1 from __future__ import absolute_import, print_function, unicode_literals
3 # Create your views here.
10 from django.views.decorators.csrf import csrf_exempt
11 from django.core.exceptions import ObjectDoesNotExist
12 from django.http import HttpResponse, HttpResponseRedirect, Http404
13 from django.shortcuts import render_to_response, get_object_or_404
14 from django.template import RequestContext
15 from django.template.loader import get_template
16 from django.contrib.auth.decorators import login_required
17 from django.conf import settings
19 from htsworkflow.auth import require_api_key
20 from experiments.models import FlowCell, Lane, LANE_STATUS_MAP
21 from experiments.admin import LaneOptions
22 from .changelist import HTSChangeList
23 from .models import Antibody, Library, Species, HTSUser
24 from .admin import LibraryOptions
25 from .results import get_flowcell_result_dict
26 from bcmagic.forms import BarcodeMagicForm
27 from htsworkflow.pipelines import runfolder
28 from htsworkflow.pipelines.eland import ResultLane
29 from htsworkflow.pipelines.samplekey import SampleKey
30 from htsworkflow.util.conversion import str_or_none, parse_flowcell_id
31 from htsworkflow.util import makebed
32 from htsworkflow.util import opener
35 LANE_LIST = [1, 2, 3, 4, 5, 6, 7, 8]
36 SAMPLES_CONTEXT_DEFAULTS = {
37 'app_name': 'Flowcell/Library Tracker',
38 'bcmagic': BarcodeMagicForm()
41 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
68 def create_library_context(cl):
70 Create a list of libraries that includes how many lanes were run
73 #for lib in library_items.object_list:
74 for lib in cl.result_list:
76 summary['library'] = lib
77 summary['library_id'] = lib.id
78 summary['library_name'] = lib.library_name
79 summary['species_name'] = lib.library_species.scientific_name
80 if lib.amplified_from_sample is not None:
81 summary['amplified_from'] = lib.amplified_from_sample.id
83 summary['amplified_from'] = ''
84 lanes_run = count_lanes(lib.lane_set)
86 for row in xrange(len(lanes_run)):
87 for col in xrange(len(lanes_run[row])):
88 if lanes_run[row][col] == 0:
89 lanes_run[row][col] = ''
90 summary['lanes_run'] = lanes_run
91 summary['is_archived'] = lib.is_archived()
92 records.append(summary)
93 cl.result_count = str(cl.paginator._count)
94 return {'library_list': records}
97 def library(request, todo_only=False):
98 queryset = Library.objects.filter(hidden__exact=0)
99 filters = {'hidden__exact': 0}
101 filters['lane'] = None
103 fcl = HTSChangeList(request, Library,
104 list_filter=['affiliations', 'library_species'],
105 search_fields=['id', 'library_name', 'amplified_from_sample__id'],
107 model_admin=LibraryOptions(Library, None),
108 extra_filters=filters
111 context = {'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
112 context.update(create_library_context(fcl))
113 t = get_template('samples/library_index.html')
114 c = RequestContext(request, context)
115 return HttpResponse(t.render(c))
118 def library_not_run(request):
119 return library(request, todo_only=True)
122 def library_to_flowcells(request, lib_id):
124 Display information about all the flowcells a library has been run on.
127 lib = Library.objects.get(id=lib_id)
129 raise Http404('Library %s does not exist' % (lib_id,))
132 flowcell_run_results = {} # aka flowcells we're looking at
133 for lane in lib.lane_set.all():
135 flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
136 if flowcell_id not in flowcell_run_results:
137 flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
138 flowcell_list.append((fc.flowcell_id, lane.lane_number))
141 lane_summary_list = []
143 for fc, lane_number in flowcell_list:
144 lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
145 lane_summary_list.extend(lane_summary)
147 eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
150 'page_name': 'Library Details',
152 'eland_results': eland_results,
153 'lane_summary_list': lane_summary_list,
155 context.update(SAMPLES_CONTEXT_DEFAULTS)
157 return render_to_response(
158 'samples/library_detail.html',
160 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, content_type="application/x-elandresult")
235 f = open(filepath, 'r')
236 return HttpResponse(f, content_type='application/x-bzip2')
239 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
241 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
243 return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
246 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
248 returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
250 fc_id, status = parse_flowcell_id(flowcell_id)
251 d = get_flowcell_result_dict(fc_id)
254 return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
257 return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
259 erd = d[cnm]['eland_results']
263 return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
268 fi = opener.autoopen(filepath, 'r')
271 name, description = makebed.make_description(fc_id, lane)
273 bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
276 return HttpResponse(bedgen)
278 return HttpResponse(bedgen, content_type="application/x-bedfile")
281 def _summary_stats(flowcell_id, lane_id, library_id):
