diff options
| -rw-r--r-- | wqflask/scripts/index.py | 16 | ||||
| -rw-r--r-- | wqflask/utility/monads.py | 26 |
2 files changed, 14 insertions, 28 deletions
diff --git a/wqflask/scripts/index.py b/wqflask/scripts/index.py index c871db43..37736951 100644 --- a/wqflask/scripts/index.py +++ b/wqflask/scripts/index.py @@ -9,7 +9,7 @@ from functools import partial import json import xapian -from utility.monads import MonadicDictCursor +from utility.monads import sql_query_mdict from wqflask.database import database_connection, xapian_writable_database @@ -39,8 +39,8 @@ def main(): # database. # pylint: disable=invalid-name with xapian_writable_database() as db: - with database_connection() as conn, conn.cursor(MonadicDictCursor) as cursor: - cursor.execute(""" + with database_connection() as conn: + for trait in sql_query_mdict(conn, """ SELECT ProbeSet.Name AS name, ProbeSet.Symbol AS symbol, ProbeSet.description AS description, @@ -70,8 +70,7 @@ def main(): INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id WHERE ProbeSetFreeze.confidentiality < 1 AND ProbeSetFreeze.public > 0 - """) - for trait in cursor.fetchall(): + """): doc = xapian.Document() termgenerator.set_document(doc) @@ -87,8 +86,8 @@ def main(): doc.set_data(json.dumps(trait.data)) write_document(db, trait["name"].bind(lambda name: f"Q{name}"), "gene", doc) - with database_connection() as conn, conn.cursor(MonadicDictCursor) as cursor: - cursor.execute(""" + with database_connection() as conn: + for i, trait in enumerate(sql_query_mdict(conn, """ SELECT Species.Name AS species, InbredSet.Name AS `group`, PublishFreeze.Name AS dataset, @@ -116,8 +115,7 @@ def main(): INNER JOIN Phenotype ON PublishXRef.PhenotypeId = Phenotype.Id INNER JOIN Publication ON PublishXRef.PublicationId = Publication.Id LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id - """) - for i, trait in enumerate(cursor.fetchall()): + """)): doc = xapian.Document() termgenerator.set_document(doc) diff --git a/wqflask/utility/monads.py b/wqflask/utility/monads.py index 3360fad2..2d708261 100644 --- a/wqflask/utility/monads.py +++ b/wqflask/utility/monads.py @@ -105,22 +105,10 @@ class MonadicDict(UserDict): except KeyError: pass -class MonadicDictCursor(DictCursor): - """Monadic version of MySQLdb.cursors.DictCursor. - - Monadic version of MySQLdb.cursors.DictCursor that returns a - MonadicDict instead of the built-in dictionary. - - Execute a SQL query and retrieve results as MonadicDict - objects. Each row object in the following code is a MonadicDict. - >>> with conn.cursor(MonadicDictCursor) as cursor: - ... cursor.execute("SELECT foo FROM bar") - ... for row in cursor.fetchall(): - ... print(row) - """ - def fetchone(self): - return Just(MonadicDict(row)) if (row := super().fetchone()) else Nothing - def fetchmany(self, size=None): - return [MonadicDict(row) for row in super().fetchmany(size=size)] - def fetchall(self): - return [MonadicDict(row) for row in super().fetchall()] + +def sql_query_mdict(conn, query): + """Execute SQL query and return a generator of MonadicDict objects.""" + with conn.cursor(DictCursor) as cursor: + cursor.execute(query) + while (row := cursor.fetchone()): + yield MonadicDict(row) |