Add "last 5 comments" to runs page

Also add a /comments page with all comments on it Fixes #396
hammerlab · Jan 16, 2015 · e75b967 · e75b967
1 parent 7b4ee73
commit e75b967
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Showing 7 changed files with 125 additions and 42 deletions.
diff --git a/cycledash/static/css/runs.css b/cycledash/static/css/runs.css
@@ -11,6 +11,14 @@ form#submit {
 #show-submit {
   float: right;
 }
+
+/* Last comments list: */
+a.all-comments {
+  font-size: 14px;
+  color: #adadad;
+}
+
+/* Runs table: */
 .runs.table {
   margin-top: 23px;
 }

diff --git a/cycledash/static/css/style.css b/cycledash/static/css/style.css
@@ -10,3 +10,29 @@ section {
   margin: auto;
 }
 img.cycle { float: right; }
+
+.comments {
+  list-style: none;
+}
+.comments .run-id {
+  font-weight: bold;
+}
+.comments .run-id a {
+  color: black;
+}
+.comments .location {
+  padding-left: 7px;
+}
+.comments .summary {
+  padding-left: 20px;
+}
+.comments .summary:before {
+  content: '“';
+  font-size: 19px;
+  padding-right: 5px;
+}
+.comments .summary:after {
+  content: '”';
+  font-size: 19px;
+  padding-left: 5px;
+}
diff --git a/cycledash/templates/comments.html b/cycledash/templates/comments.html
@@ -0,0 +1,13 @@
+{% extends "layouts/layout.html" %}
+{%- from 'macros/nav.html' import nav -%}
+{%- from 'macros/comments.html' import comment_list -%}
+
+{% block body %}
+{{ nav("runs") }}
+<main>
+  <section>
+    <h1>All Comments</h1>
+    {{ comment_list(comments) }}
+  </section>
+</main>
+{% endblock %}
diff --git a/cycledash/templates/macros/comments.html b/cycledash/templates/macros/comments.html
@@ -0,0 +1,13 @@
+{% macro comment_list(comments) -%}
+<ul class="comments">
+  {% for comment in comments -%}
+  <li>
+    <span class="run-id">
+      <a href="/runs/{{ comment['vcf_id'] }}/examine">Run {{ comment['vcf_id'] }}</a>
+    </span>
+    <span class="location">{{ comment['contig'] }}:{{ comment['position'] }}</span>
+    <span class="summary">{{ comment['comment_text']|truncate(80)}}</span>
+  </li>
+  {% endfor -%}
+</ul>
+{%- endmacro %}
diff --git a/cycledash/templates/macros/run_form.html b/cycledash/templates/macros/run_form.html
@@ -0,0 +1,44 @@
+{% macro run_form() -%}
+<form method="POST" action="/runs" role="form" id="submit">
+  <h2><button type="button" class="close" aria-hidden="true">&times;</button></h3>
+    <div class="form-group">
+      <label>Variant Caller Name:</label>
+      <input class="form-control" type="text" name="variantCallerName"
+             placeholder="Guacamole::Somatic">
+    </div>
+    <div class="form-group">
+      <label>Dataset Name:</label>
+      <input class="form-control" type="text" name="dataset"
+             placeholder="DREAM training chr20">
+    </div>
+    <div class="form-group">
+      <label>VCF Path:</label>
+      <input class="uploadable form-control" type="text" name="vcfPath"
+             placeholder="/data/somevcf.vcf">
+    </div>
+    <div class="form-group">
+      <label>Truth VCF Path:</label>
+      <input class="uploadable form-control" type="text" name="truthVcfPath"
+             placeholder="/data/true_somevcf.vcf">
+    </div>
+    <br/>
+    <h4>Optional <small>all paths should be HDFS paths to canonical data</small></h4>
+    <div class="form-group">
+      <label>Tumor BAM:</label>
+      <input class="form-control" type="text" name="tumorPath"
+             placeholder="/data/dream/tumor.chr20.bam">
+    </div>
+    <div class="form-group">
+      <label>Normal BAM:</label>
+      <input class="form-control" type="text" name="normalPath"
+             placeholder="/data/dream/normal.chr20.bam">
+    </div>
+    <div class="form-group">
+      <label>Notes, Config, Params:</label>
+      <textarea class="form-control" rows="3" name="params"
+                placeholder="command line parameters here"></textarea>
+    </div>
+
+    <button type="submit" class="btn btn-success btn-block">Submit New Run</button>
+</form>
+{%- endmacro -%}
diff --git a/cycledash/templates/runs.html b/cycledash/templates/runs.html
@@ -1,5 +1,7 @@
 {% extends "layouts/layout.html" %}
 {%- from 'macros/nav.html' import nav -%}
+{%- from 'macros/run_form.html' import run_form -%}
+{%- from 'macros/comments.html' import comment_list -%}
 
