Attempt to be robust to not having an alignment in our RunXml file

[htsworkflow.git] / htsworkflow / frontend / samples / views.py

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index afccc022586e1570b15117f0651351dbc63cfa8d..e50b5b357c2caa1b88d73cb2f2884cf0124f6158 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -9,27 +9,29 @@ try:
 except ImportError, e:
     import simplejson as json
 
 except ImportError, e:
     import simplejson as json
 

+from django.contrib.csrf.middleware import csrf_exempt

 from htsworkflow.frontend.auth import require_api_key
 from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
 from htsworkflow.frontend.samples.changelist import ChangeList
 from htsworkflow.frontend.auth import require_api_key
 from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
 from htsworkflow.frontend.samples.changelist import ChangeList

-from htsworkflow.frontend.samples.models import Library, HTSUser
-from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
+from htsworkflow.frontend.samples.models import Antibody, Library, Species, HTSUser
+from htsworkflow.frontend.samples.results import get_flowcell_result_dict

 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.eland import ResultLane
 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.eland import ResultLane

-from htsworkflow.frontend import settings
-from htsworkflow.util.conversion import unicode_or_none
+from htsworkflow.pipelines.samplekey import SampleKey
+from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id

 from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
 
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, HttpResponseRedirect, Http404
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
 
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, HttpResponseRedirect, Http404

-from django.shortcuts import render_to_response
+from django.shortcuts import render_to_response, get_object_or_404

 from django.template import RequestContext
 from django.template.loader import get_template
 from django.contrib.auth.decorators import login_required
 from django.template import RequestContext
 from django.template.loader import get_template
 from django.contrib.auth.decorators import login_required

+from django.conf import settings

 
 LANE_LIST = [1,2,3,4,5,6,7,8]
 SAMPLES_CONTEXT_DEFAULTS = {
 
 LANE_LIST = [1,2,3,4,5,6,7,8]
 SAMPLES_CONTEXT_DEFAULTS = {


@@ -37,6 +39,8 @@ SAMPLES_CONTEXT_DEFAULTS = {
     'bcmagic': BarcodeMagicForm()
 }
 
     'bcmagic': BarcodeMagicForm()
 }
 

+LOGGER = logging.getLogger(__name__)
+

 def count_lanes(lane_set):
     single = 0
     paired = 1
 def count_lanes(lane_set):
     single = 0
     paired = 1


@@ -44,7 +48,7 @@ def count_lanes(lane_set):
     medium_read = 1
     long_read = 2
     counts = [[0,0,0,],[0,0,0]]
     medium_read = 1
     long_read = 2
     counts = [[0,0,0,],[0,0,0]]

-    
+

     for lane in lane_set.all():
         if lane.flowcell.paired_end:
             lane_type = paired
     for lane in lane_set.all():
         if lane.flowcell.paired_end:
             lane_type = paired


@@ -57,7 +61,7 @@ def count_lanes(lane_set):
         else:
             read_type = long_read
         counts[lane_type][read_type] += 1
         else:
             read_type = long_read
         counts[lane_type][read_type] += 1

-        
+

     return counts
 
 def create_library_context(cl):
     return counts
 
 def create_library_context(cl):


@@ -68,6 +72,7 @@ def create_library_context(cl):
     #for lib in library_items.object_list:
     for lib in cl.result_list:
        summary = {}
     #for lib in library_items.object_list:
     for lib in cl.result_list:
        summary = {}

+       summary['library'] = lib

        summary['library_id'] = lib.id
        summary['library_name'] = lib.library_name
        summary['species_name' ] = lib.library_species.scientific_name
        summary['library_id'] = lib.id
        summary['library_name'] = lib.library_name
        summary['species_name' ] = lib.library_species.scientific_name


@@ -84,43 +89,42 @@ def create_library_context(cl):
        summary['lanes_run'] = lanes_run
        summary['is_archived'] = lib.is_archived()
        records.append(summary)
        summary['lanes_run'] = lanes_run
        summary['is_archived'] = lib.is_archived()
        records.append(summary)