283 Return the summary statistics for a given flowcell, lane, and end.
285 fc_id, status = parse_flowcell_id(flowcell_id)
286 fc_result_dict = get_flowcell_result_dict(fc_id)
291 if fc_result_dict is None:
292 err_list.append('Results for Flowcell %s not found.' % (fc_id))
293 return (summary_list, err_list)
295 for cycle_width in fc_result_dict:
296 xmlpath = fc_result_dict[cycle_width]['run_xml']
299 err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
302 run = runfolder.load_pipeline_run_xml(xmlpath)
303 # skip if we don't have available metadata.
304 if run.gerald is None or run.gerald.summary is None:
307 gerald_summary = run.gerald.summary.lane_results
308 key = SampleKey(lane=lane_id, sample='s')
309 eland_results = list(run.gerald.eland_results.find_keys(key))
310 key = SampleKey(lane=lane_id, sample=library_id)
311 eland_results.extend(run.gerald.eland_results.find_keys(key))
312 for key in eland_results:
313 eland_summary = run.gerald.eland_results.results[key]
314 # add information to lane_summary
315 eland_summary.flowcell_id = flowcell_id
317 read = key.read-1 if key.read is not None else 0
319 eland_summary.clusters = gerald_summary[read][key.lane].cluster
320 except (IndexError, KeyError) as e:
321 eland_summary.clustes = None
322 eland_summary.cycle_width = cycle_width
323 if hasattr(eland_summary, 'genome_map'):
324 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
325 eland_summary.genome_map,
326 eland_summary.mapped_reads)
328 # grab some more information out of the flowcell db
329 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
330 #pm_field = 'lane_%d_pM' % (lane_id)
331 lanes = flowcell.lane_set.filter(lane_number=lane_id)
332 eland_summary.flowcell = flowcell
333 eland_summary.lanes = lanes
335 summary_list.append(eland_summary)
337 #except Exception as e:
338 # summary_list.append("Summary report needs to be updated.")
339 # LOGGER.error("Exception: " + str(e))
341 return (summary_list, err_list)
344 def get_eland_result_type(pathname):
346 Guess the eland result file type from the filename
348 path, filename = os.path.split(pathname)
349 if 'extended' in filename:
351 elif 'multi' in filename:
353 elif 'result' in filename:
359 def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
360 fc_id, status = parse_flowcell_id(flowcell_id)
361 cur_fc = interesting_flowcells.get(fc_id, None)
365 flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
366 lanes = flowcell.lane_set.filter(lane_number=lane_number)
367 # Loop throw storage devices if a result has been archived
369 if cur_fc is not None:
370 for lts in flowcell.longtermstorage_set.all():
371 for sd in lts.storage_devices.all():
372 # Use barcode_id if it exists
373 if sd.barcode_id is not None and sd.barcode_id != '':
374 storage_id_list.append(sd.barcode_id)
377 storage_id_list.append(sd.uuid)
379 # Formatting for template use
380 if len(storage_id_list) == 0:
383 storage_ids = ', '.join(['<a href="/inventory/%s/">%s</a>' % (s, s) for s in storage_id_list])
386 for cycle in cur_fc.keys():
387 result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
388 result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
389 results.append({'flowcell_id': fc_id,
390 'flowcell': flowcell,
391 'run_date': flowcell.run_date,
394 'summary_url': make_summary_url(flowcell_id, cycle),
395 'result_url': result_link[0],
396 'result_label': result_link[1],
397 'bed_url': result_link[2],
398 'storage_ids': storage_ids})
402 def make_summary_url(flowcell_id, cycle_name):
403 url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
407 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
408 if eland_result_path is None:
411 result_type = get_eland_result_type(eland_result_path)
412 result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
413 result_label = 'eland %s' % (result_type,)
415 if result_type == 'result':
416 bed_url_pattern = '/results/%s/%s/bedfile/%s'
