Extra info in 404 response if assembly exist but not included in the datasets API

[manulera]

Is your feature request related to a problem? Please describe.

Not really a problem, but an improvement that would make my use-case easier.

I noticed that previous revision assemblies are not included in the API. For instance, for GCF_004355105:

Current version GCF_004355105.2 works, but GCF_004355105.1 gives the following:

https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_004355105.1/annotation_report

{
  "error": "Not Found",
  "code": 404,
  "message": "Your request is invalid. (For more help, see the NCBI Datasets Documentation at https://www.ncbi.nlm.nih.gov/datasets/docs/)"
}

Which is the same response as if an invalid assembly id was used.

In my website, I use a request to genome/accession/${assemblyId}/dataset_report to validate whether an assembly entered by the user exists. The issue is that I get the same response with:

• An assembly that exists, but is not included in datasets
• An assembly that does not exist

Describe the solution you'd like

It would be nice if the 404 response message was different in each case, and potentially include the identifier of the latest version.

[olearyna]

Hi manulera

Thanks for your suggestions on improving the error code messages. We appreciate your feedback and will look into improving our response system. Below are a few curl commands that might help with the issues you brought up

To check if an accession is valid, you can use the following command:

curl -X GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000001405.40%2CGCF_000001635.27%2CGCF_9999.1/check" \ -H "Accept: application/json"

For the dataset_report, you need to add the following parameter to see if there is data for an accession curl -X GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_004355105.1/dataset_report?filters.assembly_version=all_assemblies&returned_content=ASSM_ACC" -H "Accept: application/json"

You can use the following command to get the latest version:

curl -X GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000001405/dataset_report?filters.assembly_version=current&returned_content=ASSM_ACC" -H "Accept: application/json"

Please let me know if you have any more suggestions or questions.

Nuala

[manulera]

Hi @olearyna thank you so much for the swift reply. That works for my use-case, and it's great that you get the identifier of the latest assembly, so I will be able to display that for users.

Just to double-check that I got that right, all assemblies with status previous are not accessible through the annotation report, right? It's nothing special about GCF_004355105.1.

[olearyna]

Hi manulera,

Apologies, I didn't address that issue in my response. We should have annotation tables for all previous assembly versions that are annotated. For example: https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_014058445.1/annotation_report. There seems to be a bug with the example you provided. We're looking into it.

Nuala

[manulera]

Hi @olearyna, thanks for the clarification! If possible, let me know when GCF_004355105.1 is fixed, since a user is using annotations based on that assembly

[ericcox1]

Hi @manulera, This has been fixed. Please check: https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_004355105.1/annotation_report

Best, Eric

[manulera]

Thanks @ericcox1 !