samples/views.py

   1 from __future__ import absolute_import, print_function, unicode_literals
   2
   3 # Create your views here.
   4 import logging
   5 import os
   6 import sys
   7
   8 try:
   9     import json
  10 except ImportError as e:
  11     import simplejson as json
  12
  13 from django.views.decorators.csrf import csrf_exempt
  14 from django.core.exceptions import ObjectDoesNotExist
  15 from django.http import HttpResponse, HttpResponseRedirect, Http404
  16 from django.shortcuts import render_to_response, get_object_or_404
  17 from django.template import RequestContext
  18 from django.template.loader import get_template
  19 from django.contrib.auth.decorators import login_required
  20 from django.conf import settings
  21
  22 from htsworkflow.auth import require_api_key
  23 from experiments.models import FlowCell, Lane, LANE_STATUS_MAP
  24 from experiments.admin import LaneOptions
  25 from .changelist import HTSChangeList
  26 from .models import Antibody, Library, Species, HTSUser
  27 from .admin import LibraryOptions
  28 from .results import get_flowcell_result_dict
  29 from bcmagic.forms import BarcodeMagicForm
  30 from htsworkflow.pipelines import runfolder
  31 from htsworkflow.pipelines.eland import ResultLane
  32 from htsworkflow.pipelines.samplekey import SampleKey
  33 from htsworkflow.util.conversion import str_or_none, parse_flowcell_id
  34 from htsworkflow.util import makebed
  35 from htsworkflow.util import opener
  36
  37
  38 LANE_LIST = [1, 2, 3, 4, 5, 6, 7, 8]
  39 SAMPLES_CONTEXT_DEFAULTS = {
  40     'app_name': 'Flowcell/Library Tracker',
  41     'bcmagic': BarcodeMagicForm()
  42 }
  43
  44 LOGGER = logging.getLogger(__name__)
  45
  46
  47 def count_lanes(lane_set):
  48     single = 0
  49     paired = 1
  50     short_read = 0
  51     medium_read = 1
  52     long_read = 2
  53     counts = [[0, 0, 0], [0, 0, 0]]
  54
  55     for lane in lane_set.all():
  56         if lane.flowcell.paired_end:
  57             lane_type = paired
  58         else:
  59             lane_type = single
  60         if lane.flowcell.read_length < 40:
  61             read_type = short_read
  62         elif lane.flowcell.read_length < 100:
  63             read_type = medium_read
  64         else:
  65             read_type = long_read
  66         counts[lane_type][read_type] += 1
  67
  68     return counts
  69
  70
  71 def create_library_context(cl):
  72     """
  73      Create a list of libraries that includes how many lanes were run
  74     """
  75     records = []
  76     #for lib in library_items.object_list:
  77     for lib in cl.result_list:
  78         summary = {}
  79         summary['library'] = lib
  80         summary['library_id'] = lib.id
  81         summary['library_name'] = lib.library_name
  82         summary['species_name'] = lib.library_species.scientific_name
  83         if lib.amplified_from_sample is not None:
  84             summary['amplified_from'] = lib.amplified_from_sample.id
  85         else:
  86             summary['amplified_from'] = ''
  87         lanes_run = count_lanes(lib.lane_set)
  88         # suppress zeros
  89         for row in xrange(len(lanes_run)):
  90             for col in xrange(len(lanes_run[row])):
  91                 if lanes_run[row][col] == 0:
  92                     lanes_run[row][col] = ''
  93         summary['lanes_run'] = lanes_run
  94         summary['is_archived'] = lib.is_archived()
  95         records.append(summary)
  96     cl.result_count = str(cl.paginator._count)
  97     return {'library_list': records}
  98
  99
 100 def library(request, todo_only=False):
 101     queryset = Library.objects.filter(hidden__exact=0)
 102     filters = {'hidden__exact': 0}
 103     if todo_only:
 104         filters['lane'] = None
 105     # build changelist
 106     fcl = HTSChangeList(request, Library,
 107                         list_filter=['affiliations', 'library_species'],
 108                         search_fields=['id', 'library_name', 'amplified_from_sample__id'],
 109                         list_per_page=200,
 110                         model_admin=LibraryOptions(Library, None),
 111                         extra_filters=filters
 112                         )
 113
 114     context = {'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
 115     context.update(create_library_context(fcl))
 116     t = get_template('samples/library_index.html')
 117     c = RequestContext(request, context)
 118     return HttpResponse(t.render(c))
 119
 120
 121 def library_not_run(request):
 122     return library(request, todo_only=True)
 123
 124
 125 def library_to_flowcells(request, lib_id):
 126     """
