samples/views.py

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