Adjust ClinVar XML generation to latest update

[holtgrewe]

Is your feature request related to a problem? Please describe.
The ClinVar upload does not work properly, see below.

Describe the solution you'd like
Adjust the output XML format to the new, needed format.

Describe alternatives you've considered
N/A

Additional context

Thank you for the interest in submitting to ClinVar.

We updated our processing of clinical features in March 2022 to now include the qualifiers "present", "absent"
and "not tested". For example, instead of:

<TraitSet>
    <TraitSetType val_type="name">Finding</TraitSetType>
    <Trait>
        <TraitType val_type="name">Finding</TraitType>
        <XRef db="HP" id="HP:0001332"/>
    </Trait>
</TraitSet>

the new XML structure is

 <TraitSet>
    <TraitSetType val_type="name">Finding</TraitSetType>
    <Trait ClinicalFeaturesAffectedStatus="present">
        <TraitType val_type="name">Finding</TraitType>
        <XRef db="HP" id="HP:0011332"/>
    </Trait>
</TraitSet>        

If you are providing the HPO identifier, <Name> is not needed.

Also note, please include sub_id="SUB12068620" in the ClinvarSubmissionSet element.

Please update your file, delete the existing one, and upload the update.

[holtgrewe]

Resolution Proposal
Simply adjust the ClinVar XML generation code in clinvar_export.clinvar_xml.

Affected Components
VarFish Server

Affected Modules/Files
clinvar_export/clinvar_xml.py

Required Architectural Changes
None

Required Database Changes
None

Backport Possible?
Yes

Resolution Sketch
See above.

[holtgrewe]

ClinVar will shut down their XML support and is not updating their XSD any more. We will need to eventually migrate to using their API. For now, we will ignore the following issue in XSD validation

• Element 'Trait', attribute 'ClinicalFeaturesAffectedStatus': The attribute 'ClinicalFeaturesAffectedStatus' is not allowed.