htsworkflow/frontend/samples/views.py

   1 # Create your views here.
   2 import StringIO
   3 import logging
   4 import os
   5 import sys
   6
   7 try:
   8     import json
   9 except ImportError, e:
  10     import simplejson as json
  11
  12 from htsworkflow.frontend.auth import require_api_key
  13 from htsworkflow.frontend.experiments.models import FlowCell, Lane
  14 from htsworkflow.frontend.samples.changelist import ChangeList
  15 from htsworkflow.frontend.samples.models import Library, HTSUser
  16 from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
  17 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
  18 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
  19 from htsworkflow.pipelines import runfolder
  20 from htsworkflow.pipelines.eland import ResultLane
  21 from htsworkflow.frontend import settings
  22 from htsworkflow.util.conversion import unicode_or_none
  23 from htsworkflow.util import makebed
  24 from htsworkflow.util import opener
  25
  26
  27 from django.core.exceptions import ObjectDoesNotExist
  28 from django.http import HttpResponse, HttpResponseRedirect, Http404
  29 from django.shortcuts import render_to_response
  30 from django.template import RequestContext
  31 from django.template.loader import get_template
  32 from django.contrib.auth.decorators import login_required
  33
  34 LANE_LIST = [1,2,3,4,5,6,7,8]
  35 SAMPLES_CONTEXT_DEFAULTS = {
  36     'app_name': 'Flowcell/Library Tracker',
  37     'bcmagic': BarcodeMagicForm()
  38 }
  39
  40 def count_lanes(lane_set):
  41     single = 0
  42     paired = 1
  43     short_read = 0
  44     medium_read = 1
  45     long_read = 2
  46     counts = [[0,0,0,],[0,0,0]]
  47
  48     for lane in lane_set.all():
  49         if lane.flowcell.paired_end:
  50             lane_type = paired
  51         else:
  52             lane_type = single
  53         if lane.flowcell.read_length < 40:
  54             read_type = short_read
  55         elif lane.flowcell.read_length < 100:
  56             read_type = medium_read
  57         else:
  58             read_type = long_read
  59         counts[lane_type][read_type] += 1
  60
  61     return counts
  62
  63 def create_library_context(cl):
  64     """
  65     Create a list of libraries that includes how many lanes were run
  66     """
  67     records = []
  68     #for lib in library_items.object_list:
  69     for lib in cl.result_list:
  70        summary = {}
  71        summary['library_id'] = lib.id
  72        summary['library_name'] = lib.library_name
  73        summary['species_name' ] = lib.library_species.scientific_name
  74        if lib.amplified_from_sample is not None:
  75            summary['amplified_from'] = lib.amplified_from_sample.id
  76        else:
  77            summary['amplified_from'] = ''
  78        lanes_run = count_lanes(lib.lane_set)
  79        # suppress zeros
  80        for row in xrange(len(lanes_run)):
  81            for col in xrange(len(lanes_run[row])):
  82                if lanes_run[row][col] == 0:
  83                    lanes_run[row][col] = ''
  84        summary['lanes_run'] = lanes_run
  85        summary['is_archived'] = lib.is_archived()
  86        records.append(summary)
  87     cl.result_count = unicode(cl.paginator._count) + u" libraries"
  88     return {'library_list': records }
  89
  90 def library(request):
  91    # build changelist
  92     fcl = ChangeList(request, Library,
  93         list_filter=['affiliations', 'library_species'],
  94         search_fields=['id', 'library_name', 'amplified_from_sample__id'],
  95         list_per_page=200,
  96         queryset=Library.objects.filter(hidden__exact=0)
  97     )
  98
  99     context = { 'cl': fcl, 'title': 'Library Index'}
 100     context.update(create_library_context(fcl))
 101     t = get_template('samples/library_index.html')
 102     c = RequestContext(request, context)
 103
 104     app_context = {
 105         'page_name': 'Library Index',
 106         'east_region_config_div': 'changelist-filter',
 107         'body': t.render(c)
 108     }
 109     app_context.update(SAMPLES_CONTEXT_DEFAULTS)
 110
 111     app_t = get_template('flowcell_libraries_app.html')
 112     app_c = RequestContext(request, app_context)
 113     return HttpResponse( app_t.render(app_c) )
 114
 115 def library_to_flowcells(request, lib_id):
 116     """
