[bug] Many datasets are showing up with 'Pending Annotation' as Assay

[aditya-nath-sage]

There are 341 datasets in the CCKP with 'Pending Annotation' as the annotation for Assay. (https://www.cancercomplexity.synapse.org/Explore/Datasets?QueryWrapper0=%7B%22sql%22%3A%22SELECT+*+FROM+syn21897968%22%2C%22limit%22%3A25%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22tissue%22%2C%22facetValues%22%3A%5B%22Pending+Annotation%22%5D%7D%5D%7D)

This is possibly an issue with backfilling not happening when publications go from Restricted Access to Open Access. There is a process that updates publication metadata when this happens but it does not extend to Datasets at this time.
This is also a problem for Tools to a lesser extent.

[Bankso]

There is a process that updates publication metadata when this happens

This is the script that runs the status check and reports the number of publications that have moved from restricted --> open: check_publications_status.py
This script generates a manifest with the publication entries relabeled as "Open Access" and uploads it to Synapse (The most recent output is here: https://www.synapse.org/Synapse:syn66360235), but it doesn't impact the database entries.

[Bankso]

There are 341 datasets in the CCKP with 'Pending Annotation' as the annotation for Assay.

I just looked at the CCKP link above and noticed that the Pending Annotation filter in use here is for Dataset Tissue. This aligns with what I've observed during the database QC checks.

Also, Dataset Tissue is not a required column in the Dataset model, so it could be that this field is less often populated during curation.

Two ways I can think of to address this:

• change Pending Annotation to Not Applicable or Not Provided
• replace Pending Annotation with a tissue annotation that is based on Dataset Tumor Type or Dataset Description