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.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
+from django.http import HttpResponse, HttpResponseRedirect
+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):
"""
lane = getattr(lib, 'lane_%d_library' % (lane_id,))
lanes_run += len( lane.all() )
summary['lanes_run'] = lanes_run
+ summary['is_archived'] = lib.is_archived()
records.append(summary)
cl.result_count = unicode(cl.paginator._count) + u" libraries"
return {'library_list': records }
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):
"""
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('<b>Library ID:</b> %s' % (lib.library_id))
- output.append('<b>Name:</b> %s' % (lib.library_name))
- output.append('<b>Species:</b> %s' % (lib.library_species.scientific_name))
- output.append('')
-
- output.append('<b>FLOWCELL - LANE:</b>')
-
- 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('<br />')
- output.append(t.render(RequestContext(request, {'lane_summary_list': lane_summary_list})))
- output.append('<br />')
-
- if record_count == 0:
- output.append("None Found")
-
- return HttpResponse('<br />\n'.join(output))
+ 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',
+ context,
+ context_instance = RequestContext(request))
-def summaryhtm_fc_cnm(request, fc_id, cnm):
+def summaryhtm_fc_cnm(request, flowcell_id, cnm):
"""
returns a Summary.htm file if it exists.
"""
- fc_id, status = parse_flowcell_id(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
if d is None:
return HttpResponse(f)
-def result_fc_cnm_eland_lane(request, fc_id, cnm, lane):
+def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
"""
returns an eland_file upon calling.
"""
- fc_id, status = parse_flowcell_id(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
if d is None:
filepath = erd[lane]
- f = opener.autoopen(filepath, 'r')
+ #f = opener.autoopen(filepath, 'r')
+ # return HttpResponse(f, mimetype="application/x-elandresult")
+
+ f = open(filepath, 'r')
+ return HttpResponse(f, mimetype='application/x-bzip2')
- return HttpResponse(f, mimetype="application/x-elandresult")
def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
-def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=False):
+def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
"""
returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
"""
- fc_id, status = parse_flowcell_id(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
if d is None:
err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
continue
- try:
- run = load_pipeline_run_xml(xmlpath)
- gerald_summary = run.gerald.summary.lane_results
- for end in range(len(gerald_summary)):
+ run = load_pipeline_run_xml(xmlpath)
+ 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]
- # add information to lane_summary
- eland_summary.flowcell_id = flowcell_id
- eland_summary.clusters = gerald_summary[end][lane_id].cluster
- eland_summary.cycle_width = cycle_width
- eland_summary.summarized_reads = runfolder.summarize_mapped_reads(eland_summary.genome_map, eland_summary.mapped_reads)
+ 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
+ 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.mapped_reads)
- # grab some more information out of the flowcell db
- flowcell = FlowCell.objects.get(flowcell_id=fc_id)
- pm_field = 'lane_%d_pM' % (lane_id)
- eland_summary.successful_pm = getattr(flowcell, pm_field)
+ # 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)
- summary_list.append(eland_summary)
+ summary_list.append(eland_summary)
- except Exception, e:
- summary_list.append("Summary report needs to be updated.")
- logging.error("Exception: " + str(e))
+ #except Exception, e:
+ # summary_list.append("Summary report needs to be updated.")
+ # logging.error("Exception: " + str(e))
return (summary_list, err_list)
return 'result'
else:
return 'unknown'
-
+
+def _make_eland_results(flowcell_id, lane, 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)
+ # Loop throw storage devices if a result has been archived
+ storage_id_list = []
+ if cur_fc is not None:
+ for lts in flowcell.longtermstorage_set.all():
+ for sd in lts.storage_devices.all():
+ # Use barcode_id if it exists
+ if sd.barcode_id is not None and sd.barcode_id != '':
+ storage_id_list.append(sd.barcode_id)
+ # Otherwise use UUID
+ else:
+ storage_id_list.append(sd.uuid)
+
+ # Formatting for template use
+ if len(storage_id_list) == 0:
+ storage_ids = None
+ else:
+ storage_ids = ', '.join(storage_id_list)
+
+ 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)
+ results.append({'flowcell_id': fc_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],
+ 'storage_ids': storage_ids
+ })
+ 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):
+ if eland_result_path is None:
+ return ("", "", "")
+
+ 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
return ''
return '(' + '|'.join(output) + ')'
-
+
+def library_id_to_admin_url(request, lib_id):
+ 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