-    cl.result_count = unicode(cl.paginator._count) + u" libraries"
+    cl.result_count = unicode(cl.paginator._count)

     return {'library_list': records }
 
     return {'library_list': records }
 

-def library(request):
+
+def library(request, todo_only=False):
+    queryset = Library.objects.filter(hidden__exact=0)
+    if todo_only:
+        queryset = queryset.filter(lane=None)

     # build changelist
     fcl = ChangeList(request, Library,
         list_filter=['affiliations', 'library_species'],
         search_fields=['id', 'library_name', 'amplified_from_sample__id'],
         list_per_page=200,
     # build changelist
     fcl = ChangeList(request, Library,
         list_filter=['affiliations', 'library_species'],
         search_fields=['id', 'library_name', 'amplified_from_sample__id'],
         list_per_page=200,

-        queryset=Library.objects.filter(hidden__exact=0)
+        queryset=queryset

     )
 
     )
 

-    context = { 'cl': fcl, 'title': 'Library Index'}
+    context = { 'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}

     context.update(create_library_context(fcl))
     t = get_template('samples/library_index.html')
     c = RequestContext(request, context)
     context.update(create_library_context(fcl))
     t = get_template('samples/library_index.html')
     c = RequestContext(request, context)

-    
-    app_context = {
-        'page_name': 'Library Index',
-        'body': t.render(c)
-    }
-    app_context.update(SAMPLES_CONTEXT_DEFAULTS)
-    
-    app_t = get_template('flowcell_libraries_app.html')
-    app_c = RequestContext(request, app_context)
-    return HttpResponse( app_t.render(app_c) )
+    return HttpResponse( t.render(c) )
+
+
+def library_not_run(request):
+    return library(request, todo_only=True)
+

 
 def library_to_flowcells(request, lib_id):
     """
     Display information about all the flowcells a library has been run on.
     """
 
 def library_to_flowcells(request, lib_id):
     """
     Display information about all the flowcells a library has been run on.
     """

-    

     try:
     try:

-      lib = Library.objects.get(id=lib_id)
+        lib = Library.objects.get(id=lib_id)

     except:
     except:

-      return HttpResponse("Library %s does not exist" % (lib_id))
-   
+        raise Http404('Library %s does not exist' % (lib_id,))
+

     flowcell_list = []
     flowcell_run_results = {} # aka flowcells we're looking at
     for lane in lib.lane_set.all():
     flowcell_list = []
     flowcell_run_results = {} # aka flowcells we're looking at
     for lane in lib.lane_set.all():


@@ -134,10 +138,10 @@ def library_to_flowcells(request, lib_id):
     lane_summary_list = []
     eland_results = []
     for fc, lane_number in flowcell_list:
     lane_summary_list = []
     eland_results = []
     for fc, lane_number in flowcell_list:

-        lane_summary, err_list = _summary_stats(fc, lane_number)
+        lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
+        lane_summary_list.extend(lane_summary)

 
         eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
 
         eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))

-        lane_summary_list.extend(lane_summary)

 
     context = {
         'page_name': 'Library Details',
 
     context = {
         'page_name': 'Library Details',


@@ -174,28 +178,28 @@ def lanes_for(request, username=None):
         context,
         context_instance = RequestContext(request)
     )
         context,
         context_instance = RequestContext(request)
     )

-          
-    
+
+

 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
     """
     returns a Summary.htm file if it exists.
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
     """
     returns a Summary.htm file if it exists.
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)

-    
+

     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))

-    
+

     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))

-    
+

     summary_filepath = d[cnm]['summary']
     summary_filepath = d[cnm]['summary']

-    
+

     if summary_filepath is None:
         return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
     if summary_filepath is None:
         return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))

-    
+

     f = open(summary_filepath, 'r')
     f = open(summary_filepath, 'r')

-    
+

     return HttpResponse(f)
 
 
     return HttpResponse(f)
 
 


@@ -205,27 +209,27 @@ def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)

-    
+

     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))

-    
+

     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))

