-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
# Create your views here.
-import StringIO
import logging
import os
-import sys
-
-try:
- import json
-except ImportError, e:
- import simplejson as json
+import json
from django.views.decorators.csrf import csrf_exempt
-from django.core.exceptions import ObjectDoesNotExist
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
-from django.conf import settings
from htsworkflow.auth import require_api_key
-from experiments.models import FlowCell, Lane, LANE_STATUS_MAP
-from experiments.admin import LaneOptions
+from experiments.models import FlowCell, LANE_STATUS_MAP
from .changelist import HTSChangeList
-from .models import Antibody, Library, Species, HTSUser
+from .models import Antibody, Library, Species
from .admin import LibraryOptions
from .results import get_flowcell_result_dict
from bcmagic.forms import BarcodeMagicForm
from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.eland import ResultLane
from htsworkflow.pipelines.samplekey import SampleKey
-from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id
+from htsworkflow.util.conversion import str_or_none, parse_flowcell_id
from htsworkflow.util import makebed
from htsworkflow.util import opener
-
-LANE_LIST = [1,2,3,4,5,6,7,8]
+LANE_LIST = [1, 2, 3, 4, 5, 6, 7, 8]
SAMPLES_CONTEXT_DEFAULTS = {
'app_name': 'Flowcell/Library Tracker',
'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]]
+ counts = [[0, 0, 0], [0, 0, 0]]
for lane in lane_set.all():
if lane.flowcell.paired_end:
return counts
+
def create_library_context(cl):
"""
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'] = 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.id
- else:
- summary['amplified_from'] = ''
- 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)
- return {'library_list': records }
+ summary = {}
+ 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.id
+ else:
+ summary['amplified_from'] = ''
+ lanes_run = count_lanes(lib.lane_set)
+ # suppress zeros
+ for row_index, row in enumerate(lanes_run):
+ for col_index, cell in enumerate(row):
+ if lanes_run[row_index][col_index] == 0:
+ lanes_run[row_index][col_index] = ''
+ summary['lanes_run'] = lanes_run
+ summary['is_archived'] = lib.is_archived()
+ records.append(summary)
+ cl.result_count = str(cl.paginator._count)
+ return {'library_list': records}
def library(request, todo_only=False):
filters['lane'] = None
# build changelist
fcl = HTSChangeList(request, Library,
- list_filter=['affiliations', 'library_species'],
- search_fields=['id', 'library_name', 'amplified_from_sample__id'],
- list_per_page=200,
- model_admin=LibraryOptions(Library, None),
- extra_filters=filters
- )
-
- context = { 'cl': fcl, 'title': 'Library Index', 'todo_only': todo_only}
+ list_filter=['affiliations', 'library_species'],
+ search_fields=['id', 'library_name', 'amplified_from_sample__id'],
+ list_per_page=200,
+ model_admin=LibraryOptions(Library, None),
+ extra_filters=filters
+ )
+
+ 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)
- return HttpResponse( t.render(c) )
+ return HttpResponse(t.render(c))
def library_not_run(request):
raise Http404('Library %s does not exist' % (lib_id,))
flowcell_list = []
- flowcell_run_results = {} # aka flowcells we're looking at
+ flowcell_run_results = {} # aka flowcells we're looking at
for lane in lib.lane_set.all():
fc = lane.flowcell
flowcell_id, id = parse_flowcell_id(fc.flowcell_id)
return render_to_response(
'samples/library_detail.html',
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 = HTSChangeList(request, Lane,
- list_filter=[],
- search_fields=['flowcell__flowcell_id', 'library__id', 'library__library_name'],
- list_per_page=200,
- model_admin=LaneOptions,
- queryset=Lane.objects.filter(**query)
- )
-
- context = { 'lanes': fcl, 'title': 'Lane Index'}
-
- return render_to_response(
- 'samples/lanes_for.html',
- context,
- context_instance = RequestContext(request)
- )
+ context_instance=RequestContext(request))
def summaryhtm_fc_cnm(request, flowcell_id, cnm):
return HttpResponse(f, content_type='application/x-bzip2')
-
def bedfile_fc_cnm_eland_lane_ucsc(request, fc_id, cnm, lane):
"""
returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane (ucsc compatible)
fi = opener.autoopen(filepath, 'r')
# output memory file
- name, description = makebed.make_description( fc_id, lane )
+ name, description = makebed.make_description(fc_id, lane)
bedgen = makebed.make_bed_from_eland_generator(fi, name, description)
# 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
key = SampleKey(lane=lane_id, sample='s')
eland_results = list(run.gerald.eland_results.find_keys(key))
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.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)
summary_list.append(eland_summary)
- #except Exception, e:
+ #except Exception as e:
