('.txt', '.tsv'))] # The call to list is needed because keys is an iterator num_samples = len(list(pt.keys())) num_columns = len(pt.categories()) investigation_type = pt.investigation_type # Retrieve the information to download the prep template and QIIME # mapping file. See issue https://github.com/biocore/qiita/issues/1675 download_prep = [] download_qiime = [] for fp_id, fp in pt.get_filepaths(): if 'qiime' in basename(fp): download_qiime.append(fp_id) else: download_prep.append(fp_id) download_prep = download_prep[0] download_qiime = download_qiime[0] ontology = _get_ENA_ontology() job_id = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_id) if job_id: redis_info = loads(r_client.get(job_id)) processing = redis_info['status_msg'] == 'Running' if processing: alert_type = 'info' alert_msg = 'This prep template is currently being updated' else: alert_type = redis_info['return']['status'] alert_msg = redis_info['return']['message'].replace('\n', '</br>') else: processing = False alert_type = '' alert_msg = '' editable = Study(study_id).can_edit(User(user_id)) and not processing return {'status': 'success', 'message': '', 'name': name, 'files': files, 'download_prep': download_prep, 'download_qiime': download_qiime, 'num_samples': num_samples, 'num_columns': num_columns, 'investigation_type': investigation_type, 'ontology': ontology, 'artifact_attached': artifact_attached, 'study_id': study_id, 'editable': editable, 'data_type': pt.data_type(), 'alert_type': alert_type, 'alert_message': alert_msg}
def test_delete_sample_or_column(self): st = SampleTemplate(1) # Delete a sample template column obs = delete_sample_or_column(SampleTemplate, 1, "columns", "season_environment") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('season_environment', st.categories()) # Delete a sample template sample - need to add one sample that we # will remove npt.assert_warns( QiitaDBWarning, st.extend, pd.DataFrame.from_dict({'Sample1': {'taxon_id': '9606'}}, orient='index', dtype=str)) self.assertIn('1.Sample1', st.keys()) obs = delete_sample_or_column(SampleTemplate, 1, "samples", "1.Sample1") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('1.Sample1', st.keys()) # Delete a prep template column pt = PrepTemplate(2) obs = delete_sample_or_column(PrepTemplate, 2, "columns", "target_subfragment") exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('target_subfragment', pt.categories()) # Delte a prep template sample metadata = pd.DataFrame.from_dict( {'1.SKB8.640193': {'barcode': 'GTCCGCAAGTTA', 'primer': 'GTGCCAGCMGCCGCGGTAA'}, '1.SKD8.640184': {'barcode': 'CGTAGAGCTCTC', 'primer': 'GTGCCAGCMGCCGCGGTAA'}}, orient='index', dtype=str) pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata, Study(1), "16S") obs = delete_sample_or_column(PrepTemplate, pt.id, "samples", '1.SKD8.640184') exp = {'status': "success", 'message': ""} self.assertEqual(obs, exp) self.assertNotIn('1.SKD8.640184', pt.categories()) # Exception obs = delete_sample_or_column(PrepTemplate, 2, "samples", "1.SKM9.640192") exp = {'status': "danger", 'message': "Prep info file '2' has files attached, you cannot " "delete samples."} self.assertEqual(obs, exp) # No "samples" or "columns" obs = delete_sample_or_column(PrepTemplate, 2, "not_samples", "NOP") exp = {'status': 'danger', 'message': 'Unknown value "not_samples". Choose between ' '"samples" and "columns"'} self.assertEqual(obs, exp)