1 # Create your views here.
10 import simplejson as json
12 from django.contrib.csrf.middleware import csrf_exempt
13 from htsworkflow.frontend.auth import require_api_key
14 from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
15 from htsworkflow.frontend.samples.changelist import ChangeList
16 from htsworkflow.frontend.samples.models import Antibody, Library, Species, HTSUser
17 from htsworkflow.frontend.samples.results import get_flowcell_result_dict
18 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
19 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
20 from htsworkflow.pipelines import runfolder
21 from htsworkflow.pipelines.eland import ResultLane
22 from htsworkflow.pipelines.samplekey import SampleKey
23 from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id
24 from htsworkflow.util import makebed
25 from htsworkflow.util import opener
28 from django.core.exceptions import ObjectDoesNotExist
29 from django.http import HttpResponse, HttpResponseRedirect, Http404
30 from django.shortcuts import render_to_response, get_object_or_404
31 from django.template import RequestContext
32 from django.template.loader import get_template
33 from django.contrib.auth.decorators import login_required
34 from django.conf import settings
36 LANE_LIST = [1,2,3,4,5,6,7,8]
37 SAMPLES_CONTEXT_DEFAULTS = {
38 'app_name': 'Flowcell/Library Tracker',
39 'bcmagic': BarcodeMagicForm()
42 LOGGER = logging.getLogger(__name__)
44 def count_lanes(lane_set):
50 counts = [[0,0,0,],[0,0,0]]
52 for lane in lane_set.all():
53 if lane.flowcell.paired_end:
57 if lane.flowcell.read_length < 40:
58 read_type = short_read
59 elif lane.flowcell.read_length < 100:
60 read_type = medium_read
63 counts[lane_type][read_type] += 1
67 def create_library_context(cl):
69 Create a list of libraries that includes how many lanes were run
72 #for lib in library_items.object_list:
73 for lib in cl.result_list:
75 summary['library'] = lib
76 summary['library_id'] = lib.id
77 summary['library_name'] = lib.library_name
78 summary['species_name' ] = lib.library_species.scientific_name
79 if lib.amplified_from_sample is not None:
80 summary['amplified_from'] = lib.amplified_from_sample.id
82 summary['amplified_from'] = ''
83 lanes_run = count_lanes(lib.lane_set)
85 for row in xrange(len(lanes_run)):
86 for col in xrange(len(lanes_run[row])):
87 if lanes_run[row][col] == 0:
88 lanes_run[row][col] = ''
89 summary['lanes_run'] = lanes_run
90 summary['is_archived'] = lib.is_archived()
91 records.append(summary)
92 cl.result_count = unicode(cl.paginator._count)
93 return {'library_list': records }
96 def library(request, todo_only=False):
97 queryset = Library.objects.filter(hidden__exact=0)
99 queryset = queryset.filter(lane=None)
101 fcl = ChangeList(request, Library,
102 list_filter=['affiliations', 'library_species'],
103 search_fields=['id', 'library_name', 'amplified_from_sample__id'],
108 context = { 'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
109 context.update(create_library_context(fcl))
110 t = get_template('samples/library_index.html')
111 c = RequestContext(request, context)
112 return HttpResponse( t.render(c) )
115 def library_not_run(request):
116 return library(request, todo_only=True)
119 def library_to_flowcells(request, lib_id):
121 Display information about all the flowcells a library has been run on.
124 lib = Library.objects.get(id=lib_id)
126 raise Http404('Library %s does not exist' % (lib_id,))
129 flowcell_run_results = {} # aka flowcells we're looking at
130 for lane in lib.lane_set.all():
132 flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
133 if flowcell_id not in flowcell_run_results:
134 flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
135 flowcell_list.append((fc.flowcell_id, lane.lane_number))
138 lane_summary_list = []
140 for fc, lane_number in flowcell_list:
141 lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
142 lane_summary_list.extend(lane_summary)
144 eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
147 'page_name': 'Library Details',
149 'eland_results': eland_results,
150 'lane_summary_list': lane_summary_list,
152 context.update(SAMPLES_CONTEXT_DEFAULTS)
154 return render_to_response(
155 'samples/library_detail.html',
157 context_instance = RequestContext(request))
159 def lanes_for(request, username=None):
161 Generate a report of recent activity for a user
164 if username is not None:
165 user = HTSUser.objects.get(username=username)
166 query.update({'library__affiliations__users__id':user.id})
167 fcl = ChangeList(request, Lane,
169 search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
171 queryset=Lane.objects.filter(**query)
174 context = { 'lanes': fcl, 'title': 'Lane Index'}
176 return render_to_response(
177 'samples/lanes_for.html',
179 context_instance = RequestContext(request)
183 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
185 returns a Summary.htm file if it exists.
