# Create your views here.
+import StringIO
+import logging
+import os
+try:
+ import json
+except ImportError, e:
+ import simplejson as json
+
from htsworkflow.frontend.experiments.models import FlowCell
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, HttpResponseRedirect
+from django.core.exceptions import ObjectDoesNotExist
+from django.http import HttpResponse, HttpResponseRedirect, Http404
from django.shortcuts import render_to_response
from django.template import RequestContext
from django.template.loader import get_template
-
-import StringIO
-import logging
-import os
+from django.contrib.auth.decorators import login_required
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)
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):
"""
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)
-
- eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
+ 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))
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, 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:
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
+ else:
+ eland_summary = ResultLane(lane_id=lane_id, end=end)
+ # add information to lane_summary
+ eland_summary.flowcell_id = flowcell_id
+ if len(gerald_summary) > end and gerald_summary[end].has_key(lane_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)
-
- summary_list.append(eland_summary)
-
- except Exception, e:
- summary_list.append("Summary report needs to be updated.")
- logging.error("Exception: " + str(e))
+ else:
+ eland_summary.clusters = None
+ 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=flowcell_id)
+ #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)
+
+ #except Exception, e:
+ # summary_list.append("Summary report needs to be updated.")
+ # logging.error("Exception: " + str(e))
return (summary_list, err_list)
return 'unknown'
def _make_eland_results(flowcell_id, lane, interesting_flowcells):
-
- cur_fc = interesting_flowcells.get(flowcell_id, None)
+ 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([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in 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(flowcell_id, cycle, lane, result_path)
- results.append({'flowcell_id': flowcell_id,
+ 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
lib = Library.objects.get(library_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(library_id = library_id)
+ except Library.DoesNotExist, e:
+ return None
+
+ 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,
+ 'avg_lib_size': lib.avg_lib_size,
+ 'cell_line': lib.cell_line.cellline_name,
+ 'cell_line_id': lib.cell_line_id,
+ 'experiment_type': lib.experiment_type.name,
+ 'experiment_type_id': lib.experiment_type_id,
+ 'id': lib.id,
+ 'library_id': lib.library_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': lib.successful_pM,
+ 'undiluted_concentration': unicode(lib.undiluted_concentration)
+ }
+ if lib.library_type_id is None:
+ info['library_type'] = None
+ else:
+ info['library_type'] = lib.library_type.name
+ return info
+
+@login_required
+def library_json(request, library_id):
+ """
+ Return a json formatted library dictionary
+ """
+ # 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')
+
+def species_json(request, species_id):
+ """
+ Return information about a species.
+ """
+ raise Http404
+
+@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