diff options
| -rw-r--r-- | uploader/db_utils.py | 5 | ||||
| -rw-r--r-- | uploader/dbinsert.py | 22 |
2 files changed, 13 insertions, 14 deletions
diff --git a/uploader/db_utils.py b/uploader/db_utils.py index ef26398..357b3da 100644 --- a/uploader/db_utils.py +++ b/uploader/db_utils.py @@ -19,10 +19,9 @@ def parse_db_url(db_url) -> Tuple: @contextlib.contextmanager -def database_connection(db_url: Optional[str] = None) -> Iterator[mdb.Connection]: +def database_connection(db_url: str) -> Iterator[mdb.Connection]: """function to create db connector""" - host, user, passwd, db_name, db_port = parse_db_url( - db_url or app.config["SQL_URI"]) + host, user, passwd, db_name, db_port = parse_db_url(db_url) connection = mdb.connect( host, user, passwd, db_name, port=(db_port or 3306)) try: diff --git a/uploader/dbinsert.py b/uploader/dbinsert.py index 66b0c41..559dc5e 100644 --- a/uploader/dbinsert.py +++ b/uploader/dbinsert.py @@ -41,7 +41,7 @@ def genechips(): return {**acc, speciesid: (chip,)} return {**acc, speciesid: acc[speciesid] + (chip,)} - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC") return reduce(__organise_by_species__, cursor.fetchall(), {}) @@ -50,7 +50,7 @@ def genechips(): def platform_by_id(genechipid:int) -> Union[dict, None]: "Retrieve the gene platform by id" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( "SELECT * FROM GeneChip WHERE GeneChipId=%s", @@ -59,7 +59,7 @@ def platform_by_id(genechipid:int) -> Union[dict, None]: def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple: "Retrieve the studies by the related species and gene platform" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: query = ( "SELECT Species.SpeciesId, ProbeFreeze.* " @@ -83,7 +83,7 @@ def organise_groups_by_family(acc:dict, group:dict) -> dict: def tissues() -> tuple: "Retrieve type (Tissue) information from the database." - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute("SELECT * FROM Tissue ORDER BY Name") return tuple(cursor.fetchall()) @@ -158,7 +158,7 @@ def create_study(): assert form.get("inbredsetid"), "group" assert form.get("tissueid"), "type/tissue" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: values = ( form["genechipid"], @@ -190,7 +190,7 @@ def create_study(): def datasets_by_study(studyid:int) -> tuple: "Retrieve datasets associated with a study with the ID `studyid`." - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s" cursor.execute(query, (studyid,)) @@ -200,7 +200,7 @@ def datasets_by_study(studyid:int) -> tuple: def averaging_methods() -> tuple: "Retrieve averaging methods from database" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute("SELECT * FROM AvgMethod") return tuple(cursor.fetchall()) @@ -209,7 +209,7 @@ def averaging_methods() -> tuple: def dataset_datascales() -> tuple: "Retrieve datascales from database" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor() as cursor: cursor.execute( 'SELECT DISTINCT DataScale FROM ProbeSetFreeze ' @@ -261,7 +261,7 @@ def create_dataset(): assert form.get("datasetconfidentiality"), "Dataset confidentiality" assert form.get("datasetdatascale"), "Dataset Datascale" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: datasetname = form["datasetname"] cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Name=%s", @@ -299,7 +299,7 @@ def create_dataset(): def study_by_id(studyid:int) -> Union[dict, None]: "Get a study by its Id" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( "SELECT * FROM ProbeFreeze WHERE Id=%s", @@ -308,7 +308,7 @@ def study_by_id(studyid:int) -> Union[dict, None]: def dataset_by_id(datasetid:int) -> Union[dict, None]: "Retrieve a dataset by its id" - with database_connection() as conn: + with database_connection(app.config["SQL_URI"]) as conn: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( ("SELECT AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.* " |