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globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names
GNU General Public License v3.0
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discoverlife dump error #62

Closed seltmann closed 2 years ago

seltmann commented 2 years ago

@jhpoelen ran the discoverlife dump and there was an error and the file was empty. Thanks!

Using version 0.2.6

nomer dump discoverlife > discoverlife-13112021.txt using matcher [discoverlife-taxon] DiscoverLife name indexing started... WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.mapdb.Volume$ByteBufferVol (file:/usr/local/bin/nomer) to method java.nio.DirectByteBuffer.cleaner() WARNING: Please consider reporting this to the maintainers of org.mapdb.Volume$ByteBufferVol WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release java.io.IOException: Wrong index checksum, store was not closed properly and could be corrupted. java.io.IOError: java.io.IOException: Wrong index checksum, store was not closed properly and could be corrupted. at org.mapdb.StoreDirect.checkHeaders(StoreDirect.java:269) at org.mapdb.StoreDirect.(StoreDirect.java:207) at org.mapdb.DBMaker.extendStoreDirect(DBMaker.java:971) at org.mapdb.DBMaker.makeEngine(DBMaker.java:758) at org.mapdb.DBMaker.make(DBMaker.java:701) at org.globalbioticinteractions.nomer.match.DiscoverLifeTaxonService.initCache(DiscoverLifeTaxonService.java:151) at org.globalbioticinteractions.nomer.match.DiscoverLifeTaxonService.lazyInit(DiscoverLifeTaxonService.java:124) at org.globalbioticinteractions.nomer.match.DiscoverLifeTaxonService.match(DiscoverLifeTaxonService.java:52) at org.eol.globi.service.TermMatcherHierarchical.match(TermMatcherHierarchical.java:57) at org.globalbioticinteractions.nomer.util.AppendingRowHandler.onRow(AppendingRowHandler.java:34) at org.globalbioticinteractions.nomer.cmd.CmdDump.run(CmdDump.java:17) at org.globalbioticinteractions.nomer.cmd.CmdLine.run(CmdLine.java:18) at org.globalbioticinteractions.nomer.cmd.CmdLine.run(CmdLine.java:28) at org.globalbioticinteractions.nomer.Nomer.main(Nomer.java:15) Caused by: java.io.IOException: Wrong index checksum, store was not closed properly and could be corrupted. ... 14 more

jhpoelen commented 2 years ago

@seltmann thanks for sharing your detailed report. Please note that you are seeing a known issue v0.2.6 issue (see https://github.com/globalbioticinteractions/nomer/issues/61), that has been resolved in v0.2.7. Suggest to use the latest Nomer v0.2.8 to benefit from recent fixes and functionality.

Also, if you get the chance, you might want to install long-term supported versions of OpenJDK 8 or 11 (preferably OpenJDK 8) instead of the current version of java jvm (v13 I believe) that you are using now. These are the versions that Nomer is developed and tested on.

See attached screenshot from https://access.redhat.com/articles/1299013 . Screenshot from 2021-11-13 02-32-26

seltmann commented 2 years ago

@jhpoelen Ah! I see that when I install each new version of nomer the download pattern changes. I kept re-installing v0.2.6.