def create_ocp_variant_table(my_cursor): table_name = 'ocp_variant' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE ocp_variant ( ' \ 'variantName varchar(100), ' \ 'omniGene_gene_Id varchar(100), ' \ 'description_id varchar(100), ' \ 'pDot varchar(100), ' \ 'cDot varchar(100), ' \ 'gDot varchar(100), ' \ 'regionType varchar(100), ' \ 'indelType varchar(100), ' \ 'variantType varchar(100), ' \ 'variantProteinEffect varchar(100), ' \ 'jax_variant_Id varchar(100) DEFAULT NULL, ' \ 'go_variant_Id varchar(100) DEFAULT NULL, ' \ 'clinvar_variant_Id varchar(100) DEFAULT NULL, ' \ 'hot_spot_variant_Id varchar(100) DEFAULT NULL, ' \ 'exon varchar(100) , ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT ocp_variant_description_fk_es_id FOREIGN KEY (description_id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT ocp_variant_fk_omni_gene FOREIGN KEY (omniGene_gene_Id) REFERENCES omnigene (graph_id), ' \ 'CONSTRAINT ocp_variant_fk_jax_variant FOREIGN KEY (jax_variant_Id) REFERENCES jax_variant (graph_id), ' \ 'CONSTRAINT ocp_variant_fk_go_variant FOREIGN KEY (go_variant_Id) REFERENCES go_variant (graph_id), ' \ 'CONSTRAINT ocp_variant_fk_clinvar_variant FOREIGN KEY (clinvar_variant_Id) REFERENCES clinvar (graph_id), ' \ 'CONSTRAINT ocp_variant_fk_hot_spot_variant FOREIGN KEY (hot_spot_variant_Id) REFERENCES hot_spot (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_journals_table(my_cursor): table_name = 'journals' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE journals ( ' \ 'name varchar(250) NOT NULL, ' \ 'graph_id varchar(100), ' \ 'PRIMARY KEY (graph_id)' \ ')' result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_jax_synonym_table(my_cursor): table_name = 'jax_synonyms' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE jax_synonyms ( ' \ 'id MEDIUMINT NOT NULL AUTO_INCREMENT, ' \ 'name varchar(100) NOT NULL, ' \ 'jax_gene_id varchar(100), ' \ 'PRIMARY KEY (id),' \ 'CONSTRAINT jax_synonym_fk_gene_id FOREIGN KEY (jax_gene_id) REFERENCES jax_gene (graph_id) ' \ ')' result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_user_table(my_cursor): table_name = 'users' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE users ( ' \ 'name varchar(100), ' \ 'password varchar(100), ' \ 'isAdmin varchar(50), ' \ 'graph_id varchar(100) PRIMARY KEY ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_internet_references_table(my_cursor): table_name = 'internet_refs' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE internet_refs ( ' \ 'accessed_date varchar(100), ' \ 'web_address varchar(100), ' \ 'short_reference varchar(200), ' \ 'graph_id varchar(100) PRIMARY KEY ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_go_variant_table(my_cursor): table_name = 'go_variant' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE go_variant ( ' \ 'variantName varchar(100), ' \ 'geneName varchar(100), ' \ 'go_Id varchar(100), ' \ 'mutationType varchar(100), ' \ 'jaxVariant_Id varchar(100) DEFAULT NULL, ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT go_variant_fk_jax_variant FOREIGN KEY (jaxVariant_Id) REFERENCES jax_variant (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_editable_statement_table(my_cursor): table_name = 'editable_statements' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE editable_statements ( ' \ 'field varchar(100), ' \ 'statement varchar(8000), ' \ 'edit_date varchar(50), ' \ 'editor_id varchar(100), ' \ 'deleted varchar(50), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT es_fk_editor_id FOREIGN KEY (editor_id) REFERENCES users (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_hot_spot_table(my_cursor): table_name = 'hot_spot' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE hot_spot ( ' \ 'hs_name varchar(100), ' \ 'gene varchar(100), ' \ 'referenceAminoAcid varchar(10), ' \ 'variantAminoAcid varchar(10), ' \ 'hs_begin varchar(100), ' \ 'hs_end varchar(100), ' \ 'hs_position MEDIUMINT, ' \ 'graph_id varchar(100) PRIMARY KEY ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_author_ref_table(my_cursor): table_name = 'author_ref' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE author_ref ( ' \ 'id MEDIUMINT NOT NULL AUTO_INCREMENT, ' \ 'author_id varchar(100), ' \ 'ref_id varchar(100), ' \ 'PRIMARY KEY (id), ' \ 'FOREIGN KEY (author_id) ' \ 'REFERENCES authors (graph_id), ' \ 'FOREIGN KEY (ref_id) ' \ 'REFERENCES refs (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_jax_gene_table(my_cursor): table_name = 'jax_gene' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE jax_gene ( ' \ 'name varchar(100), ' \ 'canonicalTranscript varchar(50), ' \ 'chromosome varchar(50), ' \ 'entrezId varchar(50), ' \ 'jaxId varchar(50), ' \ 'description_Id varchar(50), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT