wfo returning concerning warnings

[jtmiller28]

using wfo via nomer with the following command:

cat combined-names-for-WFO.tsv | nomer append wfo --include-header > name-wfo.tsv

produced warnings: WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.mapdb.SerializerPojo$FieldInfo (file:/usr/local/bin/nomer) to field java.util.Collections$SingletonList.element WARNING: Please consider reporting this to the maintainers of org.mapdb.SerializerPojo$FieldInfo 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

Not sure if these warnings are concerning, or if something is not aligning with my name file. Attaching .txt file used for resolution combined-names-for-WFO.txt

text file was modified into a .tsv using the following code:

cat combined-names-for-WFO.txt | sed 's/^/\t/g' > combined-names-for-WFO.tsv

[jhpoelen]

@jtmiller28 thanks for sharing!

Please share the version of java you are using by:

sharing the results of:

java -version

[jtmiller28]

java -version openjdk version "11.0.16" 2022-07-19 OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu122.04) OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu122.04, mixed mode, sharing)

[jhpoelen]

See related issue https://github.com/globalbioticinteractions/nomer/issues/44 .

[jhpoelen]

@jtmiller28 thanks!

Yes, the warnings are concerning, and are related to a software library used to enable offline name matching (e.g., a java software library called "mapdb").

When using java 8, the warning are not generated. When using java 11, a warning is issued indicating that for future java versions, the illegal access might cause the java virtual machine to crash.

So, yes, this should be addressed at some point.

Can you please inspect #44 and confirm that this is the same issue?

[jhpoelen]

oh, and the name alignment should work as expected. If not, please let me know, and share some specific examples of unexpected behavior.

[jtmiller28]

Yes, that does appear to be the same issue. Should a different v. of java be used while accessing Nomer at the moment? I'm going to address some concerns I have with name alignment in a separate issue if that is fine.

[jhpoelen]

Ok, thanks for checking. I'll close this issue because it is a duplicate of #44 .

And, I'll have a look whether an upgrade to a more recent version of mapdb is feasible.

I use java8 so I don't see the warnings.

I'm going to address some concerns I have with name alignment in a separate issue if that is fine.

yes, please do share your concerns with the name mapping in a separate issue.