Merge 427f866 into 31acb67

qiita_pet/handlers/study_handlers/metadata_summary_handlers.py

@@ -16,6 +16,7 @@
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import qiita_config
 
 
 class MetadataSummaryHandler(BaseHandler):
@@ -65,14 +66,14 @@ def get(self, arguments):
             # The prep template has been provided
             template = self._get_template(PrepTemplate, prep_template)
             back_button_path = (
-                "/study/description/%s?top_tab=prep_template_tab&sub_tab=%s"
-                % (study_id, template.id))
+                "%s/study/description/%s?top_tab=prep_template_tab&sub_tab=%s"
+                % (qiita_config.portal_dir, study_id, template.id))
         elif sample_template:
             # The sample template has been provided
             template = self._get_template(SampleTemplate, sample_template)
             back_button_path = (
-                "/study/description/%s"
-                % study_id)
+                "%s/study/description/%s"
+                % (qiita_config.portal_dir, study_id))
         else:
             # Neither a sample template or a prep template has been provided
             # Fail nicely

qiita_pet/templates/ebi_submission.html

@@ -4,7 +4,7 @@
 
 <h1>Submission summary for study: <b>{{study_title}}</b></h1>
 
-<form role="form" action="/ebi_submission/{{preprocessed_data_id}}" method="post">
+<form role="form" action="{% raw qiita_config.portal_dir %}/ebi_submission/{{preprocessed_data_id}}" method="post">
     <div class="panel panel-default">
         <div class="panel-heading">
             The information below describes information contained in the sample
@@ -45,6 +45,6 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
       <b>You need to set an investigation type to continue!</b>
     {% end %}
     <br/><br/>
-    <a class="btn btn-primary" href="/study/description/{{study_id}}?top_tab=preprocessed_data_tab&sub_tab={{preprocessed_data_id}}">Return to study</a>
+    <a class="btn btn-primary" href="{% raw qiita_config.portal_dir %}/study/description/{{study_id}}?top_tab=preprocessed_data_tab&sub_tab={{preprocessed_data_id}}">Return to study</a>
 </form>
 {% end %}

qiita_pet/templates/edit_study.html

@@ -1,6 +1,6 @@
 {% extends sitebase.html %}
 {% block head %}
-<script type="text/javascript" src="/static/vendor/js/jquery.validate.min.js"></script>
+<script type="text/javascript" src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.validate.min.js"></script>
 <style>
   .custom-combobox {
     position: relative;
@@ -38,7 +38,7 @@
         // fire off ajax the request
         request = $.ajax({
           type: "GET",
-          url: '/check_study/',
+          url: '{% raw qiita_config.portal_dir %}/check_study/',
           data: {study_title: $("#study_title")[0].value {% if study %}, old_study_title: '{{study.title}}'{% end %} }
         });
 
@@ -121,7 +121,7 @@
 {% if study %}
 function cancel_edition(){
   if (confirm("Are you sure you want to go to the study description page? None of the changes will be stored")){
-    window.location.href = "/study/description/{{study.id}}";
+    window.location.href = "{% raw qiita_config.portal_dir %}/study/description/{{study.id}}";
   }
 }
 {% end %}
@@ -138,7 +138,7 @@ <h3>
 <span id="errorspan" name="errorspan" style="color: red"></span>
 <span id="messagespan" name="messagespan" style="color: red"></span>
 <br />
-<form id="create_study" name="create_study" action={%if study%}'/study/edit/{{study.id}}'{%else%}'/study/create/'{%end%} method="POST">
+<form id="create_study" name="create_study" action={%if study%}'{% raw qiita_config.portal_dir %}/study/edit/{{study.id}}'{%else%}'{% raw qiita_config.portal_dir %}/study/create/'{%end%} method="POST">
 <table>
 {% for idx, form_item in enumerate(creation_form, start=1) %}
     {% set kwargs = {'tabindex': idx, 'class_': 'form-control'} %}

qiita_pet/templates/error.html

@@ -5,6 +5,6 @@ <h1 style="text-align:center">ERROR: CODE {{status_code}}!</h1>
     <p style="text-align:center">The error has been logged and will be looked at.</p>
     <p style="text-align:center">Need help? Send us an <a href="mailto:qiita.help@gmail.com">email</a>.</p>
     {% if is_admin %}
-    <p style="text-align:center">Go to the <a href="/admin/error/">error page</a> to view the logs</p>
+    <p style="text-align:center">Go to the <a href="{% raw qiita_config.portal_dir %}/admin/error/">error page</a> to view the logs</p>
     {% end %}
 {% end %}

qiita_pet/templates/login.html

@@ -1,7 +1,7 @@
 {% extends sitebase.html %}
 {%block content %}
 <div id="login-form">
-    <form action="/auth/login/" method="post" id="login_form">
+    <form action="{% raw qiita_config.portal_dir %}/auth/login/" method="post" id="login_form">
         <fieldset>
             <label for="username">Username</label>
             <input autocapitalize="off" autocorrect="off" class="text-input" id="username" name="username" tabindex="1" type="text" value="">
@@ -20,6 +20,6 @@
         </div>
     </form>
     <br>
-    <a class="link" href="../../auth/create/">Create User</a>
+    <a class="link" href="{% raw qiita_config.portal_dir %}/auth/create/">Create User</a>
 </div>
-{% end %}
+{% end %}