 127     Display information about all the flowcells a library has been run on.
 128     """
 129     try:
 130         lib = Library.objects.get(id=lib_id)
 131     except:
 132         raise Http404('Library %s does not exist' % (lib_id,))
 133
 134     flowcell_list = []
 135     flowcell_run_results = {}  # aka flowcells we're looking at
 136     for lane in lib.lane_set.all():
 137         fc = lane.flowcell
 138         flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
 139         if flowcell_id not in flowcell_run_results:
 140             flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
 141         flowcell_list.append((fc.flowcell_id, lane.lane_number))
 142
 143     flowcell_list.sort()
 144     lane_summary_list = []
 145     eland_results = []
 146     for fc, lane_number in flowcell_list:
 147         lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
 148         lane_summary_list.extend(lane_summary)
 149
 150         eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
 151
 152     context = {
 153         'page_name': 'Library Details',
 154         'lib': lib,
 155         'eland_results': eland_results,
 156         'lane_summary_list': lane_summary_list,
 157     }
 158     context.update(SAMPLES_CONTEXT_DEFAULTS)
 159
 160     return render_to_response(
 161         'samples/library_detail.html',
 162         context,
 163         context_instance=RequestContext(request))
 164
 165
 166 def lanes_for(request, username=None):
 167     """
 168     Generate a report of recent activity for a user
 169     """
 170     query = {}
 171     if username is not None:
 172         user = HTSUser.objects.get(username=username)
 173         query.update({'library__affiliations__users__id': user.id})
 174     fcl = HTSChangeList(request, Lane,
 175                         list_filter=[],
 176                         search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
 177                         list_per_page=200,
 178                         model_admin=LaneOptions,
 179                         queryset=Lane.objects.filter(**query)
 180                         )
 181
 182     context = {'lanes': fcl, 'title': 'Lane Index'}
 183
 184     return render_to_response(
 185         'samples/lanes_for.html',
 186         context,
 187         context_instance=RequestContext(request)
 188     )
 189
 190
 191 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
 192     """
 193     returns a Summary.htm file if it exists.
 194     """
 195     fc_id, status = parse_flowcell_id(flowcell_id)
 196     d = get_flowcell_result_dict(fc_id)
 197
 198     if d is None:
 199         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 200
 201     if cnm not in d:
 202         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 203
 204     summary_filepath = d[cnm]['summary']
 205
 206     if summary_filepath is None:
 207         return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 208
 209     f = open(summary_filepath, 'r')
 210
 211     return HttpResponse(f)
 212
 213
 214 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
 215     """
 216     returns an eland_file upon calling.
 217     """
 218     fc_id, status = parse_flowcell_id(flowcell_id)
 219     d = get_flowcell_result_dict(fc_id)
 220
 221     if d is None:
 222         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 223
 224     if cnm not in d:
 225         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 226
 227     erd = d[cnm]['eland_results']
 228     lane = int(lane)
 229
 230     if lane not in erd:
 231         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 232
 233     filepath = erd[lane]
 234
 235     #f = opener.autoopen(filepath, 'r')
 236     # return HttpResponse(f, content_type="application/x-elandresult")
 237
 238     f = open(filepath, 'r')
 239     return HttpResponse(f, content_type='application/x-bzip2')
 240
 241
 242 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
 243     """
 244     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
 245     """
 246     return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
 247
 248
 249 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
 250     """
 251     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
 252     """
 253     fc_id, status = parse_flowcell_id(flowcell_id)
 254     d = get_flowcell_result_dict(fc_id)
 255
 256     if d is None:
 257         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 258
 259     if cnm not in d:
 260         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 261
 262     erd = d[cnm]['eland_results']
 263     lane = int(lane)
 264
 265     if lane not in erd:
 266         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 267
 268     filepath = erd[lane]
 269
 270     # Eland result file
 271     fi = opener.autoopen(filepath, 'r')
 272     # output memory file
 273
 274     name, description = makebed.make_description(fc_id, lane)
 275
 276     bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
 277
 278     if ucsc_compatible:
 279         return HttpResponse(bedgen)
 280     else:
 281         return HttpResponse(bedgen, content_type="application/x-bedfile")
 282
 283
 284 def _summary_stats(flowcell_id, lane_id, library_id):
 285     """
 286     Return the summary statistics for a given flowcell, lane, and end.
 287     """
 288     fc_id, status = parse_flowcell_id(flowcell_id)
 289     fc_result_dict = get_flowcell_result_dict(fc_id)
 290
 291     summary_list = []
 292     err_list = []
 293
 294     if fc_result_dict is None:
 295         err_list.append('Results for Flowcell %s not found.' % (fc_id))
 296         return (summary_list, err_list)
 297
 298     for cycle_width in fc_result_dict:
 299         xmlpath = fc_result_dict[cycle_width]['run_xml']
 300
 301         if xmlpath is None:
 302             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
 303             continue
 304
 305         run = runfolder.load_pipeline_run_xml(xmlpath)
 306         # skip if we don't have available metadata.
