Merge pull request #1166 from squirrelo/fix-1061

Fix 1061 - analysis.jobs always returns list

Author: josenavas

qiita_db/analysis.py

@@ -425,14 +425,12 @@ def jobs(self):
         Returns
         -------
         list of ints
-            Job ids for jobs in analysis
+            Job ids for jobs in analysis. Empty list if no jobs attached.
         """
         conn_handler = SQLConnectionHandler()
         sql = ("SELECT job_id FROM qiita.analysis_job WHERE "
                "analysis_id = %s".format(self._table))
         job_ids = conn_handler.execute_fetchall(sql, (self._id, ))
-        if job_ids == []:
-            return None
         return [job_id[0] for job_id in job_ids]
 
     @property

qiita_db/test/test_analysis.py

@@ -304,7 +304,7 @@ def test_retrieve_jobs(self):
     def test_retrieve_jobs_none(self):
         new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
                               "A New Analysis", Analysis(1))
-        self.assertEqual(new.jobs, None)
+        self.assertEqual(new.jobs, [])
 
     def test_retrieve_pmid(self):
         self.assertEqual(self.analysis.pmid, "121112")

qiita_pet/handlers/analysis_handlers.py

@@ -144,15 +144,14 @@ def get(self, analysis_id):
 
         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)
-                data_type = proc_data.data_type()
-                study = proc_data.study
-                dropped[data_type].append((Study(study).title, len(samples),
-                                           ', '.join(samples)))
+        for proc_data_id, samples in viewitems(dropped_samples):
+            if not samples:
+                continue
+            proc_data = ProcessedData(proc_data_id)
+            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/select_commands.html

@@ -2,7 +2,17 @@
 {% autoescape None %}
 
 {%block head%}
+
 <script>
+  function check_selection(){
+    if($('.command:checkbox:checked').length > 0){
+       return true;
+   }else {
+        $('#error').text('Please select at least one command.');
+       return false;
+   }
+  }
+
   $(function () {
     $('#data-types-tabs a:first').tab('show')
   })
@@ -12,8 +22,8 @@
 {%block content %}
 
 <h1>Select Commands</h1>
-
-<form role="form" action="/analysis/wait/{{aid}}" method="post">
+<span id="error" style="color:red"></span>
+<form role="form" action="/analysis/wait/{{aid}}" method="post" onsubmit="return check_selection()">
 <div style="padding-bottom:25px;">
     Rarefaction Depth: <input type="number" min="10" id="rarefaction-depth" name="rarefaction-depth" class="form-control" style="width:10em;">
 </div>
@@ -35,7 +45,7 @@ <h1>Select Commands</h1>
           {% for command in commands[data_type] %}
             <tr>
               <td style="width:20px;">
-                <input id="{{data_type}}#{{command.name}}" type="checkbox" name="commands" value="{{data_type}}#{{command.name}}">
+                <input id="{{data_type}}#{{command.name}}" type="checkbox" name="commands" class="command" value="{{data_type}}#{{command.name}}">
               </td>
               <td>
                 <label style="font-weight:normal;" for="{{data_type}}#{{command.name}}">{{command.name}}</label>

qiita_ware/analysis_pipeline.py

@@ -27,7 +27,15 @@ def _build_analysis_files(analysis, r_depth=None, **kwargs):
         The analysis to build files for
     r_depth : int, optional
         Rarefaction depth for biom table creation. Default None
+
+    Raises
+    ------
+    RuntimeError
+        No jobs are attached to the given analysis
     """
+    if not analysis.jobs:
+        raise RuntimeError("Analysis %d has no jobs attached!" % analysis.id)
+
     # create the biom tables and add jobs to the analysis
     analysis.status = "running"
     analysis.build_files(r_depth)