417 bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
419 return (result_url, result_label, bed_url)
422 def _files(flowcell_id, lane):
424 Sets up available files for download
428 flowcell_id, id = parse_flowcell_id(flowcell_id)
429 d = get_flowcell_result_dict(flowcell_id)
436 # c_name == 'CN-M' (i.e. C1-33)
439 if d[c_name]['summary'] is not None:
440 output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' %
441 (flowcell_id, c_name, c_name))
443 erd = d[c_name]['eland_results']
445 result_type = get_eland_result_type(erd[lane])
446 result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
447 output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
448 if result_type == 'result':
449 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
450 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
455 return '(' + '|'.join(output) + ')'
458 def library_id_to_admin_url(request, lib_id):
459 lib = Library.objects.get(id=lib_id)
460 return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
463 def library_dict(library_id):
465 Given a library id construct a dictionary containing important information
466 return None if nothing was found
469 lib = Library.objects.get(id=library_id)
470 except Library.DoesNotExist as e:
473 #lane_info = lane_information(lib.lane_set)
475 for lane in lib.lane_set.all():
476 lane_info.append({'flowcell': lane.flowcell.flowcell_id,
477 'lane_number': lane.lane_number,
479 'paired_end': lane.flowcell.paired_end,
480 'read_length': lane.flowcell.read_length,
481 'status_code': lane.status,
482 'status': LANE_STATUS_MAP[lane.status]})
486 # 'aligned_reads': lib.aligned_reads,
487 #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
488 #'amplified_from_sample_id': lib.amplified_from_sample,
489 #'antibody_name': lib.antibody_name(), # we have no antibodies.
490 'antibody_id': lib.antibody_id,
491 'cell_line_id': lib.cell_line_id,
492 'cell_line': str_or_none(lib.cell_line),
493 'experiment_type': lib.experiment_type.name,
494 'experiment_type_id': lib.experiment_type_id,
495 'gel_cut_size': lib.gel_cut_size,
496 'hidden': lib.hidden,
498 'insert_size': lib.insert_size,
499 'lane_set': lane_info,
500 'library_id': lib.id,
501 'library_name': lib.library_name,
502 'library_species': lib.library_species.scientific_name,
503 'library_species_id': lib.library_species_id,
504 #'library_type': lib.library_type.name,
505 'library_type_id': lib.library_type_id,
506 'made_for': lib.made_for,
507 'made_by': lib.made_by,
509 'replicate': lib.replicate,
510 'stopping_point': lib.stopping_point,
511 'successful_pM': str_or_none(lib.successful_pM),
512 'undiluted_concentration': str_or_none(lib.undiluted_concentration)
514 if lib.library_type_id is None:
515 info['library_type'] = None
517 info['library_type'] = lib.library_type.name
522 def library_json(request, library_id):
524 Return a json formatted library dictionary
526 require_api_key(request)
527 # what validation should we do on library_id?
529 lib = library_dict(library_id)
533 lib_json = json.dumps({'result': lib})
534 return HttpResponse(lib_json, content_type='application/json')
538 def species_json(request, species_id):
540 Return information about a species.
545 def species(request, species_id):
546 species = get_object_or_404(Species, id=species_id)
548 context = RequestContext(request,
549 {'species': species})
551 return render_to_response("samples/species_detail.html", context)
554 def antibodies(request):
555 context = RequestContext(request,
556 {'antibodies': Antibody.objects.order_by('antigene')})
557 return render_to_response("samples/antibody_index.html", context)
561 def user_profile(request):
563 Information about the user
566 'page_name': 'User Profile',
568 #'bcmagic': BarcodeMagicForm(),
569 #'select': 'settings',
571 context.update(SAMPLES_CONTEXT_DEFAULTS)
572 return render_to_response('registration/profile.html', context,
573 context_instance=RequestContext(request))