 307         if run.gerald is None or run.gerald.summary is None:
 308             continue
 309
 310         gerald_summary = run.gerald.summary.lane_results
 311         key = SampleKey(lane=lane_id, sample='s')
 312         eland_results = list(run.gerald.eland_results.find_keys(key))
 313         key = SampleKey(lane=lane_id, sample=library_id)
 314         eland_results.extend(run.gerald.eland_results.find_keys(key))
 315         for key in eland_results:
 316             eland_summary = run.gerald.eland_results.results[key]
 317             # add information to lane_summary
 318             eland_summary.flowcell_id = flowcell_id
 319
 320             read = key.read-1 if key.read is not None else 0
 321             try:
 322                 eland_summary.clusters = gerald_summary[read][key.lane].cluster
 323             except (IndexError, KeyError) as e:
 324                 eland_summary.clustes = None
 325             eland_summary.cycle_width = cycle_width
 326             if hasattr(eland_summary, 'genome_map'):
 327                 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
 328                     eland_summary.genome_map,
 329                     eland_summary.mapped_reads)
 330
 331             # grab some more information out of the flowcell db
 332             flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
 333             #pm_field = 'lane_%d_pM' % (lane_id)
 334             lanes = flowcell.lane_set.filter(lane_number=lane_id)
 335             eland_summary.flowcell = flowcell
 336             eland_summary.lanes = lanes
 337
 338             summary_list.append(eland_summary)
 339
 340         #except Exception as e:
 341         #    summary_list.append("Summary report needs to be updated.")
 342         #    LOGGER.error("Exception: " + str(e))
 343
 344     return (summary_list, err_list)
 345
 346
 347 def get_eland_result_type(pathname):
 348     """
 349     Guess the eland result file type from the filename
 350     """
 351     path, filename = os.path.split(pathname)
 352     if 'extended' in filename:
 353         return 'extended'
 354     elif 'multi' in filename:
 355         return 'multi'
 356     elif 'result' in filename:
 357         return 'result'
 358     else:
 359         return 'unknown'
 360
 361
 362 def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
 363     fc_id, status = parse_flowcell_id(flowcell_id)
 364     cur_fc = interesting_flowcells.get(fc_id, None)
 365     if cur_fc is None:
 366         return []
 367
 368     flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
 369     lanes = flowcell.lane_set.filter(lane_number=lane_number)
 370     # Loop throw storage devices if a result has been archived
 371     storage_id_list = []
 372     if cur_fc is not None:
 373         for lts in flowcell.longtermstorage_set.all():
 374             for sd in lts.storage_devices.all():
 375                 # Use barcode_id if it exists
 376                 if sd.barcode_id is not None and sd.barcode_id != '':
 377                     storage_id_list.append(sd.barcode_id)
 378                 # Otherwise use UUID
 379                 else:
 380                     storage_id_list.append(sd.uuid)
 381
 382     # Formatting for template use
 383     if len(storage_id_list) == 0:
 384         storage_ids = None
 385     else:
 386         storage_ids = ', '.join(['<a href="/inventory/%s/">%s</a>' % (s, s) for s in storage_id_list])
 387
 388     results = []
 389     for cycle in cur_fc.keys():
 390         result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
 391         result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
 392         results.append({'flowcell_id': fc_id,
 393                         'flowcell': flowcell,
 394                         'run_date': flowcell.run_date,
 395                         'cycle': cycle,
 396                         'lane': lanes[0],
 397                         'summary_url': make_summary_url(flowcell_id, cycle),
 398                         'result_url': result_link[0],
 399                         'result_label': result_link[1],
 400                         'bed_url': result_link[2],
 401                         'storage_ids': storage_ids})
 402     return results
 403
 404
 405 def make_summary_url(flowcell_id, cycle_name):
 406     url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
 407     return url
 408
 409
 410 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
 411     if eland_result_path is None:
 412         return ("", "", "")
 413
 414     result_type = get_eland_result_type(eland_result_path)
 415     result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
 416     result_label = 'eland %s' % (result_type,)
 417     bed_url = None
 418     if result_type == 'result':
 419         bed_url_pattern = '/results/%s/%s/bedfile/%s'
 420         bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
 421
 422     return (result_url, result_label, bed_url)
 423
 424
 425 def _files(flowcell_id, lane):
 426     """
 427     Sets up available files for download
 428     """
 429     lane = int(lane)
 430
 431     flowcell_id, id = parse_flowcell_id(flowcell_id)
 432     d = get_flowcell_result_dict(flowcell_id)
 433
 434     if d is None:
 435         return ''
