Issue with DocumentNoteTypes when testing

Guzman

• May 08, 2025 21:37

I'm having an issue with a test I'm writing. Part of the functionality I'm trying to test creates and reads DocumentNoteTypes, but I'm getting a NullPointerException.

A minimal example of this is the following:

@BeforeAll
static void setUp() {
    TestGeneious.initialize();

    List<DocumentNoteField> fields = new ArrayList<>();
    fields.add(DocumentNoteField.createTextNoteField("Field no.1", "The first field", "fieldCode", Collections.emptyList(), true));
    DocumentNoteType noteType = DocumentNoteUtilities.createNewNoteType("Test note", "Test code", "Test description", fields, true);
    DocumentNoteUtilities.setNoteType(noteType);
}

Running this throws:

java.lang.NullPointerException
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.c(NoteTypeStorage.java:506)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:377)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:471)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.setNoteType(NoteTypeStorage.java:425)
    at com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities.setNoteType(DocumentNoteUtilities.java:103)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.b(NoteTypeStorage.java:85)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:67)
    at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.setNoteType(NoteTypeStorage.java:418)
    at com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities.setNoteType(DocumentNoteUtilities.java:103)

Am I missing something?

Thanks!

0

• 

  Matthew Cheung

  • May 11, 2025 23:49

  Hi there,

  You can fix this by changing the 

  TestGeneious.initialize();

  to

  TestGeneious.initializePlugins("com.biomatters.plugins.local.LocalDatabasePlugin");

   

  It's not obvious so I can understand you missing it.  The problem is that using DocumentNoteTypes requires the local database to be initialized, otherwise it has no place to store the types (which are stored database wide).  

  0
• 

  Guzman

  • May 12, 2025 19:10

  Hello,
  
  Thanks for your answer. I've tried this but I still have the same issue. This is the code I run:

  @BeforeAll
  static void setUp() {
      TestGeneious.initializePlugins("com.biomatters.plugins.local.LocalDatabasePlugin");
  
      List<DocumentNoteField> fields = new ArrayList<>();
      fields.add(DocumentNoteField.createTextNoteField("Field no.1", "The first field", "fieldCode", Collections.emptyList(), true));
      DocumentNoteType noteType = DocumentNoteUtilities.createNewNoteType("Test note", "Test code", "Test description", fields, true);
      DocumentNoteUtilities.setNoteType(noteType);
  }

  And I get this error (seems like the same as before):

  
  java.lang.NullPointerException
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.c(NoteTypeStorage.java:506)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:377)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:471)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.setNoteType(NoteTypeStorage.java:425)
      at com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities.setNoteType(DocumentNoteUtilities.java:103)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.b(NoteTypeStorage.java:85)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.a(NoteTypeStorage.java:67)
      at com.biomatters.geneious.publicapi.documents.NoteTypeStorage.setNoteType(NoteTypeStorage.java:418)
      at com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities.setNoteType(DocumentNoteUtilities.java:103

  Am I missing something? Thanks!

  0
• 

  Matthew Cheung

  • May 13, 2025 22:30

  Hmmm I'm not sure why it is still failing, perhaps it is version specific.  What version of Geneious / the plugin development kit are you using?

  I'm also happy to take a closer look at your code if you don't mind sharing it.  Please send it through to support@geneious.com and mention me if you're OK to do this.

  0
• 

  Guzman

  • May 14, 2025 13:14

  Hi,
  
  Not sure how to see the plugin dev kit version, but the Geneious version I'm using is:

  Build 2022-11-28 12:49
  Java Version 11.0.17+7-LTS (64 bit)

  As for sharing the code, I don't think I can do that, however, the example I shared before should be enough to reproduce it. It's the set up method of a JUnit test. 

  0
• 

  Matthew Cheung

  • May 15, 2025 04:33

  Ah I think I know what the issue might be.  

  What is the working directory for the test run?  If you're using our plugin development kit it needs to be set to the GeneiousFiles directory so that Geneious can find the LocalDatabasePlugin.

  0
• 

  Guzman

  • May 16, 2025 20:34

  That worked!
  
  Thanks!

  0

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