jax_description_fk_es_id FOREIGN KEY (description_Id) REFERENCES editable_statements (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_es_internet_refs_table(my_cursor): table_name = 'es_internet_refs' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE es_internet_refs ( ' \ 'id MEDIUMINT NOT NULL AUTO_INCREMENT, ' \ 'es_id varchar(100), ' \ 'internet_ref_id varchar(100), ' \ 'PRIMARY KEY (id), ' \ 'FOREIGN KEY (es_id) ' \ 'REFERENCES editable_statements (graph_id), ' \ 'FOREIGN KEY (internet_ref_id) ' \ 'REFERENCES internet_refs (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_uniprot_entry_table(my_cursor): table_name = 'uniprot_entry' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE uniprot_entry ( ' \ 'name varchar(100), ' \ 'accessionNumber varchar(100), ' \ 'uniprot_id varchar(100), ' \ 'function_Id varchar(50), ' \ 'gene_Id varchar(50), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT function_fk_es_id FOREIGN KEY (function_Id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT uniprot_fk_gene_id FOREIGN KEY (gene_Id) REFERENCES mygene_info_gene (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_clinvar_table(my_cursor): table_name = 'clinvar' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE clinvar ( ' \ 'variantID varchar(100), ' \ 'gene varchar(100), ' \ 'pDot varchar(100), ' \ 'cDot varchar(100), ' \ 'significance varchar(100), ' \ 'signficanceExplanation varchar(200), ' \ 'cdot_pos BIGINT, ' \ 'pdot_pos BIGINT, ' \ 'graph_id varchar(100) PRIMARY KEY' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_hot_spot_occurrences_table(my_cursor): table_name = 'hot_spot_occurrences' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE hot_spot_occurrences ( ' \ 'id MEDIUMINT NOT NULL AUTO_INCREMENT, ' \ 'disease varchar(100) NOT NULL, ' \ 'oncoTreeCode varchar(20) NOT NULL, ' \ 'percentOccurrence varchar(10) NOT NULL, ' \ 'perThousandOccurrence MEDIUMINT NOT NULL, ' \ 'occurrences MEDIUMINT NOT NULL, ' \ 'totalSamples MEDIUMINT NOT NULL, ' \ 'hot_spot_id varchar(100), ' \ 'PRIMARY KEY (id),' \ 'CONSTRAINT hs_occurrences_fk_hotspot_id FOREIGN KEY (hot_spot_id) REFERENCES hot_spot (graph_id) ' \ ')' result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_references_table(my_cursor): table_name = 'refs' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE refs ( ' \ 'PMID varchar(20) NOT NULL, ' \ 'DOI varchar(100), ' \ 'title varchar(1000), ' \ 'journal_graph_id varchar(100), ' \ 'volume varchar(20), ' \ 'first_page varchar(20), ' \ 'last_page varchar(20), ' \ 'publication_Year varchar(20), ' \ 'short_reference varchar(200), ' \ 'abstract varchar(8000), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT refs_fk_journal_graph_id FOREIGN KEY (journal_graph_id) REFERENCES journals (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_jax_variant_table(my_cursor): table_name = 'jax_variant' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE jax_variant ( ' \ 'variantName varchar(100), ' \ 'description_id varchar(100), ' \ 'jax_Id varchar(100), ' \ 'jaxGene_gene_Id varchar(100), ' \ 'pDot varchar(100), ' \ 'cDot varchar(100), ' \ 'gDot varchar(100), ' \ 'transcript varchar(100), ' \ 'variantType varchar(100), ' \ 'proteinEffect varchar(100), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT variant_description_fk_es_id FOREIGN KEY (description_id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT variant_fk_jax_gene FOREIGN KEY (jaxGene_gene_Id) REFERENCES jax_gene (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')
def create_omnigene_table(my_cursor): table_name = 'omnigene' if not does_table_exist(my_cursor, table_name): mySql_Create_Table_Query = 'CREATE TABLE omnigene ( ' \ 'name varchar(100), ' \ 'panelName varchar(100), ' \ 'geneDescription_id varchar(100), ' \ 'oncogenicCategory_Id varchar(100), ' \ 'synonymsString_Id varchar(100), ' \ 'myGeneInfo_gene_Id varchar(100), ' \ 'jaxGene_gene_Id varchar(100), ' \ 'uniprot_entry_Id varchar(100), ' \ 'graph_id varchar(100) PRIMARY KEY, ' \ 'CONSTRAINT geneDescription_fk_es_id FOREIGN KEY (geneDescription_id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT oncogenicCategory_fk_es_id FOREIGN KEY (oncogenicCategory_Id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT synonymsString_fk_es_id FOREIGN KEY (synonymsString_Id) REFERENCES editable_statements (graph_id), ' \ 'CONSTRAINT omni_fk_mygene FOREIGN KEY (myGeneInfo_gene_Id) REFERENCES mygene_info_gene (graph_id), ' \ 'CONSTRAINT omni_fk_jax FOREIGN KEY (jaxGene_gene_Id) REFERENCES jax_gene (graph_id), ' \ 'CONSTRAINT omni_fk_uniprot FOREIGN KEY (uniprot_entry_Id) REFERENCES uniprot_entry (graph_id) ' \ ')' print(mySql_Create_Table_Query) result = my_cursor.execute(mySql_Create_Table_Query) print(f'{table_name} Table created successfully')