async def get_remote_module_config(request):
queries = request.rel_url.query
module = queries['module']
conf = au.get_remote_module_config(module)
if 'tags' not in conf:
conf['tags'] = []
response = conf
return web.json_response(response)
async def get_nowg_annot_modules(request):
# disabling this until required_annotator is included in the remote manifest.
return web.json_response({})
# Below is not run. Delete the above and change the below so that remote manifest's required_annotator is used.
queries = request.rel_url.query
job_id, dbpath = await get_jobid_dbpath(request)
conn = await aiosqlite3.connect(dbpath)
cursor = await conn.cursor()
remote_widget_modules = au.get_remote_module_infos_of_type(
'webviewerwidget')
remote_widget_names = remote_widget_modules.keys()
remote_annot_to_widgets = {}
for remote_widget_name in remote_widget_names:
conf = au.get_remote_module_config(remote_widget_name)
if 'required_annotator' in conf:
req_annot = conf['required_annotator']
if req_annot not in remote_annot_to_widgets:
remote_annot_to_widgets[req_annot] = []
remote_annot_to_widgets[req_annot].append(remote_widget_name)
wgmodules = au.get_local_module_infos_of_type('webviewerwidget')
annot_modules_with_wg = []
for wgmodule in wgmodules:
conf = wgmodules[wgmodule].conf
if 'required_annotator' in conf:
annot_module = conf['required_annotator']
if annot_module not in annot_modules_with_wg:
annot_modules_with_wg.append(annot_module)
nowg_annot_modules = {}
r = await table_exists(cursor, 'variant')
if r:
q = 'select name, displayname from variant_annotator'
await cursor.execute(q)
for r in await cursor.fetchall():
m = r[0]
if m in ['example_annotator', 'testannot', 'tagsampler']:
continue
annot_module = r[0]
displayname = r[1]
if annot_module not in annot_modules_with_wg and annot_module not in nowg_annot_modules and annot_module in remote_annot_to_widgets:
nowg_annot_modules[annot_module] = displayname
content = nowg_annot_modules
await cursor.close()
await conn.close()
return web.json_response(content)
def print_info(args):
module_name = args.module
installed = False
remote_available = False
up_to_date = False
local_info = None
remote_info = None
# Remote
try:
remote_info = au.get_remote_module_info(module_name)
if remote_info != None:
remote_available = True
except LookupError:
remote_available = False
# Local
release_note = {}
try:
local_info = au.get_local_module_info(module_name)
if local_info != None:
installed = True
del local_info.readme
release_note = local_info.conf.get('release_note', {})
else:
installed = False
except LookupError:
installed = False
if remote_available:
versions = remote_info.versions
data_sources = remote_info.data_sources
new_versions = []
for version in versions:
data_source = data_sources.get(version, None)
note = release_note.get(version, None)
if data_source:
version = version + ' (data source ' + data_source + ')'
if note:
version = version + ' ' + note
new_versions.append(version)
remote_info.versions = new_versions
del remote_info.data_sources
dump = yaml_string(remote_info)
print(dump)
# output columns
print('output columns:')
conf = au.get_remote_module_config(module_name)
if 'output_columns' in conf:
output_columns = conf['output_columns']
for col in output_columns:
desc = ''
if 'desc' in col:
desc = col['desc']
print(' {}: {}'.format(col['title'], desc))
if installed:
print('INSTALLED')
if args.local:
li_out = copy.deepcopy(local_info)
del li_out.conf
li_out.get_size()
dump = yaml_string(li_out)
print(dump)
else:
print('NOT INSTALLED')
if installed and remote_available:
if installed and local_info.version == remote_info.latest_version:
up_to_date = True
else:
up_to_date = False
if up_to_date:
print('UP TO DATE')
else:
print('NEWER VERSION EXISTS')