# 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.frontend import settings
+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 import makebed
from htsworkflow.util import opener
-from django.http import HttpResponse
+
+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
-
-import StringIO
-import logging
-import os
+from django.contrib.auth.decorators import login_required
+from django.conf import settings
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]]
+
+ 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
- lanes_run = 0
- for lane_id in LANE_LIST:
- lane = getattr(lib, 'lane_%d_library' % (lane_id,))
- lanes_run += len( lane.all() )
+ 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) + 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=['library_species','affiliations'],
- search_fields=['library_id', 'library_name'],
+ list_filter=['affiliations', 'library_species'],
+ 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)
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.
"""
- t = get_template("samples/library_detail.html")
-
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))
-
- output = []
-
- output.append('<b>Library ID:</b> %s' % (lib.library_id))
- output.append('<b>Name:</b> %s' % (lib.library_name))
- output.append('<b>Species:</b> %s' % (lib.library_species.scientific_name))
- output.append('')
-
- output.append('<b>FLOWCELL - LANE:</b>')
-
- output.extend([ '%s - Lane 1 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 1)) for fc in lib.lane_1_library.all() ])
- output.extend([ '%s - Lane 2 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 2)) for fc in lib.lane_2_library.all() ])
- output.extend([ '%s - Lane 3 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 3)) for fc in lib.lane_3_library.all() ])
- output.extend([ '%s - Lane 4 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 4)) for fc in lib.lane_4_library.all() ])
- output.extend([ '%s - Lane 5 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 5)) for fc in lib.lane_5_library.all() ])
- output.extend([ '%s - Lane 6 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 6)) for fc in lib.lane_6_library.all() ])
- output.extend([ '%s - Lane 7 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 7)) for fc in lib.lane_7_library.all() ])
- output.extend([ '%s - Lane 8 %s' % (fc.flowcell_id, _files(fc.flowcell_id, 8)) for fc in lib.lane_8_library.all() ])
-
- record_count = lib.lane_1_library.count() + \
- lib.lane_2_library.count() + \
- lib.lane_3_library.count() + \
- lib.lane_4_library.count() + \
- lib.lane_5_library.count() + \
- lib.lane_6_library.count() + \
- lib.lane_7_library.count() + \
- lib.lane_8_library.count()
-
+ raise Http404('Library %s does not exist' % (lib_id,))
+
flowcell_list = []
- flowcell_list.extend([ (fc.flowcell_id, 1) for fc in lib.lane_1_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 2) for fc in lib.lane_2_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 3) for fc in lib.lane_3_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 4) for fc in lib.lane_4_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 5) for fc in lib.lane_5_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 6) for fc in lib.lane_6_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 7) for fc in lib.lane_7_library.all() ])
- flowcell_list.extend([ (fc.flowcell_id, 8) for fc in lib.lane_8_library.all() ])
+ 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)
+ 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 = []
- for fc, lane in flowcell_list:
- lane_summary, err_list = _summary_stats(fc, lane)
-
+ eland_results = []
+ for fc, lane_number in flowcell_list:
+ lane_summary, err_list = _summary_stats(fc, lane_number, lib_id)
lane_summary_list.extend(lane_summary)
-
- for err in err_list:
- output.append(err)
-
- output.append('<br />')
- output.append(t.render(RequestContext(request, {'lane_summary_list': lane_summary_list})))
- output.append('<br />')
-
- if record_count == 0:
- output.append("None Found")
-
- return HttpResponse('<br />\n'.join(output))
-
-
-def summaryhtm_fc_cnm(request, fc_id, cnm):
+
+ eland_results.extend(_make_eland_results(fc, lane_number, flowcell_run_results))
+
+ context = {
+ 'page_name': 'Library Details',
+ 'lib': lib,
+ 'eland_results': eland_results,
+ 'lane_summary_list': lane_summary_list,
+ }
+ context.update(SAMPLES_CONTEXT_DEFAULTS)
+
+ 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 = 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(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
-
+
summary_filepath = d[cnm]['summary']
-
+
if summary_filepath is None:
return HttpResponse('<b>Summary.htm for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
-
+
f = open(summary_filepath, 'r')
-
+
return HttpResponse(f)
-def result_fc_cnm_eland_lane(request, fc_id, cnm, lane):
+def result_fc_cnm_eland_lane(request, flowcell_id, cnm, lane):
"""
returns an eland_file upon calling.
