Merge pull request #109 from carlosp420/dataset_button

Dataset button

.gitignore

@@ -24,6 +24,9 @@ htmlcov
 # old VoSeq files to ignore
 conf.php
 
+# avoid including dataset files
+voseq/create_dataset/dataset_files/*txt
+
 # avoid including migrations files
 voseq/public_interface/migrations/*
 voseq/stats/migrations/*

voseq/create_dataset/dataset.py

@@ -1,4 +1,6 @@
 import collections
+import os
+import uuid
 import re
 
 from core.utils import chain_and_flatten
@@ -26,6 +28,20 @@ def __init__(self, codon_positions, partition_by_positions, seq_objs, gene_codes
         self.warnings = []
         self.partition_list = None
 
+        self.cwd = os.path.dirname(__file__)
+        self.guid = self.make_guid()
+        self.dataset_file = os.path.join(self.cwd,
+                                         'dataset_files',
+                                         self.file_format + '_' + self.guid + '.txt',
+                                         )
+
+    def save_dataset_to_file(self, dataset_str):
+        with open(self.dataset_file, 'w') as handle:
+            handle.write(dataset_str)
+
+    def make_guid(self):
+        return uuid.uuid4().hex
+
     def get_number_chars_from_partition_list(self, partitions):
         chars = 0
         gene_codes_and_lengths = collections.OrderedDict()
@@ -132,7 +148,9 @@ def convert_lists_to_dataset(self, partitions):
         for i in partitions:
             out += '\n'
             out += '\n'.join(i)
-        return out.strip()
+        dataset_str = out.strip()
+        self.save_dataset_to_file(dataset_str)
+        return dataset_str
 
     def get_codons_in_each_partition(self, codons):
         partition_list = ()

voseq/create_dataset/templates/create_dataset/index.html

@@ -28,7 +28,7 @@ <h3>Create dataset:</h3>
     <div class="container">
       <div class="row">
 
-        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-9 col-lg-offset-1">
+        <div class="col-xs-12 col-sm-12  col-md-11 col-lg-11 ">
 
         <form action="/create_dataset/results/" method="post">
         <div class="panel panel-primary" style="min-width: 790px;">
@@ -159,6 +159,16 @@ <h3 class="panel-title"><b>Enter the required info to make yourself a ready-to-r
                         {{ form.voucher_codes }}
                       </td>
                     </tr>
+                    <tr>
+                      <td>
+                       &nbsp;
+                      </td>
+                      <td>
+                        <button type="submit" class="btn btn-info" id="submit_button">
+                          Create dataset
+                        </button>
+                      </td>
+                    </tr>
                   </table>
                 </td>
 
@@ -179,13 +189,19 @@ <h3 class="panel-title"><b>Enter the required info to make yourself a ready-to-r
                         (if geneset chosen, adds extra genes)
                       </td>
                       <td>
-                        <table class="table table-condensed table-striped">
-                          <tr>
-                            <td>
+                        <table class="table table-condensed table-striped small_fonts">
                             {% for i in form.gene_codes %}
-                              {{ i }}&nbsp;&nbsp;&nbsp;&nbsp;
+                              {% if forloop.counter == 1 %}
+                                <tr>
+                              {% endif %}
+                                  <td>
+                                  {{ i }}
+                                  </td>
+                              {% if forloop.counter|divisibleby:"4" %}
+                                </tr>
+                              {% endif %}
+
                             {% endfor %}
-                            </td>
                           </tr>
                         </table>
                       </td>
@@ -198,9 +214,7 @@ <h3 class="panel-title"><b>Enter the required info to make yourself a ready-to-r
 
         </div><!-- panel -->
 
-            <button type="submit" class="btn btn-info" id="submit_button">
-              Create dataset
-            </button>
+
         </form>
 
 

voseq/create_dataset/templates/create_dataset/results.html

@@ -62,29 +62,24 @@ <h3 class="panel-title"><b>Your dataset file:</b></h3>
 
         </div><!-- panel -->
 
-        <a href="/genbank_fasta/results/{{ protein_file }}">
+        <a href="/create_dataset/results/{{ dataset_file }}">
         <button class="btn btn-info">
           <i class="fa fa-download"></i>
           Download dataset file
         </button></a>
 
 
+          <br />
+          <br />
 
-      {% if phylip_partition_file %}
+      {% if charset_block %}
          <table class="table table-bordered">
             <tr>
               <td>
                 <textarea readonly style="height: 150px; white-space: nowrap;" class="form-control">{{ charset_block }}</textarea>
               </td>
             </tr>
           </table>
-
-      <a href="/genbank_fasta/results/{{ protein_file }}">
-        <button class="btn btn-info">
-          <i class="fa fa-download"></i>
-          Download PHYLIP partitions file
-        </button>
-      </a>
       {% endif %}
 
 

voseq/create_dataset/urls.py

@@ -8,5 +8,5 @@
     '',
     url(r'^/$', views.index, name='index'),
     url(r'^/results/$', views.results, name='results'),
-
+    url(r'^/results/(?P<file_name>.+\.txt)/$', views.serve_file, name='serve_file'),
 )

voseq/create_dataset/utils.py

@@ -1,6 +1,3 @@
-import os
-import uuid
-
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
@@ -24,17 +21,8 @@ def __init__(self, *args, **kwargs):
         self.number_taxa = len(self.voucher_codes)
         self.number_chars = None
         self.vouchers_to_drop = None
-        self.cwd = os.path.dirname(__file__)
-        self.guid = self.make_guid()
-        self.phylip_partition_file = os.path.join(self.cwd,
-                                                  'phylip_files',
-                                                  'phylip_' + self.guid + '_partitions.phy',
-                                                  )
         self.charset_block = None
 
