Display the affiliations on the public library detail page.

This involved cleaning up some of the view code to push all of the html
generation into the template and none in the view function, by modifying
the view function to feed everything to the template in the form of
variables.

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index d6647d1dba38311733d9f3d07530df9f77442a6b..3a37a8c68e1d2cd754e1c4129d213d235f68b2e7 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -10,6 +10,7 @@ from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
 from django.http import HttpResponse
+from django.shortcuts import render_to_response
 from django.template import RequestContext
 from django.template.loader import get_template
 
@@ -62,70 +63,41 @@ def library_to_flowcells(request, lib_id):
     """
     Display information about all the flowcells a library has been run on.
     """
-    t = get_template("samples/library_detail.html")
     
     try:
       lib = Library.objects.get(library_id=lib_id)
     except:
       return HttpResponse("Library %s does not exist" % (lib_id))
-    
-    output = []
-    
-    output.append('<b>Library ID:</b> %s' % (lib.library_id))
-    output.append('<b>Name:</b> %s' % (lib.library_name))
-    output.append('<b>Species:</b> %s' % (lib.library_species.scientific_name))
-    output.append('')
-    
-    output.append('<b>FLOWCELL - LANE:</b>')
-    
-    output.extend([ '%s - Lane 1 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 1)) for fc in lib.lane_1_library.all() ])
-    output.extend([ '%s - Lane 2 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 2)) for fc in lib.lane_2_library.all() ])
-    output.extend([ '%s - Lane 3 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 3)) for fc in lib.lane_3_library.all() ])
-    output.extend([ '%s - Lane 4 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 4)) for fc in lib.lane_4_library.all() ])
-    output.extend([ '%s - Lane 5 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 5)) for fc in lib.lane_5_library.all() ])
-    output.extend([ '%s - Lane 6 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 6)) for fc in lib.lane_6_library.all() ])
-    output.extend([ '%s - Lane 7 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 7)) for fc in lib.lane_7_library.all() ])
-    output.extend([ '%s - Lane 8 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 8)) for fc in lib.lane_8_library.all() ])
-    
-    record_count = lib.lane_1_library.count() + \
-                    lib.lane_2_library.count() + \
-                    lib.lane_3_library.count() + \
-                    lib.lane_4_library.count() + \
-                    lib.lane_5_library.count() + \
-                    lib.lane_6_library.count() + \
-                    lib.lane_7_library.count() + \
-                    lib.lane_8_library.count()
-    
+   
     flowcell_list = []
-    flowcell_list.extend([ (fc.flowcell_id, 1) for fc in lib.lane_1_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 2) for fc in lib.lane_2_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 3) for fc in lib.lane_3_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 4) for fc in lib.lane_4_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 5) for fc in lib.lane_5_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 6) for fc in lib.lane_6_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 7) for fc in lib.lane_7_library.all() ])
-    flowcell_list.extend([ (fc.flowcell_id, 8) for fc in lib.lane_8_library.all() ])
+    interesting_flowcells = {} # aka flowcells we're looking at
+    for lane in LANE_LIST:
+        lane_library = getattr(lib, 'lane_%d_library' % (lane,))
+        for fc in lane_library.all():
+            flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
+            if flowcell_id not in interesting_flowcells:
+                interesting_flowcells[flowcell_id] = get_flowcell_result_dict(flowcell_id)
+            flowcell_list.append((fc.flowcell_id, lane))
+
     flowcell_list.sort()
     
     lane_summary_list = []
+    eland_results = []
     for fc, lane in flowcell_list:
         lane_summary, err_list = _summary_stats(fc, lane)
         
+        eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
         lane_summary_list.extend(lane_summary)
-    
-        for err in err_list:    
-            output.append(err)
-   
-    output.append('<br />')
-    output.append(t.render(RequestContext(request, {'lane_summary_list': lane_summary_list})))
-    output.append('<br />')
-    
-    if record_count == 0:
-        output.append("None Found")
-    
-    return HttpResponse('<br />\n'.join(output))
 
