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custom database creation from CLI does not work

Open YasinEl opened this issue 7 months ago • 0 comments

Hello SIRIUS scientists :)

in SIRIUS 6.0.0 under Windows 11 I am still running into the same problem as described in https://github.com/sirius-ms/sirius/issues/106 which has been marked as completed. Specifically, creating Custom databases does not seem to work from the CLI as shown below. Notably using the very same file structures.tsv in the GUI is successful. Would be great to get help or a fix for this.

Also as a side note, I think the documentation should be updated regarding arguments (--location instead of --output).

Thanks!

sirius custom-db -i structures.tsv --name tmp_sirius_db --location output\

java.lang.NullPointerException: Name is null
	at java.base/java.lang.Enum.valueOf(Unknown Source)
	at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44)
	at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40)
	at de.unijena.bioinf.chemdb.custom.CustomDatabases.open(CustomDatabases.java:191)
	at de.unijena.bioinf.chemdb.custom.CustomDatabases.createOrOpen(CustomDatabases.java:207)
	at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:188)
	at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:144)
	at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:124)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

YasinEl avatar Jul 04 '24 22:07 YasinEl