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Custom-database CLI #106
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The custom database feature is also not working in the GUI. When I try to create a database by either typing in the SMILES code and hitting "open/create database" or by directly uploading a csv, I receive this error: java.lang.NullPointerException: Name is null Hope this helps! |
Wondering if there has been a solution to the create custom database feature in the software. As others have commented the addition of smiles strings still doesn't seem to be working. would love to have a way to bring in exports from other databases to help build up the compounds thank you David Weil |
Hello! java.lang.NullPointerException: Name is null |
Do you think you can let me know when you have a solution.
Thank you
David weil
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From: gdiazcruz ***@***.***>
Sent: Tuesday, September 12, 2023 5:31:14 AM
To: boecker-lab/sirius ***@***.***>
Cc: WEIL,DAVID (Agilent USA) ***@***.***>; Comment ***@***.***>
Subject: Re: [boecker-lab/sirius] Custom-database CLI (Issue #106)
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Hello!
I am having the same (or similar) issue with the 5.8.3 version:
java.lang.NullPointerException: Name is null
at java.base/java.lang.Enum.valueOf(Unknown Source)
at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44)
at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40)
at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99)
at de.unijena.bioinf.chemdb.SearchableDatabases.loadCustomDatabaseFromLocation(SearchableDatabases.java:195)
at de.unijena.bioinf.ms.gui.fingerid.custom_db.DatabaseDialog$ImportDatabaseDialog.lambda$runImportJob$2(DatabaseDialog.java:349)
at de.unijena.bioinf.jjobs.LoadingBackroundTask$1.compute(LoadingBackroundTask.java:35)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
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Hello SIRIUS developers,
I am currently using SIRIUS 5.6.3 CLI version and following the documentation: SIRIUS Documentation - Custom Database
so according to current documentation:
sirius --input /Users/mahnoor/SL_Sirius.tsv --name SL_Sirius custom-db --output /Users/mahnoor/SIRIUS
However, SIRIUS returns errors like: unknown options: "--input" or "output".
I think this needs an update as this command was working on SIRIUS4. Could you take a look into this issue?
Thanks,
Mahnoor
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