CNV module with limited data from staging API

[heimannch]

In the default settings of the CNV module, the production API returns: Total number of rows: 7, Number of genes: 2, but the staging returns only Total number of rows: 7, Number of genes: 2

[andrewelamb]

@heimannch Those look exactly the same?

[heimannch]

The plots and tables are different between staging and production:

• staging:

  

• production:

  

[andrewelamb]

I"ve figured out the issue, not all the results got migrated to the new database, this will be fixed with the rebuild

[heimannch]

@andrewelamb, it was brought to my attention that the version of the app before the database (shiny-iatlas) has way more results for the CNV module.

@Gibbsdavidl has mentioned that he can retrieve all the results from the API call, but they are not making it into the table in the module.

[heimannch]

Ok, I found the offending code, it's actually in iatlas-app code.

In https://github.com/CRI-iAtlas/iatlas-app/blob/staging/R/copy_number_response_server.R, line 51, the query to get the gene list is:

 iatlasGraphQLClient::query_genes(entrez = 1:100)

Which causes the app to only show the genes with entrez ids between 1 and 100. I tried to remove this argument, but then the app crashes, which might explain why this was included in the first place. After some experimentation, I concluded that the query works with no issues for the range of 1:10000:

 iatlasGraphQLClient::query_genes(entrez = 1:10000)

I will include this change in the upcoming release of iAtlas, but it doesn't look like a good long term solution. @andrewelamb, do you think there is anything we could do to be able to retrieve all gene ids available in the CNV module?

For the record, I also tried to replace iatlasGraphQLClient::query_genes(entrez = 1:100) with iatlasGraphQLClient::query_copy_number_result_genes(), and also got Error in : Bad Gateway (HTTP 502) I also tested with the staging API and got the same issues.