updates in forum and recipes

biostar/__init__.py

@@ -3,4 +3,4 @@
 __all__ = ['celery_app']
 
 
-VERSION = '2.3.3'
+VERSION = '2.3.4'

biostar/accounts/views.py

@@ -36,6 +36,7 @@
 
 RATELIMIT_KEY = settings.RATELIMIT_KEY
 
+
 def edit_profile(request):
     if request.user.is_anonymous:
         messages.error(request, "Must be logged in to edit profile")
@@ -57,7 +58,6 @@ def edit_profile(request):
             username = form.cleaned_data["username"]
             email = form.cleaned_data['email']
             User.objects.filter(pk=user.pk).update(username=username, email=email)
-            # Update user information in Profile object.
             Profile.objects.filter(user=user).update(name=form.cleaned_data['name'],
                                                      watched_tags=form.cleaned_data['watched_tags'],
                                                      location=form.cleaned_data['location'],
@@ -69,6 +69,8 @@ def edit_profile(request):
                                                      message_prefs=form.cleaned_data["message_prefs"],
                                                      html=markdown(form.cleaned_data["text"]),
                                                      digest_prefs=form.cleaned_data['digest_prefs'])
+            # Recompute watched tags
+            Profile.objects.filter(user=user).first().add_watched()
 
             return redirect(reverse("user_profile", kwargs=dict(uid=user.profile.uid)))
 

biostar/forum/api.py

@@ -192,6 +192,17 @@ def traffic(request):
     return data
 
 
+@json_response
+def api_tag(request, tag):
+    """
+    Return list of post uids that have a tag.
+    """
+    posts = Post.objects.filter(tags__name=tag.lower()).values_list('uid', flat=True)
+    posts = list(posts)
+
+    return posts
+
+
 @json_response
 def user_email(request, email):
     user = User.objects.filter(email__iexact=email.lower())

biostar/forum/auth.py

@@ -287,9 +287,10 @@ def post_tree(user, root):
 
     # Get all posts that belong to post root.
     query = Post.objects.valid_posts(u=user, root=root).exclude(pk=root.id)
+
     # Filter quarantined and deleted comments or answers.
     if user.is_anonymous or not user.profile.is_moderator:
-        query = query.exclude(Q(spam=Post.SUSPECT) | Q(status=Post.DELETED))
+        query = query.exclude(Q(spam=Post.SUSPECT) | Q(status=Post.DELETED) | Q(spam=Post.SPAM))
 
     query = query.select_related("lastedit_user__profile", "author__profile", "root__author__profile")
 

biostar/forum/models.py

@@ -35,8 +35,11 @@ def valid_posts(self, u=None, **kwargs):
         if u and u.is_authenticated and u.profile.is_moderator:
             return query
 
+        # Users get to see their own quarantined posts.
+
         # Filter for open posts that are not spam.
         query = query.filter(status=Post.OPEN, root__status=Post.OPEN)
+
         query = query.filter(models.Q(spam=Post.NOT_SPAM) | models.Q(spam=Post.DEFAULT) |
                              models.Q(root__spam=Post.NOT_SPAM) | models.Q(root__spam=Post.DEFAULT))
 

biostar/forum/search.py

@@ -13,6 +13,7 @@
 from whoosh.searching import Results
 
 import html2markdown
+import bleach
 from whoosh.qparser import MultifieldParser, OrGroup
 from whoosh.analysis import STOP_WORDS
 from whoosh.index import create_in, open_dir, exists_in
@@ -107,8 +108,9 @@ def index_exists(dirname=settings.INDEX_DIR, indexname=settings.INDEX_NAME):
 
 
 def add_index(post, writer):
-    # user html2markdown to clean text.
-    content = html2markdown.convert(post.content)
+
+    # Ensure the content is stripped of any html.
+    content = bleach.clean(post.content, styles=[], attributes={}, tags=[], strip=True)
     writer.update_document(title=post.title, url=post.get_absolute_url(),
                            type_display=post.get_type_display(),
                            content_length=len(content),

biostar/forum/static/forum.css

@@ -52,6 +52,10 @@ body > .widen.container {
 
 }
 
+.ui.form .form-wrap .field>.selection.dropdown {
+    min-width: 0 !important;
+}
+
 .voting .ui.button {
     background: none;
     padding: 5px;

biostar/forum/tasks.py

@@ -42,19 +42,6 @@ def spam_scoring(post):
         message(exc)
 