 
+    return render_to_response(
+        'samples/library_detail.html',
+        {'lib': lib,
+         'eland_results': eland_results,
+         'lane_summary_list': lane_summary_list,
+        },
+        context_instance = RequestContext(request))
+
 def summaryhtm_fc_cnm(request, fc_id, cnm):
     """
     returns a Summary.htm file if it exists.
@@ -335,7 +307,39 @@ def get_eland_result_type(pathname):
         return 'result'
     else:
         return 'unknown'
-    
+
+def _make_eland_results(flowcell_id, lane, interesting_flowcells):
+
+    cur_fc = interesting_flowcells[flowcell_id]
+    results = []
+    for cycle in cur_fc.keys():
+        result_path = cur_fc[cycle]['eland_results'][lane]
+        result_link = make_result_link(flowcell_id, cycle, lane, result_path)
+        results.append({'flowcell_id': flowcell_id,
+                        'cycle': cycle, 
+                        'lane': lane, 
+                        'summary_url': make_summary_url(flowcell_id, cycle),
+                        'result_url': result_link[0],
+                        'result_label': result_link[1],
+                        'bed_url': result_link[2],
+        })
+    return results
+
+def make_summary_url(flowcell_id, cycle_name):
+    url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
+    return url
+
+def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
+    result_type = get_eland_result_type(eland_result_path)
+    result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
+    result_label = 'eland %s' % (result_type,)
+    bed_url = None
+    if result_type == 'result':
+       bed_url_pattern = '/results/%s/%s/bedfile/%s'
+       bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
+    
+    return (result_url, result_label, bed_url)
+
 def _files(flowcell_id, lane):
     """
     Sets up available files for download

diff --git a/htsworkflow/frontend/templates/samples/library_detail.html b/htsworkflow/frontend/templates/samples/library_detail.html
index 56c937f5d58e54477648a396867d50c7de894f92..fbaf1a0c85dbc7c95401494faf3ed756ed449471 100644 (file)
--- a/htsworkflow/frontend/templates/samples/library_detail.html
+++ b/htsworkflow/frontend/templates/samples/library_detail.html
@@ -1,7 +1,4 @@
 {% load humanize %}
-
-<hr/>
-<br/>
 <style type="text/css">
   /* <![CDATA[ */
   table, td {
@@ -26,6 +23,45 @@
   /* ]]> */
 </style>
 
+<h2>About this library</h2>
+<b>Library ID</b>: {{ lib.library_id }}<br/>
+<b>Name</b>: {{ lib.library_name }}<br/>
+<b>Species</b>: {{ lib.library_species.scientific_name }}<br/>
+<b>Affiliations</b>:
+<ul>
+  {% for individual in lib.affiliations.all %}
+    <li>{{ individual.name }} ( {{ individual.contact }} )</li>
+  {% endfor %}
+</ul>
+
+<h2>Raw Result Files</h2>
+<table>
+<thead>
+  <tr>
+    <td>Cycle</td>
+    <td>Flowcell</td>
+    <td>Lane</td>
+    <td>Summary</td>
+    <td>Eland</td>
+    <td>Bed</td>
+  </tr>
+{% for result in eland_results %}
+<tr>
+  <td>{{ result.cycle }}</td>
+  <td>{{ result.flowcell_id }}</td>
+  <td>{{ result.lane }}</td>
+  <td><a href="{{ result.summary_url }}">Summary</a></td>
+  <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
+  <td>
+  {% if result.bed_url %}
+    <a href="{{ result.bed_url }}">Bed</a>
+  {% endif %}
+  </td>
+</tr>
+{% endfor %}
+</table>
+
+<h2>Lane Summary Statistics</h2>
 {% block summary_stats %}
 <table>
   <thead>
@@ -87,11 +123,12 @@
 </table>
 <br/>
 <hr/>
+<h2>Count of multi-reads</h2>
 {% for lane in lane_summary_list %}
-<h2>
+<h3>
   {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }} 
   {% if lane.end %} end {{ lane.end }}{% endif %}
-</h2>
+</h3>
   <ul>
     {% for name, counts in lane.summarized_reads.items %}
     <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>