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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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TCGAtranslateID not working? #4

Closed lwaldron closed 8 years ago

lwaldron commented 8 years ago

Shoot, has TCGA really taken down their REST interface to translate UUIDs and broken TCGAtranslateID? e.g.:

> TCGAtranslateID("00655296-ce38-4607-a99c-cb9217495e21")
No encoding supplied: defaulting to UTF-8.
Error in if (dim(id_table)[2] == 1L) { : argument is of length zero
lwaldron commented 8 years ago

Got a helpful response from Bill Wysoki at GDC:

Regarding the UUID <--> barcode mapping, this feature of the TCGA is no longer functional. However, this can be accomplished in the GDC using the API. See the following link for step-by-step instructions: https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#example-http-post-request. Running the shell command in the example will output a tab-delimited table that matches each file UUID to a TCGA among other fields that you may require. I am attaching a payload file that will allow you to access this data once you replace the example UUIDs with your own.

Payload_ID_name_barcode.example.txt

LiNk-NY commented 8 years ago

It seems to me like this can be done through R using the right packages. I'll give it a whirl.

LiNk-NY commented 8 years ago

I have added the test function under /R/TCGAtranslateUUID.R. I can't get it to work even with a valid JSON request. I could try it with the RCurl package.

schifferl commented 8 years ago

I will take a look at the JSON request and see if I can make it work too!

LiNk-NY commented 8 years ago

It seems like the request only works for certain UUIDs and not others. I was testing the function with UUIDs pulled from files on the GDC website. I tried the function again with the UUIDs provided in the example API documentation and those worked. The problem seems to be on their end..

lwaldron commented 8 years ago

By the way, their help desk seems to be responsive to requests and bug reports (support@nci-gdc.datacommons.io)...

LiNk-NY commented 8 years ago

Yes indeed, they helped me figure out the reverse translation.