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 import json
   9
  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
  18
  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
  33
  34
  35 LANE_LIST = [1, 2, 3, 4, 5, 6, 7, 8]
  36 SAMPLES_CONTEXT_DEFAULTS = {
  37     'app_name': 'Flowcell/Library Tracker',
  38     'bcmagic': BarcodeMagicForm()
  39 }
  40
  41 LOGGER = logging.getLogger(__name__)
  42
  43
  44 def count_lanes(lane_set):
  45     single = 0
  46     paired = 1
  47     short_read = 0
  48     medium_read = 1
  49     long_read = 2
  50     counts = [[0, 0, 0], [0, 0, 0]]
  51
  52     for lane in lane_set.all():
  53         if lane.flowcell.paired_end:
  54             lane_type = paired
  55         else:
  56             lane_type = single
  57         if lane.flowcell.read_length < 40:
  58             read_type = short_read
  59         elif lane.flowcell.read_length < 100:
  60             read_type = medium_read
  61         else:
  62             read_type = long_read
  63         counts[lane_type][read_type] += 1
  64
  65     return counts
  66
  67
  68 def create_library_context(cl):
  69     """
  70      Create a list of libraries that includes how many lanes were run
  71     """
  72     records = []
  73     #for lib in library_items.object_list:
  74     for lib in cl.result_list:
  75         summary = {}
  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
  82         else:
  83             summary['amplified_from'] = ''
  84         lanes_run = count_lanes(lib.lane_set)
  85         # suppress zeros
  86         for row_index, row in enumerate(lanes_run):
  87             for col_index, cell in enumerate(row):
  88                 if lanes_run[row_index][col_index] == 0:
  89                     lanes_run[row_index][col_index] = ''
  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}
  95
  96
  97 def library(request, todo_only=False):
  98     queryset = Library.objects.filter(hidden__exact=0)
  99     filters = {'hidden__exact': 0}
 100     if todo_only:
 101         filters['lane'] = None
 102     # build changelist
 103     fcl = HTSChangeList(request, Library,
 104                         list_filter=['affiliations', 'library_species'],
 105                         search_fields=['id', 'library_name', 'amplified_from_sample__id'],
 106                         list_per_page=200,
 107                         model_admin=LibraryOptions(Library, None),
 108                         extra_filters=filters
 109                         )
 110
 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))
 116
 117
 118 def library_not_run(request):
 119     return library(request, todo_only=True)
 120
 121
 122 def library_to_flowcells(request, lib_id):
 123     """
 124     Display information about all the flowcells a library has been run on.
 125     """
 126     try:
 127         lib = Library.objects.get(id=lib_id)
 128     except:
 129         raise Http404('Library %s does not exist' % (lib_id,))
 130
 131     flowcell_list = []
 132     flowcell_run_results = {}  # aka flowcells we're looking at
 133     for lane in lib.lane_set.all():
 134         fc = lane.flowcell
 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))
 139
 140     flowcell_list.sort()
 141     lane_summary_list = []
 142     eland_results = []
 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)
 146
 147         eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
 148
 149     context = {
 150         'page_name': 'Library Details',
 151         'lib': lib,
 152         'eland_results': eland_results,
 153         'lane_summary_list': lane_summary_list,
 154     }
 155     context.update(SAMPLES_CONTEXT_DEFAULTS)
 156
 157     return render_to_response(
 158         'samples/library_detail.html',
 159         context,
 160         context_instance=RequestContext(request))
 161
 162
 163 def lanes_for(request, username=None):
 164     """
 165     Generate a report of recent activity for a user
 166     """
 167     query = {}
 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,
 172                         list_filter=[],
 173                         search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
 174                         list_per_page=200,
 175                         model_admin=LaneOptions,
 176                         queryset=Lane.objects.filter(**query)
 177                         )
 178
 179     context = {'lanes': fcl, 'title': 'Lane Index'}
 180
 181     return render_to_response(
 182         'samples/lanes_for.html',
 183         context,
 184         context_instance=RequestContext(request)
 185     )
 186
 187
 188 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
 189     """
 190     returns a Summary.htm file if it exists.
 191     """
 192     fc_id, status = parse_flowcell_id(flowcell_id)
 193     d = get_flowcell_result_dict(fc_id)
 194
 195     if d is None:
 196         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 197
 198     if cnm not in d:
 199         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 200
 201     summary_filepath = d[cnm]['summary']
 202
 203     if summary_filepath is None:
 204         return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 205
 206     f = open(summary_filepath, 'r')
 207
 208     return HttpResponse(f)
 209
 210
 211 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
 212     """
 213     returns an eland_file upon calling.
 214     """
 215     fc_id, status = parse_flowcell_id(flowcell_id)
 216     d = get_flowcell_result_dict(fc_id)
 217
 218     if d is None:
 219         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 220
 221     if cnm not in d:
 222         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 223
 224     erd = d[cnm]['eland_results']
 225     lane = int(lane)
 226
 227     if lane not in erd:
 228         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 229
 230     filepath = erd[lane]
 231
 232     #f = opener.autoopen(filepath, 'r')
 233     # return HttpResponse(f, content_type="application/x-elandresult")
 234
 235     f = open(filepath, 'r')
 236     return HttpResponse(f, content_type='application/x-bzip2')
 237
 238
 239 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
 240     """
 241     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
 242     """
 243     return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
 244
 245
 246 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
 247     """
 248     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
 249     """
 250     fc_id, status = parse_flowcell_id(flowcell_id)
 251     d = get_flowcell_result_dict(fc_id)
 252
 253     if d is None:
 254         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 255
 256     if cnm not in d:
 257         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 258
 259     erd = d[cnm]['eland_results']
 260     lane = int(lane)
 261
 262     if lane not in erd:
 263         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 264
 265     filepath = erd[lane]
 266
 267     # Eland result file
 268     fi = opener.autoopen(filepath, 'r')
 269     # output memory file
 270
 271     name, description = makebed.make_description(fc_id, lane)
 272
 273     bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
 274
 275     if ucsc_compatible:
 276         return HttpResponse(bedgen)
 277     else:
 278         return HttpResponse(bedgen, content_type="application/x-bedfile")
 279
 280
 281 def _summary_stats(flowcell_id, lane_id, library_id):
 282     """
