X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=htsworkflow%2Ffrontend%2Fsamples%2Fviews.py;h=e50b5b357c2caa1b88d73cb2f2884cf0124f6158;hb=4a2529df5d2bdaa83d1661730c3791560d58df37;hp=2db0f0fd1cd2769cc267c7b717115b5b938bfa1a;hpb=77345cb40be0b31f0a1ee1c5e167a69554747cf3;p=htsworkflow.git
diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index 2db0f0f..e50b5b3 100644
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -1,26 +1,37 @@
# Create your views here.
-from htsworkflow.frontend.experiments.models import FlowCell
+import StringIO
+import logging
+import os
+import sys
+
+try:
+ import json
+except ImportError, e:
+ import simplejson as json
+
+from django.contrib.csrf.middleware import csrf_exempt
+from htsworkflow.frontend.auth import require_api_key
+from htsworkflow.frontend.experiments.models import FlowCell, Lane, LANE_STATUS_MAP
from htsworkflow.frontend.samples.changelist import ChangeList
-from htsworkflow.frontend.samples.models import Library
-from htsworkflow.frontend.samples.results import get_flowcell_result_dict, parse_flowcell_id
+from htsworkflow.frontend.samples.models import Antibody, Library, Species, HTSUser
+from htsworkflow.frontend.samples.results import get_flowcell_result_dict
from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.eland import ResultLane
-from htsworkflow.frontend import settings
+from htsworkflow.pipelines.samplekey import SampleKey
+from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id
from htsworkflow.util import makebed
from htsworkflow.util import opener
+
from django.core.exceptions import ObjectDoesNotExist
-from django.http import HttpResponse, HttpResponseRedirect
-from django.shortcuts import render_to_response
+from django.http import HttpResponse, HttpResponseRedirect, Http404
+from django.shortcuts import render_to_response, get_object_or_404
from django.template import RequestContext
from django.template.loader import get_template
from django.contrib.auth.decorators import login_required
-
-import StringIO
-import logging
-import os
+from django.conf import settings
LANE_LIST = [1,2,3,4,5,6,7,8]
SAMPLES_CONTEXT_DEFAULTS = {
@@ -28,89 +39,110 @@ SAMPLES_CONTEXT_DEFAULTS = {
'bcmagic': BarcodeMagicForm()
}
+LOGGER = logging.getLogger(__name__)
+
+def count_lanes(lane_set):
+ single = 0
+ paired = 1
+ short_read = 0
+ medium_read = 1
+ long_read = 2
+ counts = [[0,0,0,],[0,0,0]]
+
+ for lane in lane_set.all():
+ if lane.flowcell.paired_end:
+ lane_type = paired
+ else:
+ lane_type = single
+ if lane.flowcell.read_length < 40:
+ read_type = short_read
+ elif lane.flowcell.read_length < 100:
+ read_type = medium_read
+ else:
+ read_type = long_read
+ counts[lane_type][read_type] += 1
+
+ return counts
+
def create_library_context(cl):
"""
- Create a list of libraries that includes how many lanes were run
+ Create a list of libraries that includes how many lanes were run
"""
records = []
#for lib in library_items.object_list:
for lib in cl.result_list:
summary = {}
- summary['library_id'] = lib.library_id
+ summary['library'] = lib
+ summary['library_id'] = lib.id
summary['library_name'] = lib.library_name
summary['species_name' ] = lib.library_species.scientific_name
if lib.amplified_from_sample is not None:
- summary['amplified_from'] = lib.amplified_from_sample.library_id
+ summary['amplified_from'] = lib.amplified_from_sample.id
else:
summary['amplified_from'] = ''
- lanes_run = 0
- #for lane_id in LANE_LIST:
- # lane = getattr(lib, 'lane_%d_library' % (lane_id,))
- # lanes_run += len( lane.all() )
- lanes_run = lib.lane_set.count()
+ lanes_run = count_lanes(lib.lane_set)
+ # suppress zeros
+ for row in xrange(len(lanes_run)):
+ for col in xrange(len(lanes_run[row])):
+ if lanes_run[row][col] == 0:
+ lanes_run[row][col] = ''
summary['lanes_run'] = lanes_run
