1 # Create your views here.
10 import simplejson as json
12 from htsworkflow.frontend.auth import require_api_key
13 from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
14 from htsworkflow.frontend.samples.changelist import ChangeList
15 from htsworkflow.frontend.samples.models import Library, HTSUser
16 from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
17 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
18 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
19 from htsworkflow.pipelines import runfolder
20 from htsworkflow.pipelines.eland import ResultLane
21 from htsworkflow.frontend import settings
22 from htsworkflow.util.conversion import unicode_or_none
23 from htsworkflow.util import makebed
24 from htsworkflow.util import opener
27 from django.core.exceptions import ObjectDoesNotExist
28 from django.http import HttpResponse, HttpResponseRedirect, Http404
29 from django.shortcuts import render_to_response
30 from django.template import RequestContext
31 from django.template.loader import get_template
32 from django.contrib.auth.decorators import login_required
34 LANE_LIST = [1,2,3,4,5,6,7,8]
35 SAMPLES_CONTEXT_DEFAULTS = {
36 'app_name': 'Flowcell/Library Tracker',
37 'bcmagic': BarcodeMagicForm()
40 def count_lanes(lane_set):
46 counts = [[0,0,0,],[0,0,0]]
48 for lane in lane_set.all():
49 if lane.flowcell.paired_end:
53 if lane.flowcell.read_length < 40:
54 read_type = short_read
55 elif lane.flowcell.read_length < 100:
56 read_type = medium_read
59 counts[lane_type][read_type] += 1
63 def create_library_context(cl):
65 Create a list of libraries that includes how many lanes were run
68 #for lib in library_items.object_list:
69 for lib in cl.result_list:
71 summary['library_id'] = lib.id
72 summary['library_name'] = lib.library_name
73 summary['species_name' ] = lib.library_species.scientific_name
74 if lib.amplified_from_sample is not None:
75 summary['amplified_from'] = lib.amplified_from_sample.id
77 summary['amplified_from'] = ''
78 lanes_run = count_lanes(lib.lane_set)
80 for row in xrange(len(lanes_run)):
81 for col in xrange(len(lanes_run[row])):
82 if lanes_run[row][col] == 0:
83 lanes_run[row][col] = ''
84 summary['lanes_run'] = lanes_run
85 summary['is_archived'] = lib.is_archived()
86 records.append(summary)
87 cl.result_count = unicode(cl.paginator._count) + u" libraries"
88 return {'library_list': records }
92 fcl = ChangeList(request, Library,
93 list_filter=['affiliations', 'library_species'],
94 search_fields=['id', 'library_name', 'amplified_from_sample__id'],
96 queryset=Library.objects.filter(hidden__exact=0)
99 context = { 'cl': fcl, 'title': 'Library Index'}
100 context.update(create_library_context(fcl))
101 t = get_template('samples/library_index.html')
102 c = RequestContext(request, context)
105 'page_name': 'Library Index',
108 app_context.update(SAMPLES_CONTEXT_DEFAULTS)
110 app_t = get_template('flowcell_libraries_app.html')
111 app_c = RequestContext(request, app_context)
112 return HttpResponse( app_t.render(app_c) )
114 def library_to_flowcells(request, lib_id):
116 Display information about all the flowcells a library has been run on.
120 lib = Library.objects.get(id=lib_id)
122 return HttpResponse("Library %s does not exist" % (lib_id))
125 flowcell_run_results = {} # aka flowcells we're looking at
126 for lane in lib.lane_set.all():
128 flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
129 if flowcell_id not in flowcell_run_results:
130 flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
131 flowcell_list.append((fc.flowcell_id, lane.lane_number))
134 lane_summary_list = []
136 for fc, lane_number in flowcell_list:
137 lane_summary, err_list = _summary_stats(fc, lane_number)
139 eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
140 lane_summary_list.extend(lane_summary)
143 'page_name': 'Library Details',
145 'eland_results': eland_results,
146 'lane_summary_list': lane_summary_list,
148 context.update(SAMPLES_CONTEXT_DEFAULTS)
150 return render_to_response(
151 'samples/library_detail.html',
153 context_instance = RequestContext(request))
155 def lanes_for(request, username=None):
157 Generate a report of recent activity for a user
160 if username is not None:
161 user = HTSUser.objects.get(username=username)
162 query.update({'library__affiliations__users__id':user.id})
163 fcl = ChangeList(request, Lane,
165 search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
167 queryset=Lane.objects.filter(**query)
170 context = { 'lanes': fcl, 'title': 'Lane Index'}
172 return render_to_response(
173 'samples/lanes_for.html',
175 context_instance = RequestContext(request)
179 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
181 returns a Summary.htm file if it exists.
183 fc_id, status = parse_flowcell_id(flowcell_id)
184 d = get_flowcell_result_dict(fc_id)
187 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
190 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
192 summary_filepath = d[cnm]['summary']
194 if summary_filepath is None:
195 return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
197 f = open(summary_filepath, 'r')
199 return HttpResponse(f)
202 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
204 returns an eland_file upon calling.
