Merge pull request #106 from ElDeveloper/webfleshout-the-revenge

Add data type and commands selection

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)
+
+        # sort the elements to have 16S be the first tho show on the tabs
+        data_types = sorted(list(data_types))
+
+        # FIXME: Pull out from the database, see #111
+        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/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/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 %}

qiita_pet/webserver.py

@@ -17,7 +17,7 @@
 from qiita_pet.handlers.auth_handlers import (
     AuthCreateHandler, AuthLoginHandler, AuthLogoutHandler, AuthVerifyHandler)
 from qiita_pet.handlers.analysis_handlers import (
-    CreateAnalysisHandler, SelectStudiesHandler)
+    CreateAnalysisHandler, SelectStudiesHandler, SelectCommandsHandler)
 
 define("port", default=8888, help="run on the given port", type=int)
 
@@ -42,6 +42,7 @@ def __init__(self):
              {"path": STATIC_PATH}),
             (r"/analysis/1", CreateAnalysisHandler),
             (r"/analysis/2", SelectStudiesHandler),
+            (r"/analysis/3", SelectCommandsHandler),
             (r"/mockup/", MockupHandler),
             # 404 PAGE MUST BE LAST IN THIS LIST!
             (r".*", NoPageHandler)
@@ -63,4 +64,4 @@ def main():
     tornado.ioloop.IOLoop.instance().start()
 
 if __name__ == "__main__":
-    main()
+    main()