 436
 437     output = []
 438
 439     # c_name == 'CN-M' (i.e. C1-33)
 440     for c_name in d:
 441
 442         if d[c_name]['summary'] is not None:
 443             output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' %
 444                           (flowcell_id, c_name, c_name))
 445
 446         erd = d[c_name]['eland_results']
 447         if lane in erd:
 448             result_type = get_eland_result_type(erd[lane])
 449             result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
 450             output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
 451             if result_type == 'result':
 452                 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
 453                 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
 454
 455     if len(output) == 0:
 456         return ''
 457
 458     return '(' + '|'.join(output) + ')'
 459
 460
 461 def library_id_to_admin_url(request, lib_id):
 462     lib = Library.objects.get(id=lib_id)
 463     return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
 464
 465
 466 def library_dict(library_id):
 467     """
 468     Given a library id construct a dictionary containing important information
 469     return None if nothing was found
 470     """
 471     try:
 472         lib = Library.objects.get(id=library_id)
 473     except Library.DoesNotExist as e:
 474         return None
 475
 476     #lane_info = lane_information(lib.lane_set)
 477     lane_info = []
 478     for lane in lib.lane_set.all():
 479         lane_info.append({'flowcell': lane.flowcell.flowcell_id,
 480                           'lane_number': lane.lane_number,
 481                           'lane_id': lane.id,
 482                           'paired_end': lane.flowcell.paired_end,
 483                           'read_length': lane.flowcell.read_length,
 484                           'status_code': lane.status,
 485                           'status': LANE_STATUS_MAP[lane.status]})
 486
 487     info = {
 488         # 'affiliations'?
 489         # 'aligned_reads': lib.aligned_reads,
 490         #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
 491         #'amplified_from_sample_id': lib.amplified_from_sample,
 492         #'antibody_name': lib.antibody_name(), # we have no antibodies.
 493         'antibody_id': lib.antibody_id,
 494         'cell_line_id': lib.cell_line_id,
 495         'cell_line': str_or_none(lib.cell_line),
 496         'experiment_type': lib.experiment_type.name,
 497         'experiment_type_id': lib.experiment_type_id,
 498         'gel_cut_size': lib.gel_cut_size,
 499         'hidden': lib.hidden,
 500         'id': lib.id,
 501         'insert_size': lib.insert_size,
 502         'lane_set': lane_info,
 503         'library_id': lib.id,
 504         'library_name': lib.library_name,
 505         'library_species': lib.library_species.scientific_name,
 506         'library_species_id': lib.library_species_id,
 507         #'library_type': lib.library_type.name,
 508         'library_type_id': lib.library_type_id,
 509         'made_for': lib.made_for,
 510         'made_by': lib.made_by,
 511         'notes': lib.notes,
 512         'replicate': lib.replicate,
 513         'stopping_point': lib.stopping_point,
 514         'successful_pM': str_or_none(lib.successful_pM),
 515         'undiluted_concentration': str_or_none(lib.undiluted_concentration)
 516         }
 517     if lib.library_type_id is None:
 518         info['library_type'] = None
 519     else:
 520         info['library_type'] = lib.library_type.name
 521     return info
 522
 523
 524 @csrf_exempt
 525 def library_json(request, library_id):
 526     """
 527     Return a json formatted library dictionary
 528     """
 529     require_api_key(request)
 530     # what validation should we do on library_id?
 531
 532     lib = library_dict(library_id)
 533     if lib is None:
 534         raise Http404
 535
 536     lib_json = json.dumps({'result': lib})
 537     return HttpResponse(lib_json, content_type='application/json')
 538
 539
 540 @csrf_exempt
 541 def species_json(request, species_id):
 542     """
 543     Return information about a species.
 544     """
 545     raise Http404
 546
 547
 548 def species(request, species_id):
 549     species = get_object_or_404(Species, id=species_id)
 550
 551     context = RequestContext(request,
 552                              {'species': species})
 553
 554     return render_to_response("samples/species_detail.html", context)
 555
 556
 557 def antibodies(request):
 558     context = RequestContext(request,
 559                              {'antibodies': Antibody.objects.order_by('antigene')})
 560     return render_to_response("samples/antibody_index.html", context)
 561
 562
 563 @login_required
 564 def user_profile(request):
 565     """
 566     Information about the user
 567     """
 568     context = {
 569         'page_name': 'User Profile',
 570         'media': '',
 571         #'bcmagic': BarcodeMagicForm(),
 572         #'select': 'settings',
 573     }
 574     context.update(SAMPLES_CONTEXT_DEFAULTS)
 575     return render_to_response('registration/profile.html', context,
 576                               context_instance=RequestContext(request))