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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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How to execute ols-indexer.jar at Tomcat runtime ? #543

Closed chenkuncloud closed 2 years ago

chenkuncloud commented 2 years ago

Hi,

I successfully ran OLS locally .

But I found that ols-Indexer. jar could not be executed at Tomcat runtime . Error message :

Caused by: java.io.IOException: Unable to lock org.neo4j.io.fs.StoreFileChannel@2e93ff6b
    at org.neo4j.io.fs.FileLock.wrapFileChannelLock(FileLock.java:41)
    at org.neo4j.io.fs.FileLock.getOsSpecificFileLock(FileLock.java:99)
    at org.neo4j.io.fs.DefaultFileSystemAbstraction.tryLock(DefaultFileSystemAbstraction.java:85)
    at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:74)
    ... 136 common frames omitted

MongoDB - olsadmin - FAILED - message:

Error starting org.neo4j.kernel.EmbeddedGraphDatabase, OLS_HOME/neo4j

I noticed a sentence in the document https://www.ebi.ac.uk/ols/docs/installation-guide:

In contrast to that, the local tomcat server has to be down before running the ols-indexer.jar

Does that mean I have to restart Tomcat every time I update the index ?

Best Regards

serjoshua commented 2 years ago

hi @chenkun19960427,

To answer your question, yes unfortunately. The local tomcat server running with OLS is using the same index files as Solr and Neo4J, it is then mandatory to shutdown the tomcat before running the indexer.

chenkuncloud commented 2 years ago

Hi, @serjoshua

Thank you very much for your reply !

I'm going to write a timer to shut down Tomcat periodically and then execute the ols-indexer.jar .

Happy New Year !

Best Regards