From 540d33872954530c5623fa2b1b42b120838437a1 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Sat, 4 Apr 2009 00:36:43 +0000 Subject: [PATCH] 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. --- htsworkflow/frontend/samples/views.py | 104 +++++++++--------- .../templates/samples/library_detail.html | 47 +++++++- 2 files changed, 96 insertions(+), 55 deletions(-) diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py index d6647d1..3a37a8c 100644 --- 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('Library ID: %s' % (lib.library_id)) - output.append('Name: %s' % (lib.library_name)) - output.append('Species: %s' % (lib.library_species.scientific_name)) - output.append('') - - output.append('FLOWCELL - LANE:') - - 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('
') - output.append(t.render(RequestContext(request, {'lane_summary_list': lane_summary_list}))) - output.append('
') - - if record_count == 0: - output.append("None Found") - - return HttpResponse('
\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 56c937f..fbaf1a0 100644 --- a/htsworkflow/frontend/templates/samples/library_detail.html +++ b/htsworkflow/frontend/templates/samples/library_detail.html @@ -1,7 +1,4 @@ {% load humanize %} - -
-
+

About this library

+Library ID: {{ lib.library_id }}
+Name: {{ lib.library_name }}
+Species: {{ lib.library_species.scientific_name }}
+Affiliations: + + +

Raw Result Files

+ + + + + + + + + + +{% for result in eland_results %} + + + + + + + + +{% endfor %} +
CycleFlowcellLaneSummaryElandBed
{{ result.cycle }}{{ result.flowcell_id }}{{ result.lane }}Summary{{ result.result_label }} + {% if result.bed_url %} + Bed + {% endif %} +
+ +

Lane Summary Statistics

{% block summary_stats %} @@ -87,11 +123,12 @@

+

Count of multi-reads

{% for lane in lane_summary_list %} -

+

{{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }} {% if lane.end %} end {{ lane.end }}{% endif %} -

+