187 fc_id, status = parse_flowcell_id(flowcell_id)
188 d = get_flowcell_result_dict(fc_id)
191 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
194 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
196 summary_filepath = d[cnm]['summary']
198 if summary_filepath is None:
199 return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
201 f = open(summary_filepath, 'r')
203 return HttpResponse(f)
206 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
208 returns an eland_file upon calling.
210 fc_id, status = parse_flowcell_id(flowcell_id)
211 d = get_flowcell_result_dict(fc_id)
214 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
217 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
219 erd = d[cnm]['eland_results']
223 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
227 #f = opener.autoopen(filepath, 'r')
228 # return HttpResponse(f, mimetype="application/x-elandresult")
230 f = open(filepath, 'r')
231 return HttpResponse(f, mimetype='application/x-bzip2')
235 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
237 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
239 return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
242 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
244 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
246 fc_id, status = parse_flowcell_id(flowcell_id)
247 d = get_flowcell_result_dict(fc_id)
250 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
253 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
255 erd = d[cnm]['eland_results']
259 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
264 fi = opener.autoopen(filepath, 'r')
267 name, description = makebed.make_description( fc_id, lane )
269 bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
272 return HttpResponse(bedgen)
274 return HttpResponse(bedgen, mimetype="application/x-bedfile")
277 def _summary_stats(flowcell_id, lane_id, library_id):
279 Return the summary statistics for a given flowcell, lane, and end.
281 fc_id, status = parse_flowcell_id(flowcell_id)
282 fc_result_dict = get_flowcell_result_dict(fc_id)
287 if fc_result_dict is None:
288 err_list.append('Results for Flowcell %s not found.' % (fc_id))
289 return (summary_list, err_list)
291 for cycle_width in fc_result_dict:
292 xmlpath = fc_result_dict[cycle_width]['run_xml']
295 err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
298 run = load_pipeline_run_xml(xmlpath)
299 # skip if we don't have available metadata.
300 if run.gerald is None or run.gerald.summary is None:
303 gerald_summary = run.gerald.summary.lane_results
304 key = SampleKey(lane=lane_id, sample='s')
305 eland_results = list(run.gerald.eland_results.find_keys(key))
306 key = SampleKey(lane=lane_id, sample=library_id)
307 eland_results.extend(run.gerald.eland_results.find_keys(key))
308 for key in eland_results:
309 eland_summary = run.gerald.eland_results.results[key]
310 # add information to lane_summary
311 eland_summary.flowcell_id = flowcell_id
313 read = key.read-1 if key.read is not None else 0
315 eland_summary.clusters = gerald_summary[read][key.lane].cluster
316 except (IndexError, KeyError) as e:
317 eland_summary.clustes = None
318 eland_summary.cycle_width = cycle_width
319 if hasattr(eland_summary, 'genome_map'):
320 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
321 eland_summary.genome_map,
322 eland_summary.mapped_reads)
324 # grab some more information out of the flowcell db
325 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
326 #pm_field = 'lane_%d_pM' % (lane_id)
327 lanes = flowcell.lane_set.filter(lane_number=lane_id)
328 eland_summary.flowcell = flowcell
329 eland_summary.lanes = lanes
331 summary_list.append(eland_summary)
333 #except Exception, e:
334 # summary_list.append("Summary report needs to be updated.")
