Fix 1505

qiita_db/test/test_user.py

@@ -450,14 +450,26 @@ def test_user_artifacts(self):
                                     qdb.artifact.Artifact(7)]}
         self.assertEqual(obs, exp)
 
-    def test_jobs(self):
+    def test_jobs_all(self):
         PJ = qdb.processing_job.ProcessingJob
+        ignore_status = []
         # generates expected jobs
-        jobs = qdb.user.User('shared@foo.bar').jobs()
+        jobs = qdb.user.User('shared@foo.bar').jobs(ignore_status)
         self.assertEqual(jobs, [
             PJ('d19f76ee-274e-4c1b-b3a2-a12d73507c55'),
             PJ('b72369f9-a886-4193-8d3d-f7b504168e75')])
 
+        # no jobs
+        self.assertEqual(qdb.user.User('admin@foo.bar').jobs(
+            ignore_status), [])
+
+    def test_jobs_defaults(self):
+        PJ = qdb.processing_job.ProcessingJob
+        # generates expected jobs
+        jobs = qdb.user.User('shared@foo.bar').jobs()
+        self.assertEqual(jobs, [
+            PJ('d19f76ee-274e-4c1b-b3a2-a12d73507c55')])
+
         # no jobs
         self.assertEqual(qdb.user.User('admin@foo.bar').jobs(), [])
 

qiita_db/user.py

@@ -661,23 +661,43 @@ def delete_messages(self, messages):
             qdb.sql_connection.TRN.add(sql)
             qdb.sql_connection.TRN.execute()
 
-    def jobs(self):
+    def jobs(self, ignore_status=['success']):
         """Return jobs created by the user
 
         Parameters
         ----------
+        ignore_status, list of str
+            don't retieve jobs that have one of these status
 
         Returns
         -------
         list of ProcessingJob
 
         """
         with qdb.sql_connection.TRN:
-            sql_info = [self._id]
             sql = """SELECT processing_job_id
                      FROM qiita.processing_job
+                     LEFT JOIN qiita.processing_job_status
+                        USING (processing_job_status_id)
                      WHERE email = %s
-                     ORDER BY heartbeat DESC"""
+                  """
+
+            if ignore_status:
+                sql_info = [self._id, tuple(ignore_status)]
+                sql += "    AND processing_job_status NOT IN %s"
+            else:
+                sql_info = [self._id]
+
+            sql += """
+                     ORDER BY CASE processing_job_status
+                            WHEN 'in_construction' THEN 1
+                            WHEN 'running' THEN 2
+                            WHEN 'queued' THEN 3
+                            WHEN 'waiting' THEN 4
+                            WHEN 'error' THEN 5
+                            WHEN 'success' THEN 6
+                        END, heartbeat DESC"""
+
             qdb.sql_connection.TRN.add(sql, sql_info)
             return [qdb.processing_job.ProcessingJob(p[0])
                     for p in qdb.sql_connection.TRN.execute_fetchindex()]

qiita_pet/handlers/api_proxy/tests/test_user.py

@@ -46,24 +46,8 @@ def test_user_jobs_get_req(self):
                     'threads': 1,
                     'sortmerna_coverage': 0.97},
                  'name': 'Pick closed-reference OTUs',
-                 'processing_job_workflow_id': ''},
-                {'id': 'b72369f9-a886-4193-8d3d-f7b504168e75',
-                 'status': 'success',
-                 'heartbeat': '2015-11-22 21:15:00',
-                 'params': {
-                    'max_barcode_errors': 1.5,
-                    'sequence_max_n': 0,
-                    'max_bad_run_length': 3,
-                    'phred_offset': u'auto',
-                    'rev_comp': False,
-                    'phred_quality_threshold': 3,
-                    'input_data': 1,
-                    'rev_comp_barcode': False,
-                    'rev_comp_mapping_barcodes': True,
-                    'min_per_read_length_fraction': 0.75,
-                    'barcode_type': u'golay_12'},
-                 'name': 'Split libraries FASTQ',
-                 'processing_job_workflow_id': 1}]}
+                 'step': 'generating demux file',
+                 'processing_job_workflow_id': ''}]}
         self.assertEqual(obs, exp)
 
 

qiita_pet/handlers/api_proxy/user.py

@@ -11,26 +11,26 @@
 
 
 @execute_as_transaction
-def user_jobs_get_req(user):
+def user_jobs_get_req(user, limit=30):
     """Gets the json of jobs
 
     Parameters
     ----------
-    prep_id : int
-        PrepTemplate id to get info for
-    user_id : str
-        User requesting the sample template info
+    user : User
+        The user from which you want to return all jobs
+    limit : int, optional
+        Maximum jobs to send, negative values will return all
 
     Returns
     -------
     dict of objects
     {'status': status,
      'message': message,
-     'template': {sample: {column: value, ...}, ...}
+     'template': {{column: value, ...}, ...}
     """
 
     response = []
-    for j in user.jobs():
+    for i, j in enumerate(user.jobs()):
         name = j.command.name
         hb = j.heartbeat
         hb = "" if hb is None else hb.strftime("%Y-%m-%d %H:%M:%S")
@@ -42,6 +42,7 @@ def user_jobs_get_req(user):
             'params': j.parameters.values,
             'status': j.status,
             'heartbeat': hb,
+            'step': j.step,
             'processing_job_workflow_id': wid})
 
     return {'status': 'success',

qiita_pet/static/css/style.css

@@ -1,9 +1,29 @@
+#qiita-main {
+  position: relative;
+  height: 100%;
+  width: 100%;
+}
+#qiita-processing {
+  position: absolute;
+  height: 100%;
+  width: 0%;
+  right: 0;
+  top: 0;
+}
 #template-content{
   padding: 10px;
   height: 100%;
   width: 100%;
 }
 
