Merge pull request #229 from carlosp420/overview_table

Overview table

.gitignore

@@ -32,6 +32,7 @@ voseq/create_dataset/dataset_files/*txt
 
 # avoid including migrations files
 voseq/public_interface/migrations/*
+voseq/overview_table/migrations/*
 voseq/stats/migrations/*
 
 # avoid including doc files for modules

HISTORY.rst

@@ -7,6 +7,7 @@ HISTORY
 pre-release v2.0.0-alpha-4 (2015-xx-xx)
 +++++++++++++++++++++++++++++++++++++++
 
+- **Interactive overview table** to browse taxa and the genes sequenced for them.
 - **Easy instalation** and deployment using Vagrant virtual machines. Install
   and configure VoSeq and all its dependencies with the command ``vagrant up``.
 

Makefile

@@ -64,7 +64,7 @@ test:
 	rm -rf htmlcov .coverage
 	coverage run --source voseq voseq/manage.py test -v 2 blast_local blast_local_full blast_ncbi blast_new \
 	    core create_dataset genbank_fasta public_interface stats view_genes genbank_fasta gene_table \
-	    voucher_table gbif \
+	    voucher_table gbif overview_table \
 	    --settings=voseq.settings.testing
 
 travis_test:
@@ -73,5 +73,5 @@ travis_test:
 	rm -rf htmlcov .coverage
 	coverage run --source voseq voseq/manage.py test -v 2 blast_local blast_local_full blast_ncbi blast_new \
 	    core create_dataset genbank_fasta public_interface stats view_genes genbank_fasta gene_table \
-	    voucher_table gbif \
+	    voucher_table gbif overview_table \
 	    --settings=voseq.settings.travis

voseq/overview_table/models.py

@@ -0,0 +1,16 @@
+from django.db import models
+
+
+class OverviewTable(models.Model):
+    """Bulk create does not work on inherited models so we need to create a new
+    one.
+    """
+    sequence_string = models.TextField(help_text="HTML string of cells with length of"
+                                                 "sequences for each gene.")
+    o_code = models.CharField(max_length=300)
+    orden = models.TextField(blank=True)
+    superfamily = models.TextField(blank=True)
+    family = models.TextField(blank=True)
+    subfamily = models.TextField(blank=True)
+    genus = models.TextField(blank=True)
+    species = models.TextField(blank=True)

