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CRI-iAtlas / iatlasGraphQLClient

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extracellular network function `iatlasGraphQLClient::query_nodes()` not working #16

Closed heimannch closed 3 months ago

heimannch commented 9 months ago 
> x <- iatlasGraphQLClient::query_nodes()
Error in create_result_from_cursor_paginated_api_query(query_args = query_args,  : 
  object 'query_file' not found
andrewelamb commented 9 months ago

@heimannch Do you know where in the code this is happening?

heimannch commented 9 months ago

Do you mean the app code or the api code? In the app, this function is being called in extracellular_network_main_server.R -> extracellular_networks_functions.R

andrewelamb commented 9 months ago

I mean where is iatlasGraphQLClient::query_nodes() being called without any arguments. It's not meant to be.

heimannch commented 9 months ago

Ah, nowhere in the code. I just did that because I thought it would be helpful in debugging - the issue is that no network is displayed in the Extracellular Network module.

andrewelamb commented 9 months ago

I can't run the app locally so I can't diagnose something like this. If there's an error, or a iatlasGraphQLClient function that returning the wrong information, then I could help.

heimannch commented 9 months ago

When I run the app, the issue when running the extracellular network module is Error in : Gateway Timeout (HTTP 504).

I get this error when I select genesets (Immunomodulators and Extracellular Network Genes), but if I select few genes everything works fine. I’m assuming this issue is due to settings of the staging API, or the geneset information.