+td.more-info-processing-jobs{
+  cursor: pointer;
+  background: url('../img//details_open.png') no-repeat center center;
+}
+tr.shown td.more-info-processing-jobs {
+    background: url('../img//details_close.png') no-repeat center center;
+}
+
 /* table in the study description that holds the investigation type elements */
 .investigation-type-table td {
   padding-top: 6px;

qiita_pet/static/js/qiita.js

@@ -29,18 +29,50 @@ function bootstrapAlert(message, severity, timeout){
     alertDiv.append('<p style="text-align:center">Need help? Send us an <a href="mailto:qiita.help@gmail.com">email</a>.</p>');
   }
 
-  $('body').prepend(alertDiv);
+  $('#qiita-main').prepend(alertDiv);
 
   if(timeout > 0) {
    window.setTimeout(function() { $('#alert-message').alert('close'); }, timeout);
   }
 }
 
+function format_extra_info_processing_jobs ( data ) {
+    // `data` is the original data object for the row
+    // 0: blank +/- button
+    // 1: heartbeat
+    // 2: name
+    // 3: status
+    // 4: step
+    // 5: id
+    // 6: params
+    // 7: processing_job_workflow_id
+
+    let row = '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
+                '<tr>'+
+                    '<td><b>ID:</b></td>'+
+                    '<td>'+ data[5] +'</td>'+
+                '</tr>'+
+                '<tr>'+
+                    '<td colspan="2"><h5>Parameters:</h5>'+ data[6] +'</td>'+
+                '</tr>';
+    if (data[7] !== '' && data[3] === 'in_construction') {
+      row += '<tr>'+
+                '<td colspan="2">'+
+                  '<button class="btn btn-danger btn-sm" onclick="remove_job(\''+ data[5] + "', '" + data[7] +'\');">'+
+                  '<span class="glyphicon glyphicon-trash"></span></button>'+
+                '</td>'
+             '</tr>';
+    }
+    row += '</table>';
+
+    return row
+}
+
+
 function show_hide(div) {
 	$('#' + div).toggle();
 }
 
-
 function delete_analysis(aname, analysis_id) {
   if (confirm('Are you sure you want to delete analysis: ' + aname + '?')) {
     var form = $("<form>")
@@ -58,3 +90,21 @@ function delete_analysis(aname, analysis_id) {
     form.submit();
   }
 }
+
+function show_hide_process_list() {
+  if ($("#qiita-main").width() == $("#qiita-main").parent().width()) {
+    // let's update the job list
+    processing_jobs_vue.update_processing_job_data();
+    $("#qiita-main").width("76%");
+    $("#user-studies-table").width("76%");
+    $("#studies-table").width("76%");
+    $("#qiita-processing").width("24%");
+    $("#qiita-processing").show();
+  } else {
+    $("#qiita-main").width("100%");
+    $("#user-studies-table").width("100%");
+    $("#studies-table").width("100%");
+    $("#qiita-processing").width("0%");
+    $("#qiita-processing").hide();
+  }
+}

qiita_pet/templates/admin_approval.html

@@ -1,7 +1,5 @@
 {% extends sitebase.html %}
 {% block head %}
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js" type="text/javascript"></script>
 
 <script type="text/javascript">
 $(document).ready(function() {

qiita_pet/templates/error_log.html

@@ -3,10 +3,6 @@
 {% from future.utils import viewitems %}
 {% from qiita_core.qiita_settings import qiita_config %}
 
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
-
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
-
 <script type="text/javascript">
 $(document).ready(function() {
     $('#error-table').dataTable({"order": [[1, "asc"]]});

qiita_pet/templates/index.html

@@ -3,7 +3,7 @@
 {% end %}
 
 {%block content %}
-<div id="jumbotron" class="jumbotron">
+<div id="jumbotron" class="jumbotron" style="border-radius: 10px; padding: 30px">
   <h1>{% raw portal_styling.index_header%}</h1>
   {% raw portal_styling.index_text%}
 </div>

qiita_pet/templates/list_studies.html

@@ -5,18 +5,10 @@
 <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/select2.min.css" type="text/css">
 
 <style>
-#alert-message {
-  position: fixed;
-  top: 50px;
-  left: 40px;
-  z-index:100;
-}
 td.details-control {
   cursor: pointer;
 }
 </style>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.plugin.natural.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/select2.min.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/js/sharing.js"></script>
@@ -302,6 +294,8 @@ <h3 class="gray-msg">Other Studies</h3>
             </tr>
         </thead>
     </table>
+  </div>
+</div>
 <!--Abstract Modal-->
 <div class="modal fade" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true" id="study-abstract-modal">
   <div class="modal-dialog modal-med">

qiita_pet/templates/portals_edit.html

@@ -1,7 +1,6 @@
 {% extends sitebase.html%}
 
 {%block head%}
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
 <style type="text/css">
   .navlist li
   {
@@ -11,15 +10,7 @@
   .portal-select {
     width: 15em;
   }
-  #alert-message {
-    position: fixed;
-    top: 55px;
-    left:30%;
-    z-index:100;
-    white-space: nowrap;
-  }
 </style>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
 <script type="text/javascript">
 function check_submit(action) {
   //disable submit buttons