diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 25 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 11 |
2 files changed, 23 insertions, 13 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 572db080..f87914d5 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -1,6 +1,7 @@ import datetime import json import os +import re from collections import namedtuple from itertools import groupby @@ -250,17 +251,21 @@ def update_phenotype(dataset_id: str, name: str): file_.save(new_file_name) publishdata_id = "" lines = [] + split_point = "" with open(new_file_name, "r") as f: lines = f.read() - first_line = lines.split('\n', 1)[0] - publishdata_id = first_line.split("Id:")[-1].strip() + for line in lines.split("\n"): + if "# Publish Data Id:" in line: + split_point = line + publishdata_id = re.findall(r'\b\d+\b', line)[0] + break with open(new_file_name, "w") as f: - f.write(lines.split("\n\n")[-1]) + f.write(lines.split(f"{split_point}\n")[-1].strip()) csv_ = get_trait_csv_sample_data(conn=conn, trait_name=str(name), phenotype_id=str(phenotype_id)) with open(uploaded_file_name, "w") as f_: - f_.write(csv_.split("\n\n")[-1]) + f_.write(csv_.split(str(publishdata_id))[-1].strip()) r = run_cmd(cmd=("csvdiff " f"'{uploaded_file_name}' '{new_file_name}' " "--format json")) @@ -423,9 +428,15 @@ def list_diffs(): gn_proxy_url=current_app.config.get("GN2_PROXY")) return render_template( "display_files.html", - approved=files.get("approved"), - rejected=files.get("rejected"), - waiting=files.get("waiting")) + approved=sorted(files.get("approved"), + reverse=True, + key=lambda d: d.get("time_stamp")), + rejected=sorted(files.get("rejected"), + reverse=True, + key=lambda d: d.get("time_stamp")), + waiting=sorted(files.get("waiting"), + reverse=True, + key=lambda d: d.get("time_stamp"))) @metadata_edit.route("/diffs/<name>") diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 2cbaffd6..55d9ebbe 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -131,9 +131,8 @@ def handle_generic_exceptions(e): time_str = now.strftime('%l:%M%p UTC %b %d, %Y') # get the stack trace and send it to the logger exc_type, exc_value, exc_traceback = sys.exc_info() - formatted_lines = {f"{request.url} ({time_str}) " - f" {traceback.format_exc().splitlines()}"} - + formatted_lines = (f"{request.url} ({time_str}) \n" + f"{traceback.format_exc()}") _message_templates = { werkzeug.exceptions.NotFound: ("404: Not Found: " f"{time_str}: {request.url}"), @@ -142,8 +141,8 @@ def handle_generic_exceptions(e): werkzeug.exceptions.RequestTimeout: ("408: Request Timeout: " f"{time_str}: {request.url}")} # Default to the lengthy stack trace! - logger.error(_message_templates.get(exc_type, - formatted_lines)) + app.logger.error(_message_templates.get(exc_type, + formatted_lines)) # Handle random animations # Use a cookie to have one animation on refresh animation = request.cookies.get(err_msg[:32]) @@ -152,7 +151,7 @@ def handle_generic_exceptions(e): "./wqflask/static/gif/error") if fn.endswith(".gif")]) resp = make_response(render_template("error.html", message=err_msg, - stack=formatted_lines, + stack={formatted_lines}, error_image=animation, version=GN_VERSION)) |