import StringIO
import logging
import os
+import sys
+
try:
import json
except ImportError, e:
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.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
return HttpResponse("Library %s does not exist" % (lib_id))
flowcell_list = []
- interesting_flowcells = {} # aka flowcells we're looking at
- #for lane in LANE_LIST:
+ flowcell_run_results = {} # aka flowcells we're looking at
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)
+ if flowcell_id not in flowcell_run_results:
+ flowcell_run_results[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_number in flowcell_list:
lane_summary, err_list = _summary_stats(fc, lane_number)
- eland_results.extend(_make_eland_results(fc, lane_number, interesting_flowcells))
+ eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
lane_summary_list.extend(lane_summary)
context = {
summary_list.append("Summary report needs to be updated.")
logging.error("Exception: " + str(e))
- print "----------------------------------"
- print "-- DOES NOT SUPPORT PAIRED END ---"
- print "----------------------------------"
+ print >>sys.stderr, "----------------------------------"
+ print >>sys.stderr, "-- DOES NOT SUPPORT PAIRED END ---"
+ print >>sys.stderr, "----------------------------------"
lane_results = results.gerald.summary[0][lane]
lrs = lane_results
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} )
+
info = {
# 'affiliations'?
# 'aligned_reads': lib.aligned_reads,
#'antibody_name': lib.antibody_name(), # we have no antibodies.
'antibody_id': lib.antibody_id,
'avg_lib_size': lib.avg_lib_size,
- 'cell_line': lib.cell_line.cellline_name,
'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,
'id': lib.id,
+ 'lane_set': lane_info,
'library_id': lib.id,
'library_name': lib.library_name,
'library_species': lib.library_species.scientific_name,
'notes': lib.notes,
'replicate': lib.replicate,
'stopping_point': lib.stopping_point,
- 'successful_pM': lib.successful_pM,
- 'undiluted_concentration': unicode(lib.undiluted_concentration)
+ '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