 
-def tpatt(tag):
-    """
-    Return pattern matching a tag found in comma separated string.
-    (?i)             : case-insensitive flag
-    ^{tag}\\s*,      : matches beginning
-    ,\\s*{tag}\\s*,  : matches middle
-    ,\\s*{tag}$      : matches end
-    ^{tag}[^\\w+]    : matches single entry ( no commas )
-    """
-    patt = fr"(?i)(^{tag}\s*,|,\s*{tag}\s*,|,\s*{tag}$|^{tag}$)"
-    return patt
-
-
 @task
 def notify_watched_tags(post, extra_context):
     """
@@ -63,7 +50,7 @@ def notify_watched_tags(post, extra_context):
     from biostar.accounts.models import User
     from django.conf import settings
 
-    users = [User.objects.filter(profile__watched_tags__iregex=tpatt(tag.name)).distinct()
+    users = [User.objects.filter(profile__watched__name=tag.name).distinct()
              for tag in post.root.tags.all()]
 
     # Flatten nested users queryset and get email.

biostar/forum/templates/accounts/edit_profile.html

@@ -1,9 +1,26 @@
 {% extends "forum_base.html" %}
 {% load forum_tags %}
 {% load accounts_tags %}
+{% load static %}
 
 {% block headtitle %}Edit Profile{% endblock %}
 
+{% block head %}
+    <script async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" id="MathJax-script"></script>
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
+    <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
+    <link disabled rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/styles/default.min.css">
+    <script async src="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/highlight.min.js"></script>
+{% endblock %}
+
+{% block js %}
+
+    <script src="{% static 'semantic.min.js' %}"></script>
+    <script src="{% static 'prism.js' %}"></script>
+    <script src="{% static 'setup.js' %}{% randparam %}"></script>
+    <script src="{% static 'forum.js' %}{% randparam %}"></script>
+{% endblock %}
+
 {% block content %}
 
     <div class="ui horizontal segments no-shadow">

biostar/forum/templates/accounts/user_profile.html

@@ -21,6 +21,7 @@
     <script src="{% static 'forum.js' %}{% randparam %}"></script>
 {% endblock %}
 
+
 {% block content %}
 
     <div class="ui stackable three column grid profile" data-value="{{ target.profile.id }}">

biostar/forum/templates/banners/menu-topics.html

@@ -18,19 +18,18 @@
 
             {% if counts.messages.count %}
 
-                <div class="ui green large label">
+                <div class="ui green label">
                     <i class="envelope icon"></i>Messages ({{ counts.messages.count }})
                    </div>
             {%  else %}
                  <i class="envelope icon"></i> Messages
             {% endif %}
 
         </a>
-        <a class="item {% activate tab "myvotes" %}"
-           href="{% url 'myvotes' %}">
+        <a class="item {% activate tab "myvotes" %}" href="{% url 'myvotes' %}">
 
             {% if counts.votes.count %}
-                <div class="ui pink label"><i class="heart icon"></i> New Votes ({{ counts.votes.count }})</div>
+                <div class="ui pink label"><i class="heart icon"></i> Votes ({{ counts.votes.count }})</div>
             {%  else %}
                 <i class="heart icon"></i> Votes
             {% endif %}

