1 # Create your views here.
10 import simplejson as json
12 from django.views.decorators.csrf 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.experiments.admin import LaneOptions
16 from htsworkflow.frontend.samples.changelist import HTSChangeList
17 from htsworkflow.frontend.samples.models import Antibody, Library, Species, HTSUser
18 from htsworkflow.frontend.samples.admin import LibraryOptions
19 from htsworkflow.frontend.samples.results import get_flowcell_result_dict
20 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
21 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
22 from htsworkflow.pipelines import runfolder
23 from htsworkflow.pipelines.eland import ResultLane
24 from htsworkflow.pipelines.samplekey import SampleKey
25 from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id
26 from htsworkflow.util import makebed
27 from htsworkflow.util import opener
30 from django.core.exceptions import ObjectDoesNotExist
31 from django.http import HttpResponse, HttpResponseRedirect, Http404
32 from django.shortcuts import render_to_response, get_object_or_404
33 from django.template import RequestContext
34 from django.template.loader import get_template
35 from django.contrib.auth.decorators import login_required
36 from django.conf import settings
38 LANE_LIST = [1,2,3,4,5,6,7,8]
39 SAMPLES_CONTEXT_DEFAULTS = {
40 'app_name': 'Flowcell/Library Tracker',
41 'bcmagic': BarcodeMagicForm()
44 LOGGER = logging.getLogger(__name__)
46 def count_lanes(lane_set):
52 counts = [[0,0,0,],[0,0,0]]
54 for lane in lane_set.all():
55 if lane.flowcell.paired_end:
59 if lane.flowcell.read_length < 40:
60 read_type = short_read
61 elif lane.flowcell.read_length < 100:
62 read_type = medium_read
65 counts[lane_type][read_type] += 1
69 def create_library_context(cl):
71 Create a list of libraries that includes how many lanes were run
74 #for lib in library_items.object_list:
75 for lib in cl.result_list:
77 summary['library'] = lib
78 summary['library_id'] = lib.id
79 summary['library_name'] = lib.library_name
80 summary['species_name' ] = lib.library_species.scientific_name
81 if lib.amplified_from_sample is not None:
82 summary['amplified_from'] = lib.amplified_from_sample.id
84 summary['amplified_from'] = ''
85 lanes_run = count_lanes(lib.lane_set)
87 for row in xrange(len(lanes_run)):
88 for col in xrange(len(lanes_run[row])):
89 if lanes_run[row][col] == 0:
90 lanes_run[row][col] = ''
91 summary['lanes_run'] = lanes_run
92 summary['is_archived'] = lib.is_archived()
93 records.append(summary)
94 cl.result_count = unicode(cl.paginator._count)
95 return {'library_list': records }
98 def library(request, todo_only=False):
99 queryset = Library.objects.filter(hidden__exact=0)
100 filters = {'hidden__exact': 0}
104 fcl = HTSChangeList(request, Library,
105 list_filter=['affiliations', 'library_species'],
106 search_fields=['id', 'library_name', 'amplified_from_sample__id'],
108 model_admin=LibraryOptions(Library, None),
109 extra_filters=filters
112 context = { 'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
113 context.update(create_library_context(fcl))
114 t = get_template('samples/library_index.html')
115 c = RequestContext(request, context)
116 return HttpResponse( t.render(c) )
119 def library_not_run(request):
120 return library(request, todo_only=True)
123 def library_to_flowcells(request, lib_id):
125 Display information about all the flowcells a library has been run on.
128 lib = Library.objects.get(id=lib_id)
130 raise Http404('Library %s does not exist' % (lib_id,))
133 flowcell_run_results = {} # aka flowcells we're looking at
134 for lane in lib.lane_set.all():
136 flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
137 if flowcell_id not in flowcell_run_results:
138 flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
139 flowcell_list.append((fc.flowcell_id, lane.lane_number))
142 lane_summary_list = []
144 for fc, lane_number in flowcell_list:
145 lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
146 lane_summary_list.extend(lane_summary)
148 eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
151 'page_name': 'Library Details',
153 'eland_results': eland_results,
154 'lane_summary_list': lane_summary_list,
156 context.update(SAMPLES_CONTEXT_DEFAULTS)
158 return render_to_response(
159 'samples/library_detail.html',
161 context_instance = RequestContext(request))
163 def lanes_for(request, username=None):
165 Generate a report of recent activity for a user
168 if username is not None:
169 user = HTSUser.objects.get(username=username)
170 query.update({'library__affiliations__users__id':user.id})
171 fcl = HTSChangeList(request, Lane,
173 search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
175 model_admin=LaneOptions,
176 queryset=Lane.objects.filter(**query)
179 context = { 'lanes': fcl, 'title': 'Lane Index'}
181 return render_to_response(
182 'samples/lanes_for.html',
184 context_instance = RequestContext(request)
188 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
190 returns a Summary.htm file if it exists.