-    
+

     erd = d[cnm]['eland_results']
     lane = int(lane)
     erd = d[cnm]['eland_results']
     lane = int(lane)

-    
+

     if lane not in erd:
         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
     if lane not in erd:
         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))

-    
+

     filepath = erd[lane]
     filepath = erd[lane]

-    
+

     #f = opener.autoopen(filepath, 'r')
     # return HttpResponse(f, mimetype="application/x-elandresult")
 
     f = open(filepath, 'r')
     return HttpResponse(f, mimetype='application/x-bzip2')
     #f = opener.autoopen(filepath, 'r')
     # return HttpResponse(f, mimetype="application/x-elandresult")
 
     f = open(filepath, 'r')
     return HttpResponse(f, mimetype='application/x-bzip2')

-    
+

 
 
 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
 
 
 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):


@@ -241,36 +245,36 @@ def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=F
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)
     """
     fc_id, status = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(fc_id)

-    
+

     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
     if d is None:
         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))

-    
+

     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
     if cnm not in d:
         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))

-    
+

     erd = d[cnm]['eland_results']
     lane = int(lane)
     erd = d[cnm]['eland_results']
     lane = int(lane)

-    
+

     if lane not in erd:
         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
     if lane not in erd:
         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))

-    
+

     filepath = erd[lane]
     filepath = erd[lane]

-    
+

     # Eland result file
     fi = opener.autoopen(filepath, 'r')
     # output memory file
     # Eland result file
     fi = opener.autoopen(filepath, 'r')
     # output memory file

-    
+

     name, description = makebed.make_description( fc_id, lane )
     name, description = makebed.make_description( fc_id, lane )

-    
+

     bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
     bedgen = makebed.make_bed_from_eland_generator(fi, name, description)

-    
+

     if ucsc_compatible:
         return HttpResponse(bedgen)
     else:
         return HttpResponse(bedgen, mimetype="application/x-bedfile")
 
 
     if ucsc_compatible:
         return HttpResponse(bedgen)
     else:
         return HttpResponse(bedgen, mimetype="application/x-bedfile")
 
 

-def _summary_stats(flowcell_id, lane_id):
+def _summary_stats(flowcell_id, lane_id, library_id):

     """
     Return the summary statistics for a given flowcell, lane, and end.
     """
     """
     Return the summary statistics for a given flowcell, lane, and end.
     """


@@ -279,112 +283,60 @@ def _summary_stats(flowcell_id, lane_id):
 
     summary_list = []
     err_list = []
 
     summary_list = []
     err_list = []

-    
+

     if fc_result_dict is None:
         err_list.append('Results for Flowcell %s not found.' % (fc_id))
         return (summary_list, err_list)
 
     for cycle_width in fc_result_dict:
         xmlpath = fc_result_dict[cycle_width]['run_xml']
     if fc_result_dict is None:
         err_list.append('Results for Flowcell %s not found.' % (fc_id))
         return (summary_list, err_list)
 
     for cycle_width in fc_result_dict:
         xmlpath = fc_result_dict[cycle_width]['run_xml']

-        
+

         if xmlpath is None:
             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
             continue
         if xmlpath is None:
             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
             continue

-        
+

         run = load_pipeline_run_xml(xmlpath)
         run = load_pipeline_run_xml(xmlpath)

+        # skip if we don't have available metadata.
+        if run.gerald is None or run.gerald.summary is None:
+            continue
+        

         gerald_summary = run.gerald.summary.lane_results
         gerald_summary = run.gerald.summary.lane_results

-        for end in range(len(gerald_summary)):
-            end_summary = run.gerald.eland_results.results[end]
-            if end_summary.has_key(lane_id):
-                eland_summary = run.gerald.eland_results.results[end][lane_id]
-            else:
-                eland_summary = ResultLane(lane_id=lane_id, end=end)
+        key = SampleKey(lane=lane_id, sample='s')
+        eland_results = list(run.gerald.eland_results.find_keys(key))
+        key = SampleKey(lane=lane_id, sample=library_id)
+        eland_results.extend(run.gerald.eland_results.find_keys(key))
+        for key in eland_results:
+            eland_summary = run.gerald.eland_results.results[key]

