def get_valid_report_types():
reporter_infos = au.get_local_module_infos(types=['reporter'])
report_types = [x.name.split('reporter')[0] for x in reporter_infos]
report_types = [
v for v in report_types
if not v in ['text', 'pandas', 'stdout', 'example']
]
return report_types
def get_annotators(request):
out = {}
for local_info in au.get_local_module_infos(types=['annotator']):
module_name = local_info.name
if local_info.type == 'annotator':
out[module_name] = {
'name': module_name,
'version': local_info.version,
'type': local_info.type,
'title': local_info.title,
'description': local_info.description,
'developer': local_info.developer
}
return web.json_response(out)
async def load_live_modules(module_names=[]):
global live_modules
global live_mapper
global include_live_modules
global exclude_live_modules
print('populating live annotators')
conf = au.get_system_conf()
if 'live' in conf:
live_conf = conf['live']
if 'include' in live_conf:
include_live_modules = live_conf['include']
else:
include_live_modules = []
if 'exclude' in live_conf:
exclude_live_modules = live_conf['exclude']
else:
exclude_live_modules = []
else:
include_live_modules = []
exclude_live_modules = []
if live_mapper is None:
cravat_conf = au.get_cravat_conf()
if 'genemapper' in cravat_conf:
default_mapper = cravat_conf['genemapper']
else:
default_mapper = 'hg38'
live_mapper = get_live_mapper(default_mapper)
modules = au.get_local_module_infos(types=['annotator'])
for module in modules:
if module.name in live_modules:
continue
if module.name not in module_names:
if module.name in exclude_live_modules:
continue
if len(include_live_modules
) > 0 and module.name not in include_live_modules:
continue
if 'secondary_inputs' in module.conf:
continue
annotator = get_live_annotator(module.name)
if annotator is None:
continue
live_modules[module.name] = annotator
print('done populating live annotators')
def get_valid_report_types():
reporter_infos = au.get_local_module_infos(types=['reporter'])
report_types = [x.name.split('reporter')[0] for x in reporter_infos]
return report_types
