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authorMunyoki Kilyungi2022-09-05 10:21:06 +0300
committerBonfaceKilz2022-09-08 14:26:19 +0300
commit8aef689bb1ab735ad4605af8b8b282672f92d2cf (patch)
tree92506b8120f4223bfe92784ce7bd83d70ecae20b /.gitignore
parentc341c4565126c47c78f220871d9e334dbe5aec73 (diff)
downloadgenenetwork2-8aef689bb1ab735ad4605af8b8b282672f92d2cf.tar.gz
Replace g.db with database_connection() context manager
* wqflask/base/data_set.py (DatasetType.set_dataset_key): Replace g.db with "database_connection()". (DatasetGroup.get_mapping_methods): Ditto. (DataSet.get_accession_id): Ditto. (DataSet.retrieve_other_names): Rework "if ... else" logic to get rid of "query" and "_vars" variables. Also, nest "try ... except" block within "database_connection". (DataSet.chunk_dataset): Replace g.db with "database_connection()". (DataSet.get_probeset_data): Ditto. (DataSet.get_trait_data): Ditto. (PhenotypeDataSet.get_trait_info): Ditto. (PhenotypeDataSet.retrieve_sample_data): Ditto. (GenotypeDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.get_trait_info): Ditto. (MrnaAssayDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.retrieve_genes): Ditto. (TempDataSet): Ditto. (geno_mrna_confidentiality): Ditto. (query_table_timestamp): Ditto. * wqflask/wqflask/api/router.py: Replace "flask.g" with database_connection import. (get_species_list): Replace g.db with "database_connection()". (get_species_info): Ditto. (get_groups_list): Ditto. (get_group_info): Ditto. (get_datasets_for_group): Ditto. (get_dataset_info): Ditto. (fetch_traits): Ditto. (all_sample_data): Ditto. (trait_sample_data): Ditto. (get_trait_info): Ditto. (get_dataset_trait_ids): Ditto. (get_samplelist): Ditto. (get_group_id_from_dataset): Ditto. (get_group_id): Ditto.
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