Misc small fixes

qiita_db/support_files/patches/python_patches/62.py

@@ -2,8 +2,29 @@
 # Adding a new command into Qiita/Alpha: delete_analysis
 
 from qiita_db.software import Software, Command
+from qiita_db.sql_connection import TRN
 
 # Create the delete study command
 Command.create(Software.from_name_and_version('Qiita', 'alpha'),
                'delete_analysis', 'Deletes a full analysis',
                {'analysis_id': ['integer', None]})
+
+# Make sure that all validate commands have the "analysis" parameter
+with TRN:
+    # Get all validate commands that are missing the analysis parameter
+    sql = """SELECT command_id
+             FROM qiita.software_command sc
+             WHERE name = 'Validate' AND NOT (
+                SELECT EXISTS(SELECT *
+                              FROM qiita.command_parameter
+                              WHERE parameter_name = 'analysis'
+                                AND command_id = sc.command_id));"""
+    TRN.add(sql)
+    sql = """INSERT INTO qiita.command_parameter
+                (command_id, parameter_name, parameter_type,
+                 required, default_value, name_order, check_biom_merge)
+             VALUES (6, 'analysis', 'analysis', false, NULL, NULL, false)"""
+    sql_params = [[cmd_id, 'analysis', 'analysis', False, None, None, False]
+                  for cmd_id in TRN.execute_fetchflatten()]
+    TRN.add(sql, sql_params, many=True)
+    TRN.execute()

qiita_pet/handlers/api_proxy/artifact.py

@@ -218,7 +218,8 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
                 'template': prep_template_id,
                 'files': dumps(cleaned_filepaths),
                 'artifact_type': artifact_type,
-                'name': name
+                'name': name,
+                'analysis': None,
                 }), True)
 
     # Submit the job

qiita_pet/static/js/networkVue.js

@@ -23,10 +23,29 @@ Vue.component('processing-graph', {
   template: '<div class="row">' +
               '<div class="row" id="network-header-div">' +
                 '<div class="col-md-12">' +
-                  '<h4><a class="btn btn-info" id="show-hide-network-btn" onclick="toggleNetworkGraph();">Hide</a><i> Processing network </i></h4>' +
-                  'Graph navigation: <a class="btn btn-danger" id="interaction-btn">Disabled</a></br>' +
-                  '<div id="run-btn-div"><a class="btn btn-success" id="run-btn"><span class="glyphicon glyphicon-play"></span> Run workflow</a><span class="blinking-message">  Don\'t forget to hit "Run" once you are done with your workflow!</span></div>' +
-                  '<b>Click circles for more information - This graph will refresh in <span id="countdown-span"></span> seconds or reload <a href="#" id="refresh-now-link">now</a></b>' +
+                  // Processing Network header and Show/hide button
+                  '<div class="row">' +
+                    '<div class="col-md-2">' +
+                      '<h4>Processing network</h4>' +
+                    '</div>' +
+                    '<div class="col-md-1">' +
+                      '<a class="btn btn-info form-control" id="show-hide-network-btn" onclick="toggleNetworkGraph();">Hide</a>' +
+                    '</div>' +
+                  '</div>' +
+                  // Run workflow button
+                  '<div class="row" id="run-btn-div">' +
+                    '<div class="col-md-2">' +
+                      '<h4><span class="blinking-message">Start workflow:</h4></span>' +
+                    '</div>' +
+                    '<div class="col-md-1">' +
+                      '<a class="btn btn-success form-control" id="run-btn"><span class="glyphicon glyphicon-play"></span> Run</a>' +
+                    '</div>' +
+                  '</div>' +
+                  '<div class="row">' +
+                    '<div class="col-md-12">' +
+                      '<b>Click circles for more information - This graph will refresh in <span id="countdown-span"></span> seconds or reload <a href="#" id="refresh-now-link">now</a></b>' +
+                    '</div>' +
+                  '</div>' +
                 '</div>' +
               '</div>' +
               '<div class="row">' +
@@ -45,40 +64,6 @@ Vue.component('processing-graph', {
             '</div>',
   props: ['portal', 'graph-endpoint', 'jobs-endpoint', 'no-init-jobs-callback', 'is-analysis-pipeline'],
   methods: {
-    /**
-     *
-     * Enables the graph interaction
-     *
-     **/
-    enableGraphInteraction: function () {
-      let vm = this;
-      $('#interaction-btn').removeClass('btn-danger').addClass('btn-success').html('Enabled');
-      options = {interaction: { dragNodes: false,
-                                    dragView: true,
-                                    zoomView: true,
-                                    selectConnectedEdges: true,
-                                    navigationButtons: true,
-                                    keyboard: false}};
-      vm.network.setOptions(options);
-    },
-
-    /**
-     *
-     * Disables the graph interaction
-     *
-     **/
-    disableGraphInteraction: function() {
-      let vm = this;
-      $('#interaction-btn').removeClass('btn-success').addClass('btn-danger').html('Disabled');
-      options = {interaction: { dragNodes: false,
-                                dragView: false,
-                                zoomView: false,
-                                selectConnectedEdges: false,
-                                navigationButtons: false,
-                                keyboard: false}};
-      vm.network.setOptions(options);
-    },
-
     /**
      *
      * Resets the zoom view of the graph
@@ -90,20 +75,6 @@ Vue.component('processing-graph', {
         vm.network.fit();
       }
     },
-    /**
-     *
-     * Enables/Disables the interaction with the graph
-     *
-     **/
-    toggleGraphInteraction: function () {
-      let vm = this;
-      var options;
-      if ($('#interaction-btn').hasClass('btn-danger')) {
-        vm.enableGraphInteraction();
-      } else {
-        vm.disableGraphInteraction();
-      }
-    },
 
