metadatacenter / cedar-project

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Constrain Sequencing Platform to a predefined list of platforms #950

Open marcosmro opened 5 years ago

marcosmro commented 5 years ago

Using free-text entry for the Sequencing Platform field (instrument_model in the submission.xml file) has generated NCBI processing issues in previous submissions. For example, entering "Illumina HiSeq2500" instead of "Illumina HiSeq 2500" generates the following processing error:

<Response error_source="system" status="processed-error">
      <Message severity="error-stop">An error occurred during submission processing. Please contact SRA helpdesk for more information. Please do not create another (duplicate) submission with the same data.</Message>
</Response>
marcosmro commented 5 years ago

A spreadsheet with the list of instrument models can be downloaded from the SRA submission portal (templates tab, SRA section): https://submit.ncbi.nlm.nih.gov/templates/. Available here too: SRA_metadata_acc.xlsx

The tab labelled "Library and Platform Terms" contains the valid values for the following attributes in the submission.xml file:

We need to update the MiAIRR template to constrain the corresponding fields to those values.