335 # LOGGER.error("Exception: " + str(e))
337 return (summary_list, err_list)
340 def get_eland_result_type(pathname):
342 Guess the eland result file type from the filename
344 path, filename = os.path.split(pathname)
345 if 'extended' in filename:
347 elif 'multi' in filename:
349 elif 'result' in filename:
354 def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
355 fc_id, status = parse_flowcell_id(flowcell_id)
356 cur_fc = interesting_flowcells.get(fc_id, None)
360 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
361 lanes = flowcell.lane_set.filter(lane_number=lane_number)
362 # Loop throw storage devices if a result has been archived
364 if cur_fc is not None:
365 for lts in flowcell.longtermstorage_set.all():
366 for sd in lts.storage_devices.all():
367 # Use barcode_id if it exists
368 if sd.barcode_id is not None and sd.barcode_id != '':
369 storage_id_list.append(sd.barcode_id)
372 storage_id_list.append(sd.uuid)
374 # Formatting for template use
375 if len(storage_id_list) == 0:
378 storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
381 for cycle in cur_fc.keys():
382 result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
383 result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
384 results.append({'flowcell_id': fc_id,
385 'flowcell': flowcell,
386 'run_date': flowcell.run_date,
389 'summary_url': make_summary_url(flowcell_id, cycle),
390 'result_url': result_link[0],
391 'result_label': result_link[1],
392 'bed_url': result_link[2],
393 'storage_ids': storage_ids
397 def make_summary_url(flowcell_id, cycle_name):
398 url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
401 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
402 if eland_result_path is None:
405 result_type = get_eland_result_type(eland_result_path)
406 result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
407 result_label = 'eland %s' % (result_type,)
409 if result_type == 'result':
410 bed_url_pattern = '/results/%s/%s/bedfile/%s'
411 bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
413 return (result_url, result_label, bed_url)
415 def _files(flowcell_id, lane):
417 Sets up available files for download
421 flowcell_id, id = parse_flowcell_id(flowcell_id)
422 d = get_flowcell_result_dict(flowcell_id)
429 # c_name == 'CN-M' (i.e. C1-33)
432 if d[c_name]['summary'] is not None:
433 output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
434 % (flowcell_id, c_name, c_name))
436 erd = d[c_name]['eland_results']
438 result_type = get_eland_result_type(erd[lane])
439 result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
440 output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
441 if result_type == 'result':
442 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
443 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
448 return '(' + '|'.join(output) + ')'
450 def library_id_to_admin_url(request, lib_id):
451 lib = Library.objects.get(id=lib_id)
452 return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
454 def library_dict(library_id):
456 Given a library id construct a dictionary containing important information
457 return None if nothing was found
460 lib = Library.objects.get(id = library_id)
461 except Library.DoesNotExist, e:
464 #lane_info = lane_information(lib.lane_set)
466 for lane in lib.lane_set.all():
467 lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
468 'lane_number': lane.lane_number,
470 'paired_end': lane.flowcell.paired_end,
471 'read_length': lane.flowcell.read_length,
472 'status_code': lane.status,
473 'status': LANE_STATUS_MAP[lane.status]} )
477 # 'aligned_reads': lib.aligned_reads,
478 #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
479 #'amplified_from_sample_id': lib.amplified_from_sample,
480 #'antibody_name': lib.antibody_name(), # we have no antibodies.
481 'antibody_id': lib.antibody_id,
482 'cell_line_id': lib.cell_line_id,
483 'cell_line': unicode_or_none(lib.cell_line),
484 'experiment_type': lib.experiment_type.name,
485 'experiment_type_id': lib.experiment_type_id,
486 'gel_cut_size': lib.gel_cut_size,
487 'hidden': lib.hidden,
489 'insert_size': lib.insert_size,
490 'lane_set': lane_info,
491 'library_id': lib.id,
492 'library_name': lib.library_name,
493 'library_species': lib.library_species.scientific_name,
494 'library_species_id': lib.library_species_id,
495 #'library_type': lib.library_type.name,
496 'library_type_id': lib.library_type_id,
497 'made_for': lib.made_for,
498 'made_by': lib.made_by,
500 'replicate': lib.replicate,
501 'stopping_point': lib.stopping_point,
502 'successful_pM': unicode_or_none(lib.successful_pM),
503 'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
505 if lib.library_type_id is None:
506 info['library_type'] = None
508 info['library_type'] = lib.library_type.name
512 def library_json(request, library_id):
514 Return a json formatted library dictionary
516 require_api_key(request)
517 # what validation should we do on library_id?
519 lib = library_dict(library_id)
523 lib_json = json.dumps(lib)
524 return HttpResponse(lib_json, mimetype='application/json')
527 def species_json(request, species_id):
529 Return information about a species.
533 def species(request, species_id):
534 species = get_object_or_404(Species, id=species_id)
536 context = RequestContext(request,
537 { 'species': species })
539 return render_to_response("samples/species_detail.html", context)
541 def antibodies(request):
542 context = RequestContext(request,
543 {'antibodies': Antibody.objects.order_by('antigene')})
544 return render_to_response("samples/antibody_index.html", context)
547 def user_profile(request):
549 Information about the user
552 'page_name': 'User Profile',
554 #'bcmagic': BarcodeMagicForm(),
555 #'select': 'settings',
557 context.update(SAMPLES_CONTEXT_DEFAULTS)
558 return render_to_response('registration/profile.html', context,
559 context_instance=RequestContext(request))