Merge branch 'master' of https://github.com/biocore/qiita into disable-make-processed-data-public

Author: josenavas

INSTALL.md

@@ -113,3 +113,7 @@ As a general rule of thumb you will want to have an updated version of Python
 H5PY is known to cause a few problems, however their [installation
 instructions](http://docs.h5py.org/en/latest/build.html) are a great resource
 to troubleshoot your system in case any of the steps above fail.
+
+## Troubleshooting installation issues with matplotlib
+
+In the event that you get `_tkinter.TclError: no display name and no $DISPLAY environment variable` error while trying to generate figures that rely on matplotlib, you should create a matplotlib rc file. This configuration file should have `backend : agg`. For more information you should visit the [matplotlib configuration](http://matplotlib.org/users/customizing.html) and [troubleshooting](http://matplotlib.org/faq/troubleshooting_faq.html#locating-matplotlib-config-dir) page.

qiita_db/test/test_study.py

@@ -441,7 +441,11 @@ def test_create_unknown_db_col(self):
 
     def test_delete(self):
         title = "Fried chicken microbiome"
-        study = Study.create(User('test@foo.bar'), title, [1], self.info)
+        # the study is assigned to investigation 1
+        study = Study.create(User('test@foo.bar'), title, [1], self.info,
+                             Investigation(1))
+        # sharing with other user
+        study.share(User("shared@foo.bar"))
         study.delete(study.id)
         self.assertFalse(study.exists(title))
 

qiita_pet/handlers/analysis_handlers.py

@@ -30,6 +30,7 @@
                            check_access_to_analysis_result,
                            filepath_ids_to_rel_paths)
 from qiita_db.exceptions import QiitaDBUnknownIDError
+from qiita_db.study import Study
 
 SELECT_SAMPLES = 2
 SELECT_COMMANDS = 3
@@ -141,14 +142,17 @@ def get(self, analysis_id):
             jobres[jobject.datatype].append((jobject.command[0],
                                              jobject.results))
 
-        dropped = {}
         dropped_samples = analysis.dropped_samples
+        dropped = defaultdict(list)
         if dropped_samples:
             for proc_data_id, samples in viewitems(dropped_samples):
+                if not samples:
+                    continue
                 proc_data = ProcessedData(proc_data_id)
-                key = "Data type %s, Study: %s" % (proc_data.data_type(),
-                                                   proc_data.study)
-                dropped[key] = samples
+                data_type = proc_data.data_type()
+                study = proc_data.study
+                dropped[data_type].append((Study(study).title, len(samples),
+                                           ', '.join(samples)))
 
         self.render("analysis_results.html",
                     jobres=jobres, aname=analysis.name, dropped=dropped,

qiita_pet/templates/analysis_results.html

@@ -11,44 +11,60 @@
 
 
 <div class="row">
-  <h1>Analysis {{aname}}</h1>
-
-  {% if dropped %}
-    <h3>Dropped Samples</h3>
-    These samples were dropped during processing due to rarefaction:
-    <table width="100%">
-    {% for study, samples in viewitems(dropped) %}
-      <tr>
-        <td width="5%">For {{study}}:</td>
-        <td width="80%"><small>{{', '.join(samples)}}</small></td>
-      </tr>
-    {% end %}
-    </table>
-    <br/>
-  {% end %}
+  <h1>&nbsp;Analysis: <u>{{aname}}</u></h1>
 </div>
 
 
+<div class="row" width='100%'>
+  <div class="col-md-12">
+    <div class="panel-group" id="accordion">
+      {% if dropped %}
+        <div class="panel panel-default">
+          <div class="panel-heading">
+            <h3 class="panel-title"><a data-toggle="collapse" data-parent="#accordion" href="#dropped-samples">Dropped Samples</a></h3>
+          </div>
+          <div id="dropped-samples" class="panel-collapse collapse">
+              <div class="panel-body">
+                  {% for data_type, studies in viewitems(dropped) %}
+                    <b><u>{{data_type}}</u></b>
+                    <br/><br/>
+                    {% for title, num_samples, samples in studies %}
+                      <b>{{title}}:</b>
+                      <br/>
+                      Total dropped: {{num_samples}}
+                      <br/>
+                      {{samples}}<br/>
+                    {% end %}
+                    <hr>
+                  {% end %}
+              </div>
+          </div>
+        </div>
+      {% end %}
+    </div>
+  </div>
+</div>
+
 <div class="row" width='100%'>
   <div class="col-md-2">
     <div class="panel-group" id="accordion">
-{% for data_type, jobs in jobres.items() %}
+      {% for data_type, jobs in jobres.items() %}
         <div class="panel panel-default">
           <div class="panel-heading">
             <h3 class="panel-title"><a data-toggle="collapse" data-parent="#accordion" href="#{{data_type}}">{{data_type}}</a></h3>
           </div>
           <div id="{{data_type}}" class="panel-collapse collapse">
-{% for job, results in jobs%}
+            {% for job, results in jobs%}
               <div class="panel-body">
                 {{job}}<br />
-  {% if len(results) == 0 %}
+                {% if len(results) == 0 %}
                   <h3 style="color:red">ERROR</h3>
-  {% end %}
-  {%for result in results%}
+                {% end %}
+                {%for result in results%}
                   <a href='{{"/results/%s" % result}}' target="resframe">{{basename(result)}}</a><br />
-  {% end %}
+                {% end %}
               </div>
-{% end %}
+            {% end %}
           </div>
         </div>
       {% end %}