Use gn-libs code for db connection.

Use the code in gn-libs to connect to the database, rather than a
local module.

19 files changed, 30 insertions, 26 deletions

diff --git a/scripts/insert_data.py b/scripts/insert_data.py
index 4b2e5f3..67038f8 100644
--- a/scripts/insert_data.py
+++ b/scripts/insert_data.py
@@ -10,11 +10,11 @@ from typing import Tuple, Iterator
 import MySQLdb as mdb
 from redis import Redis
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 
 from functional_tools import take
 
 from quality_control.file_utils import open_file
-from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 
 # Set up logging
diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py
index e3577b6..1b0a052 100644
--- a/scripts/insert_samples.py
+++ b/scripts/insert_samples.py
@@ -6,8 +6,8 @@ import argparse
 
 import MySQLdb as mdb
 from redis import Redis
+from gn_libs.mysqldb import database_connection
 
-from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 from uploader.species.models import species_by_id
 from uploader.population.models import population_by_id
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py
index ade9862..4efc3e0 100644
--- a/scripts/process_rqtl2_bundle.py
+++ b/scripts/process_rqtl2_bundle.py
@@ -11,6 +11,7 @@ from logging import Logger, getLogger, StreamHandler
 
 import MySQLdb as mdb
 from redis import Redis
+from gn_libs.mysqldb import database_connection
 
 from functional_tools import take
 
@@ -19,7 +20,6 @@ import r_qtl.r_qtl2_qc as rqc
 import r_qtl.exceptions as rqe
 
 from uploader import jobs
-from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 
 from scripts.cli_parser import init_cli_parser
diff --git a/scripts/qc.py b/scripts/qc.py
index 6de051f..b00f4c1 100644
--- a/scripts/qc.py
+++ b/scripts/qc.py
@@ -5,14 +5,14 @@ import mimetypes
 from typing import Union, Callable
 from argparse import ArgumentParser
 
+from gn_libs.mysqldb import database_connection
+
 from functional_tools import take
 
 from quality_control.utils import make_progress_calculator
 from quality_control.errors import InvalidValue, DuplicateHeading
 from quality_control.parsing import FileType, strain_names, collect_errors
 
-from uploader.db_utils import database_connection
-
 from .cli_parser import init_cli_parser
 
 
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index fc95d13..9f9248c 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -12,12 +12,12 @@ from typing import Union, Sequence, Callable, Iterator
 
 import MySQLdb as mdb
 from redis import Redis
+from gn_libs.mysqldb import database_connection
 
 from quality_control.errors import InvalidValue
 from quality_control.checks import decimal_points_error
 
 from uploader import jobs
-from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 
 from r_qtl import r_qtl2 as rqtl2
diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py
index bc4cd9f..b45e1dc 100644
--- a/scripts/rqtl2/entry.py
+++ b/scripts/rqtl2/entry.py
@@ -5,9 +5,9 @@ from argparse import Namespace
 
 from redis import Redis
 from MySQLdb import Connection
+from gn_libs.mysqldb import database_connection
 
 from uploader import jobs
-from uploader.db_utils import database_connection
 from uploader.check_connections import check_db, check_redis
 
 from scripts.redis_logger import setup_redis_logger
diff --git a/scripts/validate_file.py b/scripts/validate_file.py
index a40d7e7..52e55ec 100644
--- a/scripts/validate_file.py
+++ b/scripts/validate_file.py
@@ -8,12 +8,12 @@ from zipfile import ZipFile, is_zipfile
 import jsonpickle
 from redis import Redis
 from redis.exceptions import ConnectionError # pylint: disable=[redefined-builtin]
+from gn_libs.mysqldb import database_connection
 
 from quality_control.utils import make_progress_calculator
 from quality_control.parsing import FileType, strain_names, collect_errors
 
 from uploader import jobs
-from uploader.db_utils import database_connection
 
 from .cli_parser import init_cli_parser
 from .qc import add_file_validation_arguments
diff --git a/uploader/check_connections.py b/uploader/check_connections.py
index 2561e55..c9b9aa3 100644
--- a/uploader/check_connections.py
+++ b/uploader/check_connections.py
@@ -4,8 +4,7 @@ import traceback
 
 import redis
 import MySQLdb
-
-from uploader.db_utils import database_connection
+from gn_libs.mysqldb import database_connection
 
 def check_redis(uri: str):
     "Check the redis connection"
diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py
index 32ca359..6d8ce80 100644
--- a/uploader/expression_data/dbinsert.py
+++ b/uploader/expression_data/dbinsert.py
@@ -7,16 +7,17 @@ from datetime import datetime
 
 from redis import Redis
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (
     flash, request, url_for, Blueprint, redirect, render_template,
     current_app as app)
 
 from uploader import jobs
 from uploader.authorisation import require_login
+from uploader.db_utils import with_db_connection
 from uploader.population.models import populations_by_species
 from uploader.species.models import all_species, species_by_id
 from uploader.platforms.models import platform_by_species_and_id
-from uploader.db_utils import with_db_connection, database_connection
 
 dbinsertbp = Blueprint("dbinsert", __name__)
 
diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py
index bbe6538..7629f3e 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -8,6 +8,7 @@ from zipfile import ZipFile, is_zipfile
 import jsonpickle
 from redis import Redis
 from werkzeug.utils import secure_filename
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -21,8 +22,8 @@ from uploader import jobs
 from uploader.datautils import order_by_family
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
+from uploader.db_utils import with_db_connection
 from uploader.species.models import all_species, species_by_id
-from uploader.db_utils import with_db_connection, database_connection
 from uploader.population.models import (populations_by_species,
                                         population_by_species_and_id)
 