     /**
      *
@@ -689,10 +660,10 @@ Vue.component('processing-graph', {
         },
         interaction: {
           dragNodes: false,
-          dragView: false,
-          zoomView: false,
-          selectConnectedEdges: false,
-          navigationButtons: false,
+          dragView: true,
+          zoomView: true,
+          selectConnectedEdges: true,
+          navigationButtons: true,
           keyboard: false
         },
         groups: {
@@ -728,13 +699,6 @@ Vue.component('processing-graph', {
           }
         }
       });
-
-      // Make sure that the button and the behavior matches
-      if ($('#interaction-btn').hasClass('btn-danger')) {
-        vm.disableGraphInteraction();
-      } else {
-        vm.enableGraphInteraction();
-      }
     },
 
     /**
@@ -1019,8 +983,6 @@ Vue.component('processing-graph', {
     $('#run-btn').on('click', function() { vm.runWorkflow(); });
     $('#run-btn-div').hide();
 
-    $('#interaction-btn').on('click', vm.toggleGraphInteraction);
-
     $('#refresh-now-link').on('click', function () {
       vm.countdownPoll = 15;
       vm.update_job_status();

qiita_pet/static/js/sampleTemplateVue.js

@@ -335,12 +335,12 @@ Vue.component('sample-template-page', {
 
       // The two "pills"
       $ul = $('<ul>').addClass('nav nav-pills').appendTo($col);
-      $li = $('<li>').appendTo($ul);
+      $li = $('<li>').css('border', '1px solid #428bca').css('border-radius', '5px').appendTo($ul);
       if (vm.rowType == 'column') {
         $li.addClass('active');
       }
       $('<a>').attr('data-toggle', 'tab').attr('href', '#sample-info-tab').appendTo($li).append('Sample Information');
-      $li = $('<li>').appendTo($ul);
+      $li = $('<li>').css('border', '1px solid #428bca').css('border-radius', '5px').appendTo($ul);
       if (vm.rowType == 'sample') {
         $li.addClass('active');
       }

qiita_pet/static/vendor/css/bootstrap-toggle.min.css

@@ -0,0 +1,28 @@
+/*! ========================================================================
+ * Bootstrap Toggle: bootstrap-toggle.css v2.2.0
+ * http://www.bootstraptoggle.com
+ * ========================================================================
+ * Copyright 2014 Min Hur, The New York Times Company
+ * Licensed under MIT
+ * ======================================================================== */
+.checkbox label .toggle,.checkbox-inline .toggle{margin-left:-20px;margin-right:5px}
+.toggle{position:relative;overflow:hidden}
+.toggle input[type=checkbox]{display:none}
+.toggle-group{position:absolute;width:200%;top:0;bottom:0;left:0;transition:left .35s;-webkit-transition:left .35s;-moz-user-select:none;-webkit-user-select:none}
+.toggle.off .toggle-group{left:-100%}
+.toggle-on{position:absolute;top:0;bottom:0;left:0;right:50%;margin:0;border:0;border-radius:0}
+.toggle-off{position:absolute;top:0;bottom:0;left:50%;right:0;margin:0;border:0;border-radius:0}
+.toggle-handle{position:relative;margin:0 auto;padding-top:0;padding-bottom:0;height:100%;width:0;border-width:0 1px}
+.toggle.btn{min-width:59px;min-height:34px}
+.toggle-on.btn{padding-right:24px}
+.toggle-off.btn{padding-left:24px}
+.toggle.btn-lg{min-width:79px;min-height:45px}
+.toggle-on.btn-lg{padding-right:31px}
+.toggle-off.btn-lg{padding-left:31px}
+.toggle-handle.btn-lg{width:40px}
+.toggle.btn-sm{min-width:50px;min-height:30px}
+.toggle-on.btn-sm{padding-right:20px}
+.toggle-off.btn-sm{padding-left:20px}
+.toggle.btn-xs{min-width:35px;min-height:22px}
+.toggle-on.btn-xs{padding-right:12px}
+.toggle-off.btn-xs{padding-left:12px}

