Troubleshooting Operations

Here we describe how to troubleshoot issues with system operations. As with all the troubleshooting sections, this section will be enhanced based on experiences with the deployed OntoPortal systems.

Because of the complexity of troubleshooting, initially only limited troubleshooting information is available on this page. The BMIR BioPortal team has a detailed troubleshooting guide for cases where the system is severely misbehaving; until we make part of this document, contact us if you think you need this information.

For troubleshooting installations, see the Troubleshooting Installations section.

For troubleshooting ontology submissions, see the Troubleshooting Submissions section.

General conditions

System slow or dead

# To be provided.

System producing incorrect or inconsistent responses

# To be provided.

User interface displaying error message instead of content

# To be provided.

Missing or odd search results

If concepts that should be found during a search are not found, the problem is likely a faulty index for that ontology. (Possibly the indexing of the last submission of the ontology was interrupted.) The fix is to re-index the ontology.

Check for indexed acronyms

This should report results if they exist, as it’s a wildcard search:

! possibly following link should use :8080 address

http://data.{my-appliance-hostname}/search?q=*&ontologies=OBI

Also it’s possible to look at SOLR directly; this gives you all acronyms in the index:

http://{my-appliance-hostname}:8080/solr/select?q=&rows=0&facet=true&facet.limit=-1&facet.field=submissionAcronym

For more specific SOLR queries, the SOLR admin interface is available at:

http://{my-appliance-hostname}:8080/solr/

In those interfaces, use the ‘Core Selector’ to choose ‘Collection1’ (likely the only choice available). In the ‘Query’ utility that appears, enter parameters such as ‘q’ text field entry: ‘submissionAcronym:AERO’.

To re-index an ontology, follow the instructions in Search Index Management

https://github.com/ncbo/ncbo_cron/blob/master/bin/ncbo_ontology_index

Specific diagnostic errors

ontologies_report.json is missing

When running some jobs you may see the error

ontologies_report.json : No such file or directory

To fix it, create an ontologies_report.json file at the following location: /srv/reports/ontologies_report.json

The file has to be owned by ncbobp:ncbobp and to have permission 666

Advanced troubleshooting of specific systems

Troubleshooting ncbo_cron

See ncbo-cron Reference for details.