From dc0109d07824f779e85e0ededa794a1d868c8af0 Mon Sep 17 00:00:00 2001
From: carlosp420 <mycalesis@gmail.com>
Date: Tue, 20 Jan 2015 11:40:33 +0200
Subject: [PATCH] genbank fasta: result page

---
 .../templates/genbank_fasta/results.html      | 129 ++++++++----------
 voseq/genbank_fasta/utils.py                  |   8 +-
 voseq/genbank_fasta/views.py                  |  11 +-
 3 files changed, 73 insertions(+), 75 deletions(-)

diff --git a/voseq/genbank_fasta/templates/genbank_fasta/results.html b/voseq/genbank_fasta/templates/genbank_fasta/results.html
index 93f189ec..4c43098d 100644
--- a/voseq/genbank_fasta/templates/genbank_fasta/results.html
+++ b/voseq/genbank_fasta/templates/genbank_fasta/results.html
@@ -4,7 +4,7 @@
 {% block content %}
 <div class="explorer-container">
   <div class="container">
-    <h3>Create GenBank FASTA file:</h3>
+    <h3>Results:</h3>
 
 
     <div class="container">
@@ -12,89 +12,76 @@ <h3>Create GenBank FASTA file:</h3>
 
         <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 FASTA file to be submitted to GenBank</b></h3>
+            <h3 class="panel-title"><b>Sequences that already have GenBank accession numbers:
+              <span class="badge"><b>{{ items_with_accession|length }}</b></span>
+              <br />
+              These will be ignored</b></h3>
           </div>
 
-              {% csrf_token %}
+          <ul class="list-group">
+            {% for i in items_with_accession %}
+              <li class="list-group-item">{{ i.voucher_code }} for {{ i.gene_code }} = {{ i.accession }}</li>
+            {% endfor %}
+          </ul>
+        </div><!-- panel -->
 
-        <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_gene_code_list">... and/or a list of codes: </label>
-                      </td>
-                      <td>
-                        {% for i in form.gene_code_list.errors %}
-                        <div class="alert alert-warning">{{ i }}</div>
-                        {% endfor %}
-                        {{ form.gene_code_list }}
-                      </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>
 
+        <h3>
+          This is your nucleotide FASTA file to import into Sequin
+          (<a href="http://www.ncbi.nlm.nih.gov/Sequin/">http://www.ncbi.nlm.nih.gov/Sequin/</a>)
+        </h3>
+
+        <button type="submit" class="btn btn-info" id="submit_button">
+          <i class="fa fa-download"></i>
+          Download nucleotide file
+        </button>
+        <br />
+        <br />
+        <div class="panel panel-primary" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>Your nucleotide file:</b></h3>
+          </div>
+
+          <table class="table table-bordered">
+            <tr>
+              <td>
+                <textarea readonly style="height: 250px; white-space: nowrap;" class="form-control">{{ fasta }}</textarea>
+              </td>
             </tr>
-        </table><!-- big -->
+          </table>
 
         </div><!-- panel -->
 
-            <button type="submit" class="btn btn-info" id="submit_button">
-                Make GenBank FASTA
-            </button>
-        </form>
 
 
+        <h3>
+          This is your protein file to use in case you have introns.
+          Load it in Sequin after your nucleotide file to link nucleotides to
+          protein and identify the introns.
+        </h3>
 
+        <button type="submit" class="btn btn-info" id="submit_button">
+          <i class="fa fa-download"></i>
+          Download protein file
+        </button>
+        <br />
+        <br />
+        <div class="panel panel-primary" style="min-width: 790px;">
+          <div class="panel-heading">
+            <h3 class="panel-title"><b>Your protein file:</b></h3>
+          </div>
+
+          <table class="table table-bordered">
+            <tr>
+              <td>
+                <textarea readonly style="height: 250px; white-space: nowrap;" class="form-control">{{ protein }}</textarea>
+              </td>
+            </tr>
+          </table>
+
+        </div><!-- panel -->
 
 
 
diff --git a/voseq/genbank_fasta/utils.py b/voseq/genbank_fasta/utils.py
index 2a32f135..d0823018 100644
--- a/voseq/genbank_fasta/utils.py
+++ b/voseq/genbank_fasta/utils.py
@@ -75,7 +75,13 @@ def get_datasets(self):
                         continue
 
                     if s.accession.strip() != '':
-                        self.items_with_accession.append((code, gene_code, s.accession))
+                        self.items_with_accession.append(
+                            {
+                                'voucher_code': code,
+                                'gene_code': gene_code,
+                                'accession': s.accession,
+                            },
+                        )
                     else:
                         seq_id = v.genus + '_' + v.species + '_' + code
                         seq_description = '[org=' + v.genus + ' ' + v.species + ']'
diff --git a/voseq/genbank_fasta/views.py b/voseq/genbank_fasta/views.py
index 52008c01..9a464791 100644
--- a/voseq/genbank_fasta/views.py
+++ b/voseq/genbank_fasta/views.py
@@ -36,12 +36,17 @@ def results(request):
             gene_codes = utils.get_gene_codes(cleaned_data)
 
             print(voucher_codes, gene_codes)
-            items_with_accession, fasta, proteins = utils.get_results(voucher_codes, gene_codes)
-            result = ''
+            res = utils.Results(voucher_codes, gene_codes)
+            res.get_datasets()
+            items_with_accession = res.items_with_accession
+            fasta = res.fasta
+            protein = res.protein
 
             return render(request, 'genbank_fasta/results.html',
                           {
-                              'result': result,
+                              'items_with_accession': items_with_accession,
+                              'fasta': fasta,
+                              'protein': protein,
                               'version': version,
                               'stats': stats,
                           },