+
+def library_id_to_admin_url(request, lib_id):
+ lib = Library.objects.get(id=lib_id)
+ return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
+
+def library_dict(library_id):
+ """
+ Given a library id construct a dictionary containing important information
+ return None if nothing was found
+ """
+ try:
+ lib = Library.objects.get(id = library_id)
+ except Library.DoesNotExist, e:
+ return None
+
+ #lane_info = lane_information(lib.lane_set)
+ lane_info = []
+ 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]} )
+
+ 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,
+ #'antibody_name': lib.antibody_name(), # we have no antibodies.
+ 'antibody_id': lib.antibody_id,
+ 'cell_line_id': lib.cell_line_id,
+ 'cell_line': unicode_or_none(lib.cell_line),
+ 'experiment_type': lib.experiment_type.name,
+ 'experiment_type_id': lib.experiment_type_id,
+ 'gel_cut_size': lib.gel_cut_size,
+ 'hidden': lib.hidden,
+ 'id': lib.id,
+ 'insert_size': lib.insert_size,
+ 'lane_set': lane_info,
+ 'library_id': lib.id,
+ 'library_name': lib.library_name,
+ 'library_species': lib.library_species.scientific_name,
+ 'library_species_id': lib.library_species_id,
+ #'library_type': lib.library_type.name,
+ 'library_type_id': lib.library_type_id,
+ 'made_for': lib.made_for,
+ 'made_by': lib.made_by,
+ 'notes': lib.notes,
+ 'replicate': lib.replicate,
+ 'stopping_point': lib.stopping_point,
+ 'successful_pM': unicode_or_none(lib.successful_pM),
+ 'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
+ }
+ if lib.library_type_id is None:
+ info['library_type'] = None
+ else:
+ 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?
+
+ lib = library_dict(library_id)
+ if lib is None:
+ raise Http404
+
+ 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(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):
+ """
+ Information about the user
+ """
+ context = {
+ 'page_name': 'User Profile',
+ 'media': '',
+ #'bcmagic': BarcodeMagicForm(),
+ #'select': 'settings',
+ }
+ context.update(SAMPLES_CONTEXT_DEFAULTS)
+ return render_to_response('registration/profile.html', context,
+ context_instance=RequestContext(request))
+
+