diff options
| -rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 1 |
3 files changed, 1 insertions, 36 deletions
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index ba998e91..8a9dc79d 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -30,14 +30,6 @@ logger = getLogger(__name__ ) #output: cursor instance #function: connect to database and return cursor instance ########################################################################### -def getCursor(): - try: - logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)") - con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) - cursor = con.cursor() - return cursor - except: - return None def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index e2a0a479..c7dbc972 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -872,32 +872,6 @@ if __name__ == "__main__": dataset_name = "HC_M2_0606_P" dataset = create_dataset(db_conn, dataset_name) - #cursor.execute(""" - # SELECT ProbeSet.Name as TNAME, 0 as thistable, - # ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, - # ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, - # ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, - # ProbeSet.name_num as TNAME_NUM - # FROM ProbeSetXRef, ProbeSet, Geno - # WHERE ProbeSetXRef.LRS > 99.0 and - # ABS(ProbeSet.Mb-Geno.Mb) < 5 and - # ProbeSetXRef.Locus = Geno.name and - # Geno.SpeciesId = 1 and - # ProbeSet.Chr = Geno.Chr and - # ProbeSet.Id = ProbeSetXRef.ProbeSetId and - # ProbeSetXRef.ProbeSetFreezeId = 112""") - - #logger.debug(pf(cursor.fetchall())) - #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run() - #results = RifSearch("diabetes", dataset, cursor, db_conn).run() - #results = WikiSearch("nicotine", dataset, cursor, db_conn).run() - #results = CisLrsSearch(['99'], '>', dataset, cursor, db_conn).run() # cisLRS > 99 - #results = LrsSearch('99', '>', dataset, cursor, db_conn).run() - #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run() - #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run() - #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() - #results = GoSearch("0045202", dataset, cursor, db_conn).run() - - logger.debug("results are:", pf(results)) + db_conn.close() diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 49b47123..2089f9de 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -72,7 +72,6 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) - @app.before_request def connect_db(): db = getattr(g, '_database', None) |