biostar/forum/templates/base_view.html

@@ -9,3 +9,32 @@
     <link disabled rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/styles/default.min.css">
     <script async src="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/highlight.min.js"></script>
 {% endblock %}
+
+{% block css %}
+    <link rel="stylesheet" href="{% static 'autocomplete/tribute.css' %}" />
+    <link rel="stylesheet" href="{% static 'autocomplete/at.who.css' %}" />
+    <link href="{% static 'pagedown.css' %}" type="text/css" media="all" rel="stylesheet">
+    <link href="{% static 'prism.css' %}" rel="stylesheet">
+    <link href="{% static 'pagedown/demo/browser/demo.css' %}" type="text/css" media="all" rel="stylesheet">
+{% endblock %}
+
+
+{% block js %}
+    <script src="{% static 'autocomplete/tribute.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown/Markdown.Converter.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown-extra/pagedown/Markdown.Converter.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown/Markdown.Sanitizer.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown/Markdown.Editor.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown-extra/Markdown.Extra.js' %}"></script>
+    <script type="text/javascript" src="{% static 'pagedown_init.js' %}{% randparam %}"></script>
+
+    <script src="{% static 'semantic.min.js' %}"></script>
+    <script src="{% static 'prism.js' %}"></script>
+    <script src="{% static 'setup.js' %}{% randparam %}"></script>
+
+    <script src="{% static 'markdown-it.js' %}"></script>
+    <script src="{% static 'autocomplete/at.who.js' %}"></script>
+    <script src="{% static 'effects.js' %}{% randparam %}"></script>
+    <script src="{% static 'inplace.js' %}{% randparam %}"></script>
+    <script src="{% static 'forum.js' %}{% randparam %}"></script>
+{% endblock %}

biostar/forum/templates/forum_base.html

@@ -56,26 +56,24 @@
     {#% recaptcha_init %#}
 
     {#  CSS compression. #}
-    {% compress css inline %}
+    {% compress css %}
+
         <link href="{% static 'semantic.min.css' %}" rel="stylesheet">
         {#  Preload key requests #}
-        <link href="{% static 'prism.css' %}" rel="stylesheet">
         <link href="{% static 'forum.css' %}{% randparam %}" rel="stylesheet">
         {% block cssfile %}
         {% endblock %}
 
     {% endcompress %}
 
     {# Javascript compression. #}
-    {% compress js inline %}
+    {% compress js %}
 
         {% block jsfile %}
         {% endblock %}
 
     {% endcompress %}
 
-
-
     {# Optional css header content. #}
     {% block css %}
     {% endblock %}
@@ -86,6 +84,8 @@
     {% endblock %}
 
 </head>
+
+
 <body>
 
 <div class="ui inverted container widen">
@@ -120,6 +120,8 @@
     {% endblock %}
 </div>
 
+
 </body>
+
 </html>
 

biostar/forum/templates/new_post.html

@@ -8,33 +8,6 @@
 
 <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
 
-{% block css %}
-    <link href="{% static 'autocomplete/at.who.css' %}" rel="stylesheet">
-    <link rel="stylesheet" href="{% static 'autocomplete/tribute.css' %}"/>
-    <link href=" {% static 'pagedown.css' %}" type="text/css" media="all" rel="stylesheet">
-    <link href="{% static 'pagedown/demo/browser/demo.css' %}" type="text/css" media="all" rel="stylesheet">
-{% endblock %}
-
-{% block js %}
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Converter.js' %}"></script>
-    <script src="{% static 'autocomplete/tribute.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown-extra/pagedown/Markdown.Converter.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Sanitizer.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Editor.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown-extra/Markdown.Extra.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown_init.js' %}"></script>
-
-    <script src="{% static 'semantic.min.js' %}"></script>
-    <script src="{% static 'prism.js' %}"></script>
-    <script src="{% static 'setup.js' %}{% randparam %}"></script>
-    <script src="{% static 'forum.js' %}{% randparam %}"></script>
-
-    <script src="{% static 'markdown-it.js' %}"></script>
-    <script src="{% static 'autocomplete/at.who.js' %}"></script>
-    <script src="{% static 'autocomplete/caret.js' %}"></script>
-    <script src="{% static 'effects.js' %}{% randparam %}"></script>
-    <script src="{% static 'inplace.js' %}{% randparam %}"></script>
-{% endblock %}
 