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 44c98b1..4c3e634 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -4,8 +4,9 @@ from datetime import datetime
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
+from flask import current_app as app
 
-from uploader.db_utils import debug_query
+from gn_libs.mysqldb import debug_query
 
 def genocode_by_population(
         conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
@@ -38,7 +39,7 @@ def genotype_markers(
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, (species_id,))
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall())
 
 
@@ -64,7 +65,7 @@ def genotype_dataset(
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, _params)
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0821eca..e6b1ba7 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -1,5 +1,6 @@
 """Views for the genotypes."""
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -11,7 +12,6 @@ from flask import (flash,
 from uploader.ui import make_template_renderer
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
-from uploader.db_utils import database_connection
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.request_checks import with_species, with_population
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 9324601..73b1cce 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -5,8 +5,9 @@ from datetime import datetime
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
+from flask import current_app as app
 
-from uploader.db_utils import debug_query
+from gn_libs.mysqldb import debug_query
 
 def datasets_by_population(
         conn: mdb.Connection,
@@ -68,7 +69,7 @@ def dataset_phenotypes(conn: mdb.Connection,
             f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, (population_id, dataset_id))
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall())
 
 
@@ -201,7 +202,7 @@ def phenotypes_data(conn: mdb.Connection,
                   f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, (population_id, dataset_id))
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall())
 
 
@@ -228,5 +229,5 @@ def save_new_dataset(cursor: Cursor,
         "%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, "
         "%(users)s)",
         params)
-    debug_query(cursor)
+    debug_query(cursor, app.logger)
     return {**params, "Id": cursor.lastrowid}
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 02e8078..79aab81 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -8,6 +8,7 @@ from functools import wraps
 from redis import Redis
 from requests.models import Response
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -24,7 +25,6 @@ from uploader import jobs
 from uploader.files import save_file#, fullpath
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
-from uploader.db_utils import database_connection
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.request_checks import with_species, with_population
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index 2d61b6a..c20ab44 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -1,5 +1,6 @@
 """The endpoints for the platforms"""
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (
     flash,
     request,
@@ -10,7 +11,6 @@ from flask import (
 
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
-from uploader.db_utils import database_connection
 from uploader.species.models import all_species, species_by_id
 from uploader.datautils import safe_int, order_by_family, enumerate_sequence
 
diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py
index 9968bd6..436eca0 100644
--- a/uploader/population/rqtl2.py
+++ b/uploader/population/rqtl2.py
@@ -12,6 +12,7 @@ import MySQLdb as mdb
 from redis import Redis
 from MySQLdb.cursors import DictCursor
 from werkzeug.utils import secure_filename
+from gn_libs.mysqldb import database_connection
 from flask import (
     flash,
     escape,
@@ -29,7 +30,7 @@ from r_qtl import r_qtl2
 from uploader import jobs
 from uploader.files import save_file, fullpath
 from uploader.species.models import all_species
-from uploader.db_utils import with_db_connection, database_connection
+from uploader.db_utils import with_db_connection
 
 from uploader.authorisation import require_login
 from uploader.platforms.models import platform_by_id, platforms_by_species
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 36201ba..4f985f5 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -3,6 +3,7 @@ import json
 import base64
 
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -15,7 +16,6 @@ from uploader.oauth2.client import oauth2_post
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.genotypes.views import genotypesbp
-from uploader.db_utils import database_connection
 from uploader.datautils import enumerate_sequence
 from uploader.phenotypes.views import phenotypesbp
 from uploader.expression_data.views import exprdatabp
diff --git a/uploader/request_checks.py b/uploader/request_checks.py
index a24b2f7..f1d8027 100644
--- a/uploader/request_checks.py
+++ b/uploader/request_checks.py
@@ -4,10 +4,10 @@ These are useful for reusability, and hence maintainability of the code.
 """
 from functools import wraps
 
+from gn_libs.mysqldb import database_connection
 from flask import flash, url_for, redirect, current_app as app
 
 from uploader.species.models import species_by_id
-from uploader.db_utils import database_connection
 from uploader.population.models import population_by_species_and_id
 
 def with_species(redirect_uri: str):
diff --git a/uploader/species/views.py b/uploader/species/views.py
index 10715a5..fee5c75 100644
--- a/uploader/species/views.py
+++ b/uploader/species/views.py
@@ -1,5 +1,6 @@
 """Endpoints handling species."""
 from pymonad.either import Left, Right, Either
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -10,7 +11,6 @@ from flask import (flash,
 from uploader.population import popbp
 from uploader.platforms import platformsbp
 from uploader.ui import make_template_renderer
-from uploader.db_utils import database_connection
 from uploader.oauth2.client import oauth2_get, oauth2_post
 from uploader.authorisation import require_login, require_token
 from uploader.datautils import order_by_family, enumerate_sequence