 283     Return the summary statistics for a given flowcell, lane, and end.
 284     """
 285     fc_id, status = parse_flowcell_id(flowcell_id)
 286     fc_result_dict = get_flowcell_result_dict(fc_id)
 287
 288     summary_list = []
 289     err_list = []
 290
 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)
 294
 295     for cycle_width in fc_result_dict:
 296         xmlpath = fc_result_dict[cycle_width]['run_xml']
 297
 298         if xmlpath is None:
 299             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
 300             continue
 301
 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:
 305             continue
 306
 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
 316
 317             read = key.read-1 if key.read is not None else 0
 318             try:
 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)
 327
 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
 334
 335             summary_list.append(eland_summary)
 336
 337         #except Exception as e:
 338         #    summary_list.append("Summary report needs to be updated.")
 339         #    LOGGER.error("Exception: " + str(e))
 340
 341     return (summary_list, err_list)
 342
 343
 344 def get_eland_result_type(pathname):
 345     """
 346     Guess the eland result file type from the filename
 347     """
 348     path, filename = os.path.split(pathname)
 349     if 'extended' in filename:
 350         return 'extended'
 351     elif 'multi' in filename:
 352         return 'multi'
 353     elif 'result' in filename:
 354         return 'result'
 355     else:
 356         return 'unknown'
 357
 358
 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)
 362     if cur_fc is None:
 363         return []
 364
 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
 368     storage_id_list = []
 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)
 375                 # Otherwise use UUID
 376                 else:
 377                     storage_id_list.append(sd.uuid)
 378
 379     # Formatting for template use
 380     if len(storage_id_list) == 0:
 381         storage_ids = None
 382     else:
 383         storage_ids = ', '.join(['<a href="/inventory/%s/">%s</a>' % (s, s) for s in storage_id_list])
 384
 385     results = []
 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,
 392                         'cycle': cycle,
 393                         'lane': lanes[0],
 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})
 399     return results
 400
 401
 402 def make_summary_url(flowcell_id, cycle_name):
 403     url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
 404     return url
 405
 406
 407 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
 408     if eland_result_path is None:
 409         return ("", "", "")
 410
 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,)
 414     bed_url = None
 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)
 418
 419     return (result_url, result_label, bed_url)
 420
 421
 422 def _files(flowcell_id, lane):
 423     """
 424     Sets up available files for download
 425     """
 426     lane = int(lane)
 427
 428     flowcell_id, id = parse_flowcell_id(flowcell_id)
 429     d = get_flowcell_result_dict(flowcell_id)
 430
 431     if d is None:
 432         return ''
 433
 434     output = []
 435
 436     # c_name == 'CN-M' (i.e. C1-33)
 437     for c_name in d:
 438
 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))
 442
 443         erd = d[c_name]['eland_results']
 444         if lane in erd:
 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))
 451
 452     if len(output) == 0:
 453         return ''
 454
 455     return '(' + '|'.join(output) + ')'
 456
 457
 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,))
 461
 462
 463 def library_dict(library_id):
 464     """
 465     Given a library id construct a dictionary containing important information
 466     return None if nothing was found
 467     """
 468     try:
 469         lib = Library.objects.get(id=library_id)
 470     except Library.DoesNotExist as e:
 471         return None
 472
 473     #lane_info = lane_information(lib.lane_set)
 474     lane_info = []
 475     for lane in lib.lane_set.all():
 476         lane_info.append({'flowcell': lane.flowcell.flowcell_id,
 477                           'lane_number': lane.lane_number,
 478                           'lane_id': lane.id,
 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]})
 483
 484     info = {
 485         # 'affiliations'?
 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,
 497         'id': lib.id,
 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,
 508         'notes': lib.notes,
 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)
 513         }
 514     if lib.library_type_id is None:
 515         info['library_type'] = None
 516     else:
 517         info['library_type'] = lib.library_type.name
 518     return info
 519
 520
 521 @csrf_exempt
 522 def library_json(request, library_id):
 523     """
 524     Return a json formatted library dictionary
 525     """
 526     require_api_key(request)
 527     # what validation should we do on library_id?
 528
 529     lib = library_dict(library_id)
 530     if lib is None:
 531         raise Http404
 532
 533     lib_json = json.dumps({'result': lib})
 534     return HttpResponse(lib_json, content_type='application/json')
 535
 536
 537 @csrf_exempt
 538 def species_json(request, species_id):
 539     """
 540     Return information about a species.
 541     """
 542     raise Http404
 543
 544
 545 def species(request, species_id):
 546     species = get_object_or_404(Species, id=species_id)
 547
 548     context = RequestContext(request,
 549                              {'species': species})
 550
 551     return render_to_response("samples/species_detail.html", context)
 552
 553
 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)
 558
 559
 560 @login_required
 561 def user_profile(request):
 562     """
 563     Information about the user
 564     """
 565     context = {
 566         'page_name': 'User Profile',
 567         'media': '',
 568         #'bcmagic': BarcodeMagicForm(),
 569         #'select': 'settings',
 570     }
 571     context.update(SAMPLES_CONTEXT_DEFAULTS)
 572     return render_to_response('registration/profile.html', context,
 573                               context_instance=RequestContext(request))