 117     Display information about all the flowcells a library has been run on.
 118     """
 119
 120     try:
 121       lib = Library.objects.get(id=lib_id)
 122     except:
 123       return HttpResponse("Library %s does not exist" % (lib_id))
 124
 125     flowcell_list = []
 126     flowcell_run_results = {} # aka flowcells we're looking at
 127     for lane in lib.lane_set.all():
 128         fc = lane.flowcell
 129         flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
 130         if flowcell_id not in flowcell_run_results:
 131             flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
 132         flowcell_list.append((fc.flowcell_id, lane.lane_number))
 133
 134     flowcell_list.sort()
 135     lane_summary_list = []
 136     eland_results = []
 137     for fc, lane_number in flowcell_list:
 138         lane_summary, err_list = _summary_stats(fc, lane_number)
 139
 140         eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
 141         lane_summary_list.extend(lane_summary)
 142
 143     context = {
 144         'page_name': 'Library Details',
 145         'lib': lib,
 146         'eland_results': eland_results,
 147         'lane_summary_list': lane_summary_list,
 148     }
 149     context.update(SAMPLES_CONTEXT_DEFAULTS)
 150
 151     return render_to_response(
 152         'samples/library_detail.html',
 153         context,
 154         context_instance = RequestContext(request))
 155
 156 def lanes_for(request, username=None):
 157     """
 158     Generate a report of recent activity for a user
 159     """
 160     query = {}
 161     if username is not None:
 162         user = HTSUser.objects.get(username=username)
 163         query.update({'library__affiliations__users__id':user.id})
 164     fcl = ChangeList(request, Lane,
 165         list_filter=[],
 166         search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
 167         list_per_page=200,
 168         queryset=Lane.objects.filter(**query)
 169     )
 170
 171     context = { 'lanes': fcl, 'title': 'Lane Index'}
 172
 173     return render_to_response(
 174         'samples/lanes_for.html',
 175         context,
 176         context_instance = RequestContext(request)
 177     )
 178
 179
 180 def summaryhtm_fc_cnm(request, flowcell_id, cnm):
 181     """
 182     returns a Summary.htm file if it exists.
 183     """
 184     fc_id, status = parse_flowcell_id(flowcell_id)
 185     d = get_flowcell_result_dict(fc_id)
 186
 187     if d is None:
 188         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 189
 190     if cnm not in d:
 191         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 192
 193     summary_filepath = d[cnm]['summary']
 194
 195     if summary_filepath is None:
 196         return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 197
 198     f = open(summary_filepath, 'r')
 199
 200     return HttpResponse(f)
 201
 202
 203 def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
 204     """
 205     returns an eland_file upon calling.
 206     """
 207     fc_id, status = parse_flowcell_id(flowcell_id)
 208     d = get_flowcell_result_dict(fc_id)
 209
 210     if d is None:
 211         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 212
 213     if cnm not in d:
 214         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 215
 216     erd = d[cnm]['eland_results']
 217     lane = int(lane)
 218
 219     if lane not in erd:
 220         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 221
 222     filepath = erd[lane]
 223
 224     #f = opener.autoopen(filepath, 'r')
 225     # return HttpResponse(f, mimetype="application/x-elandresult")
 226
 227     f = open(filepath, 'r')
 228     return HttpResponse(f, mimetype='application/x-bzip2')
 229
 230
 231
 232 def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
 233     """
 234     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
 235     """
 236     return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
 237
 238
 239 def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
 240     """
 241     returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
 242     """
 243     fc_id, status = parse_flowcell_id(flowcell_id)
 244     d = get_flowcell_result_dict(fc_id)
 245
 246     if d is None:
 247         return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
 248
 249     if cnm not in d:
 250         return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
 251
 252     erd = d[cnm]['eland_results']
 253     lane = int(lane)
 254
 255     if lane not in erd:
 256         return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
 257
 258     filepath = erd[lane]
 259
 260     # Eland result file
 261     fi = opener.autoopen(filepath, 'r')
 262     # output memory file
 263
 264     name, description = makebed.make_description( fc_id, lane )
 265
 266     bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
 267
 268     if ucsc_compatible:
 269         return HttpResponse(bedgen)
 270     else:
 271         return HttpResponse(bedgen, mimetype="application/x-bedfile")
 272
 273
 274 def _summary_stats(flowcell_id, lane_id):
 275     """