qiita_pet/static/vendor/js/resumable-uploader.js

@@ -73,10 +73,10 @@
        this.resumable.on('fileProgress', function(file){
            $this.setFileProgress(file.uniqueIdentifier, file.progress());
            $this.setProgress($this.resumable.progress());
-
            // Apply a thumbnail
            if(file.chunks.length>0 && file.chunks[0].status()=='success' && file.chunks[file.chunks.length-1].status()=='success'){
-             $('#uploader_status').append('~~ Upload Finished: <i>' + file.fileName + '</i> ~~<br/>');
+             var alphaNumFileName = file.fileName.replace(/[^0-9a-z]/gi, '');
+             $('#file-icon-' + alphaNumFileName).removeClass('blinking-message glyphicon-circle-arrow-up').addClass('glyphicon-ok');
              $this.setFileThumbnail(file.uniqueIdentifier, target_prefix + '/api/photo/frame?time=10&study_id='+encodeURIComponent(this.study_id)+'&resumableIdentifier='+encodeURIComponent(file.uniqueIdentifier));
            }
          });
@@ -138,16 +138,18 @@
        }
 
        var listNode = $(document.createElement('div'));
+       var alphaNumFileName = fileName.replace(/[^0-9a-z]/gi, '');
+       var iconClass = resumableFile.uploaded !== undefined ? 'glyphicon-ok' : 'blinking-message glyphicon-circle-arrow-up';
+       var html = '<div class="row" class="checkbox">' +
+                    '<label>' + fileName + '&nbsp; <input type="checkbox" value="' + dirId + '-' + fileName  + '" name="files_to_erase">&nbsp;</label>' +
+                    '<i id="file-icon-' + alphaNumFileName + '" class="glyphicon ' + iconClass + '"></i>';
+
        if (is_admin) {
-         listNode.html('<div class="row" class="checkbox"><label>' + fileName +
-                       '&nbsp; <input type="checkbox" value="' + dirId + '-' +
-                       fileName  + '" name="files_to_erase"></label>' +
-                       '&nbsp;<a href="' + url + fileName + '">download</a></div>');
-       } else {
-         listNode.html('<div class="row" class="checkbox"><label>' + fileName +
-                       '&nbsp; <input type="checkbox" value="' + dirId + '-' +
-                       fileName  + '" name="files_to_erase"></label></div>');
+         html = html + '&nbsp;<a href="' + url + fileName + '">download</a>';
        }
+
+       html = html + '</div>';
+       listNode.html(html);
        this.uploaderList.append(listNode);
 
        var editNode = $(document.createElement('div'));
@@ -164,6 +166,7 @@
          var x = {};
          var editStatus = 'editing';
        }
+
        var file = {
          resumableFile:resumableFile,
          listNode:listNode,

qiita_pet/static/vendor/licences/boostrap-toggle_license.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2011-2014 Min Hur, The New York Times Company
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

qiita_pet/templates/sitebase.html

@@ -31,11 +31,12 @@
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery-ui.theme.min.css" type="text/css">
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/bootstrap.min.css" type="text/css">
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/bootstrap-theme.min.css" type="text/css">
+    <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/bootstrap-toggle.min.css" type="text/css">
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/chosen.css" type="text/css">
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.min.css" type="text/css">
     <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/css/style.css" type="text/css">
-    <link rel="stylesheet" src="{% raw qiita_config.portal_dir %}/static/vendor/css/vis.min.css" type="text/css">
-    <link rel="stylesheet" src="{% raw qiita_config.portal_dir %}/static/vendor/css/vis-network.min.css" type="text/css">
+    <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/vis.min.css" type="text/css">
+    <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/vis-network.min.css" type="text/css">
     {% if portal_styling.custom_css %}
     <style type="text/css">
       {% raw portal_styling.custom_css %}
@@ -44,6 +45,7 @@
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery-2.1.0.min.js"></script>
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery-ui.min.js"></script>
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/bootstrap.min.js"></script>
+    <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/bootstrap-toggle.min.js"></script>
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/chosen.jquery.min.js"></script>
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js" type="text/javascript"></script>
     <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/vue.min.js"></script>