qiita_pet/templates/lost_pass.html

@@ -1,6 +1,6 @@
 {%extends sitebase.html%}
 {%block head%}
-<script type="text/javascript" src="/static/vendor/js/jquery.validate.min.js"></script>
+<script type="text/javascript" src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.validate.min.js"></script>
 <script type="text/javascript">
 // http://www.9lessons.info/2012/04/bootstrap-registration-form-tutorial.html
 $(document).ready(function() {
@@ -33,7 +33,7 @@
 <div style='width: 50%;'>
 <h1>Lost Password</h1>
 <h3>Enter email for account</h3>
-<form class="form-horizontal" role="form" action="/auth/forgot/" method="post" id="lost_pass" name="lost_pass">
+<form class="form-horizontal" role="form" action="{% raw qiita_config.portal_dir %}/auth/forgot/" method="post" id="lost_pass" name="lost_pass">
 <div class="form-group">
     <label for="email" class="col-sm-2 control-label">Email</label>
     <div class="col-sm-10">

qiita_pet/templates/portals_edit.html

@@ -1,7 +1,7 @@
 {% extends sitebase.html%}
 
 {%block head%}
-<link rel="stylesheet" href="/static/vendor/css/jquery.dataTables.css" type="text/css">
+<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
 <style type="text/css">
   .navlist li
   {
@@ -19,7 +19,7 @@
     white-space: nowrap;
   }
 </style>
-<script src="/static/vendor/js/jquery.dataTables.min.js"></script>
+<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
@@ -57,7 +57,7 @@
       bootstrapAlert(data, "danger", 2200);
     }
     else {
-      $('#info-table').DataTable().ajax.url("/admin/portals/studiesAJAX/" + echo).load();
+      $('#info-table').DataTable().ajax.url("{% raw qiita_config.portal_dir %}/admin/portals/studiesAJAX/" + echo).load();
       bootstrapAlert(data, "success", 2200);
     }
     $("#portal").val('');
@@ -99,7 +99,7 @@
       { 'mRender': render_checkbox, 'mData': 2, 'aTargets': [ 0 ] }
     ],
     "ajax": {
-      "url": "/admin/portals/studiesAJAX/?sEcho=" + Math.floor(Math.random()*1001) + "&view-portal=QIITA",
+      "url": "{% raw qiita_config.portal_dir %}/admin/portals/studiesAJAX/?sEcho=" + Math.floor(Math.random()*1001) + "&view-portal=QIITA",
       "aoColumns": [
         {"sSortDataType": "dom-checkbox", "bSearchable": false, "bSortable": false},
         {% for h in headers %}
@@ -120,7 +120,7 @@
 
   $('#view-portal').change(function() {
     var echo = "?sEcho=" + Math.floor(Math.random()*1001) + "&view-portal=" + $("#view-portal").val();
-    $('#info-table').DataTable().ajax.url("/admin/portals/studiesAJAX/" + echo).load();
+    $('#info-table').DataTable().ajax.url("{% raw qiita_config.portal_dir %}/admin/portals/studiesAJAX/" + echo).load();
   });
 });
 </script>

qiita_pet/templates/select_commands.html

@@ -23,7 +23,7 @@
 
 <h1>Select Commands</h1>
 <span id="error" style="color:red"></span>
-<form role="form" action="/analysis/wait/{{aid}}" method="post" onsubmit="return check_selection()">
+<form role="form" action="{% raw qiita_config.portal_dir %}/analysis/wait/{{aid}}" method="post" onsubmit="return check_selection()">
 
 <div>
 <table class="table">

qiita_pet/templates/show_analyses.html

@@ -14,7 +14,7 @@
 
 <div id='no-analyses' class='jumbotron'>
   <h1>No Analyses available</h1>
-  <h3><a href="/study/list/">Create an analysis</a></h3>
+  <h3><a href="{% raw qiita_config.portal_dir %}/study/list/">Create an analysis</a></h3>
 </div>
 
