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Merged
merged 3 commits into from
Feb 20, 2016
Merged

fixing some files! #1652

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de2b96b
fixing some files!
antgonza Feb 19, 2016
a10e4af
Fixing comments
josenavas Feb 20, 2016
427f866
Adding missing import
josenavas Feb 20, 2016
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9 changes: 5 additions & 4 deletions qiita_pet/handlers/study_handlers/metadata_summary_handlers.py
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Expand Up @@ -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):
Expand Down Expand Up @@ -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))
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qiita_config is not imported in this file - I'm assuming that flake8 will complain

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
Expand Down
4 changes: 2 additions & 2 deletions qiita_pet/templates/ebi_submission.html
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Expand Up @@ -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
Expand Down Expand Up @@ -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 %}
8 changes: 4 additions & 4 deletions qiita_pet/templates/edit_study.html
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@@ -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;
Expand Down Expand Up @@ -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 %} }
});

Expand Down Expand Up @@ -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 %}
Expand All @@ -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'} %}
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/error.html
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Expand Up @@ -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 %}
6 changes: 3 additions & 3 deletions qiita_pet/templates/login.html
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@@ -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="">
Expand All @@ -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 %}
4 changes: 2 additions & 2 deletions qiita_pet/templates/lost_pass.html
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@@ -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() {
Expand Down Expand Up @@ -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">
Expand Down
10 changes: 5 additions & 5 deletions qiita_pet/templates/portals_edit.html
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@@ -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
{
Expand All @@ -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
Expand Down Expand Up @@ -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('');
Expand Down Expand Up @@ -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 %}
Expand All @@ -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>
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/select_commands.html
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Expand Up @@ -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">
Expand Down
10 changes: 5 additions & 5 deletions qiita_pet/templates/show_analyses.html
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Expand Up @@ -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 %}
Expand All @@ -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>
Expand Down
6 changes: 3 additions & 3 deletions qiita_pet/templates/stats.html
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Expand Up @@ -14,7 +14,7 @@
streetViewControl: false,
mapTypeControl: false
};

var map = new google.maps.Map(document.getElementById('map-canvas'),
mapOptions);

Expand All @@ -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 %}
Expand Down Expand Up @@ -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 %}
Expand Down
8 changes: 4 additions & 4 deletions qiita_pet/templates/study_description.html
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Expand Up @@ -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")
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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>
Expand Down
10 changes: 5 additions & 5 deletions qiita_pet/templates/upload.html
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Expand Up @@ -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>

Expand Down Expand Up @@ -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: [] };
Expand Down