Merge a3a632f into bcf4a24

qiita_pet/handlers/analysis_handlers.py

@@ -1,9 +1,12 @@
 from tornado.web import authenticated
+from collections import defaultdict
 
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_db.user import User
 from qiita_db.analysis import Analysis
 from qiita_db.study import Study
+from qiita_db.data import ProcessedData
+from qiita_db.metadata_template import SampleTemplate
 # login code modified from https://gist.github.com/guillaumevincent/4771570
 
 
@@ -31,4 +34,47 @@ def post(self):
         analysis = Analysis.create(User(user), name, description)
 
         self.render('select_studies.html', user=user, aid=analysis.id,
-                    studies=studies)
+                    studies=studies)
+
+
+class SelectCommandsHandler(BaseHandler):
+    """Select commands to be executed"""
+    @authenticated
+    def post(self):
+        analysis_id = self.get_argument('analysis-id')
+        study_args = self.get_arguments('studies')
+        split = [x.split("#") for x in study_args]
+
+        # build dictionary of studies and datatypes selected
+        # as well a set of unique datatypes selected
+        study_dts = defaultdict(list)
+        data_types = set()
+        for study_id, data_type in split:
+            study_dts[study_id].append(data_type)
+            data_types.add(data_type)
+
+        # make sure the data types are unique
+        data_types = sorted(list(data_types))
+
+        # FIXME: Pull out from the database!!
+        commands = {'16S': ['Alpha Diversity', 'Beta Diversity',
+                            'Summarize Taxa'],
+                    '18S': ['Alpha Diversity', 'Beta Diversity',
+                            'Summarize Taxa'],
+                    'Metabolomic': ['Summarize Taxa']}
+
+        self.render('select_commands.html', user=self.get_current_user(),
+                    commands=commands, data_types=data_types, aid=analysis_id)
+
+        analysis = Analysis(analysis_id)
+
+        for study_id in study_dts:
+            study = Study(study_id)
+            processed_data = {ProcessedData(pid).data_type: pid for pid in
+                              study.processed_data}
+
+            sample_ids = SampleTemplate(study.id).keys()
+            for data_type in study_dts[study.id]:
+                samples = [(processed_data[data_type], sid) for sid in
+                           sample_ids]
+                analysis.add_samples(samples)

qiita_pet/static/css/style.css

@@ -2,75 +2,3 @@
   padding: 20px;
 }
 
-/* navbar code from http://line25.com/tutorials/how-to-create-a-pure-css-dropdown-menu */
-nav {
-    padding: 0px;
-    margin: 0px;
-    font-size: 18px;
-    text-align: center;
-}
-
-nav ul ul {
-    display: none;
-}
-
-nav ul li:hover > ul {
-    display: block;
-}
-
-
-nav ul {
-    background: #A7A9AC; 
-    padding: 0 20px; 
-    list-style: none;
-    position: relative;
-}
-    nav ul:after {
-        content: ""; 
-        clear: both; 
-        display: block;
-    }
-
-    nav ul li {
-        float: left;
-    }
-        nav ul li:hover {
-            background: #999;
-        }
-            nav ul li:hover a {
-                color: #000;
-            }
-
-        nav ul li a {
-            display: block; 
-            padding: 10px 10px;
-            color: #000; 
-            text-decoration: none;
-
-        }
-
-
-    nav ul ul {
-        background: #999; 
-        border-radius: 0px; 
-        padding: 0;
-        position: absolute; top: 100%;
-    }
-        nav ul ul li {
-            float: none; 
-            border-top: 1px solid #999;
-            border-bottom: 1px solid #999; 
-            position: relative;
-        }
-            nav ul ul li a {
-                padding: 10px 10px;
-                color: #000;
-            }   
-                nav ul ul li a:hover {
-                    background: #888;
-                }
-
-    nav ul ul ul {
-        position: absolute; left: 100%; 
-        top:0;
-    }

qiita_pet/templates/404.html

@@ -1,4 +1,4 @@
-{%extends base.html%}
+{%extends sitebase.html%}
 {%block content%}
 <h1>404: Page not found!</h1>
 {%end%}

qiita_pet/templates/index.html

@@ -4,6 +4,15 @@
 
 {%block content %}
 <div class="jumbotron">
-  <h2>Welcome to Qiita.</h2>
+  <h1>Welcome to Qiita</h1>
+  <p align="justify">
+    Qiita is a development effort powering the data analysis and storage for the Human Microbiome Project phase two of the Human Microbiome Project, a new three-year "multi-omic" study investigating the roles played by microbes and their interactions with the human body. Using inflammatory bowel disease as our focus, this project will delve into the relationship between the microbiome and disease.
+  </p>
+  </ br>
+  <p align="right">
+    <small>
+        <i>Text taken from <a href="https://ibdmdb.org">https://ibdmdb.org</a>.</i>
+    </small>
+  </p>
 </div>
-{% end %}
+{% end %}

qiita_pet/templates/select_commands.html

@@ -0,0 +1,48 @@
+{% extends sitebase.html %}
+{% autoescape None %}
+
+{%block head%}
+<script>
+  $(function () {
+    $('#data-types-tabs a:first').tab('show')
+  })
+</script>
+{%end%}
+
+{%block content %}
+
+<h1>Select Commands</h1>
+
+<ul class="nav nav-tabs" id="data-types-tabs">
+  {% for data_type in data_types %}
+    <li><a href="#{{ data_type }}" data-toggle="tab">{{ data_type }}</a></li>
+  {% end %}
+</ul>
+
+<form role="form" action="/analysis/wait/" method="post">
+  <input type="hidden" name="analysis-id" value="{{aid}}">
+  <div class="tab-content" style="height:300px">
+    {% for data_type in data_types %}
+      <div class="tab-pane" id="{{ data_type }}">
+            <table class="table">
+              <tr>
+                <th style="width:20px;"></th>
+                <th>Command</th>
+              </tr>
+              {% for command in commands[data_type] %}
+                <tr>
+                  <td style="width:20px;">
+                    <input id="{{data_type}}#{{command}}" type="checkbox" name="commands" value="{{data_type}}#{{command}}">
+                  </td>
+                  <td>
+                    <label style="font-weight:normal;" for="{{data_type}}#{{command}}">{{command}}</label>
+                  </td>
+                </tr>
+              {% end %}
+            </table>
+      </div>
+    {% end %}
+  </div>
+  <button type="submit" class="btn btn-default">Start Processing</button>
+</form>
+{% end %}

qiita_pet/templates/select_studies.html

@@ -16,20 +16,25 @@ <h1>Studies</h1>
     <input type="hidden" name="analysis-id" value="{{aid}}">
       <table class="table table-hover">
         <tr>
-          <th> </th>
+          <th>Data Types</th>
           <th>Study Name</th>
           <th>Description</th>
         </tr>
         {% for study in studies %}
         <tr>
-          <td><input type="checkbox" name="studies" value="{{study.id}}"></td>
-          <td>{{study.title}}</td>
-          <td>{{study.info["study_description"]}}</td>
+          <td>
+          {% for data_type in study.data_types %}
+              <input type="checkbox" name="studies" value="{{study.id}}#{{data_type}}">{{data_type}}
+              <br />
+          {% end %}
+          </td>
+          <td style="vertical-align:middle;">{{study.title}}</td>
+          <td style="vertical-align:middle;">{{study.info["study_description"]}}</td>
         </tr>
         {% end %}
       </table>
       <button type="submit" class="btn btn-default">Select studies</button>
       </form>
     </div>
 
-{% end %}
+{% end %}