summary['is_archived'] = lib.is_archived()
records.append(summary)
- cl.result_count = unicode(cl.paginator._count) + u" libraries"
+ cl.result_count = unicode(cl.paginator._count)
return {'library_list': records }
-def library(request):
- # build changelist
+
+def library(request, todo_only=False):
+ queryset = Library.objects.filter(hidden__exact=0)
+ if todo_only:
+ queryset = queryset.filter(lane=None)
+ # build changelist
fcl = ChangeList(request, Library,
list_filter=['affiliations', 'library_species'],
- search_fields=['library_id', 'library_name', 'amplified_from_sample__library_id'],
+ search_fields=['id', 'library_name', 'amplified_from_sample__id'],
list_per_page=200,
- queryset=Library.objects.filter(hidden__exact=0)
+ queryset=queryset
)
- context = { 'cl': fcl, 'title': 'Library Index'}
+ context = { 'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
context.update(create_library_context(fcl))
t = get_template('samples/library_index.html')
c = RequestContext(request, context)
-
- app_context = {
- 'page_name': 'Library Index',
- 'east_region_config_div': 'changelist-filter',
- 'body': t.render(c)
- }
- app_context.update(SAMPLES_CONTEXT_DEFAULTS)
-
- app_t = get_template('flowcell_libraries_app.html')
- app_c = RequestContext(request, app_context)
- return HttpResponse( app_t.render(app_c) )
+ return HttpResponse( t.render(c) )
+
+
+def library_not_run(request):
+ return library(request, todo_only=True)
+
def library_to_flowcells(request, lib_id):
"""
Display information about all the flowcells a library has been run on.
"""
-
try:
- lib = Library.objects.get(library_id=lib_id)
+ lib = Library.objects.get(id=lib_id)
except:
- return HttpResponse("Library %s does not exist" % (lib_id))
-
+ raise Http404('Library %s does not exist' % (lib_id,))
+
flowcell_list = []
- interesting_flowcells = {} # aka flowcells we're looking at
- #for lane in LANE_LIST:
+ flowcell_run_results = {} # aka flowcells we're looking at
for lane in lib.lane_set.all():
- #lane_library = getattr(lib, 'lane_%d_library' % (lane,))
- #for fc in lane_library.all():
fc = lane.flowcell
flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
- if flowcell_id not in interesting_flowcells:
- interesting_flowcells[flowcell_id] = get_flowcell_result_dict(flowcell_id)
- flowcell_list.append((fc.flowcell_id, lane))
+ if flowcell_id not in flowcell_run_results:
+ flowcell_run_results[flowcell_id] = get_flowcell_result_dict(flowcell_id)
+ flowcell_list.append((fc.flowcell_id, lane.lane_number))
flowcell_list.sort()
-
lane_summary_list = []
eland_results = []
- for fc, lane in flowcell_list:
- lane_summary, err_list = _summary_stats(fc, lane)
-
- eland_results.extend(_make_eland_results(fc, lane, interesting_flowcells))
+ for fc, lane_number in flowcell_list:
+ lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
lane_summary_list.extend(lane_summary)
+ eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
+
context = {
'page_name': 'Library Details',
'lib': lib,
@@ -124,26 +156,50 @@ def library_to_flowcells(request, lib_id):
context,
context_instance = RequestContext(request))
+def lanes_for(request, username=None):
+ """
+ Generate a report of recent activity for a user
+ """
+ query = {}
+ if username is not None:
+ user = HTSUser.objects.get(username=username)
+ query.update({'library__affiliations__users__id':user.id})
+ fcl = ChangeList(request, Lane,
+ list_filter=[],
+ search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
+ list_per_page=200,
+ queryset=Lane.objects.filter(**query)
+ )
+
+ context = { 'lanes': fcl, 'title': 'Lane Index'}
+
+ return render_to_response(
+ 'samples/lanes_for.html',
+ context,
+ context_instance = RequestContext(request)
+ )
+
+
def summaryhtm_fc_cnm(request, flowcell_id, cnm):
"""
returns a Summary.htm file if it exists.