192 fc_id, status = parse_flowcell_id(flowcell_id)
193 d = get_flowcell_result_dict(fc_id)
196 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
199 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
201 summary_filepath = d[cnm]['summary']
203 if summary_filepath is None:
204 return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
206 f = open(summary_filepath, 'r')
208 return HttpResponse(f)
211 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
213 returns an eland_file upon calling.
215 fc_id, status = parse_flowcell_id(flowcell_id)
216 d = get_flowcell_result_dict(fc_id)
219 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
222 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
224 erd = d[cnm]['eland_results']
228 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
232 #f = opener.autoopen(filepath, 'r')
233 # return HttpResponse(f, mimetype="application/x-elandresult")
235 f = open(filepath, 'r')
236 return HttpResponse(f, mimetype='application/x-bzip2')
240 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
242 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
244 return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
247 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
249 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
251 fc_id, status = parse_flowcell_id(flowcell_id)
252 d = get_flowcell_result_dict(fc_id)
255 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
258 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
260 erd = d[cnm]['eland_results']
264 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
269 fi = opener.autoopen(filepath, 'r')
272 name, description = makebed.make_description( fc_id, lane )
274 bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
277 return HttpResponse(bedgen)
279 return HttpResponse(bedgen, mimetype="application/x-bedfile")
282 def _summary_stats(flowcell_id, lane_id, library_id):
284 Return the summary statistics for a given flowcell, lane, and end.
286 fc_id, status = parse_flowcell_id(flowcell_id)
287 fc_result_dict = get_flowcell_result_dict(fc_id)
292 if fc_result_dict is None:
293 err_list.append('Results for Flowcell %s not found.' % (fc_id))
294 return (summary_list, err_list)
296 for cycle_width in fc_result_dict:
297 xmlpath = fc_result_dict[cycle_width]['run_xml']
300 err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
303 run = load_pipeline_run_xml(xmlpath)
304 gerald_summary = run.gerald.summary.lane_results
305 key = SampleKey(lane=lane_id, sample='s')
306 eland_results = list(run.gerald.eland_results.find_keys(key))
307 key = SampleKey(lane=lane_id, sample=library_id)
308 eland_results.extend(run.gerald.eland_results.find_keys(key))
309 for key in eland_results:
310 eland_summary = run.gerald.eland_results.results[key]
311 # add information to lane_summary
312 eland_summary.flowcell_id = flowcell_id
314 read = key.read-1 if key.read is not None else 0
316 eland_summary.clusters = gerald_summary[read][key.lane].cluster
317 except (IndexError, KeyError) as e:
318 eland_summary.clustes = None
319 eland_summary.cycle_width = cycle_width
320 if hasattr(eland_summary, 'genome_map'):
321 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
322 eland_summary.genome_map,
323 eland_summary.mapped_reads)
325 # grab some more information out of the flowcell db
326 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
327 #pm_field = 'lane_%d_pM' % (lane_id)
328 lanes = flowcell.lane_set.filter(lane_number=lane_id)
329 eland_summary.flowcell = flowcell
330 eland_summary.lanes = lanes
332 summary_list.append(eland_summary)
334 #except Exception, e:
335 # summary_list.append("Summary report needs to be updated.")