             # add information to lane_summary
             eland_summary.flowcell_id = flowcell_id
             # add information to lane_summary
             eland_summary.flowcell_id = flowcell_id

-            if len(gerald_summary) > end and gerald_summary[end].has_key(lane_id):
-                eland_summary.clusters = gerald_summary[end][lane_id].cluster
-            else:
-                eland_summary.clusters = None
+
+            read = key.read-1 if key.read is not None else 0
+            try:
+                eland_summary.clusters = gerald_summary[read][key.lane].cluster
+            except (IndexError, KeyError) as e:
+                eland_summary.clustes = None

             eland_summary.cycle_width = cycle_width
             if hasattr(eland_summary, 'genome_map'):
             eland_summary.cycle_width = cycle_width
             if hasattr(eland_summary, 'genome_map'):

-                eland_summary.summarized_reads = runfolder.summarize_mapped_reads( 
-                                                   eland_summary.genome_map, 
+                eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
+                                                   eland_summary.genome_map,

                                                    eland_summary.mapped_reads)
 
             # grab some more information out of the flowcell db
             flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
             #pm_field = 'lane_%d_pM' % (lane_id)
                                                    eland_summary.mapped_reads)
 
             # grab some more information out of the flowcell db
             flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
             #pm_field = 'lane_%d_pM' % (lane_id)

-            lane_obj = flowcell.lane_set.get(lane_number=lane_id)
-            eland_summary.successful_pm = lane_obj.pM
+            lanes = flowcell.lane_set.filter(lane_number=lane_id)
+            eland_summary.flowcell = flowcell
+            eland_summary.lanes = lanes

 
             summary_list.append(eland_summary)
 
         #except Exception, e:
         #    summary_list.append("Summary report needs to be updated.")
 
             summary_list.append(eland_summary)
 
         #except Exception, e:
         #    summary_list.append("Summary report needs to be updated.")

-        #    logging.error("Exception: " + str(e))
-    
+        #    LOGGER.error("Exception: " + str(e))
+

     return (summary_list, err_list)
 
     return (summary_list, err_list)
 

-def _summary_stats_old(flowcell_id, lane):
-    """
-    return a dictionary of summary stats for a given flowcell_id & lane.
-    """
-    fc_id, status = parse_flowcell_id(flowcell_id)
-    fc_result_dict = get_flowcell_result_dict(fc_id)
-    
-    dict_list = []
-    err_list = []
-    summary_list = []
-    
-    if fc_result_dict is None:
-        err_list.append('Results for Flowcell %s not found.' % (fc_id))
-        return (dict_list, err_list, summary_list)
-    
-    for cnm in fc_result_dict:
-    
-        xmlpath = fc_result_dict[cnm]['run_xml']
-        
-        if xmlpath is None:
-            err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
-            continue
-        
-        tree = ElementTree.parse(xmlpath).getroot()
-        results = runfolder.PipelineRun(pathname='', xml=tree)
-        try:
-            lane_report = runfolder.summarize_lane(results.gerald, lane)
-            summary_list.append(os.linesep.join(lane_report))
-        except Exception, e:
-            summary_list.append("Summary report needs to be updated.")
-            logging.error("Exception: " + str(e))
-       
-        print >>sys.stderr, "----------------------------------"
-        print >>sys.stderr, "-- DOES NOT SUPPORT PAIRED END ---"
-        print >>sys.stderr, "----------------------------------"
-        lane_results = results.gerald.summary[0][lane]
-        lrs = lane_results
-        
-        d = {}
-        
-        d['average_alignment_score'] = lrs.average_alignment_score
-        d['average_first_cycle_intensity'] = lrs.average_first_cycle_intensity
-        d['cluster'] = lrs.cluster
-        d['lane'] = lrs.lane
-        d['flowcell'] = flowcell_id
-        d['cnm'] = cnm
-        d['percent_error_rate'] = lrs.percent_error_rate
-        d['percent_intensity_after_20_cycles'] = lrs.percent_intensity_after_20_cycles
-        d['percent_pass_filter_align'] = lrs.percent_pass_filter_align
-        d['percent_pass_filter_clusters'] = lrs.percent_pass_filter_clusters
-        
-        #FIXME: function finished, but need to take advantage of
-        #   may need to take in a list of lanes so we only have to
-        #   load the xml file once per flowcell rather than once
-        #   per lane.
-        dict_list.append(d)
-    
-    return (dict_list, err_list, summary_list)
-    
-    
+