 276     Return the summary statistics for a given flowcell, lane, and end.
 277     """
 278     fc_id, status = parse_flowcell_id(flowcell_id)
 279     fc_result_dict = get_flowcell_result_dict(fc_id)
 280
 281     summary_list = []
 282     err_list = []
 283
 284     if fc_result_dict is None:
 285         err_list.append('Results for Flowcell %s not found.' % (fc_id))
 286         return (summary_list, err_list)
 287
 288     for cycle_width in fc_result_dict:
 289         xmlpath = fc_result_dict[cycle_width]['run_xml']
 290
 291         if xmlpath is None:
 292             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
 293             continue
 294
 295         run = load_pipeline_run_xml(xmlpath)
 296         gerald_summary = run.gerald.summary.lane_results
 297         for end in range(len(gerald_summary)):
 298             end_summary = run.gerald.eland_results.results[end]
 299             if end_summary.has_key(lane_id):
 300                 eland_summary = run.gerald.eland_results.results[end][lane_id]
 301             else:
 302                 eland_summary = ResultLane(lane_id=lane_id, end=end)
 303             # add information to lane_summary
 304             eland_summary.flowcell_id = flowcell_id
 305             if len(gerald_summary) > end and gerald_summary[end].has_key(lane_id):
 306                 eland_summary.clusters = gerald_summary[end][lane_id].cluster
 307             else:
 308                 eland_summary.clusters = None
 309             eland_summary.cycle_width = cycle_width
 310             if hasattr(eland_summary, 'genome_map'):
 311                 eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
 312                                                    eland_summary.genome_map,
 313                                                    eland_summary.mapped_reads)
 314
 315             # grab some more information out of the flowcell db
 316             flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
 317             #pm_field = 'lane_%d_pM' % (lane_id)
 318             lane_obj = flowcell.lane_set.get(lane_number=lane_id)
 319             eland_summary.successful_pm = lane_obj.pM
 320
 321             summary_list.append(eland_summary)
 322
 323         #except Exception, e:
 324         #    summary_list.append("Summary report needs to be updated.")
 325         #    logging.error("Exception: " + str(e))
 326
 327     return (summary_list, err_list)
 328
 329 def _summary_stats_old(flowcell_id, lane):
 330     """
 331     return a dictionary of summary stats for a given flowcell_id & lane.
 332     """
 333     fc_id, status = parse_flowcell_id(flowcell_id)
 334     fc_result_dict = get_flowcell_result_dict(fc_id)
 335
 336     dict_list = []
 337     err_list = []
 338     summary_list = []
 339
 340     if fc_result_dict is None:
 341         err_list.append('Results for Flowcell %s not found.' % (fc_id))
 342         return (dict_list, err_list, summary_list)
 343
 344     for cnm in fc_result_dict:
 345
 346         xmlpath = fc_result_dict[cnm]['run_xml']
 347
 348         if xmlpath is None:
 349             err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
 350             continue
 351
 352         tree = ElementTree.parse(xmlpath).getroot()
 353         results = runfolder.PipelineRun(pathname='', xml=tree)
 354         try:
 355             lane_report = runfolder.summarize_lane(results.gerald, lane)
 356             summary_list.append(os.linesep.join(lane_report))
 357         except Exception, e:
 358             summary_list.append("Summary report needs to be updated.")
