Chunlei Wu
Chunlei Wu
Currently, our genomic_pos and genomic_pos_hg19 fields are coming from Ensembl, therefore, only available for those species included in Ensembl release. We should find out a good data source from NCBI...
The current gene summary data (`summary` field) from MyGene.info API are extracted from the RefSeq records (see the current [refseq data source](https://github.com/biothings/mygene.info/tree/master/src/hub/dataload/sources/refseq)). It appears that Refseq does not contain all...
Looks like couchdb-lucene server always loads the config file from "./conf/couchdb-lucene.ini". It will be nice if it can accept an alternative config file, maybe something like: ./bin/run --conf alt_couchdb-lucene.ini My...
This should be a standalone helper function (e.g. can be under `utils/es_reindex.py`) used only from the Python/iPython console manually when needed. It helps to reindex an existing index by transferring...
This can be a new type of Dumper class, which triggers a docker container (typically runs on a different server) to run and generate the output file, and then stop...
Our current documentation site at https://docs.biothings.io/ does not contain API document from `biothings.hub` module. It was due to some errors in the past, let's re-evaluate to see if we can...
Not sure how the current list is organized or sorted: https://docs.biothings.io/en/latest/apidoc/biothings.hub.commands.html
for both elasticsearch-py and elasticsearch-dsl packages, their ES8 support is complete. We should test and upgrade. All of our hubs are now using ES8, but we should target the support...
In this Hub instance for outbreak.info, we have implemented a `auto_archive` feature to archive old builds automatically as a hub hook: https://github.com/outbreak-info/outbreak.api/blob/master/hooks/auto_archive.py This feature is generally useful for all hubs...