 def get_eland_result_type(pathname):
     """
     Guess the eland result file type from the filename
 def get_eland_result_type(pathname):
     """
     Guess the eland result file type from the filename


@@ -399,13 +351,14 @@ def get_eland_result_type(pathname):
     else:
         return 'unknown'
 
     else:
         return 'unknown'
 

-def _make_eland_results(flowcell_id, lane, interesting_flowcells):
+def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):

     fc_id, status = parse_flowcell_id(flowcell_id)
     cur_fc = interesting_flowcells.get(fc_id, None)
     if cur_fc is None:
       return []
 
     flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
     fc_id, status = parse_flowcell_id(flowcell_id)
     cur_fc = interesting_flowcells.get(fc_id, None)
     if cur_fc is None:
       return []
 
     flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)

+    lanes = flowcell.lane_set.filter(lane_number=lane_number)

     # Loop throw storage devices if a result has been archived
     storage_id_list = []
     if cur_fc is not None:
     # Loop throw storage devices if a result has been archived
     storage_id_list = []
     if cur_fc is not None:


@@ -417,7 +370,7 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
                 # Otherwise use UUID
                 else:
                     storage_id_list.append(sd.uuid)
                 # Otherwise use UUID
                 else:
                     storage_id_list.append(sd.uuid)

-        
+

     # Formatting for template use
     if len(storage_id_list) == 0:
         storage_ids = None
     # Formatting for template use
     if len(storage_id_list) == 0:
         storage_ids = None


@@ -426,12 +379,13 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
 
     results = []
     for cycle in cur_fc.keys():
 
     results = []
     for cycle in cur_fc.keys():

-        result_path = cur_fc[cycle]['eland_results'].get(lane, None)
-        result_link = make_result_link(fc_id, cycle, lane, result_path)
+        result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
+        result_link = make_result_link(fc_id, cycle, lanes[0], result_path)

         results.append({'flowcell_id': fc_id,
         results.append({'flowcell_id': fc_id,

+                        'flowcell': flowcell,

                         'run_date': flowcell.run_date,
                         'run_date': flowcell.run_date,

-                        'cycle': cycle, 
-                        'lane': lane, 
+                        'cycle': cycle,
+                        'lane': lanes[0],

                         'summary_url': make_summary_url(flowcell_id, cycle),
                         'result_url': result_link[0],
                         'result_label': result_link[1],
                         'summary_url': make_summary_url(flowcell_id, cycle),
                         'result_url': result_link[0],
                         'result_label': result_link[1],


@@ -455,7 +409,7 @@ def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
     if result_type == 'result':
        bed_url_pattern = '/results/%s/%s/bedfile/%s'
        bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
     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):
     return (result_url, result_label, bed_url)
 
 def _files(flowcell_id, lane):


@@ -466,19 +420,19 @@ def _files(flowcell_id, lane):
 
     flowcell_id, id = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(flowcell_id)
 
     flowcell_id, id = parse_flowcell_id(flowcell_id)
     d = get_flowcell_result_dict(flowcell_id)

-    
+

     if d is None:
         return ''
     if d is None:
         return ''

-    
+

     output = []
     output = []

-    
+

     # c_name == 'CN-M' (i.e. C1-33)
     for c_name in d:
     # c_name == 'CN-M' (i.e. C1-33)
     for c_name in d:

-        
+

         if d[c_name]['summary'] is not None:
             output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
                           % (flowcell_id, c_name, c_name))
         if d[c_name]['summary'] is not None:
             output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
                           % (flowcell_id, c_name, c_name))

