start with forms

Makefile

@@ -1,5 +1,5 @@
 help:
-	@echo "serve - remove build artifacts"
+	@echo "serve - runserver for development"
 	@echo "test - use testing settings and SQlite3 database"
 
 serve: index stats
@@ -16,7 +16,7 @@ import:
 	python voseq/manage.py migrate_db --dumpfile=test_db_dump.xml --settings=voseq.settings.local
 
 index:
-	python voseq/manage.py rebuild_index
+	python voseq/manage.py rebuild_index --settings=voseq.settings.local
 
 stats:
 	python voseq/manage.py create_stats --settings=voseq.settings.local

voseq/create_dataset/admin.py

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

voseq/create_dataset/forms.py

@@ -0,0 +1,66 @@
+from django import forms
+
+from public_interface.models import Genes
+from public_interface.models import GeneSets
+from public_interface.models import TaxonSets
+
+
+class CreateDatasetForm(forms.Form):
+    file_format = forms.ChoiceField(
+        label='Choose file format',
+        choices=[
+            ('TNT', 'TNT format'),
+            ('NEXUS', 'NEXUS format'),
+            ('PHY', 'PHYLIP format'),
+            ('FASTA', 'Unaligned FASTA format'),
+        ]
+    )
+
+    outgroup = forms.CharField(
+        label='Outgroup (code, for NEXUS and TNT)',
+        help_text='Voucher code for using that specimen\'s sequence as '
+                  'outgroup in NEXUS and TNT datasets.',
+    )
+    """
+    taxonset = forms.ModelChoiceField(
+        TaxonSets.objects.all(),
+        label='Choose taxonset',
+        required=False,
+        empty_label='Choose taxonset',
+    )
+    geneset = forms.ModelChoiceField(
+        GeneSets.objects.all(),
+        label='Choose geneset',
+        required=False,
+        empty_label='Choose geneset',
+    )
+    gene_codes = forms.ModelMultipleChoiceField(
+        Genes.objects.all(),
+        label='Check to select your alignment/gene',
+        required=False,
+        widget=forms.CheckboxSelectMultiple(),
+    )
+    voucher_codes = forms.CharField(
+        widget=forms.Textarea,
+        label='... and/or a list of voucher codes',
+        required=False,
+    )
+    """
+
+    def clean(self):
+        """Overwriting validator method of class form."""
+        cleaned_data = super(GenBankFastaForm, self).clean()
+        taxonset = cleaned_data.get("taxonset")
+        voucher_codes = cleaned_data.get("voucher_codes")
+
+        geneset = cleaned_data.get("geneset")
+        gene_codes = cleaned_data.get("gene_codes")
+        print(gene_codes)
+
+        if taxonset is None and voucher_codes.strip() == '':
+            raise forms.ValidationError("You need to enter at least some "
+                                        "voucher codes or select a taxonset.")
+
+        if geneset is None and len(gene_codes) < 1:
+            raise forms.ValidationError("You need to enter at least some "
+                                        "gene codes or select a geneset.")