 359             logging.error("Exception: " + str(e))
 360
 361         print >>sys.stderr, "----------------------------------"
 362         print >>sys.stderr, "-- DOES NOT SUPPORT PAIRED END ---"
 363         print >>sys.stderr, "----------------------------------"
 364         lane_results = results.gerald.summary[0][lane]
 365         lrs = lane_results
 366
 367         d = {}
 368
 369         d['average_alignment_score'] = lrs.average_alignment_score
 370         d['average_first_cycle_intensity'] = lrs.average_first_cycle_intensity
 371         d['cluster'] = lrs.cluster
 372         d['lane'] = lrs.lane
 373         d['flowcell'] = flowcell_id
 374         d['cnm'] = cnm
 375         d['percent_error_rate'] = lrs.percent_error_rate
 376         d['percent_intensity_after_20_cycles'] = lrs.percent_intensity_after_20_cycles
 377         d['percent_pass_filter_align'] = lrs.percent_pass_filter_align
 378         d['percent_pass_filter_clusters'] = lrs.percent_pass_filter_clusters
 379
 380         #FIXME: function finished, but need to take advantage of
 381         #   may need to take in a list of lanes so we only have to
 382         #   load the xml file once per flowcell rather than once
 383         #   per lane.
 384         dict_list.append(d)
 385
 386     return (dict_list, err_list, summary_list)
 387
 388
 389 def get_eland_result_type(pathname):
 390     """
 391     Guess the eland result file type from the filename
 392     """
 393     path, filename = os.path.split(pathname)
 394     if 'extended' in filename:
 395         return 'extended'
 396     elif 'multi' in filename:
 397         return 'multi'
 398     elif 'result' in filename:
 399         return 'result'
 400     else:
 401         return 'unknown'
 402
 403 def _make_eland_results(flowcell_id, lane, interesting_flowcells):
 404     fc_id, status = parse_flowcell_id(flowcell_id)
 405     cur_fc = interesting_flowcells.get(fc_id, None)
 406     if cur_fc is None:
 407       return []
 408
 409     flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
 410     # Loop throw storage devices if a result has been archived
 411     storage_id_list = []
 412     if cur_fc is not None:
 413         for lts in flowcell.longtermstorage_set.all():
 414             for sd in lts.storage_devices.all():
 415                 # Use barcode_id if it exists
 416                 if sd.barcode_id is not None and sd.barcode_id != '':
 417                     storage_id_list.append(sd.barcode_id)
 418                 # Otherwise use UUID
 419                 else:
 420                     storage_id_list.append(sd.uuid)
 421
 422     # Formatting for template use
 423     if len(storage_id_list) == 0:
 424         storage_ids = None
 425     else:
 426         storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
 427
 428     results = []
 429     for cycle in cur_fc.keys():
 430         result_path = cur_fc[cycle]['eland_results'].get(lane, None)
 431         result_link = make_result_link(fc_id, cycle, lane, result_path)
 432         results.append({'flowcell_id': fc_id,
 433                         'run_date': flowcell.run_date,
 434                         'cycle': cycle,
 435                         'lane': lane,
 436                         'summary_url': make_summary_url(flowcell_id, cycle),
 437                         'result_url': result_link[0],
 438                         'result_label': result_link[1],
 439                         'bed_url': result_link[2],
 440                         'storage_ids': storage_ids
 441         })
 442     return results
 443
 444 def make_summary_url(flowcell_id, cycle_name):
 445     url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
 446     return url
 447
 448 def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
 449     if eland_result_path is None:
 450         return ("", "", "")
 451
 452     result_type = get_eland_result_type(eland_result_path)
 453     result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
 454     result_label = 'eland %s' % (result_type,)
 455     bed_url = None
 456     if result_type == 'result':
 457        bed_url_pattern = '/results/%s/%s/bedfile/%s'
 458        bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
 459
 460     return (result_url, result_label, bed_url)
 461
 462 def _files(flowcell_id, lane):
 463     """
 464     Sets up available files for download
 465     """
 466     lane = int(lane)
 467
