Adding support for existing Biosample

[cgirardot]

The tool currently does not support submitting data where the sample already exist in BioSample.
This could be achieved by adding an optional biosample column in the samples.tsv and modifying the ENA_template_samples_XYZ.xml

Reading theSRA.sample.xsd, it is unclear to me how to pass the biosample ref; would it be something like

<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.sample.xsd">
    <SAMPLE alias="mysample" center_name="Genomics Core Facility">
        <TITLE>my_sample</TITLE>
        <SAMPLE_NAME>
            <TAXON_ID>9606</TAXON_ID>
            <SCIENTIFIC_NAME>Homo sapiens</SCIENTIFIC_NAME>
        </SAMPLE_NAME>
        <DESCRIPTION>blah blah </DESCRIPTION>
	<SAMPLE_LINKS>
  		<SAMPLE_LINK>
                    <XREF_LINK>
                            <DB>biosample</DB>
                            <ID>289</ID>
                            <LABEL>SAMN00000289</LABEL>
                    </XREF_LINK>
		</SAMPLE_LINK>
	</SAMPLE_LINKS>
…
    </SAMPLE>
</SAMPLE_SET>

see xref example here

[bedroesb]

This is a great proposal, and something we implemented in the MARS project in the repository api components, so we can have a look there.

[bedroesb]

From ENA: se the SAMPLE_DESCRIPTOR for this

[cgirardot]

I see the SAMPLE_DESCRIPTOR gets filled in with <SAMPLE_DESCRIPTOR refname="${row.sample_alias}"/>, so it seems it is only a matter of injecting the BioSample accession as a sample_alias. No code change seems required.
I have a use case, I will try and report here