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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Load latest working version of Ontology onto PROD #154

Closed shirey closed 1 year ago

AlanSimmons commented 1 year ago

@shirey Latest version of neo4j graph has the following integrations:

UBERON PATO CL DOID OBI EDAM HSAPDV SBO MI CHEBI MP (fixed) ORDO UNIPROTKB (new; custom) PR (fixed) UO (new) HUSAT (new) HUBMAP (new) CCF (new version)

AlanSimmons commented 1 year ago

The Production neo4j can be rebuilt either via the instructions here or via a direct copy of the neo4j database folder from my local laptop.

AlanSimmons commented 1 year ago

@yuanzhou I have an archive of CSV files that can be copied to the prod neo4j instance to build a new ontology database.

yuanzhou commented 1 year ago

@shirey @AlanSimmons I'm thinking we should do a rebuild on DEV VM first along with the recent ontology-api updates. And once you and @ChuckKollar give me the green light, I can copy over the neo4j data directory generated on DEV to PROD and release the ontology-api as well.

AlanSimmons commented 1 year ago

Rebuilding in the DEV VM requires access that I do not have--e.g.,

`Go to the host and update from the repository.

$ ssh -i ~/.ssh/id_rsa_e2c.pem cpk36@neo4j.dev.hubmapconsortium.org $ sudo /bin/su - centos $ cd hubmap/ontology-api

NOTE: this is a Git reposntory https://github.com/hubmapconsortium/ontology-api.git so make sure that you are in the right branch...

$ git pull`

AlanSimmons commented 1 year ago

The code snippet is from the instructions in the readme.

yuanzhou commented 1 year ago

@AlanSimmons I can rebuild the ontology neo4j on DEV. @ChuckKollar can you rebuild the ontology-api on DEV since I don't know much about the recent changes?