-        
+

         erd = d[c_name]['eland_results']
         if lane in erd:
             result_type = get_eland_result_type(erd[lane])
         erd = d[c_name]['eland_results']
         if lane in erd:
             result_type = get_eland_result_type(erd[lane])


@@ -487,10 +441,10 @@ def _files(flowcell_id, lane):
             if result_type == 'result':
                 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
                 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
             if result_type == 'result':
                 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
                 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))

-    
+

     if len(output) == 0:
         return ''
     if len(output) == 0:
         return ''

-    
+

     return '(' + '|'.join(output) + ')'
 
 def library_id_to_admin_url(request, lib_id):
     return '(' + '|'.join(output) + ')'
 
 def library_id_to_admin_url(request, lib_id):


@@ -512,16 +466,17 @@ def library_dict(library_id):
     for lane in lib.lane_set.all():
         lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
                            'lane_number': lane.lane_number,
     for lane in lib.lane_set.all():
         lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
                            'lane_number': lane.lane_number,

+                           'lane_id': lane.id,

                            'paired_end': lane.flowcell.paired_end,
                            'read_length': lane.flowcell.read_length,
                            'status_code': lane.status,
                            'status': LANE_STATUS_MAP[lane.status]} )
                            'paired_end': lane.flowcell.paired_end,
                            'read_length': lane.flowcell.read_length,
                            'status_code': lane.status,
                            'status': LANE_STATUS_MAP[lane.status]} )

-        
+

     info = {
         # 'affiliations'?
         # 'aligned_reads': lib.aligned_reads,
         #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
     info = {
         # 'affiliations'?
         # 'aligned_reads': lib.aligned_reads,
         #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...

-        #'amplified_from_sample_id': lib.amplified_from_sample, 
+        #'amplified_from_sample_id': lib.amplified_from_sample,

         #'antibody_name': lib.antibody_name(), # we have no antibodies.
         'antibody_id': lib.antibody_id,
         'cell_line_id': lib.cell_line_id,
         #'antibody_name': lib.antibody_name(), # we have no antibodies.
         'antibody_id': lib.antibody_id,
         'cell_line_id': lib.cell_line_id,


@@ -553,13 +508,14 @@ def library_dict(library_id):
         info['library_type'] = lib.library_type.name
     return info
 
         info['library_type'] = lib.library_type.name
     return info
 

+@csrf_exempt

 def library_json(request, library_id):
     """
     Return a json formatted library dictionary
     """
     require_api_key(request)
     # what validation should we do on library_id?
 def library_json(request, library_id):
     """
     Return a json formatted library dictionary
     """
     require_api_key(request)
     # what validation should we do on library_id?

-    
+

     lib = library_dict(library_id)
     if lib is None:
         raise Http404
     lib = library_dict(library_id)
     if lib is None:
         raise Http404


@@ -567,12 +523,26 @@ def library_json(request, library_id):
     lib_json = json.dumps(lib)
     return HttpResponse(lib_json, mimetype='application/json')
 
     lib_json = json.dumps(lib)
     return HttpResponse(lib_json, mimetype='application/json')
 

+@csrf_exempt

 def species_json(request, species_id):
     """
     Return information about a species.
     """
     raise Http404
 
 def species_json(request, species_id):
     """
     Return information about a species.
     """
     raise Http404
 

+def species(request, species_id):
+    species = get_object_or_404(Species, id=species_id)
+
+    context = RequestContext(request,
+                             { 'species': species })
+
+    return render_to_response("samples/species_detail.html", context)
+
+def antibodies(request):
+    context = RequestContext(request,
+                             {'antibodies': Antibody.objects.order_by('antigene')})
+    return render_to_response("samples/antibody_index.html", context)
+

 @login_required
 def user_profile(request):
     """
 @login_required
 def user_profile(request):
     """


@@ -588,3 +558,4 @@ def user_profile(request):
     return render_to_response('registration/profile.html', context,
                               context_instance=RequestContext(request))
 
     return render_to_response('registration/profile.html', context,
                               context_instance=RequestContext(request))
 

+