Dennis Hendriksen

Exception when reading FlexBuffer fixed untyped Vector [Java, 2.0.3]

3

```java package org.molgenis.vcfflatbuffers; import static com.google.flatbuffers.FlexBuffersBuilder.BUILDER_FLAG_SHARE_ALL; import com.google.flatbuffers.ByteBufferReadWriteBuf; import com.google.flatbuffers.FlexBuffers; import com.google.flatbuffers.FlexBuffers.Vector; import com.google.flatbuffers.FlexBuffersBuilder; import java.nio.ByteBuffer; public class FlexBufferApp { public static void main(String[] args) { FlexBuffersBuilder builder = new...

VCF output with invalid QUAL values based on Locale

1

Consider htsjdk.variant.vcf.VCFEncoder: ```java private static final String QUAL_FORMAT_STRING = "%.2f"; private static final String QUAL_FORMAT_EXTENSION_TO_TRIM = ".00"; private static String formatQualValue(final double qual) { String s = String.format(QUAL_FORMAT_STRING, qual); if...

### How to Reproduce 1. Import ```molgenis-platform-integration-tests/src/test/resources/owl/biobank_ontology.owl.zip``` 2. Open SORTA and start a new task 3. Upload ```molgenis-platform-integration-tests/src/test/resources/txt/sorta_test_2.txt``` 4. Run the matching algorithm 5. Inspect the progress bar ### Expected...

Ontology deletion non-practical

1

### How to Reproduce - Sign in as superuser - Import [molgenis.test.obo.zip](https://github.com/molgenis/molgenis/files/2433706/molgenis.test.obo.zip) using the 'Advanced data import' plugin in the 'Import data' menu - Navigate to the 'Data Explorer' plugin...

### How to Reproduce ### Expected behavior ### Observed behavior

Query of type 'not' on nullable mref incorrect results

2

### How to Reproduce - Sign in as superuser - Import [it_emx_mrefnullable.xlsx](https://github.com/molgenis/molgenis/files/4133449/it_emx_mrefnullable.xlsx) using the 'Advanced data import' plugin - GET ```/api/data/it_emx_nullablemref_Dataset?q=nullableRef!=ref2``` ### Expected behavior - 3 results: row0, row1 and...

Query of type 'in' on nullable mref incorrect results

2

### How to Reproduce - Sign in as superuser - Import [it_emx_mrefnullable.xlsx](https://github.com/molgenis/molgenis/files/4133449/it_emx_mrefnullable.xlsx) using the 'Advanced data import' plugin - a) GET ```/api/data/it_emx_nullablemref_Dataset?q=nullableRef!=in=('')``` - b) GET ```/api/data/it_emx_nullablemref_Dataset?q=nullableRef!=in=('',ref2)``` ### Expected behavior -...

Deleting system beacon package fails

2

### How to Reproduce - Start MOLGENIS with an empty database - Stop MOLGENS - Remove ```molgenis-beacon``` module and all references - Start MOLGENIS ### Expected behavior - ```sys_beacon``` package...

No handler found for Directory plugin

3

### How to Reproduce - As superuser navigate to the 'Menu manager' plugin in the 'Admin' menu - Create menu item for plugin 'directory and save the new menu layout...