-# Create your views here.
\ No newline at end of file
+# 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.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
+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):
+ """
+ Create a list of libraries that includes how many lanes were run
+ """
+ records = []
+ #for lib in library_items.object_list:
+ for lib in cl.result_list:
+ summary = {}
+ summary['library_id'] = lib.library_id
+ summary['library_name'] = lib.library_name
+ summary['species_name' ] = lib.library_species.scientific_name
+ if lib.amplified_from_sample is not None:
+ summary['amplified_from'] = lib.amplified_from_sample.library_id
+ 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() )
+ 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 }
+
+def library(request):
+ # build changelist
+ fcl = ChangeList(request, Library,
+ list_filter=['affiliations', 'library_species'],
+ search_fields=['library_id', 'library_name', 'amplified_from_sample__library_id'],
+ list_per_page=200,
+ queryset=Library.objects.filter(hidden__exact=0)
+ )
+
+ context = { 'cl': fcl, 'title': 'Library Index'}
+ context.update(create_library_context(fcl))
+ t = get_template('samples/library_index.html')
+ c = RequestContext(request, context)
+
+ 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.
+ """
+
+ try:
+ lib = Library.objects.get(library_id=lib_id)
+ except:
+ return HttpResponse("Library %s does not exist" % (lib_id))
+
+ flowcell_list = []
+ interesting_flowcells = {} # aka flowcells we're looking at
+ #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_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',
+ context,
+ context_instance = RequestContext(request))
+
+def summaryhtm_fc_cnm(request, flowcell_id, cnm):
+ """
+ returns a Summary.htm file if it exists.
+ """
+ fc_id, status = parse_flowcell_id(flowcell_id)
+ d = get_flowcell_result_dict(fc_id)
+
+ if d is None:
+ return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
+
+ if cnm not in d:
+ return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
+
+ summary_filepath = d[cnm]['summary']
+
+ if summary_filepath is None:
+ return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
+
+ f = open(summary_filepath, 'r')
+
+ return HttpResponse(f)
+
+
+def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
+ """
+ returns an eland_file upon calling.
+ """
+ fc_id, status = parse_flowcell_id(flowcell_id)
+ d = get_flowcell_result_dict(fc_id)
+
+ if d is None:
+ return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
+
+ if cnm not in d:
+ return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
+
+ erd = d[cnm]['eland_results']
+ lane = int(lane)
+
+ if lane not in erd:
+ return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
+
+ filepath = erd[lane]
+
+ #f = opener.autoopen(filepath, 'r')
+ # return HttpResponse(f, mimetype="application/x-elandresult")
+
+ f = open(filepath, 'r')
+ return HttpResponse(f, mimetype='application/x-bzip2')
+
+
+
+def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
+ """
+ returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
+ """
+ return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
+
+
+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(flowcell_id)
+ d = get_flowcell_result_dict(fc_id)
+
+ if d is None:
+ return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
+
+ if cnm not in d:
+ return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
+
+ erd = d[cnm]['eland_results']
+ lane = int(lane)
+
+ if lane not in erd:
+ return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
+
+ filepath = erd[lane]
+
+ # Eland result file
+ fi = opener.autoopen(filepath, 'r')
+ # output memory file
+
+ name, description = makebed.make_description( fc_id, lane )
+
+ bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
+
+ if ucsc_compatible:
+ return HttpResponse(bedgen)
+ else:
+ return HttpResponse(bedgen, mimetype="application/x-bedfile")
+
+
+def _summary_stats(flowcell_id, lane_id):
+ """
+ Return the summary statistics for a given flowcell, lane, and end.
+ """
+ fc_id, status = parse_flowcell_id(flowcell_id)
+ fc_result_dict = get_flowcell_result_dict(fc_id)
+
+ summary_list = []
+ err_list = []
+
+ if fc_result_dict is None:
+ err_list.append('Results for Flowcell %s not found.' % (fc_id))
+ return (summary_list, err_list)
+
+ for cycle_width in fc_result_dict:
+ xmlpath = fc_result_dict[cycle_width]['run_xml']
+
+ if xmlpath is None:
+ err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
+ continue
+
+ 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]
+ 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
+ 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)
+
+def _summary_stats_old(flowcell_id, lane):
+ """
+ return a dictionary of summary stats for a given flowcell_id & lane.
+ """
+ fc_id, status = parse_flowcell_id(flowcell_id)
+ fc_result_dict = get_flowcell_result_dict(fc_id)
+
+ dict_list = []
+ err_list = []
+ summary_list = []
+
+ if fc_result_dict is None:
+ err_list.append('Results for Flowcell %s not found.' % (fc_id))
+ return (dict_list, err_list, summary_list)
+
+ for cnm in fc_result_dict:
+
+ xmlpath = fc_result_dict[cnm]['run_xml']
+
+ if xmlpath is None:
+ err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
+ continue
+
+ tree = ElementTree.parse(xmlpath).getroot()
+ results = runfolder.PipelineRun(pathname='', xml=tree)
+ try:
+ lane_report = runfolder.summarize_lane(results.gerald, lane)
+ summary_list.append(os.linesep.join(lane_report))
+ except Exception, e:
+ summary_list.append("Summary report needs to be updated.")
+ logging.error("Exception: " + str(e))
+
+ print "----------------------------------"
+ print "-- DOES NOT SUPPORT PAIRED END ---"
+ print "----------------------------------"
+ lane_results = results.gerald.summary[0][lane]
+ lrs = lane_results
+
+ d = {}
+
+ d['average_alignment_score'] = lrs.average_alignment_score
+ d['average_first_cycle_intensity'] = lrs.average_first_cycle_intensity
+ d['cluster'] = lrs.cluster
+ d['lane'] = lrs.lane
+ d['flowcell'] = flowcell_id
+ d['cnm'] = cnm
+ d['percent_error_rate'] = lrs.percent_error_rate
+ d['percent_intensity_after_20_cycles'] = lrs.percent_intensity_after_20_cycles
+ d['percent_pass_filter_align'] = lrs.percent_pass_filter_align
+ d['percent_pass_filter_clusters'] = lrs.percent_pass_filter_clusters
+
+ #FIXME: function finished, but need to take advantage of
+ # may need to take in a list of lanes so we only have to
+ # load the xml file once per flowcell rather than once
+ # per lane.
+ dict_list.append(d)
+
+ return (dict_list, err_list, summary_list)
+
+
+def get_eland_result_type(pathname):
+ """
+ Guess the eland result file type from the filename
+ """
+ path, filename = os.path.split(pathname)
+ if 'extended' in filename:
+ return 'extended'
+ elif 'multi' in filename:
+ return 'multi'
+ elif 'result' in filename:
+ 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([ '<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(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
+ """
+ lane = int(lane)
+
+ flowcell_id, id = parse_flowcell_id(flowcell_id)
+ d = get_flowcell_result_dict(flowcell_id)
+
+ if d is None:
+ return ''
+
+ output = []
+
+ # c_name == 'CN-M' (i.e. C1-33)
+ for c_name in d:
+
+ if d[c_name]['summary'] is not None:
+ output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
+ % (flowcell_id, c_name, c_name))
+
+ erd = d[c_name]['eland_results']
+ if lane in erd:
+ result_type = get_eland_result_type(erd[lane])
+ result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
+ output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
+ if result_type == 'result':
+ bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
+ output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
+
+ if len(output) == 0:
+ 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,))
+
+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