voseq/overview_table/templates/overview_table/index.html

@@ -0,0 +1,151 @@
+{% extends 'public_interface/base.html' %}
+
+{% block title %}
+  VoSeq | Overview table
+{% endblock title %}
+
+{% load staticfiles %}
+{% block additional_css %}
+  <link rel="stylesheet" type="text/css" href="{% static 'css/dataTables.bootstrap.css' %}">
+{% endblock additional_css %}
+
+{% block content %}
+<div class="explorer-container">
+  <div class="container">
+    <h3>Interactive overview table:</h3>
+
+
+    <div class="container">
+      <div class="row">
+
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-12">
+
+
+          <table class="table table-condensed table-striped small_fonts">
+            {% for i in genes %}
+              {% if forloop.counter == 1 %}
+                <tr>
+              {% endif %}
+                <td>
+                  <input type="checkbox" class="toggle-vis" data-column="{{ forloop.counter|add:6 }}">
+                    {{ i.gene_code }}
+                  </input>
+                </td>
+
+              {% if forloop.counter|divisibleby:"4" %}
+                </tr>
+              {% endif %}
+
+            {% endfor %}
+            </tr>
+          </table>
+
+          <table id="datatable" class="display table table-striped table-hover" width="100%">
+              <thead>
+                  <tr>
+                    <th>Code</th>
+                    <th>Order</th>
+                    <th>Superfamily</th>
+                    <th>Family</th>
+                    <th>Subfamily</th>
+                    <th>Genus</th>
+                    <th>Species</th>
+                    {% for i in genes %}
+                      <th class="genes">{{ i.gene_code }}</th>
+                    {% endfor %}
+              </thead>
+              <tbody>
+
+                {% for item in data %}
+                  <tr>
+                    <td><a href="/p/{{ item.o_code }}/">{{ item.o_code }}</a></td>
+                    <td>{{ item.orden }}</td>
+                    <td>{{ item.superfamily }}</td>
+                    <td>{{ item.family }}</td>
+                    <td>{{ item.subfamily }}</td>
+                    <td>{{ item.genus }}</td>
+                    <td>{{ item.species }}</td>
+                    {{ item.sequence_string|safe }}
+                  </tr>
+                {% endfor %}
+
+              </tbody>
+          </table>
+
+
+        </div><!-- col -->
+
+      </div><!-- row -->
+
+      <div class="row"><!-- pagination -->
+        {% if data.has_previous or data.has_next %}
+          <nav class="text-center">
+            <ul class="pagination">
+              {% if data.has_previous %}
+              <li>
+                <a href="?page={{ data.previous_page_number }}" aria-label="Previous">
+                  <span aria-hidden="true">&laquo;</span>
+                </a>
+              </li>
+              {% endif %}
+
+              {% for i in page_range %}
+                {% if i > data.number|add:"-10" and i < data.number|add:"10" %}
+                  {% if data.number == i %}
+                    <li class="active">
+                  {% else %}
+                    <li>
+                  {% endif %}
+                      <a href="?{{ url_encoded_query }}&amp;page={{ i }}">{{ i }}</a>
+                    </li>
+                {% endif %}
+              {% endfor %}
+
+              {% if data.has_next %}
+              <li>
+                <a href="?page={{ data.next_page_number }}" aria-label="Next">
+                  <span aria-hidden="true">&raquo;</span>
+                </a>
+              </li>
+              {% endif %}
+            </ul>
+          </nav>
+        {% endif %}
+      </div><!-- pagination -->
+    </div><!-- container -->
+
+
+  </div>
+</div>
+{% endblock content %}
+
+
+{% block additional_javascript_footer %}
+  <script type="text/javascript" charset="utf8" src="{% static 'js/jquery.dataTables.min.js' %}"></script>
+  <script type="text/javascript" charset="utf8" src="{% static 'js/dataTables.bootstrap.min.js' %}"></script>
+<script>
+  $(document).ready( function () {
+      var table = $('#datatable').DataTable(
+          {
+              "paging": false,
+              "scrollY": 600,
+              "info": false
+          }
+      );
+
+      table.columns( '.genes' ).visible(false, false);
+      table.columns.adjust().draw(false);
+
+      $('input.toggle-vis').on('click', function(e) {
+        e.preventDefault();
+
+        // Get the column API object
+        var column = table.column( $(this).attr('data-column') );
+
+        // Toggle the visibility
+        column.visible( ! column.visible() );
+      });
+  });
+</script>
+
+{% endblock additional_javascript_footer %}

voseq/overview_table/tests.py

@@ -0,0 +1,33 @@
+from django.test import TestCase
+from django.core.management import call_command
+from django.test import Client
+
+from overview_table.utils import OverviewTableMaker
+
+
+class TestOverviewTable(TestCase):
+    def setUp(self):
+        args = []
+        opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
+        cmd = 'migrate_db'
+        call_command(cmd, *args, **opts)
+        call_command('create_stats')
+
+    def test_utils(self):
+        o = OverviewTableMaker()
+        expected = 3
+        result = len(o.items)
+        self.assertEqual(expected, result)
+
+
+class TestViews(TestCase):
+    def test_index_view(self):
+        args = []
+        opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
+        cmd = 'migrate_db'
+        call_command(cmd, *args, **opts)
+        call_command('create_stats')
+
+        c = Client()
+        response = c.get('/view_table/')
+        self.assertEqual(200, response.status_code)

voseq/overview_table/urls.py

@@ -0,0 +1,10 @@
+from django.conf.urls import patterns
+from django.conf.urls import url
+
+from . import views
+
+
+urlpatterns = patterns(
+    '',
+    url(r'^/$', views.index, name='index'),
+)