-    def make_guid(self):
-        return uuid.uuid4().hex
-
     def get_charset_block(self):
         charset_block = []
 
@@ -99,7 +87,9 @@ def convert_lists_to_dataset(self, partitions):
                             out += [' ' * 55 + line[-1] + '\n']
 
         self.get_charset_block()
-        return ''.join(out)
+        dataset_str = ''.join(out)
+        self.save_dataset_to_file(dataset_str)
+        return dataset_str
 
 
 class CreateTNT(Dataset):
@@ -145,7 +135,9 @@ def convert_lists_to_dataset(self, partitions):
                         out += '\n' + i
 
         out += '\n;\nproc/;'
-        return out.strip()
+        dataset_str = out.strip()
+        self.save_dataset_to_file(dataset_str)
+        return dataset_str
 
 
 class CreateNEXUS(Dataset):
@@ -218,7 +210,9 @@ def convert_lists_to_dataset(self, partitions):
         out += self.get_charset_block()
         out += self.get_partitions_block()
         out += self.get_final_block()
-        return '\n'.join(out)
+        dataset_str = '\n'.join(out)
+        self.save_dataset_to_file(dataset_str)
+        return dataset_str
 
 
 class CreateDataset(object):
@@ -246,7 +240,7 @@ def __init__(self, cleaned_data):
         self.gene_codes_metadata = self.get_gene_codes_metadata()
         self.warnings = []
         self.outgroup = cleaned_data['outgroup']
-        self.phylip_partition_file = None
+        self.dataset_file = None
         self.charset_block = None
         self.dataset_str = self.create_dataset()
 
@@ -261,6 +255,7 @@ def create_dataset(self):
                                 self.file_format)
             fasta_dataset = fasta.from_seq_objs_to_dataset()
             self.warnings += fasta.warnings
+            self.dataset_file = fasta.dataset_file
             return fasta_dataset
 
         if self.file_format == 'PHY':
@@ -270,8 +265,7 @@ def create_dataset(self):
                                self.minimum_number_of_genes)
             phylip_dataset = phy.from_seq_objs_to_dataset()
             self.warnings += phy.warnings
-            self.phylip_partition_file = phy.phylip_partition_file
-            print(">>>>>>>>>>>>> self.charset_block", phy.charset_block)
+            self.dataset_file = phy.dataset_file
             self.charset_block = phy.charset_block
             return phylip_dataset
 
@@ -282,6 +276,7 @@ def create_dataset(self):
                             self.minimum_number_of_genes)
             tnt_dataset = tnt.from_seq_objs_to_dataset()
             self.warnings += tnt.warnings
+            self.dataset_file = tnt.dataset_file
             return tnt_dataset
 
         if self.file_format == 'NEXUS':
@@ -291,6 +286,7 @@ def create_dataset(self):
                                 self.minimum_number_of_genes)
             nexus_dataset = nexus.from_seq_objs_to_dataset()
             self.warnings += nexus.warnings
+            self.dataset_file = nexus.dataset_file
             return nexus_dataset
 
     def create_seq_record(self, s):

voseq/create_dataset/views.py

@@ -1,7 +1,9 @@
+import os
 import re
 
 from django.shortcuts import render
 from django.http import HttpResponseRedirect
+from django.http import HttpResponse
 
 from core.utils import get_version_stats
 from .forms import CreateDatasetForm
@@ -28,19 +30,19 @@ def results(request):
         if form.is_valid():
             print(">>>>", form.cleaned_data)
             dataset_creator = CreateDataset(form.cleaned_data)
-            dataset = dataset_creator.dataset_str
+            dataset = dataset_creator.dataset_str[0:1500] + '\n...\n\n\n' + '#######\nComplete dataset file available for download.\n#######'
             errors = dataset_creator.errors
             warnings = dataset_creator.warnings
 
-            phylip_file = dataset_creator.phylip_partition_file
-            if phylip_file is not None:
-                phylip_partition_file = re.search('(phylip_[a-z0-9]+_partitions\.phy)', phylip_file).groups()[0]
+            dataset_file_abs = dataset_creator.dataset_file
+            if dataset_file_abs is not None:
+                dataset_file = re.search('([A-Z]+_[a-z0-9]+\.txt)', dataset_file_abs).groups()[0]
             else:
-                phylip_partition_file = False
+                dataset_file = False
 
             return render(request, 'create_dataset/results.html',
                           {
-                              'phylip_partition_file': phylip_partition_file,
+                              'dataset_file': dataset_file,
                               'charset_block': dataset_creator.charset_block,
                               'dataset': dataset,
                               'errors': errors,
@@ -60,3 +62,17 @@ def results(request):
                           )
     else:
         return HttpResponseRedirect('/create_dataset/')
+
+
+def serve_file(request, file_name):
+    cwd = os.path.dirname(__file__)
+    dataset_file = os.path.join(cwd,
+                                'dataset_files',
+                                file_name,
+                                )
+    response = HttpResponse(open(dataset_file, 'r').read(), content_type='application/text')
+    response['Content-Disposition'] = 'attachment; filename=dataset_file.txt'
+
+    if os.path.isfile(dataset_file):
+        os.remove(dataset_file)
+    return response

voseq/public_interface/static/css/pi.css

@@ -62,3 +62,8 @@ body {
     font-family: 'Source Code Pro', Courier, serif;
     font-weight: 600;
 }
+
+.small_fonts {
+    font-family: 'Source Code Pro', sans-serif;
+    font-size: 12px;
+}