336 # LOGGER.error("Exception: " + str(e))
338 return (summary_list, err_list)
341 def get_eland_result_type(pathname):
343 Guess the eland result file type from the filename
345 path, filename = os.path.split(pathname)
346 if 'extended' in filename:
348 elif 'multi' in filename:
350 elif 'result' in filename:
355 def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
356 fc_id, status = parse_flowcell_id(flowcell_id)
357 cur_fc = interesting_flowcells.get(fc_id, None)
361 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
362 lanes = flowcell.lane_set.filter(lane_number=lane_number)
363 # Loop throw storage devices if a result has been archived
365 if cur_fc is not None:
366 for lts in flowcell.longtermstorage_set.all():
367 for sd in lts.storage_devices.all():
368 # Use barcode_id if it exists
369 if sd.barcode_id is not None and sd.barcode_id != '':
370 storage_id_list.append(sd.barcode_id)
373 storage_id_list.append(sd.uuid)
375 # Formatting for template use
376 if len(storage_id_list) == 0:
379 storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
382 for cycle in cur_fc.keys():
383 result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
384 result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
385 results.append({'flowcell_id': fc_id,
386 'flowcell': flowcell,
387 'run_date': flowcell.run_date,
390 'summary_url': make_summary_url(flowcell_id, cycle),
391 'result_url': result_link[0],
392 'result_label': result_link[1],
393 'bed_url': result_link[2],
394 'storage_ids': storage_ids
398 def make_summary_url(flowcell_id, cycle_name):
399 url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
402 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
403 if eland_result_path is None:
406 result_type = get_eland_result_type(eland_result_path)
407 result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
408 result_label = 'eland %s' % (result_type,)
410 if result_type == 'result':
411 bed_url_pattern = '/results/%s/%s/bedfile/%s'
412 bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
414 return (result_url, result_label, bed_url)
416 def _files(flowcell_id, lane):
418 Sets up available files for download
422 flowcell_id, id = parse_flowcell_id(flowcell_id)
423 d = get_flowcell_result_dict(flowcell_id)
430 # c_name == 'CN-M' (i.e. C1-33)
433 if d[c_name]['summary'] is not None:
434 output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
435 % (flowcell_id, c_name, c_name))
437 erd = d[c_name]['eland_results']
439 result_type = get_eland_result_type(erd[lane])
440 result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
441 output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
442 if result_type == 'result':
443 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
444 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
449 return '(' + '|'.join(output) + ')'
451 def library_id_to_admin_url(request, lib_id):
452 lib = Library.objects.get(id=lib_id)
453 return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
455 def library_dict(library_id):
457 Given a library id construct a dictionary containing important information
458 return None if nothing was found
461 lib = Library.objects.get(id = library_id)
462 except Library.DoesNotExist, e:
465 #lane_info = lane_information(lib.lane_set)
467 for lane in lib.lane_set.all():
468 lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
469 'lane_number': lane.lane_number,
471 'paired_end': lane.flowcell.paired_end,
472 'read_length': lane.flowcell.read_length,
473 'status_code': lane.status,
474 'status': LANE_STATUS_MAP[lane.status]} )
478 # 'aligned_reads': lib.aligned_reads,
479 #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
480 #'amplified_from_sample_id': lib.amplified_from_sample,
481 #'antibody_name': lib.antibody_name(), # we have no antibodies.
482 'antibody_id': lib.antibody_id,
483 'cell_line_id': lib.cell_line_id,
484 'cell_line': unicode_or_none(lib.cell_line),
485 'experiment_type': lib.experiment_type.name,
486 'experiment_type_id': lib.experiment_type_id,
487 'gel_cut_size': lib.gel_cut_size,
488 'hidden': lib.hidden,
490 'insert_size': lib.insert_size,
491 'lane_set': lane_info,
492 'library_id': lib.id,
493 'library_name': lib.library_name,
494 'library_species': lib.library_species.scientific_name,
495 'library_species_id': lib.library_species_id,
496 #'library_type': lib.library_type.name,
497 'library_type_id': lib.library_type_id,
498 'made_for': lib.made_for,
499 'made_by': lib.made_by,
501 'replicate': lib.replicate,
502 'stopping_point': lib.stopping_point,
503 'successful_pM': unicode_or_none(lib.successful_pM),
504 'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
506 if lib.library_type_id is None:
507 info['library_type'] = None
509 info['library_type'] = lib.library_type.name
513 def library_json(request, library_id):
515 Return a json formatted library dictionary
517 require_api_key(request)
518 # what validation should we do on library_id?
520 lib = library_dict(library_id)
524 lib_json = json.dumps(lib)
525 return HttpResponse(lib_json, mimetype='application/json')
528 def species_json(request, species_id):
530 Return information about a species.
534 def species(request, species_id):
535 species = get_object_or_404(Species, id=species_id)
537 context = RequestContext(request,
538 { 'species': species })
540 return render_to_response("samples/species_detail.html", context)
542 def antibodies(request):
543 context = RequestContext(request,
544 {'antibodies': Antibody.objects.order_by('antigene')})
545 return render_to_response("samples/antibody_index.html", context)
548 def user_profile(request):
550 Information about the user
553 'page_name': 'User Profile',
555 #'bcmagic': BarcodeMagicForm(),
556 #'select': 'settings',
558 context.update(SAMPLES_CONTEXT_DEFAULTS)
559 return render_to_response('registration/profile.html', context,
560 context_instance=RequestContext(request))