 {% block container %}
     <div class="ui bottom attached create-post segment">

biostar/forum/templates/post_view.html

@@ -10,33 +10,6 @@
     <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
 
-{% block css %}
-    <link rel="stylesheet" href="{% static 'autocomplete/tribute.css' %}" />
-    <link rel="stylesheet" href="{% static 'autocomplete/at.who.css' %}" />
-    <link href="{% static 'pagedown.css' %}" type="text/css" media="all" rel="stylesheet">
-    <link href="{% static 'pagedown/demo/browser/demo.css' %}" type="text/css" media="all" rel="stylesheet">
-{% endblock %}
-
-
-{% block js %}
-    <script src="{% static 'autocomplete/tribute.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Converter.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown-extra/pagedown/Markdown.Converter.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Sanitizer.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown/Markdown.Editor.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown-extra/Markdown.Extra.js' %}"></script>
-    <script type="text/javascript" src="{% static 'pagedown_init.js' %}{% randparam %}"></script>
-
-    <script src="{% static 'semantic.min.js' %}"></script>
-    <script src="{% static 'prism.js' %}"></script>
-    <script src="{% static 'setup.js' %}{% randparam %}"></script>
-
-    <script src="{% static 'markdown-it.js' %}"></script>
-    <script src="{% static 'autocomplete/at.who.js' %}"></script>
-    <script src="{% static 'effects.js' %}{% randparam %}"></script>
-    <script src="{% static 'inplace.js' %}{% randparam %}"></script>
-    <script src="{% static 'forum.js' %}{% randparam %}"></script>
-{% endblock %}
 
 {% block body %}
 

biostar/forum/urls.py

@@ -63,6 +63,7 @@
     # Api calls
     path(r'api/traffic/', api.traffic, name='api_traffic'),
     path(r'api/user/<str:uid>/', api.user_details, name='api_user'),
+    path(r'api/tag/<str:tag>/', api.api_tag, name='api_tag'),
     path(r'api/tags/list/', api.tags_list, name='api_tags_list'),
     path(r'api/post/<str:uid>/', api.post_details, name='api_post'),
     path(r'api/vote/<str:uid>/', api.vote_details, name='api_vote'),

biostar/forum/views.py

@@ -112,7 +112,10 @@ def get_posts(user, topic="", tag="", order="", limit=None):
     elif topic == FOLLOWING and user.is_authenticated:
         query = query.filter(subs__user=user).exclude(subs__type=Subscription.NO_MESSAGES)
     elif topic == MYPOSTS and user.is_authenticated:
-        query = query.filter(author=user)
+        # Show users all of there posts ( deleted, spam, or quarantined )
+        query = Post.objects.filter(author=user)
+        #query = query.filter(author=user)
+
     elif topic == MYVOTES and user.is_authenticated:
         query = query.filter(votes__post__author=user)
     elif topic == MYTAGS and user.is_authenticated:

biostar/recipes/forms.py

@@ -244,8 +244,9 @@ def clean(self):
             if not cleaned_data.get("data_name"):
                 raise forms.ValidationError("Name is required with text inputs.")
 
-        total_count = Data.objects.filter(owner=self.user).count()
-        if total_count >= settings.MAX_DATA:
+        total_count = Data.objects.filter(owner=self.user, deleted=False).count()
+
+        if total_count >= settings.MAX_DATA and not self.user.profile.is_moderator:
             raise forms.ValidationError(f"Exceeded maximum amount of data:{settings.MAX_DATA}.")
         return cleaned_data
 

biostar/recipes/static/engine.css

@@ -37,8 +37,7 @@ body {
 }
 
 .ui-droppable-hover {
-    border: #10ee0a dotted 5px !important;
-    height: 50% !important;
+    border-bottom: #10ee0a solid 5px !important;
 }
 
 .draggable {

conf/scripts/server-cleanup.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# Load the conda commands.
+source ~/miniconda3/etc/profile.d/conda.sh
+
+export POSTGRES_HOST=/var/run/postgresql
+
+# Activate the conda environemnt.
+conda activate engine
+
+# Set the configuration module.
+export DJANGO_SETTINGS_MODULE=conf.run.site_settings
+
+python manage.py cleanup