search

sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
78 stars 17 forks source link

argument "src" is null #85

Closed SarahLenn closed 1 year ago

SarahLenn commented 1 year ago

Dear all,

I am using Sirius via the GUI. I am currently running into an issue. I am trying to create a custom database from a list of smiles. I get the error below. I have tried to uninstall and reinstall Sirius without much success. Would you have any suggestion ?

Thank you very much for your help, Kind regards, Sarah Lennon

Oct 03, 2022 9:51:45 AM de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow run GRAVE: error when storing custom db java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: argument "src" is null at java.base/java.util.concurrent.FutureTask.report(Unknown Source) at java.base/java.util.concurrent.FutureTask.get(Unknown Source) at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:205) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.run(CustomDBOptions.java:102) at de.unijena.bioinf.ms.gui.compute.jjobs.Jobs$ComputationJJob.compute(Jobs.java:261) at de.unijena.bioinf.ms.gui.compute.jjobs.Jobs$ComputationJJob.compute(Jobs.java:231) 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$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: java.lang.IllegalArgumentException: argument "src" is null at com.fasterxml.jackson.databind.ObjectMapper._assertNotNull(ObjectMapper.java:4829) at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3673) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.lambda$getTags$2(FileBlobStorage.java:88) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.withWriteLock(FileBlobStorage.java:228) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.getTags(FileBlobStorage.java:86) at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40) at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99) at de.unijena.bioinf.chemdb.custom.CustomDatabase.createOrOpen(CustomDatabase.java:107) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:130) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:90) ... 5 more

Oct 03, 2022 9:51:45 AM de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow run GRAVE: error when storing custom db java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: argument "src" is null at java.base/java.util.concurrent.FutureTask.report(Unknown Source) at java.base/java.util.concurrent.FutureTask.get(Unknown Source) at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:205) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.run(CustomDBOptions.java:102) at de.unijena.bioinf.ms.gui.compute.jjobs.Jobs$ComputationJJob.compute(Jobs.java:261) at de.unijena.bioinf.ms.gui.compute.jjobs.Jobs$ComputationJJob.compute(Jobs.java:231) 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$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: java.lang.IllegalArgumentException: argument "src" is null at com.fasterxml.jackson.databind.ObjectMapper._assertNotNull(ObjectMapper.java:4829) at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3673) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.lambda$getTags$2(FileBlobStorage.java:88) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.withWriteLock(FileBlobStorage.java:228) at de.unijena.bioinf.storage.blob.file.FileBlobStorage.getTags(FileBlobStorage.java:86) at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40) at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99) at de.unijena.bioinf.chemdb.custom.CustomDatabase.createOrOpen(CustomDatabase.java:107) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:130) at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:90) ... 5 more

Oct 03, 2022 9:51:45 AM de.unijena.bioinf.chemdb.SearchableDatabases getCustomDatabaseByPath GRAVE: argument "src" is null Oct 03, 2022 9:51:45 AM de.unijena.bioinf.chemdb.SearchableDatabases getCustomDatabaseByPath GRAVE: argument "src" is null

mfleisch commented 1 year ago

Hey Sarah, which version of SIRIUS are your using? Can you please describe how exactly you have tried to create the custom-db?

Best Markus

SarahLenn commented 1 year ago

Hi Markus,

Thank you for your answer ! I am using Sirius 5.5.7. I think I have got an idea how I made this happened, but I am not sure how to fix it. I created a database using a list of smiles and a location on one of our server. I did not realise Sirius was going to import all the .json file here. So I stopped the process and decided to change the location from the server to local on my laptop and I deleted what Sirius has been imported by Sirius. Since then, I am not able to create a custom DB anymore and I get that argument "src" is null. I have also tried to install Sirius on another computer, I still have the same issue. I might have corrupted something related to my account. Is this possible ?

Thank you ! Kind regards, Sarah

mfleisch commented 1 year ago

Hey Sarah, the import process for custom databases will be improved with the upcoming release, including better checks of the location.

The location for the custom db must either:

To fix your problem please try deleting the .sirius-5.5 directory in your user home directory. This should remove the faulty configuration that is likely to be the reason for this problem.

Best Markus

SarahLenn commented 1 year ago

Hi Markus,

Thank you very much for your answer, it has indeed fixed my issue!

kind regards,

Sarah