diff options
| -rw-r--r-- | scripts/phenotypes_bulk_edit.py | 7 | ||||
| -rw-r--r-- | uploader/publications/pubmed.py | 6 |
2 files changed, 10 insertions, 3 deletions
diff --git a/scripts/phenotypes_bulk_edit.py b/scripts/phenotypes_bulk_edit.py index 6d277e5..30933a6 100644 --- a/scripts/phenotypes_bulk_edit.py +++ b/scripts/phenotypes_bulk_edit.py @@ -6,15 +6,16 @@ from pathlib import Path from typing import Iterator from functools import reduce -import requests -from lxml import etree from MySQLdb.cursors import DictCursor from gn_libs import jobs, mysqldb, sqlite3 import uploader.publications.pubmed as pmed from uploader.publications.misc import publications_differences -from uploader.publications.models import fetch_phenotype_publications +from uploader.phenotypes.views import BULK_EDIT_COMMON_FIELDNAMES +from uploader.publications.models import ( + create_new_publications, fetch_phenotype_publications) + logging.basicConfig( format="%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s: %(message)s") logger = logging.getLogger(__name__) diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py index d984d99..9ad2ac0 100644 --- a/uploader/publications/pubmed.py +++ b/uploader/publications/pubmed.py @@ -1,4 +1,10 @@ """Module to interact with NCBI's PubMed""" +import logging + +import requests +from lxml import etree + +logger = logging.getLogger(__name__) def __pub_date__(pubdate: etree.Element): |