 {% block head %}
 <link rel="stylesheet" href="static/css/runs.css">
@@ -9,48 +11,12 @@
 {{ nav("runs") }}
 <main>
   <h2>Runs Directory <button id="show-submit" class="btn btn-default">Submit New Run</button></h2>
-  <form method="POST" action="/runs" role="form" id="submit">
-    <h2><button type="button" class="close" aria-hidden="true">&times;</button></h3>
-      <div class="form-group">
-        <label>Variant Caller Name:</label>
-        <input class="form-control" type="text" name="variantCallerName"
-               placeholder="Guacamole::Somatic">
-      </div>
-      <div class="form-group">
-        <label>Dataset Name:</label>
-        <input class="form-control" type="text" name="dataset"
-               placeholder="DREAM training chr20">
-      </div>
-      <div class="form-group">
-        <label>VCF Path:</label>
-        <input class="uploadable form-control" type="text" name="vcfPath"
-               placeholder="/data/somevcf.vcf">
-      </div>
-      <div class="form-group">
-        <label>Truth VCF Path:</label>
-        <input class="uploadable form-control" type="text" name="truthVcfPath"
-               placeholder="/data/true_somevcf.vcf">
-      </div>
-      <br/>
-      <h4>Optional <small>all paths should be HDFS paths to canonical data</small></h4>
-      <div class="form-group">
-        <label>Tumor BAM:</label>
-        <input class="form-control" type="text" name="tumorPath"
-               placeholder="/data/dream/tumor.chr20.bam">
-      </div>
-      <div class="form-group">
-        <label>Normal BAM:</label>
-        <input class="form-control" type="text" name="normalPath"
-               placeholder="/data/dream/normal.chr20.bam">
-      </div>
-      <div class="form-group">
-        <label>Notes, Config, Params:</label>
-        <textarea class="form-control" rows="3" name="params"
-                  placeholder="command line parameters here"></textarea>
-      </div>
+  {{ run_form() }}
 
-      <button type="submit" class="btn btn-success btn-block">Submit New Run</button>
-  </form>
+  {% if last_comments -%}
+  <h4>Last {{ last_comments|length}} Comments: <a href="/comments" class="all-comments">(see all)</a></h4>
+  {{ comment_list(last_comments) }}
+  {%- endif %}
 
   <table class="runs table condenses table-hover">
     <thead>

diff --git a/cycledash/views.py b/cycledash/views.py
@@ -65,8 +65,13 @@ def runs():
             q = select(vcfs.c + [num_comments]).select_from(joined).group_by(
                 vcfs.c.id).order_by(desc(vcfs.c.id))
             vcfs = [dict(v) for v in con.execute(q).fetchall()]
+
+            q = select(user_comments.c).order_by(
+                desc(user_comments.c.last_modified)).limit(5)
+            last_comments = [dict(c) for c in con.execute(q).fetchall()]
         if 'text/html' in request.accept_mimetypes:
-            return render_template('runs.html', runs=vcfs, run_kvs=RUN_ADDL_KVS)
+            return render_template('runs.html', runs=vcfs, run_kvs=RUN_ADDL_KVS,
+                                   last_comments=last_comments)
         elif 'application/json' in request.accept_mimetypes:
             return jsonify({'runs': vcfs})
 
@@ -92,6 +97,14 @@ def download_vcf(run_id):
     return send_file(fd, as_attachment=True, attachment_filename=filename)
 
 
+@app.route('/comments')
+def all_comments():
+    with tables(db, 'user_comments') as (con, user_comments):
+        q = select(user_comments.c).order_by(
+            desc(user_comments.c.last_modified))
+        comments = [dict(c) for c in con.execute(q).fetchall()]
+    return render_template('comments.html', comments=comments)
+
 @app.route('/runs/<vcf_id>/comments', methods=['GET', 'POST'])
 def comments(vcf_id):
     if request.method == 'POST':