diff options
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/update_rif_table.py | 49 |
1 files changed, 21 insertions, 28 deletions
diff --git a/scripts/update_rif_table.py b/scripts/update_rif_table.py index 5318020..89ad947 100755 --- a/scripts/update_rif_table.py +++ b/scripts/update_rif_table.py @@ -87,36 +87,29 @@ def update_rif(sqluri: str): generif_basics_path, ) genedict = parse_gene_info_from_ncbi(gene_info_path) - insert_query = """ - INSERT IGNORE INTO GeneRIF_BASIC - SET GeneRIF_BASIC.`SpeciesId`=%s, - GeneRIF_BASIC.`GeneId`=%s, - GeneRIF_BASIC.`symbol`=%s, - GeneRIF_BASIC.`PubMed_ID`=%s, - GeneRIF_BASIC.`createtime`=%s, - GeneRIF_BASIC.`comment`=%s, - GeneRIF_BASIC.`TaxID`=%s, - VersionId=%s - """ + insert_query = """ INSERT IGNORE INTO GeneRIF_BASIC + (SpeciesId, GeneId, symbol, PubMed_Id, createtime, comment, TaxID, VersionId) + VALUES (%s, %s, %s, %s, %s, %s, %s, %s) + """ with database_connection(sql_uri=sqluri) as con: - with con.cursor() as cursor: - for row in read_tsv_file(generif_basics_path): - if row["#Tax ID"] not in TAX_IDS: - continue - species_id = TAX_IDS[row["#Tax ID"]] - symbol = genedict.get(row["Gene ID"], "") - insert_values = ( - species_id, # SpeciesId - row["Gene ID"], # GeneId - symbol, # symbol - row["PubMed ID (PMID) list"], # PubMed_ID - row["last update timestamp"], # createtime - row["GeneRIF text"], # comment - row["#Tax ID"], # TaxID - VERSION_ID, # VersionId - ) - cursor.execute(insert_query, insert_values) + cursor = con.cursor() + for row in read_tsv_file(generif_basics_path): + if row["#Tax ID"] not in TAX_IDS: + continue + species_id = TAX_IDS[row["#Tax ID"]] + symbol = genedict.get(row["Gene ID"], "") + insert_values = ( + species_id, # SpeciesId + row["Gene ID"], # GeneId + symbol, # symbol + row["PubMed ID (PMID) list"], # PubMed_ID + row["last update timestamp"], # createtime + row["GeneRIF text"], # comment + row["#Tax ID"], # TaxID + VERSION_ID, # VersionId + ) + cursor.execute(insert_query, insert_values) print( f"Generif_BASIC table updated. In case of error, you can do use VersionID={VERSION_ID} to find rows inserted with this script" ) |