On this page you will find some guidelines on how Advanced administration of the BioPortal Virtual Appliance. To proceed you will need a ssh connexion to your Appliance.
To simplify the examples we will consider we are using a Virtual Appliance deployed at http://my-bioportal-vm/

NCBO architecture diagram

Solr search index

Access to solr

It is hosted by the tomcat on the port 8082

http://my-bioportal-vm:8082/solr

There are 2 cores:

core1 is used for search
core2 is used when doing a full reindexing (it allows the search to work fine when reindexing the whole bioportal)

To swap the 2 cores:

Go to core admin tab
Select core1
Hit the "Swap" button

Reindex all ontologies in core2

Re-indexing in the core2 allows the BioPortal Appliance to not stop working during the reindexing (you just have to swap the cores when the reindexing is over)

bin/ncbo_ontology_index -a -l logs/reindexing_all.log -c http://my-bioportal-vm:8082/solr/core2

Reindex only the specified ontologies in core2

bin/ncbo_ontology_index -o STY,SNOMED -l logs/reindexing_STY_SNOMED.log -c http://my-bioportal-vm:8082/solr/core2

Updating the Annotator cache and dictionary

See the Annotator Documentation

Common troubles

ontologies_report.json is missing

When running some job you can face the following error:

ontologies_report.json : No such file or directory

To avoid it you have to create a ontologies_report.json file at the following location:

/srv/reports/ontologies_report.json

It has to be owned by ncbobp:ncbobp and to have permission 666

Advanced Administration

Contents