URL Configuration and Germplasm Implementation

[Gouripriya5]

Hello Matthijs,

I wanted to inform you that I have successfully implemented the Germplasm GET/Attributes and GET/AttributeValues endpoints. However, I have a question regarding the URLs we should use for the Germplasm endpoints.

Currently, for genotyping, we use the following URL: https://agent.ipk-gatersleben.de/genotyping/brapi/v2/callsets or Samples

For Germplasm, I have been using: /genotyping/brapi/v2/attributes or attributevalues

My question is whether I should implement a different URL specifically for Germplasm, such as: https://agent.ipk-gatersleben.de/germplasm/brapi/v2/attributes

Or if the existing URL (/genotyping/brapi/v2/attributes) is sufficient. Which URL would be best to use for the BrAPI proxy?

Your guidance on this matter would be greatly appreciated. Thank you!

Best regards,
Priya.

[Gouripriya5]

Hi Priya,

Both options are possible for the proxy. However, if you are using a different germplasm URL, a separate serverinfo endpoint will be needed as well. You can choose the option that makes the most sense for your implementation and local infrastructure. Please let me know when the new endpoints are online and available.

Best,

Matthijs

[Gouripriya5]

How ever you decide. The argument to need for multiple servierinfo endpoints is relevant. So, maybe there is still time to move also /genotype URL to a unique common URL scheme. This cause of curse additional work to re-adjust program code and Proxy prototype and GITHub Doku. But now its not rolled out and the effects could be handled.

What do you think?

Thanks!
Matthias

[Gouripriya5]

Hello Matthijs,

I am using the same URL that is used for genotyping. The germplasm endpoints are now online and available. Please check and let me know if everything is working correctly.

GET/ Attributes :

https://agent.ipk-gatersleben.de/genotyping/brapi/v2/attributes
https://agent.ipk-gatersleben.de/genotyping/brapi/v2/attributes?ATTRIBUTEDBID=10352

GET/ AttributeValues:

https://agent.ipk-gatersleben.de/genotyping/brapi/v2/attributevalues
https://agent.ipk-gatersleben.de/genotyping/brapi/v2/attributevalues?GERMPLASMDBID=121888

Thanks.
Best regards
Priya.

[Gouripriya5]

Hi Priya,

I had a quick look at the server details and noticed a few points that need attention:

• The server info at https://agent.ipk-gatersleben.de/genotyping/brapi/v2/serverinfo needs to be updated with the new endpoints.
• The names are all uppercased, which does not comply with the specified naming conventions.

Best,
Matthijs

[Gouripriya5]

Hello @matthijsbrouwer

I've updated the server info with the new endpoints and adjusted the names to comply with the naming conventions.
Can you please double check that I have done everything correctly?
Thanks!

[matthijsbrouwer]

I still see uppercased names for attributes and I think for example scale is required in the response.

[Gouripriya5]

Hello @matthijsbrouwer for now Uppercased issue has fixed. Please check the updated response.

I’m working on including the "scale" field in the response. I’ll update you once that is implemented.

[matthijsbrouwer]

Some comments on BrAPI implementation by AGENT database backend:

• studies and germplasm not yet included in serverinfo
• samples:
  • output has observationUnitId: "None", but this probably should be observationUnitId: null
• callsets:
  • callSetDbId SAMEA8867410 has callSetName Diabas, but using this as parameter returns zero results
• attributes:
  • scale required in response but missing
  • attributeDbId 11028 has attributeCategory Phenological, but using this as parameter returns zero results
  • attributeDbId 10352 has attributeName Sowing Date, but using this as parameter returns zero results
• attributevalues:
  • attributeValueDbId 220308 has attributeName Thousand Kernel Weight, but using this as parameter returns zero results