206 fc_id, status = parse_flowcell_id(flowcell_id)
207 d = get_flowcell_result_dict(fc_id)
210 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
213 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
215 erd = d[cnm]['eland_results']
219 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
223 #f = opener.autoopen(filepath, 'r')
224 # return HttpResponse(f, mimetype="application/x-elandresult")
226 f = open(filepath, 'r')
227 return HttpResponse(f, mimetype='application/x-bzip2')
231 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
233 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
235 return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
238 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
240 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
242 fc_id, status = parse_flowcell_id(flowcell_id)
243 d = get_flowcell_result_dict(fc_id)
246 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
249 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
251 erd = d[cnm]['eland_results']
255 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
260 fi = opener.autoopen(filepath, 'r')
263 name, description = makebed.make_description( fc_id, lane )
265 bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
268 return HttpResponse(bedgen)
270 return HttpResponse(bedgen, mimetype="application/x-bedfile")
273 def _summary_stats(flowcell_id, lane_id):
275 Return the summary statistics for a given flowcell, lane, and end.
277 fc_id, status = parse_flowcell_id(flowcell_id)
278 fc_result_dict = get_flowcell_result_dict(fc_id)
283 if fc_result_dict is None:
284 err_list.append('Results for Flowcell %s not found.' % (fc_id))
285 return (summary_list, err_list)
287 for cycle_width in fc_result_dict:
288 xmlpath = fc_result_dict[cycle_width]['run_xml']
291 err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
294 run = load_pipeline_run_xml(xmlpath)
295 gerald_summary = run.gerald.summary.lane_results
296 for end in range(len(gerald_summary)):
297 end_summary = run.gerald.eland_results.results[end]
298 if end_summary.has_key(lane_id):
299 eland_summary = run.gerald.eland_results.results[end][lane_id]
301 eland_summary = ResultLane(lane_id=lane_id, end=end)
302 # add information to lane_summary
303 eland_summary.flowcell_id = flowcell_id
304 if len(gerald_summary) > end and gerald_summary[end].has_key(lane_id):
305 eland_summary.clusters = gerald_summary[end][lane_id].cluster
307 eland_summary.clusters = None
308 eland_summary.cycle_width = cycle_width
309 if hasattr(eland_summary, 'genome_map'):
310 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
311 eland_summary.genome_map,
312 eland_summary.mapped_reads)
314 # grab some more information out of the flowcell db
315 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
316 #pm_field = 'lane_%d_pM' % (lane_id)
317 lane_obj = flowcell.lane_set.get(lane_number=lane_id)
318 eland_summary.successful_pm = lane_obj.pM
320 summary_list.append(eland_summary)
322 #except Exception, e:
323 # summary_list.append("Summary report needs to be updated.")
324 # logging.error("Exception: " + str(e))
326 return (summary_list, err_list)
328 def _summary_stats_old(flowcell_id, lane):
330 return a dictionary of summary stats for a given flowcell_id & lane.
332 fc_id, status = parse_flowcell_id(flowcell_id)
333 fc_result_dict = get_flowcell_result_dict(fc_id)
339 if fc_result_dict is None:
340 err_list.append('Results for Flowcell %s not found.' % (fc_id))
341 return (dict_list, err_list, summary_list)
343 for cnm in fc_result_dict:
345 xmlpath = fc_result_dict[cnm]['run_xml']
348 err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
351 tree = ElementTree.parse(xmlpath).getroot()
352 results = runfolder.PipelineRun(pathname='', xml=tree)
354 lane_report = runfolder.summarize_lane(results.gerald, lane)
355 summary_list.append(os.linesep.join(lane_report))
357 summary_list.append("Summary report needs to be updated.")
