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| author | Frederick Muriuki Muriithi | 2024-01-11 02:26:46 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-11 02:26:46 +0300 |
| commit | 88a8bc0b458f079e93757057080f1ec0dc842fd8 (patch) | |
| tree | 99479c603dc3a0f17f5d1e550ba69789a7f9419b | |
| parent | 242491b97183203a77b5b8634f6e8825c8b101fa (diff) | |
| download | gn-uploader-88a8bc0b458f079e93757057080f1ec0dc842fd8.tar.gz | |
Cleanup linting and typing errors.
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 14 |
1 files changed, 9 insertions, 5 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 3b9e987..5c3da85 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -57,8 +57,9 @@ def cross_reference_individuals(dbconn: mdb.Connection, """Cross reference any inserted individuals.""" with dbconn.cursor(cursorclass=DictCursor) as cursor: paramstr = ", ".join(["%s"] * len(individuals)) - cursor.execute(f"SELECT Id FROM Strain WHERE Name IN ({paramstr})", - individuals) + cursor.execute("SELECT Id FROM Strain " + f"WHERE SpeciesId=%s AND Name IN ({paramstr})", + (speciesid,) + individuals) ids = ({"popid": populationid, "indid": row["Id"]} for row in cursor.fetchall()) cursor.executemany( @@ -71,7 +72,8 @@ def cross_reference_individuals(dbconn: mdb.Connection, def insert_genotype_data(dbconn: mdb.Connection, speciesid: int, genotypes: tuple[dict, ...], - individuals: tuple[str, ...]) -> tuple[int, tuple[int, ...]]: + individuals: tuple[str, ...]) -> tuple[ + int, tuple[dict, ...]]: """Insert the genotype data values into the database.""" with dbconn.cursor(cursorclass=DictCursor) as cursor: paramstr = ", ".join(["%s"] * len(individuals)) @@ -108,7 +110,7 @@ def insert_genotype_data(dbconn: mdb.Connection, def cross_reference_genotypes(dbconn: mdb.Connection, datasetid: int, - dataids: tuple[int, ...]) -> int: + dataids: tuple[dict, ...]) -> int: """Cross-reference the data to the relevant dataset.""" with dbconn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( @@ -155,6 +157,7 @@ def install_genotypes(dbconn: mdb.Connection, cross_reference_genotypes(dbconn, datasetid, dataids) count = count + len(batch) + cdata = rqtl2.control_data(zfile) if "gmap" in cdata: logger.info("Loading genetic mapping info.") # TODO: load gmap files @@ -167,7 +170,8 @@ def install_genotypes(dbconn: mdb.Connection, except rqtl2.InvalidFormat as exc: logger.error(str(exc)) logger.info("There are no genotypes to load.") - except Exception as _exc: + except Exception as _exc:# pylint: disable=[broad-except] + # Narrow this exception with time. logger.error("Failing with exception: %s", traceback.format_exc()) return 3 |