voseq/overview_table/utils.py

@@ -0,0 +1,47 @@
+from public_interface.models import Genes
+from public_interface.models import Sequences
+from public_interface.models import Vouchers
+
+
+class OverviewTableMaker(object):
+    def __init__(self):
+        self.genes = Genes.objects.all().order_by('gene_code').values('gene_code')
+        self.items = self.get_vouchers_with_sequences()
+
+    def get_vouchers_with_sequences(self):
+        unique_vouchers = self.get_unique()
+        sequences = Sequences.objects.all().values('code', 'gene_code', 'total_number_bp')
+        sequences = self.convert_to_dict(sequences)
+
+        for voucher in unique_vouchers:
+            code = voucher['code']
+            voucher['sequence_string'] = self.build_sequence_string(sequences[code])
+
+        return unique_vouchers
+
+    def get_unique(self):
+        v = Vouchers.objects.all().filter(sequences__code__isnull=False).values('code', 'orden', 'superfamily', 'family',
+                                                                                'subfamily', 'genus', 'species').distinct()
+        return v
+
+    def convert_to_dict(self, sequences):
+        new_seqs = {}
+        for i in sequences:
+            code = i['code']
+            if code not in new_seqs:
+                new_seqs[code] = {}
+            del i['code']
+            new_seqs[code][i['gene_code']] = i['total_number_bp']
+        return new_seqs
+
+    def build_sequence_string(self, sequences):
+        my_string = []
+        for gene in self.genes:
+            gene_code = gene['gene_code']
+            try:
+                my_string.append(str(sequences[gene_code]))
+            except KeyError:
+                my_string.append('')
+
+        my_string = '<td>' + '</td><td>'.join(my_string) + '</td>'
+        return my_string

voseq/overview_table/views.py

@@ -0,0 +1,37 @@
+from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
+from django.shortcuts import render
+
+from core.utils import get_version_stats
+from core.utils import get_username
+from public_interface.models import Genes
+from overview_table.models import OverviewTable
+
+
+def index(request):
+    version, stats = get_version_stats()
+    username = get_username(request)
+
+    genes = Genes.objects.all().order_by('gene_code')
+    vouchers = OverviewTable.objects.all()
+
+    paginator = Paginator(vouchers, 100)
+
+    page = request.GET.get('page')
+    try:
+        vouchers_for_page = paginator.page(page)
+    except PageNotAnInteger:
+        vouchers_for_page = paginator.page(1)
+    except EmptyPage:
+        vouchers_for_page = paginator.page(paginator.num_pages)
+
+    return render(request,
+                  'overview_table/index.html',
+                  {
+                      'username': username,
+                      'version': version,
+                      'stats': stats,
+                      'data': vouchers_for_page,
+                      'genes': genes,
+                      'page_range': paginator.page_range,
+                  },
+                  )

voseq/public_interface/models.py

@@ -114,7 +114,7 @@ class Vouchers(models.Model):
         (LOST, 'lost'),
         (UNKNOWN, 'unknown'),
     )
-    code = models.TextField(unique=True, primary_key=True, help_text="Voucher code.")
+    code = models.CharField(max_length=300, unique=True, primary_key=True, help_text="Voucher code.")
     orden = models.TextField(blank=True)
     superfamily = models.TextField(blank=True)
     family = models.TextField(blank=True)
@@ -173,7 +173,7 @@ class Sequences(models.Model):
     time_edited = models.DateTimeField(auto_now=True, null=True, blank=True)
     notes = models.TextField(blank=True)
     genbank = models.BooleanField()
-    # total_number_bp = models.IntegerField(blank=True, null=True)
+    total_number_bp = models.IntegerField(blank=True, null=True)
     number_ambiguous_bp = models.IntegerField(blank=True, null=True)
 
     class Meta:
@@ -183,8 +183,7 @@ def save(self, *args, **kwargs):
         ambiguous_seq_length = self.sequences.count('?') + self.sequences.count('-')
         ambiguous_seq_length += self.sequences.count('N') + self.sequences.count('n')
         self.number_ambiguous_bp = ambiguous_seq_length
-        # TODO save length of sequence string as *total_number_bp*
-        # self.total_number_bp = len(self.sequences)
+        self.total_number_bp = len(str(self.sequences))
         super(Sequences, self).save(*args, **kwargs)
 
     def __str__(self):