"""
fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('Results for Flowcell %s not found.' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('Results for Flowcell %s; %s not found.' % (fc_id, cnm))
-
+
summary_filepath = d[cnm]['summary']
-
+
if summary_filepath is None:
return HttpResponse('Summary.htm for Flowcell %s; %s not found.' % (fc_id, cnm))
-
+
f = open(summary_filepath, 'r')
-
+
return HttpResponse(f)
@@ -153,27 +209,27 @@ def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
"""
fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('Results for Flowcell %s not found.' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('Results for Flowcell %s; %s not found.' % (fc_id, cnm))
-
+
erd = d[cnm]['eland_results']
lane = int(lane)
-
+
if lane not in erd:
return HttpResponse('Results for Flowcell %s; %s; lane %s not found.' % (fc_id, cnm, lane))
-
+
filepath = erd[lane]
-
+
#f = opener.autoopen(filepath, 'r')
# return HttpResponse(f, mimetype="application/x-elandresult")
f = open(filepath, 'r')
return HttpResponse(f, mimetype='application/x-bzip2')
-
+
def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
@@ -189,36 +245,36 @@ def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=F
"""
fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('Results for Flowcell %s not found.' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('Results for Flowcell %s; %s not found.' % (fc_id, cnm))
-
+
erd = d[cnm]['eland_results']
lane = int(lane)
-
+
if lane not in erd:
return HttpResponse('Results for Flowcell %s; %s; lane %s not found.' % (fc_id, cnm, lane))
-
+
filepath = erd[lane]
-
+
# Eland result file
fi = opener.autoopen(filepath, 'r')
# output memory file
-
+
name, description = makebed.make_description( fc_id, lane )
-
+
bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
-
+
if ucsc_compatible:
return HttpResponse(bedgen)
else:
return HttpResponse(bedgen, mimetype="application/x-bedfile")
-def _summary_stats(flowcell_id, lane_id):
+def _summary_stats(flowcell_id, lane_id, library_id):
"""
Return the summary statistics for a given flowcell, lane, and end.
"""
@@ -227,108 +283,60 @@ def _summary_stats(flowcell_id, lane_id):
summary_list = []
err_list = []
-
+
if fc_result_dict is None:
err_list.append('Results for Flowcell %s not found.' % (fc_id))
return (summary_list, err_list)
for cycle_width in fc_result_dict:
xmlpath = fc_result_dict[cycle_width]['run_xml']
-
+
if xmlpath is None:
err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cycle_width))
continue
-
+
run = load_pipeline_run_xml(xmlpath)
+ # skip if we don't have available metadata.
+ if run.gerald is None or run.gerald.summary is None:
+ continue
+
gerald_summary = run.gerald.summary.lane_results
- for end in range(len(gerald_summary)):
- end_summary = run.gerald.eland_results.results[end]
- if end_summary.has_key(lane_id):
- eland_summary = run.gerald.eland_results.results[end][lane_id]
- else:
- eland_summary = ResultLane(lane_id=lane_id, end=end)
+ key = SampleKey(lane=lane_id, sample='s')
+ eland_results = list(run.gerald.eland_results.find_keys(key))
+ key = SampleKey(lane=lane_id, sample=library_id)
+ eland_results.extend(run.gerald.eland_results.find_keys(key))
+ for key in eland_results:
+ eland_summary = run.gerald.eland_results.results[key]
# add information to lane_summary
eland_summary.flowcell_id = flowcell_id
- eland_summary.clusters = gerald_summary[end][lane_id].cluster
+
+ read = key.read-1 if key.read is not None else 0
+ try:
+ eland_summary.clusters = gerald_summary[read][key.lane].cluster
+ except (IndexError, KeyError) as e:
+ eland_summary.clustes = None
eland_summary.cycle_width = cycle_width
if hasattr(eland_summary, 'genome_map'):
- eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
- eland_summary.genome_map,
+ eland_summary.summarized_reads = runfolder.summarize_mapped_reads(
+ eland_summary.genome_map,
eland_summary.mapped_reads)
# grab some more information out of the flowcell db
flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
- pm_field = 'lane_%d_pM' % (lane_id)
- eland_summary.successful_pm = getattr(flowcell, pm_field)
+ #pm_field = 'lane_%d_pM' % (lane_id)
+ lanes = flowcell.lane_set.filter(lane_number=lane_id)
+ eland_summary.flowcell = flowcell
+ eland_summary.lanes = lanes
summary_list.append(eland_summary)
#except Exception, e:
# summary_list.append("Summary report needs to be updated.")
- # logging.error("Exception: " + str(e))
-
+ # LOGGER.error("Exception: " + str(e))
+
return (summary_list, err_list)
-def _summary_stats_old(flowcell_id, lane):
- """
- return a dictionary of summary stats for a given flowcell_id & lane.
