ChIP-Input experiments not validating

[sitag]

As per https://github.com/IHEC/ihec-ecosystems/blob/master/docs/metadata/1.0/Ihec_metadata_specification.md , things like

<EXPERIMENT_ATTRIBUTE><TAG>CHIP_PROTOCOL</TAG><VALUE></VALUE></EXPERIMENT_ATTRIBUTE>

should validate. But when we parse this xml, the json gets None for "chip_protocol" and this fails against https://github.com/IHEC/ihec-ecosystems/blob/master/schemas/json/experiment.json#L135 as it is not a string.

[sitag]

@juettemann you might need to keep this in mind.

[dzerbino]

Hello @sitag,

I'm not sure I agree with your reading of the spec. It says: CHIP_PROTOCOL - The ChIP protocol used, or 'Input'..

As I understand it, the XML example you provided should not validate.

Cheers,

Daniel

[sitag]

@dzerbino Sorry, I meant nullable attributes like "CHIP_ANTIBODY"

[dzerbino]

OK, here's one possible solution: each time a property is of type "string" without any constraints (e.g. enum, regex etc), then we replace "string" with ["string","null"]

[sitag]

@dzerbino There was some discussion (with @dbujold ) about supporting lists for attributes and not strings, in which case a NA value is an empty list (?) ..are we moving forward with lists or staying with strings?

[dzerbino]

Hello @sitag,

That's a good point:

• My proposes solution is only a short term solution for EpiMap
• The lists (due V1.1) would be the long term one, assuming that NA is indeed an empty list

Cheers,

Daniel

[sitag]

submitted ["string", "null"] fix. https://github.com/IHEC/ihec-ecosystems/pull/60/commits/15bf5ec2e39d41423894ea19e913ae6c77afb44f

[dzerbino]

Can we close then?

[sitag]

sure ...assuming it looks good to you