from htsworkflow.frontend.samples.changelist import ChangeList
from htsworkflow.frontend.samples.models import Library
from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
+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 import makebed
from htsworkflow.util import opener
from django.shortcuts import render_to_response
from django.template import RequestContext
from django.template.loader import get_template
+from django.contrib.auth.decorators import login_required
import StringIO
import logging
import os
LANE_LIST = [1,2,3,4,5,6,7,8]
+SAMPLES_CONTEXT_DEFAULTS = {
+ 'app_name': 'Flowcell/Library Tracker',
+ 'bcmagic': BarcodeMagicForm()
+}
def create_library_context(cl):
"""
else:
summary['amplified_from'] = ''
lanes_run = 0
- for lane_id in LANE_LIST:
- lane = getattr(lib, 'lane_%d_library' % (lane_id,))
- lanes_run += len( lane.all() )
+ #for lane_id in LANE_LIST:
+ # lane = getattr(lib, 'lane_%d_library' % (lane_id,))
+ # lanes_run += len( lane.all() )
+ lanes_run = lib.lane_set.count()
summary['lanes_run'] = lanes_run
summary['is_archived'] = lib.is_archived()
records.append(summary)
context.update(create_library_context(fcl))
t = get_template('samples/library_index.html')
c = RequestContext(request, context)
- return HttpResponse( t.render(c) )
+
+ app_context = {
+ 'page_name': 'Library Index',
+ 'east_region_config_div': 'changelist-filter',
+ '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) )
def library_to_flowcells(request, lib_id):
"""
flowcell_list = []
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))
+ #for lane in LANE_LIST:
+ for lane in lib.lane_set.all():
+ #lane_library = getattr(lib, 'lane_%d_library' % (lane,))
+ #for fc in lane_library.all():
+ fc = lane.flowcell
+ 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.lane_number))
flowcell_list.sort()
lane_summary_list = []
eland_results = []
- for fc, lane in flowcell_list:
- lane_summary, err_list = _summary_stats(fc, lane)
+ for fc, lane_number in flowcell_list:
+ lane_summary, err_list = _summary_stats(fc, lane_number)
- eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
+ eland_results.extend(_make_eland_results(fc, lane_number, interesting_flowcells))
lane_summary_list.extend(lane_summary)
+ context = {
+ 'page_name': 'Library Details',
+ 'lib': lib,
+ 'eland_results': eland_results,
+ 'lane_summary_list': lane_summary_list,
+ }
+ context.update(SAMPLES_CONTEXT_DEFAULTS)
+
return render_to_response(
'samples/library_detail.html',
- {'lib': lib,
- 'eland_results': eland_results,
- 'lane_summary_list': lane_summary_list,
- },
+ context,
context_instance = RequestContext(request))
def summaryhtm_fc_cnm(request, flowcell_id, cnm):
run = load_pipeline_run_xml(xmlpath)
gerald_summary = run.gerald.summary.lane_results
for end in range(len(gerald_summary)):
- eland_summary = run.gerald.eland_results.results[end][lane_id]
+ 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)
# add information to lane_summary
eland_summary.flowcell_id = flowcell_id
- eland_summary.clusters = gerald_summary[end][lane_id].cluster
+ 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 = 'n/a'
eland_summary.cycle_width = cycle_width
if hasattr(eland_summary, 'genome_map'):
eland_summary.summarized_reads = runfolder.summarize_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.successful_pm = getattr(flowcell, pm_field)
+ #pm_field = 'lane_%d_pM' % (lane_id)
+ lane_obj = flowcell.lane_set.get(lane_number=lane_id)
+ eland_summary.successful_pm = lane_obj.pM
summary_list.append(eland_summary)
if len(storage_id_list) == 0:
storage_ids = None
else:
- storage_ids = ', '.join(storage_id_list)
+ storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
results = []
for cycle in cur_fc.keys():
lib = Library.objects.get(library_id=lib_id)
return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
+@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))
projects / htsworkflow.git / blobdiff