CSBC/PS-ON Manifests Validator Give Reload Error when uploading Datasets and Tools

[brynnz22]

When attempting to validate the datasets and tools manifests using the CSBC Manifests Validator, a reload error occurs immediately.

To reproduce error:

1. Pick appropriate manifest

2. attach manifest to upload
   datasets_manifest_update_2021-03-25.xlsx
   tools_manifest_update_2021-03-25.xlsx

3. Include the additional standard terms sheet
   additional_standard_terms_update_2021_03_25.xlsx

4. Click validate

[jaeddy]

Figured out the problem:

The error occurs when in line 365 of server.R:

syn_store(synapseclient$Table(portal_table[[type]], new_portal_row))

... specifically:

Warning: Error in py_call_impl: SynapseHTTPError: 400 Client Error: 
Value at [0,15] was not a valid STRING_LIST. Not a JSON Array: True

The problem appears to be with two spots in utils.R, which I suspect were introduced when we decided not to create new publication entities for now. That is, in both dataset_row() and tool_row(), there's a step that looks like this:

    publicationId = NA,

However, R (or Python?) gets confused by this missing value and ends up treating it as a logical (lgl) type, which then makes Synapse upset because it doesn't recognize the NA as a STRING_LIST. Instead, these lines should look like this:

    publicationId = "",

... where "" is recognized as a valid "empty list" by Synapse.

The dataset manifest upload seems to be working now, and I'll test with tools next. If everything uploads successfully, I'll create a PR with the fix.