def get(self):
# {
# "python-package-info": [
# "aiocron 1.6",
# "aiohttp 3.6.2",
# "async-timeout 3.0.1",
# ...
# ],
# "codebase": {
# "repository-url": "https://github.com/biothings/biothings.api.git",
# "commit-hash": "8715a8ebcf49bc436bca24b1ce1a35f1777a7c4c"
# },
# "biothings": {
# "repository-url": "https://github.com/biothings/biothings.api.git",
# "commit-hash": "f3ca99a1f5261a70eaef196bbab1163302c16859",
# "master-commits": "2478",
# "version": "0.10.0"
# },
# "python-info": {
# "version": "3.9.5 (tags/v3.9.5:0a7dcbd, May 3 2021, 17:27:52)",
# "version_info": {
# "major": 3,
# "minor": 9,
# "micro": 5
# }
# }
# }
try:
return get_software_info(self._repo)
except Exception:
return {}
async def get(self):
_raw = await self.web_settings.metadata.refresh(self.biothing_type)
_meta = self.web_settings.metadata.biothing_metadata[self.biothing_type]
if self.args.raw:
raise Finish(_raw)
elif self.args.dev:
_meta['software'] = get_software_info(
app_dir=self.web_settings.devinfo.get_git_repo_path())
_meta['cluster'] = await get_es_versions(
client=self.web_settings.connections.async_client)
_meta['hosts'] = self.web_settings.connections.async_client.transport.info
else: # remove correlation info
_meta.pop('_biothing', None)
_meta.pop('_indices', None)
_meta = self.extras(_meta) # override here
self.finish(dict(sorted(_meta.items())))
def extras(self, _meta):
appdir = self.web_settings.devinfo.get_git_repo_path()
commit = get_software_info(appdir).get('commit-hash', '')
_meta['available_fields'] = 'http://mygene.info/metadata/fields'
_meta['app_revision'] = commit
_meta['genome_assembly'] = {}
_meta['taxonomy'] = {}
for s, d in self.web_settings.TAXONOMY.items():
if 'tax_id' in d:
_meta['taxonomy'][s] = int(d['tax_id'])
if 'assembly' in d:
_meta['genome_assembly'][s] = d['assembly']
if "source" not in _meta:
# occurs when loaded from scratch, not from a change/diff file
_meta["source"] = None
return _meta
def _get_software_info(self):
''' Override me '''
return get_software_info(app_dir=self.app_dir)
def _fill_software_info(self,_meta):
kwargs = self.get_query_params()
debug = kwargs.pop('dev', False)
if debug:
_meta['software'] = get_software_info()
