Guillaume Poirier-Morency
Guillaume Poirier-Morency
ChEBI is a fast evolving ontology and having to wait until a restart can impede curation efforts.
[Gemma - http-nio-8181-exec-919 (2024-04-10 14:20:58,470)] ERROR org.directwebremoting.util.CommonsLoggingOutput.error(75) | No converter found for 'org.glassfish.jersey.message.internal.OutboundJaxrsResponse' [Slack Message](https://pavlidis-lab.slack.com/archives/C02LZHP6RB3/p1712784058671559)
It's getting in the way of the 1.31.3 release and is not super urgent. ``` org.springframework.dao.InvalidDataAccessApiUsageException: object references an unsaved transient instance - save the transient instance before flushing: ubic.gemma.model.genome.biosequence.BioSequence;...
Ontology search and inference is critical for the browser performance. I suggest that we keep track of some relevant metrics: - [x] timers for getChildren() and getParent() - [ ]...
We have probably hundreds of dangling Slack API metrics thread in production because of that. Here's what we have in the QA server: 
[Gemma - pool-6-thread-15 (2024-03-13 14:15:20,773)] ERROR ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.runDifferentialExpressionAnalyses(187) | Error during differential expression analysis: could not initialize proxy - no Session [Slack Message](https://pavlidis-lab.slack.com/archives/C02LZHP6RB3/p1710364520956899)
When inference is done on the clause, it would be very useful to have labels to use for displaying attached somewhere in the payload. In GemBrow, we have to resort...
Data that is made available in Gemma is available under CC-BY-SA 4.0. To prevent confusion, all the tabular datasets that we produce should have a mention of the license under...