Skip to content

Fixes #2398 #2658

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 9 commits into from
Sep 11, 2018
Merged

Fixes #2398 #2658

Show file tree
Hide file tree
Changes from 7 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
9797a1a
Fixes #2398
Sep 1, 2018
ad34d04
Resolving conflict with another new patch file.
Sep 1, 2018
c73bd55
Merge branch 'dev' of http://github.com/biocore/qiita into dev
Sep 4, 2018
8aed862
Rename file
Sep 4, 2018
f6cfb15
67.py renamed to 66.py. minor edit to edit_study.html
Sep 4, 2018
043f5eb
Update study title only if UTF-8 characters were removed.
Sep 4, 2018
7b5f42d
Merge branch 'dev' of http://github.com/biocore/qiita into dev
Sep 5, 2018
6b099ca
UTF-8 stripper now processes all study-types.
Sep 10, 2018
ebd99b0
66.py now passes flake8 tests.
Sep 10, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 16 additions & 5 deletions qiita_db/support_files/patches/python_patches/66.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,15 +1,26 @@
# August 6, 2018
# Create parameters for the ssh/scp remote file upload commands


from json import loads, dumps

from qiita_db.sql_connection import TRN
from qiita_db.software import Software, Command
from qiita_db.exceptions import (QiitaDBError, QiitaDBDuplicateError)
from qiita_db.util import convert_to_id
from qiita_db.study import Study
from re import sub

# August 31, 2018
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This patch needs to be moved to its own file.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I can do this in my PR as I'm fixing conflicts; however, in the past we have decided to have only one patch per release cycle ... thus; the idea of having in the same patch

# Strip any UTF-8 characters that are not also printable ASCII characters
# from study titles. As some analysis packages cannot interpret UTF-8
# characters, it becomes important to remove them from study titles, as
# they are used as metadata/identifiers when creating new analyses.
studies = Study.get_by_status('public')
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just realized that this will only loop over the public studies and we need to check all studies ...

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looking through the methods, I haven't yet seen a way to enumerate through all of the studies, regardless of status (Study.get_all() or similar). It looks like the source of truth for the set of valid status strings is ultimately the qiita.visibility table, which lists the following:
awaiting_approval
sandbox
private
public

A nested loop to process each status in turn isn't horrible, but this might be a good time to write a get_all(), if it's not already available.

Another alternative would be to simply perform the same action in SQL directly. It looks like the only state we're changing through the API is study_title in the qiita.study table. The update statement below has already been tested, and could be placed in 66.sql:

update qiita.study set study_title = REGEXP_REPLACE(study_title,'[^\x20-\x7E]+','','g');

What do you think?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good point, perhaps we should open an issue about making sure that all objects have an iter method. Anyway, we normally do:

studies = Study.get_by_status('private').union(
    Study.get_by_status('public')).union(Study.get_by_status('sandbox'))


for study in studies:
new_title = sub(r'[^\x20-\x7E]+', '', study.title)
if new_title != study.title:
study.title = new_title


# August 6, 2018
# Create parameters for the ssh/scp remote file upload commands
# Copied from patch 58.py. Couldn't import due to how patching system works
def create_command(software, name, description, parameters, outputs=None,
analysis_only=False):
Expand Down
13 changes: 10 additions & 3 deletions qiita_pet/templates/edit_study.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
{% extends sitebase.html %}
{% block head %}
<script type="text/javascript" src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.validate.min.js"></script>
<script type = "text/javascript"
src = "{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.validate.min.js">
</script>
<style>
.custom-combobox {
position: relative;
Expand Down Expand Up @@ -32,7 +34,9 @@
var title = $(this).val();
// removing any duplicated whitespaces
title = title.replace(/ +(?= )/g, '');
// removing wite spaces from the front of the text
//remove all utf-8 encoded characters that are not also printable ASCII characters.
title = title.replace(/[^\x20-\x7E]+/g, "");
// removing white spaces from the front of the text
$(this).val(title.trimLeft());
});
$("#create_study").validate({
Expand Down Expand Up @@ -156,8 +160,11 @@ <h3>
{% if form_item.label.text == 'Environmental Packages' %}
{% set kwargs['size'] = len(form_item.choices) %}
{% set additional_info = 'You can select multiple entries by control-clicking (mac: command-clicking)' %}
{% elif form_item.label.text == 'Principan Investigator'%}
{% elif form_item.label.text == 'Principal Investigator'%}
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

thanks!

{% set kwargs['class_'] = kwargs['class_'] + ' chzn-select' %}
{% elif form_item.label.text == 'Study Title'%}
{% set additional_info = 'Study titles may only contain ASCII characters' %}

{% end %}
<tr>
<td width="20%">{% raw form_item.label %} <br /> <small>{{additional_info}}</small></td>
Expand Down