"""
- fc_id, status = parse_flowcell_id(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
-
+
erd = d[cnm]['eland_results']
lane = int(lane)
-
+
if lane not in erd:
return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (fc_id, cnm, lane))
-
+
filepath = erd[lane]
-
- f = opener.autoopen(filepath, 'r')
-
- return HttpResponse(f, mimetype="application/x-elandresult")
+
+ #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):
return bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=True)
-def bedfile_fc_cnm_eland_lane(request, fc_id, cnm, lane, ucsc_compatible=False):
+def bedfile_fc_cnm_eland_lane(request, flowcell_id, cnm, lane, ucsc_compatible=False):
"""
returns a bed file for a given flowcell, CN-M (i.e. C1-33), and lane
"""
- fc_id, status = parse_flowcell_id(fc_id)
+ fc_id, status = parse_flowcell_id(flowcell_id)
d = get_flowcell_result_dict(fc_id)
-
+
if d is None:
return HttpResponse('<b>Results for Flowcell %s not found.</b>' % (fc_id))
-
+
if cnm not in d:
return HttpResponse('<b>Results for Flowcell %s; %s not found.</b>' % (fc_id, cnm))
-
+
erd = d[cnm]['eland_results']
lane = int(lane)
-
+
if lane not in erd:
return HttpResponse('<b>Results for Flowcell %s; %s; lane %s not found.</b>' % (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.
"""
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
- try:
- run = load_pipeline_run_xml(xmlpath)
- gerald_summary = run.gerald.summary.lane_results
- for end in range(len(gerald_summary)):
- eland_summary = run.gerald.eland_results.results[end][lane_id]
- # add information to lane_summary
- eland_summary.flowcell_id = flowcell_id
- eland_summary.clusters = gerald_summary[end][lane_id].cluster
- eland_summary.cycle_width = cycle_width
- eland_summary.summarized_reads = runfolder.summarize_mapped_reads(eland_summary.mapped_reads)
-
- # grab some more information out of the flowcell db
- flowcell = FlowCell.objects.get(flowcell_id=fc_id)
- pm_field = 'lane_%d_pM' % (lane_id)
- eland_summary.successful_pm = getattr(flowcell, pm_field)
-
- summary_list.append(eland_summary)
-
- except Exception, e:
- summary_list.append("Summary report needs to be updated.")
- logging.error("Exception: " + str(e))
-
+ gerald_summary = run.gerald.summary.lane_results
+ 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
+
+ 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.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)
+ 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.")
+ # LOGGER.error("Exception: " + str(e))
+
return (summary_list, err_list)
-def _summary_stats_old(flowcell_id, lane):
+
+def get_eland_result_type(pathname):
"""
- return a dictionary of summary stats for a given flowcell_id & lane.
+ Guess the eland result file type from the filename
"""
+ path, filename = os.path.split(pathname)
+ if 'extended' in filename:
+ return 'extended'
+ elif 'multi' in filename:
+ return 'multi'
+ elif 'result' in filename:
+ return 'result'
+ else:
+ return 'unknown'
+
+def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
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)
-
-
-
-
+ 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:
+ for lts in flowcell.longtermstorage_set.all():
+ for sd in lts.storage_devices.all():
+ # Use barcode_id if it exists
+ if sd.barcode_id is not None and sd.barcode_id != '':
+ storage_id_list.append(sd.barcode_id)
+ # Otherwise use UUID
+ else:
+ storage_id_list.append(sd.uuid)
+
+ # Formatting for template use
+ 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 ])
+
+ results = []
+ for cycle in cur_fc.keys():
+ 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,
+ '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],
+ 'bed_url': result_link[2],
+ '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_type = get_eland_result_type(eland_result_path)
+ result_url = '/results/%s/%s/eland_result/%s' % (flowcell_id, cycle_name, lane)
+ 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)
+
+ return (result_url, result_label, bed_url)
+
def _files(flowcell_id, lane):
"""
Sets up available files for download
"""
+ lane = int(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('<a href="/results/%s/%s/summary/">summary(%s)</a>' \
% (flowcell_id, c_name, c_name))
-
+
erd = d[c_name]['eland_results']
-
- if int(lane) in erd:
- output.append('<a href="/results/%s/%s/eland_result/%s">eland_result(%s)</a>' % (flowcell_id, c_name, lane, c_name))
- output.append('<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>' % (flowcell_id, c_name, lane, c_name))
-
+ if lane in erd:
+ result_type = get_eland_result_type(erd[lane])
+ result_url_pattern = '<a href="/results/%s/%s/eland_result/%s">eland %s(%s)</a>'
+ output.append(result_url_pattern % (flowcell_id, c_name, lane, result_type, c_name))
+ if result_type == 'result':
+ bed_url_pattern = '<a href="/results/%s/%s/bedfile/%s">bedfile(%s)</a>'
+ 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(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):
+ """
+ Information about the user
+ """
+ context = {
+ '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