# summary_list.append("Summary report needs to be updated.")
# LOGGER.error("Exception: " + str(e))
else:
return 'unknown'
+
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 []
+ return []
flowcell = FlowCell.objects.get(flowcell_id=flowcell_id)
lanes = flowcell.lane_set.filter(lane_number=lane_number)
if len(storage_id_list) == 0:
storage_ids = None
else:
- storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
+ storage_ids = ', '.join(['<a href="/inventory/%s/">%s</a>' % (s, s) for s in storage_id_list])
results = []
for cycle in cur_fc.keys():
'result_url': result_link[0],
'result_label': result_link[1],
'bed_url': result_link[2],
- 'storage_ids': storage_ids
- })
+ 'storage_ids': storage_ids})
return results
+
def make_summary_url(flowcell_id, cycle_name):
url = '/results/%s/%s/summary/' % (flowcell_id, cycle_name)
return url
+
def make_result_link(flowcell_id, cycle_name, lane, eland_result_path):
if eland_result_path is None:
return ("", "", "")
result_label = 'eland %s' % (result_type,)
bed_url = None
if result_type == 'result':
- bed_url_pattern = '/results/%s/%s/bedfile/%s'
- bed_url = bed_url_pattern % (flowcell_id, cycle_name, lane)
+ 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):
"""
Sets up available files for download
for c_name in d:
if d[c_name]['summary'] is not None:
- output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
- % (flowcell_id, c_name, c_name))
+ output.append('<a href="/results/%s/%s/summary/">summary(%s)</a>' %
+ (flowcell_id, c_name, c_name))
erd = d[c_name]['eland_results']
if lane in erd:
return '(' + '|'.join(output) + ')'
+
def library_id_to_admin_url(request, 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:
+ lib = Library.objects.get(id=library_id)
+ except Library.DoesNotExist as 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]} )
+ 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'?
#'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),
+ 'cell_line': str_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,
'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)
+ 'successful_pM': str_or_none(lib.successful_pM),
+ 'undiluted_concentration': str_or_none(lib.undiluted_concentration)
}
if lib.library_type_id is None:
info['library_type'] = None
info['library_type'] = lib.library_type.name
return info
+
@csrf_exempt
def library_json(request, library_id):
"""
if lib is None:
raise Http404
- lib_json = json.dumps(lib)
+ lib_json = json.dumps({'result': lib})
return HttpResponse(lib_json, content_type='application/json')
+
@csrf_exempt
def species_json(request, species_id):
"""
"""
raise Http404
+
def species(request, species_id):
species = get_object_or_404(Species, id=species_id)
context = RequestContext(request,
- { 'species': species })
+ {'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):
"""
Information about the user
"""
context = {
- 'page_name': 'User Profile',
- 'media': '',
- #'bcmagic': BarcodeMagicForm(),
- #'select': 'settings',
- }
+ 'page_name': 'User Profile',
+ 'media': '',
+ #'bcmagic': BarcodeMagicForm(),
+ #'select': 'settings',
+ }
context.update(SAMPLES_CONTEXT_DEFAULTS)
return render_to_response('registration/profile.html', context,
context_instance=RequestContext(request))
projects / htsworkflow.git / blobdiff