def test_get_idx_types(self):
self.assertJSONEqual(
json.dumps(ElasticSettings.get_idx_types('MARKER')),
json.dumps({
'MARKER': {
'type': 'marker',
'description': 'dbsnp',
'search': True,
'auth_public': True
}
}))
def _build_score_functions(idx_dict):
''' Build an array of ScoreFunction instances for boosting query results. '''
# create function score query to return documents with greater weights.
score_fns = [ScoreFunction.create_score_function('field_value_factor', field='tags.weight', missing=1.0)]
# create a function score that increases the score of markers.
if ElasticSettings.idx('MARKER') is not None and ElasticSettings.idx('MARKER') in idx_dict['idx']:
type_filter = Filter(Query({"type": {"value": ElasticSettings.get_idx_types('MARKER')['MARKER']['type']}}))
score_fns.append(ScoreFunction.create_score_function('weight', 2, function_filter=type_filter.filter))
logger.debug("Add marker type score function.")
# create a function score that increases the score of publications tagged with disease.
if ElasticSettings.idx('PUBLICATION') is not None and ElasticSettings.idx('PUBLICATION') in idx_dict['idx']:
score_fns.append(ScoreFunction.create_score_function('weight', 2,
function_filter=ExistsFilter('tags.disease').filter))
logger.debug("Add publication disease tag score function.")
return score_fns
def chicpea(request):
queryDict = request.GET
user = request.user
context = dict()
context['title'] = 'Capture HiC Plotter'
context['admin_url_path'] = settings.ADMIN_URL_PATH
context['RECAPTCHA_KEY'] = settings.RECAPTCHA_KEY
# context['tissue'] = 'Total_CD4_Activated'
context['searchTerm'] = random.choice(getattr(chicp_settings, 'DEFAULT_GENES'))
if queryDict.get("term"):
context['searchTerm'] = queryDict.get("term")
if queryDict.get("tissue"):
context['tissue'] = queryDict.get("tissue")
else:
context['default_target'] = getattr(chicp_settings, 'DEFAULT_TARGET')
context['default_tissue'] = getattr(chicp_settings, 'DEFAULT_TISSUE')
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
user=user, idx_keys=None, idx_type_keys=None)
indexes = list()
tissues = list()
for target in getattr(chicp_settings, 'CP_TARGET'):
if 'CP_TARGET_'+target not in idx_keys_auth:
continue
indexes.append({"value": target, "text": ElasticSettings.get_label('CP_TARGET_'+target)})
elasticJSON = Search(idx=ElasticSettings.idx('CP_TARGET_'+target)).get_mapping(mapping_type="gene_target")
tissueList = list(elasticJSON[ElasticSettings.idx('CP_TARGET_'+target)]
['mappings']['gene_target']['_meta']['tissue_type'].keys())
utils.tissues['CP_TARGET_'+target] = tissueList
tissueList.sort()
for t in tissueList:
tissues.append({"value": t, "text": t.replace("_", " "), "class": target})
context['allIndexes'] = indexes
context['allTissues'] = tissues
snpTracks = OrderedDict()
defaultTrack = getattr(chicp_settings, 'DEFAULT_TRACK')
for group in getattr(chicp_settings, 'CP_STATS'):
if 'CP_STATS_'+group not in idx_keys_auth:
continue
if group == 'UD':
if settings.INCLUDE_USER_UPLOADS:
context['allow_user_uploads'] = True
else:
continue
snp_tracks = list()
for track, details in (ElasticSettings.get_idx_types(idx_name='CP_STATS_'+group, user='******')).items():
if 'CP_STATS_'+group+'.'+track not in idx_type_keys_auth:
continue
snp_tracks.append({"value": track.lower(), "text": details['label']})
if defaultTrack == '':
defaultTrack = track.lower()
snpTracks[ElasticSettings.get_label('CP_STATS_'+group)] = sorted(snp_tracks, key=itemgetter('text'))
context['snpTracks'] = snpTracks
if queryDict.get("snp_track"):
context['snp_track'] = queryDict.get("snp_track")
else:
context['snp_track'] = defaultTrack
return render(request, 'chicp/index.html', context, content_type='text/html')
def chicpea(request):
queryDict = request.GET
user = request.user
context = dict()
context['title'] = 'Capture HiC Plotter'
context['admin_url_path'] = settings.ADMIN_URL_PATH
context['RECAPTCHA_KEY'] = settings.RECAPTCHA_KEY
# context['tissue'] = 'Total_CD4_Activated'
context['searchTerm'] = random.choice(getattr(chicp_settings, 'DEFAULT_GENES'))
if queryDict.get("term"):
context['searchTerm'] = queryDict.get("term")
if queryDict.get("tissue"):
context['tissue'] = queryDict.get("tissue")
else:
context['default_target'] = getattr(chicp_settings, 'DEFAULT_TARGET')
context['default_tissue'] = getattr(chicp_settings, 'DEFAULT_TISSUE')
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
user=user, idx_keys=None, idx_type_keys=None)
indexes = list()
tissues = list()
for target in getattr(chicp_settings, 'CP_TARGET'):
if 'CP_TARGET_'+target not in idx_keys_auth:
continue
indexes.append({"value": target, "text": ElasticSettings.get_label('CP_TARGET_'+target)})
elasticJSON = Search(idx=ElasticSettings.idx('CP_TARGET_'+target)).get_mapping(mapping_type="gene_target")
tissueList = list(elasticJSON[ElasticSettings.idx('CP_TARGET_'+target)]
['mappings']['gene_target']['_meta']['tissue_type'].keys())
utils.tissues['CP_TARGET_'+target] = tissueList
tissueList.sort()
for t in tissueList:
tissues.append({"value": t, "text": t.replace("_", " "), "class": target})
context['allIndexes'] = indexes
context['allTissues'] = tissues
snpTracks = OrderedDict()
defaultTrack = getattr(chicp_settings, 'DEFAULT_TRACK')
for group in getattr(chicp_settings, 'CP_STATS'):
if 'CP_STATS_'+group not in idx_keys_auth:
continue
if group == 'UD':
if settings.INCLUDE_USER_UPLOADS:
context['allow_user_uploads'] = True
else:
continue
snp_tracks = list()
for track, details in (ElasticSettings.get_idx_types(idx_name='CP_STATS_'+group, user='******')).items():
if 'CP_STATS_'+group+'.'+track not in idx_type_keys_auth:
continue
snp_tracks.append({"value": track.lower(), "text": details['label']})
if defaultTrack == '':
defaultTrack = track.lower()
snpTracks[ElasticSettings.get_label('CP_STATS_'+group)] = sorted(snp_tracks, key=itemgetter('text'))
context['snpTracks'] = snpTracks
if queryDict.get("snp_track"):
context['snp_track'] = queryDict.get("snp_track")
else:
context['snp_track'] = defaultTrack
return render(request, 'chicp/index.html', context, content_type='text/html')