 {% if analyses %}
@@ -34,19 +34,19 @@ <h3><a href="/study/list/">Create an analysis</a></h3>
       {% if status == "in_construction"%}
         <tr>
           <td>
-            <a href="/analysis/{{analysis.step}}?aid={{analysis.id}}">{{analysis.name}}</a>
+            <a href="{% raw qiita_config.portal_dir %}/analysis/{{analysis.step}}?aid={{analysis.id}}">{{analysis.name}}</a>
       {% elif status == "running" %}
         <tr class="active">
           <td>
-            <a href="/analysis/wait/{{analysis.id}}">{{analysis.name}}</a>
+            <a href="{% raw qiita_config.portal_dir %}/analysis/wait/{{analysis.id}}">{{analysis.name}}</a>
       {% elif status == "completed" %}
         <tr class="success">
           <td>
-            <a href="/analysis/results/{{analysis.id}}">{{analysis.name}}</a>
+            <a href="{% raw qiita_config.portal_dir %}/analysis/results/{{analysis.id}}">{{analysis.name}}</a>
       {% elif status == "error" %}
         <tr class="danger">
           <td>
-            <a href="/analysis/results/{{analysis.id}}">{{analysis.name}}</a>
+            <a href="{% raw qiita_config.portal_dir %}/analysis/results/{{analysis.id}}">{{analysis.name}}</a>
       {% else %}
         <tr class="active">
           <td>

qiita_pet/templates/stats.html

@@ -14,7 +14,7 @@
     streetViewControl: false,
     mapTypeControl: false
   };
-  
+
   var map = new google.maps.Map(document.getElementById('map-canvas'),
       mapOptions);
 
@@ -27,7 +27,7 @@
       new google.maps.Size(40, 37),
       new google.maps.Point(0, 0),
       new google.maps.Point(12, 35));
-  
+
   {% for lat, lng in lat_longs %}
       setMarker(map, {{ lat }}, {{ lng }}, pinImage, pinShadow, pinColor);
   {% end %}
@@ -75,7 +75,7 @@ <h3>{{ random_study_title }}</h3>
       <p align="justify">{{ random_study_info['study_abstract'] }}</p>
       <p>
       {% if user is not None %}
-          <a href="/study/description/{{ random_study_id }}">Go to the study <span class="glyphicon glyphicon-arrow-right"></span></a>
+          <a href="{% raw qiita_config.portal_dir %}/study/description/{{ random_study_id }}">Go to the study <span class="glyphicon glyphicon-arrow-right"></span></a>
       {% else %}
           <h4>Log in above to see this and other public studies</h4>
       {% end %}

qiita_pet/templates/study_description.html

@@ -162,7 +162,7 @@
     var qual = result[6];
 
     var form = $("<form>")
-    .attr("action", "/study/create_raw_data")
+    .attr("action", "{% raw qiita_config.portal_dir %}/study/create_raw_data")
     .attr("method", "post")
     .append($("<input>")
       .attr("type", "hidden")
@@ -207,7 +207,7 @@
     bootstrapAlert("You need to select a raw data used in a previous study");
   } else {
     var form = $("<form>")
-      .attr("action", "/study/create_raw_data")
+      .attr("action", "{% raw qiita_config.portal_dir %}/study/create_raw_data")
       .attr("method", "post")
       .append($("<input>")
         .attr("type", "hidden")
@@ -577,9 +577,9 @@ <h2><i>{{study_alias}}</i></h2>
   <tr>
     <td style="vertical-align: middle; text-align:left; width: 50%;" colspan="2">
       {% if show_edit_btn %}
-        <a class="btn btn-default glyphicon glyphicon-edit" href="/study/edit/{{study.id}}" title="Edit the study information" style="margin:5px; word-spacing: -10px;"> Edit</a>
+        <a class="btn btn-default glyphicon glyphicon-edit" href="{% raw qiita_config.portal_dir %}/study/edit/{{study.id}}" title="Edit the study information" style="margin:5px; word-spacing: -10px;"> Edit</a>
       {% end %}
-      <a href="/study/upload/{{study.id}}" class="btn btn-default glyphicon glyphicon-upload" title="Upload study files" style="margin:5px; word-spacing: -10px;"> Upload</a>
+      <a href="{% raw qiita_config.portal_dir %}/study/upload/{{study.id}}" class="btn btn-default glyphicon glyphicon-upload" title="Upload study files" style="margin:5px; word-spacing: -10px;"> Upload</a>
       <a class="btn btn-danger glyphicon glyphicon-trash" style="display: inline-block;" data-toggle="modal" data-target="#delete-study"> Delete-study</a>
     </td>
   </tr>

qiita_pet/templates/upload.html

@@ -11,7 +11,7 @@
         <li>fastq or fastq.gz (gziped fastq) for sequences. Note that zip files can not be processed</li>
         <li>tab separated text files for sample and prep templates, the extension should be txt</li>
       </ul>
-      <a href="/study/description/{{study_id}}">Go to study description</a>
+      <a href="{% raw qiita_config.portal_dir %}/study/description/{{study_id}}">Go to study description</a>
     </td>
   </tr>
 
@@ -62,10 +62,10 @@
 
 
 <!-- Upload required files and JS code -->
-<script src="/static/vendor/js/resumable.js"></script>
-<script src="/static/vendor/js/resumable-uploader.js"></script>
-<script src="/static/vendor/js/underscore.min.js"></script>
-<script src="/static/vendor/js/string.min.js"></script>
+<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/resumable.js"></script>
+<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/resumable-uploader.js"></script>
+<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/underscore.min.js"></script>
+<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/string.min.js"></script>
 
 <script>
   var meta = { fileType: [] };