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metadatacenter / cedar-template-editor

Web application containing the CEDAR Template Designer, Metadata Editor, and Metadata Explorer
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Add support for updating BioSample submissions #782

Open marcosmro opened 5 years ago

marcosmro commented 5 years ago

Our current MiAIRR submission pipeline is not able to deal with BioSample updates. If a given biosample identifier is already in the NCBI systems and a user needs to update the metadata for that biosample or submit new data files for it, our current submission system will return an error. Currently, the only way of dealing with this situation is contacting the NCBI staff and ask them to manually update the BioSample metadata/data.

The NCBI staff will send us an example of the XML file that CEDAR could use to support BioSample updates.

graybeal commented 5 years ago

Yuriy Skripchenko writes September 14:

I have also attached an example XML file for updating a BioSample. You will notice that there is the PrimaryId tag in the BioSample/SampleId block. BioSample required that both the PrimaryId and the SPUID tags are present in that section in the same order as in the example XML. You will also need to generate a new Identifier/SPUID tag for this transaction.