- """
- fc_id, status = parse_flowcell_id(flowcell_id)
- fc_result_dict = get_flowcell_result_dict(fc_id)
-
- dict_list = []
- err_list = []
- summary_list = []
-
- if fc_result_dict is None:
- err_list.append('Results for Flowcell %s not found.' % (fc_id))
- return (dict_list, err_list, summary_list)
-
- for cnm in fc_result_dict:
-
- xmlpath = fc_result_dict[cnm]['run_xml']
-
- if xmlpath is None:
- err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
- continue
-
- tree = ElementTree.parse(xmlpath).getroot()
- results = runfolder.PipelineRun(pathname='', xml=tree)
- try:
- lane_report = runfolder.summarize_lane(results.gerald, lane)
- summary_list.append(os.linesep.join(lane_report))
- except Exception, e:
- summary_list.append("Summary report needs to be updated.")
- logging.error("Exception: " + str(e))
-
- print "----------------------------------"
- print "-- DOES NOT SUPPORT PAIRED END ---"
- print "----------------------------------"
- lane_results = results.gerald.summary[0][lane]
- lrs = lane_results
-
- d = {}
-
- d['average_alignment_score'] = lrs.average_alignment_score
- d['average_first_cycle_intensity'] = lrs.average_first_cycle_intensity
- d['cluster'] = lrs.cluster
- d['lane'] = lrs.lane
- d['flowcell'] = flowcell_id
- d['cnm'] = cnm
- d['percent_error_rate'] = lrs.percent_error_rate
- d['percent_intensity_after_20_cycles'] = lrs.percent_intensity_after_20_cycles
- d['percent_pass_filter_align'] = lrs.percent_pass_filter_align
- d['percent_pass_filter_clusters'] = lrs.percent_pass_filter_clusters
-
- #FIXME: function finished, but need to take advantage of
- # may need to take in a list of lanes so we only have to
- # load the xml file once per flowcell rather than once
- # per lane.
- dict_list.append(d)
-
- return (dict_list, err_list, summary_list)
-
-
+
def get_eland_result_type(pathname):
"""
Guess the eland result file type from the filename
@@ -343,13 +351,14 @@ def get_eland_result_type(pathname):
else:
return 'unknown'
-def _make_eland_results(flowcell_id, lane, interesting_flowcells):
+def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
fc_id, status = parse_flowcell_id(flowcell_id)
cur_fc = interesting_flowcells.get(fc_id, None)
if cur_fc is None:
return []
flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
+ lanes = flowcell.lane_set.filter(lane_number=lane_number)
# Loop throw storage devices if a result has been archived
storage_id_list = []
if cur_fc is not None:
@@ -361,7 +370,7 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
# Otherwise use UUID
else:
storage_id_list.append(sd.uuid)
-
+
# Formatting for template use
if len(storage_id_list) == 0:
storage_ids = None
@@ -370,11 +379,13 @@ def _make_eland_results(flowcell_id, lane, interesting_flowcells):
results = []
for cycle in cur_fc.keys():
- result_path = cur_fc[cycle]['eland_results'].get(lane, None)
- result_link = make_result_link(fc_id, cycle, lane, result_path)
+ result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
+ result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
results.append({'flowcell_id': fc_id,
- 'cycle': cycle,
- 'lane': lane,
+ 'flowcell': flowcell,
+ 'run_date': flowcell.run_date,
+ 'cycle': cycle,
+ 'lane': lanes[0],
'summary_url': make_summary_url(flowcell_id, cycle),
'result_url': result_link[0],
'result_label': result_link[1],
@@ -398,7 +409,7 @@ def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
if result_type == 'result':
bed_url_pattern = '/results/%s/%s/bedfile/%s'
bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
-
+
return (result_url, result_label, bed_url)
def _files(flowcell_id, lane):
@@ -409,19 +420,19 @@ def _files(flowcell_id, lane):
flowcell_id, id = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(flowcell_id)
-
+
if d is None:
return ''
-
+
output = []
-
+
# c_name == 'CN-M' (i.e. C1-33)
for c_name in d:
-
+
if d[c_name]['summary'] is not None:
output.append('summary(%s)' \
% (flowcell_id, c_name, c_name))
-
+
erd = d[c_name]['eland_results']
if lane in erd:
result_type = get_eland_result_type(erd[lane])
@@ -430,16 +441,108 @@ def _files(flowcell_id, lane):
if result_type == 'result':
bed_url_pattern = 'bedfile(%s)'
output.append(bed_url_pattern % (flowcell_id, c_name, lane, c_name))
-
+
if len(output) == 0:
return ''
-
+
return '(' + '|'.join(output) + ')'
def library_id_to_admin_url(request, lib_id):
- lib = Library.objects.get(library_id=lib_id)
+ lib = Library.objects.get(id=lib_id)
return HttpResponseRedirect('/admin/samples/library/%s' % (lib.id,))
+def library_dict(library_id):
+ """
+ Given a library id construct a dictionary containing important information
+ return None if nothing was found
+ """
+ try:
+ lib = Library.objects.get(id = library_id)
+ except Library.DoesNotExist, e:
+ return None
+
+ #lane_info = lane_information(lib.lane_set)
+ lane_info = []
+ for lane in lib.lane_set.all():
+ lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
+ 'lane_number': lane.lane_number,
+ 'lane_id': lane.id,
+ 'paired_end': lane.flowcell.paired_end,
+ 'read_length': lane.flowcell.read_length,
+ 'status_code': lane.status,
+ 'status': LANE_STATUS_MAP[lane.status]} )
+
+ info = {
+ # 'affiliations'?
+ # 'aligned_reads': lib.aligned_reads,
+ #'amplified_into_sample': lib.amplified_into_sample, # into is a colleciton...
+ #'amplified_from_sample_id': lib.amplified_from_sample,
+ #'antibody_name': lib.antibody_name(), # we have no antibodies.
+ 'antibody_id': lib.antibody_id,
+ 'cell_line_id': lib.cell_line_id,
+ 'cell_line': unicode_or_none(lib.cell_line),
+ 'experiment_type': lib.experiment_type.name,
+ 'experiment_type_id': lib.experiment_type_id,
+ 'gel_cut_size': lib.gel_cut_size,
+ 'hidden': lib.hidden,
+ 'id': lib.id,
+ 'insert_size': lib.insert_size,
+ 'lane_set': lane_info,
+ 'library_id': lib.id,
+ 'library_name': lib.library_name,
+ 'library_species': lib.library_species.scientific_name,
+ 'library_species_id': lib.library_species_id,
+ #'library_type': lib.library_type.name,
+ 'library_type_id': lib.library_type_id,
+ 'made_for': lib.made_for,
+ 'made_by': lib.made_by,
+ 'notes': lib.notes,
+ 'replicate': lib.replicate,
+ 'stopping_point': lib.stopping_point,
+ 'successful_pM': unicode_or_none(lib.successful_pM),
+ 'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
+ }
+ if lib.library_type_id is None:
+ info['library_type'] = None
+ else:
+ info['library_type'] = lib.library_type.name
+ return info
+
+@csrf_exempt
+def library_json(request, library_id):
+ """
+ Return a json formatted library dictionary
+ """
+ require_api_key(request)
+ # what validation should we do on library_id?
+
+ lib = library_dict(library_id)
+ if lib is None:
+ raise Http404
+
+ lib_json = json.dumps(lib)
+ return HttpResponse(lib_json, mimetype='application/json')
+
+@csrf_exempt
+def species_json(request, species_id):
+ """
+ Return information about a species.
+ """
+ raise Http404
+
+def species(request, species_id):
+ species = get_object_or_404(Species, id=species_id)
+
+ context = RequestContext(request,
+ { 'species': species })
+
+ return render_to_response("samples/species_detail.html", context)
+
+def antibodies(request):
+ context = RequestContext(request,
+ {'antibodies': Antibody.objects.order_by('antigene')})
+ return render_to_response("samples/antibody_index.html", context)
+
@login_required
def user_profile(request):
"""
@@ -454,3 +557,5 @@ def user_profile(request):
context.update(SAMPLES_CONTEXT_DEFAULTS)
return render_to_response('registration/profile.html', context,
context_instance=RequestContext(request))
+
+