Changed nested fields fail to upload to dataverse-server ( dataset.update() )

[JulianRein]

Hi there,

I want to add some "samples" (= several subfields in a sample-field) to a easyDataverse-dataset.
However, it seems dataset.update() fails to actually upload the easyDataverse-obj / in-memory object to the dataverse server.
Likely because dataset._extract_changes() / dataset.[metadatablock].extract_changed() / base.extract_changed() does not register them somehow.

As a workaround, I tried to set base._changed manually, but no idea what to add there.

Any ideas how to fix this?

I added the "samples" like this:
dataset.sample_se.add_sample_field_se(sample_name_se='testSampleProg', sample_description_se='BRAAAAAAINS!', sequencing_batch_se='1', replicate_se='1', sample_prep_date_se='2025-03-12', tissue_type_se='Brain', cell_line_se=None, cell_type_se='Cells, Cultured', treatment_se='H2O2', um_is_se='No', paired_end_se='single-end', platform_se='Illumina MiniSeq System', molecule_se='PolyA-selected RNA', count_table_se=None, fastq_file_se='testdir/testfile.fastq', paired_end2_se=None, comment_se=None, )

I attached the metadatablock in question.

sample_se.tsv

I tried to combine
dataset.sample_se.to_dataverse_json() with easyDataverse.uploader.update_dataset
but the resulting JSON is apparently not quite a fit for the API.

[JR-1991]

@JulianRein thanks for submitting the issue! I guess the underlying problem indeed is that the _extract_changes method does not see the actual changes. This likely, because something has been added, but none of the objects added have _changed set and thus the updater assumes there is nothing to update.

I will try to reproduce your error and get back to you once I have found the underlying problem.

[JR-1991]

@JulianRein, I’ve identified the issue. As expected, the _changed attribute wasn’t populated, which caused the update to fail. I’ve opened a PR (#65) for your review. Please don’t mind the failing CI; it’s due to another bug that has been resolved elsewhere and needs to be updated here.

[JulianRein]

Thank you very much for the quick resolution! Tested it and the .update() works now (after removing and re-installing the package. Maybe bump the version number a little?)