 468     flowcell_id, id = parse_flowcell_id(flowcell_id)
 469     d = get_flowcell_result_dict(flowcell_id)
 470
 471     if d is None:
 472         return ''
 473
 474     output = []
 475
 476     # c_name == 'CN-M' (i.e. C1-33)
 477     for c_name in d:
 478
 479         if d[c_name]['summary'] is not None:
 480             output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
 481                           % (flowcell_id, c_name, c_name))
 482
 483         erd = d[c_name]['eland_results']
 484         if lane in erd:
 485             result_type = get_eland_result_type(erd[lane])
 486             result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
 487             output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
 488             if result_type == 'result':
 489                 bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
 490                 output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
 491
 492     if len(output) == 0:
 493         return ''
 494
 495     return '(' + '|'.join(output) + ')'
 496
 497 def library_id_to_admin_url(request, lib_id):
 498     lib = Library.objects.get(id=lib_id)
 499     return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
 500
 501 def library_dict(library_id):
 502     """
 503     Given a library id construct a dictionary containing important information
 504     return None if nothing was found
 505     """
 506     try:
 507         lib = Library.objects.get(id = library_id)
 508     except Library.DoesNotExist, e:
 509         return None
 510
 511     #lane_info = lane_information(lib.lane_set)
 512     lane_info = []
 513     for lane in lib.lane_set.all():
 514         lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
 515                            'lane_number': lane.lane_number} )
 516
 517     info = {
 518         # 'affiliations'?
 519         # 'aligned_reads': lib.aligned_reads,
 520         #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
 521         #'amplified_from_sample_id': lib.amplified_from_sample,
 522         #'antibody_name': lib.antibody_name(), # we have no antibodies.
 523         'antibody_id': lib.antibody_id,
 524         'avg_lib_size': lib.avg_lib_size,
 525         'cell_line_id': lib.cell_line_id,
 526         'cell_line': unicode_or_none(lib.cell_line),
 527         'experiment_type': lib.experiment_type.name,
 528         'experiment_type_id': lib.experiment_type_id,
 529         'id': lib.id,
 530         'lane_set': lane_info,
 531         'library_id': lib.id,
 532         'library_name': lib.library_name,
 533         'library_species': lib.library_species.scientific_name,
 534         'library_species_id': lib.library_species_id,
 535         #'library_type': lib.library_type.name,
 536         'library_type_id': lib.library_type_id,
 537         'made_for': lib.made_for,
 538         'made_by': lib.made_by,
 539         'notes': lib.notes,
 540         'replicate': lib.replicate,
 541         'stopping_point': lib.stopping_point,
 542         'successful_pM': unicode_or_none(lib.successful_pM),
 543         'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
 544         }
 545     if lib.library_type_id is None:
 546         info['library_type'] = None
 547     else:
 548         info['library_type'] = lib.library_type.name
 549     return info
 550
 551 def library_json(request, library_id):
 552     """
 553     Return a json formatted library dictionary
 554     """
 555     require_api_key(request)
 556     # what validation should we do on library_id?
 557
 558     lib = library_dict(library_id)
 559     if lib is None:
 560         raise Http404
 561
 562     lib_json = json.dumps(lib)
 563     return HttpResponse(lib_json, mimetype='application/json')
 564
 565 def species_json(request, species_id):
 566     """
 567     Return information about a species.
 568     """
 569     raise Http404
 570
 571 @login_required
 572 def user_profile(request):
 573     """
 574     Information about the user
 575     """
 576     context = {
 577                 'page_name': 'User Profile',
 578                 'media': '',
 579                 #'bcmagic': BarcodeMagicForm(),
 580                 #'select': 'settings',
 581             }
 582     context.update(SAMPLES_CONTEXT_DEFAULTS)
 583     return render_to_response('registration/profile.html', context,
 584                               context_instance=RequestContext(request))
 585