358 logging.error("Exception: " + str(e))
360 print >>sys.stderr, "----------------------------------"
361 print >>sys.stderr, "-- DOES NOT SUPPORT PAIRED END ---"
362 print >>sys.stderr, "----------------------------------"
363 lane_results = results.gerald.summary[0][lane]
368 d['average_alignment_score'] = lrs.average_alignment_score
369 d['average_first_cycle_intensity'] = lrs.average_first_cycle_intensity
370 d['cluster'] = lrs.cluster
372 d['flowcell'] = flowcell_id
374 d['percent_error_rate'] = lrs.percent_error_rate
375 d['percent_intensity_after_20_cycles'] = lrs.percent_intensity_after_20_cycles
376 d['percent_pass_filter_align'] = lrs.percent_pass_filter_align
377 d['percent_pass_filter_clusters'] = lrs.percent_pass_filter_clusters
379 #FIXME: function finished, but need to take advantage of
380 # may need to take in a list of lanes so we only have to
381 # load the xml file once per flowcell rather than once
385 return (dict_list, err_list, summary_list)
388 def get_eland_result_type(pathname):
390 Guess the eland result file type from the filename
392 path, filename = os.path.split(pathname)
393 if 'extended' in filename:
395 elif 'multi' in filename:
397 elif 'result' in filename:
402 def _make_eland_results(flowcell_id, lane, interesting_flowcells):
403 fc_id, status = parse_flowcell_id(flowcell_id)
404 cur_fc = interesting_flowcells.get(fc_id, None)
408 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
409 # Loop throw storage devices if a result has been archived
411 if cur_fc is not None:
412 for lts in flowcell.longtermstorage_set.all():
413 for sd in lts.storage_devices.all():
414 # Use barcode_id if it exists
415 if sd.barcode_id is not None and sd.barcode_id != '':
416 storage_id_list.append(sd.barcode_id)
419 storage_id_list.append(sd.uuid)
421 # Formatting for template use
422 if len(storage_id_list) == 0:
425 storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
428 for cycle in cur_fc.keys():
429 result_path = cur_fc[cycle]['eland_results'].get(lane, None)
430 result_link = make_result_link(fc_id, cycle, lane, result_path)
431 results.append({'flowcell_id': fc_id,
432 'run_date': flowcell.run_date,
435 'summary_url': make_summary_url(flowcell_id, cycle),
436 'result_url': result_link[0],
437 'result_label': result_link[1],
438 'bed_url': result_link[2],
439 'storage_ids': storage_ids
443 def make_summary_url(flowcell_id, cycle_name):
444 url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
447 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
448 if eland_result_path is None:
451 result_type = get_eland_result_type(eland_result_path)
452 result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
453 result_label = 'eland %s' % (result_type,)
455 if result_type == 'result':
456 bed_url_pattern = '/results/%s/%s/bedfile/%s'
457 bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
459 return (result_url, result_label, bed_url)
461 def _files(flowcell_id, lane):
463 Sets up available files for download
467 flowcell_id, id = parse_flowcell_id(flowcell_id)
468 d = get_flowcell_result_dict(flowcell_id)
475 # c_name == 'CN-M' (i.e. C1-33)
478 if d[c_name]['summary'] is not None:
479 output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
480 % (flowcell_id, c_name, c_name))
482 erd = d[c_name]['eland_results']
484 result_type = get_eland_result_type(erd[lane])
485 result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
486 output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
487 if result_type == 'result':
488 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
489 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
494 return '(' + '|'.join(output) + ')'
496 def library_id_to_admin_url(request, lib_id):
497 lib = Library.objects.get(id=lib_id)
498 return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
500 def library_dict(library_id):
502 Given a library id construct a dictionary containing important information
503 return None if nothing was found
506 lib = Library.objects.get(id = library_id)
507 except Library.DoesNotExist, e:
510 #lane_info = lane_information(lib.lane_set)
512 for lane in lib.lane_set.all():
513 lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
514 'lane_number': lane.lane_number,
515 'paired_end': lane.flowcell.paired_end,
516 'read_length': lane.flowcell.read_length,
517 'status_code': lane.status,
518 'status': LANE_STATUS_MAP[lane.status]} )
522 # 'aligned_reads': lib.aligned_reads,
523 #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
524 #'amplified_from_sample_id': lib.amplified_from_sample,
525 #'antibody_name': lib.antibody_name(), # we have no antibodies.
526 'antibody_id': lib.antibody_id,
527 'cell_line_id': lib.cell_line_id,
528 'cell_line': unicode_or_none(lib.cell_line),
529 'experiment_type': lib.experiment_type.name,
530 'experiment_type_id': lib.experiment_type_id,
531 'gel_cut_size': lib.gel_cut_size,
532 'hidden': lib.hidden,
534 'insert_size': lib.insert_size,
535 'lane_set': lane_info,
536 'library_id': lib.id,
537 'library_name': lib.library_name,
538 'library_species': lib.library_species.scientific_name,
539 'library_species_id': lib.library_species_id,
540 #'library_type': lib.library_type.name,
541 'library_type_id': lib.library_type_id,
542 'made_for': lib.made_for,
543 'made_by': lib.made_by,
545 'replicate': lib.replicate,
546 'stopping_point': lib.stopping_point,
547 'successful_pM': unicode_or_none(lib.successful_pM),
548 'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
550 if lib.library_type_id is None:
551 info['library_type'] = None
553 info['library_type'] = lib.library_type.name
556 def library_json(request, library_id):
558 Return a json formatted library dictionary
560 require_api_key(request)
561 # what validation should we do on library_id?
563 lib = library_dict(library_id)
567 lib_json = json.dumps(lib)
568 return HttpResponse(lib_json, mimetype='application/json')
570 def species_json(request, species_id):
572 Return information about a species.
577 def user_profile(request):
579 Information about the user
582 'page_name': 'User Profile',
584 #'bcmagic': BarcodeMagicForm(),
585 #'select': 'settings',
587 context.update(SAMPLES_CONTEXT_DEFAULTS)
588 return render_to_response('registration/profile.html', context,
589 context_instance=RequestContext(request))