diff options
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 11 | ||||
| -rw-r--r-- | uploader/phenotypes/models.py | 3 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 7 | ||||
| -rw-r--r-- | uploader/population/rqtl2.py | 2 | ||||
| -rw-r--r-- | uploader/publications/models.py | 2 | ||||
| -rw-r--r-- | uploader/publications/views.py | 3 |
6 files changed, 9 insertions, 19 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index 9c636b9..e4802b7 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -1,16 +1,17 @@ import sys import uuid import json +import time import logging import argparse import datetime +from typing import Any from pathlib import Path from zipfile import ZipFile -from typing import Any, Union from urllib.parse import urljoin from functools import reduce, partial -from MySQLdb.cursors import Cursor, DictCursor +from MySQLdb.cursors import DictCursor from gn_libs import jobs, mysqldb, sqlite3, monadic_requests as mrequests @@ -23,9 +24,7 @@ from uploader.phenotypes.models import ( save_phenotypes_data, create_new_phenotypes, quick_save_phenotypes_data) -from uploader.publications.models import ( - create_new_publications, - fetch_publication_by_id) +from uploader.publications.models import fetch_publication_by_id from scripts.rqtl2.bundleutils import build_line_joiner, build_line_splitter @@ -180,7 +179,7 @@ def save_numeric_data( except Exception as _exc: logger.debug("Could not use `LOAD … INFILE`, using raw query", exc_info=True) - import time;time.sleep(60) + time.sleep(60) return save_phenotypes_data( conn, table, diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index ed14993..4a1b2d5 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -9,9 +9,10 @@ from typing import Optional, Iterable import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor -from functional_tools import take from gn_libs.mysqldb import debug_query +from functional_tools import take + logger = logging.getLogger(__name__) diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 4a9df8b..04cdc3b 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,15 +1,12 @@ """Views handling ('classical') phenotypes.""" import sys -import csv import uuid import json import logging -import tempfile from typing import Any from pathlib import Path from zipfile import ZipFile from functools import wraps, reduce -from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING from urllib.parse import urljoin, urlparse, ParseResult, urlunparse, urlencode import datetime @@ -18,7 +15,6 @@ from redis import Redis from pymonad.either import Left from requests.models import Response from MySQLdb.cursors import DictCursor -from werkzeug.utils import secure_filename from gn_libs import sqlite3 from gn_libs import jobs as gnlibs_jobs @@ -31,7 +27,6 @@ from flask import (flash, jsonify, redirect, Blueprint, - send_file, current_app as app) # from r_qtl import r_qtl2 as rqtl2 @@ -53,7 +48,6 @@ from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.publications.models import fetch_publication_by_id from uploader.request_checks import with_species, with_population -from uploader.samples.models import samples_by_species_and_population from uploader.input_validation import (encode_errors, decode_errors, is_valid_representative_name) @@ -64,7 +58,6 @@ from .models import (dataset_by_id, save_new_dataset, dataset_phenotypes, datasets_by_population, - phenotypes_data_by_ids, phenotype_publication_data) phenotypesbp = Blueprint("phenotypes", __name__) diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py index 044cdd4..97d4854 100644 --- a/uploader/population/rqtl2.py +++ b/uploader/population/rqtl2.py @@ -12,9 +12,9 @@ import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection +from markupsafe import escape from flask import ( flash, - escape, request, url_for, redirect, diff --git a/uploader/publications/models.py b/uploader/publications/models.py index b199991..f37b67d 100644 --- a/uploader/publications/models.py +++ b/uploader/publications/models.py @@ -1,6 +1,6 @@ """Module to handle persistence and retrieval of publication to/from MariaDB""" import logging -from typing import Iterable, Optional +from typing import Iterable from MySQLdb.cursors import DictCursor diff --git a/uploader/publications/views.py b/uploader/publications/views.py index 0608a35..e7aa412 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -1,7 +1,6 @@ """Endpoints for publications""" import json -from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection from flask import ( flash, @@ -21,8 +20,6 @@ from .models import ( from .datatables import fetch_publications -from gn_libs.debug import __pk__ - pubbp = Blueprint("publications", __name__) |