voseq/create_dataset/models.py

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

voseq/create_dataset/templates/create_dataset/index.html

@@ -0,0 +1,138 @@
+{% extends 'public_interface/base.html' %}
+
+
+{% block additional_css %}
+  {% load staticfiles %}
+  <link rel="stylesheet" href="{% static 'css/jquery-ui.min.css' %}">
+  <link rel="stylesheet" href="{% static 'css/jquery-ui.structure.min.css' %}">
+  <link rel="stylesheet" href="{% static 'css/jquery-ui.theme.min.css' %}">
+{% endblock additional_css %}
+
+
+{% block content %}
+<div class="explorer-container">
+  <div class="container">
+    <h3>Create dataset:</h3>
+
+    <div class="alert alert-info" role="alert">
+      <b>Select sequences you want for a dataset by entering the voucher codes and gene codes.</b>
+    </div>
+
+    <div class="container">
+      <div class="row">
+
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-9 col-lg-offset-1">
+
+        <form action="/genbank_fasta/results/" method="post">
+        <div class="panel panel-primary" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>Enter the required info to make yourself a ready-to-run dataset</b></h3>
+          </div>
+
+
+
+          {{ form.as_p }}
+<i class="fa fa-exclamation-triangle"></i> Warning! your dataset will not necessarily be properly aligned!
+<a title="You need to be sure that your data is aligned!" href="#"><i class="fa fa-question-circle"></i></a>
+              {% csrf_token %}
+
+          {% for i in form.non_field_errors %}
+          <div class="alert alert-warning">{{ i }}</div>
+          {% endfor %}
+        <table class="table table-bordered"><!-- big -->
+            <tr>
+                <td>
+                  <table class="table table-bordered">
+                    <tr>
+                      <td>
+                        <label for="id_taxonset">Choose taxonset: </label>
+                      </td>
+                      <td>
+                        {% for i in form.taxonset.errors %}
+                        <div class="alert alert-warning">{{ i }}</div>
+                        {% endfor %}
+                        {{ form.taxonset }}
+                      </td>
+                    </tr>
+                    <tr>
+                      <td>
+                        <label for="id_voucher_codes">... and/or a list of voucher codes: </label>
+                      </td>
+                      <td>
+                        {% for i in form.voucher_codes.errors %}
+                        <div class="alert alert-warning">{{ i }}</div>
+                        {% endfor %}
+                        {{ form.voucher_codes }}
+                      </td>
+                    </tr>
+                  </table>
+                </td>
+
+                <td>
+                  <table class="table table-bordered">
+                    <tr>
+                      <td>
+                        <label for="id_geneset">Choose geneset: </label>
+                      </td>
+                      <td>
+                        {% for i in form.geneset.errors %}
+                        <div class="alert alert-warning">{{ i }}</div>
+                        {% endfor %}
+                        {{ form.geneset }}
+                      </td>
+                    </tr>
+                    <tr>
+                      <td>
+                        Check to select your alignment/gene:<br />
+                        <br />
+                        (if geneset chosen, adds extra genes)
+                      </td>
+                      <td>
+                        <table class="table table-condensed table-striped">
+                          <tr>
+                            {% for i in form.gene_codes %}
+                            <td>
+                              {{ i }}
+                            </td>
+                            {% endfor %}
+                          </tr>
+                        </table>
+                      </td>
+                    </tr>
+                  </table>
+                </td>
+
+            </tr>
+        </table><!-- big -->
+
+        </div><!-- panel -->
+
+            <button type="submit" class="btn btn-info" id="submit_button">
+                Make GenBank FASTA1
+            </button>
+        </form>
+
+
+
+
+
+
+
+        </div><!-- col -->
+
+      </div><!-- row -->
+    </div><!-- container -->
+
+
+  </div>
+</div>
+{% endblock content %}
+
+
+{% block additional_javascript_footer %}
+<script>
+  $(function() {
+    $( document ).tooltip();
+  });
+</script>
+{% endblock additional_javascript_footer %}

voseq/create_dataset/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

voseq/create_dataset/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/create_dataset/views.py

@@ -0,0 +1,14 @@
+from django.shortcuts import render
+
+from .forms import CreateDatasetForm
+
+
+def index(request):
+    form = CreateDatasetForm()
+
+    return render(request,
+                  'create_dataset/index.html',
+                  {
+                      'form': form,
+                  },
+                  )

voseq/public_interface/templates/public_interface/base.html

@@ -104,6 +104,7 @@
                 <ul class="dropdown-menu" role="menu">
                   <li><a href="/genes/">View genes</a></li>
                   <li><a href="/blast_new/">Blast new sequence</a></li>
+                  <li><a href="/create_dataset/">Create new dataset</a></li>
                   <li><a href="/genbank_fasta/">Create GenBank FASTA file</a></li>
                 </ul>
               </div>

voseq/voseq/settings/base.py

@@ -40,6 +40,7 @@
     # my apps
     'core',
     'public_interface',
+    'create_dataset',
     'blast_local',
     'blast_local_full',
     'blast_ncbi',

voseq/voseq/urls.py

@@ -3,12 +3,14 @@
 
 urlpatterns = patterns(
     '',
+    url(r'^create_dataset', include('create_dataset.urls', namespace='create_dataset')),
     url(r'^genbank_fasta', include('genbank_fasta.urls', namespace='genbank_fasta')),
     url(r'^blast_local', include('blast_local.urls', namespace='blast_local')),
     url(r'^blast_local_full', include('blast_local_full.urls', namespace='blast_local_full')),
     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'^', include('public_interface.urls', namespace='public_interace')),
+
     url(r'^admin/', include(admin.site.urls)),
 )