start app for dumping data for GBIF

voseq/gbif/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

voseq/gbif/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

voseq/gbif/templates/gbif/index.html

@@ -0,0 +1,93 @@
+{% extends 'public_interface/base.html' %}
+
+
+
+{% block content %}
+<div class="explorer-container">
+  <div class="container">
+    <h3>Integration with GBIF:</h3>
+    <hr>
+
+
+    <div class="container">
+      <div class="row">
+
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-11 ">
+          <p>
+            You can share your information hosted in VoSeq with GBIF.
+          </p>
+
+          <p>
+            <b>GBIF</b> prefers data owners to use their
+            <a href="http://www.gbif.org/ipt">Integrated Publishing Toolkit (IPT)</a>. This means that
+            you can install their IPT software to produce a resource in Darwin Core format that can be
+            harvested by GBIF. In addition to the actual data in your VoSeq installation, <b>IPT allows you
+            to include a rich variety of metadata</b> for GBIF.
+          </p>
+
+          <p>
+            VoSeq is able to produce a <b>dump file</b> containing all the data you own. Then you can import
+            this file into a IPT installation and choose which types of data you want to publish via
+            GBIF. Once you include all the metadata required by GBIF you have two choices in order to
+            expose your data taken from GBIF website:
+          </p>
+
+          <ul class="list-group">
+            <li class="list-group-item"><h4>By setting up a dynamic server software:</h4>
+              <ul class="list-group">
+                <li class="list-group-item">- Acquire hardware with a permanent Internet connection (a regular PC is sufficient).</li>
+                <li class="list-group-item">- Install data publishing software. GBIF recommends the Integrated Publishing Toolkit (IPT). You will need a web server such as Apache.</li>
+                <li class="list-group-item">- Configure the software for your local data structure; this is the "mapping" process. Please follow the documentation of your chosen publishing software for this process.</li>
+                <li class="list-group-item">- Register your service with GBIF and sign the GBIF Data Sharing Agreement.</li>
+              </ul>
+            </li>
+            <li class="list-group-item"><h4>Create an archive for your entire dataset:</h4>
+              <ul class="list-group">
+                <li class="list-group-item">- This scenario doesn't require a permanent Internet connection.</li>
+                <li class="list-group-item">- You simply need to create a Darwin Core Archive, upload it to a repository (for example an IPT repository installed by your GBIF Participant Node, an institutional FTP or web server, or a service like Dropbox or the Internet Archive).</li>
+                <li class="list-group-item">- You then just need to register the public URL for the storage location of your archive with GBIF.</li>
+              </ul>
+            </li>
+        </ul>
+
+
+        <button class="btn btn-primary" onClick="dump_data();">Dump data for GBIF</button>
+
+
+        </div><!-- col -->
+
+      </div><!-- row -->
+    </div><!-- container -->
+
+
+  </div>
+</div>
+{% endblock content %}
+
+
+{% block additional_javascript_footer %}
+  <script type="text/javascript">
+
+        function dump_data() {
+          $.post('dump_data.php', { request: "count_data" },
+            function(data) {
+              var out = '';
+
+              out =  "<br /><br /><p>A total of <b>" + data.count + "</b> records were processed for GBIF. ";
+              out += "<br />A MS EXCEL will be created with all data for GBIF. <a href='dump_data.php?request=make_file'>Click here to Download</a>. ";
+              out += "<p>Submit to GBIF by using an installation of their ";
+              out += "<a href='http://www.gbif.org/informatics/infrastructure/publishing/#c889'>Integrated Publishing Toolkit (IPT)</a>.</p>";
+              out += "<p>See <a href='http://carlosp420.github.io/VoSeq/#integration-with-gbif'>VoSeq documentation</a> on how to upload this dump file into IPT.</p>";
+
+              $('#output').empty().html('<img src="images/loading.gif" />').fadeIn('slow', function(){}).delay(1000).fadeOut('slow', function() {
+                                                                    $('#output').html(out).show();
+                                                                    });
+
+            }, "json");
+
+          // make and download MS EXCEL file
+          $.get('dump_data.php', { request: "make_file" });
+        }
+
+  </script>
+{% endblock additional_javascript_footer %}

voseq/gbif/tests.py

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+from django.test import TestCase
+
+# Create your tests here.

voseq/gbif/urls.py

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+from django.conf.urls import patterns
+from django.conf.urls import url
+
+from . import views
+
+
+urlpatterns = patterns(
+    '',
+    url(r'^/$', views.index, name='index'),
+    url(r'^/results/$', views.results, name='results'),
+)

voseq/gbif/views.py

@@ -0,0 +1,17 @@
+from django.shortcuts import render
+
+from core.utils import get_version_stats
+
+
+def index(request):
+    version, stats = get_version_stats()
+    return render(request, 'gbif/index.html',
+                  {
+                      'version': version,
+                      'stats': stats,
+                  },
+                  )
+
+
+def results(request):
+    return ''

voseq/voseq/settings/base.py

@@ -50,6 +50,7 @@
     'genbank_fasta',
     'gene_table',
     'voucher_table',
+    'gbif',
 )
 
 MIDDLEWARE_CLASSES = (

voseq/voseq/urls.py

@@ -12,6 +12,7 @@
     url(r'^blast_ncbi', include('blast_ncbi.urls', namespace='blast_ncbi')),
     url(r'^blast_new', include('blast_new.urls', namespace='blast_new')),
     url(r'^genes', include('view_genes.urls', namespace='view_genes')),
+    url(r'^share_data_gbif', include('gbif.urls', namespace='gbif')),
     url(r'^', include('public_interface.urls', namespace='public_interace')),
 
     url(r'^admin/', include(admin.site.urls)),