Fix multiple conditions parsing

[northwestwitch]

This PR adds | fixes:

• Fix validation error die to uppercase multipleConditionExplanation (fix ClinVar upload issues.. #114 )

How to prepare for test:

• Download the scout submission mentioned in the issue as json and convert MultipleConditionExplanation to lower case

How to test:

• Try to validate the submission against the schema using this service: https://www.jsonschemavalidator.net/

Expected outcome:

• Validation should pass

Review:

• Code approved by
• Tests executed by CR

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[northwestwitch]

After downloading the submission in question from Scout:

• Submission with uppercase (MultipleConditionExplanation)

• After fixing the field name with lowercase (multipleConditionExplanation):

The remaining error in the validation is due to one of the variants that has an empty observedIn field. This variant in ANKRD11 has also other issues so better fixing it before doing the submission

[northwestwitch]

Other errors I see in the submission:

Perhaps download it as json and inspect it before submitting it as it is?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.02%. Comparing base (ef00987) to head (9e3135f).
Report is 7 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #115   +/-   ##
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  Coverage   95.02%   95.02%           
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  Files          11       11           
  Lines         462      462           
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  Hits          439      439           
  Misses         23       23           

Flag	Coverage Δ
unittests	95.02% <100.00%> (ø)

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[dnil]

Other errors I see in the submission:
...
Perhaps download it as json and inspect it before submitting it as it is?

I wonder how they got in there? Added before fixes?

[northwestwitch]

I wonder how they got in there? Added before fixes?

The errors? Could have happened before or after. The check for what's included in the associated conditions is not that strict, even if it kind of pre-fills the field for you already (so if you stick to what's there you should be fine). I wonder if we should make it super strict instead.. Like if you add an HP term then it should have the format HP:0000356 and not HP:HP:0000356 or HP:somedisease and so on..

[dnil]

I wonder how they got in there? Added before fixes?

The errors? Could have happened before or after. The check for what's included in the associated conditions is not that strict, even if it kind of pre-fills the field for you already (so if you stick to what's there you should be fine). I wonder if we should make it super strict instead.. Like if you add an HP term then it should have the format HP:0000356 and not HP:HP:0000356 or HP:somedisease and so on..

Ah, ofcourse - they are manual adds?! I was wondering how they ended up there, and was searching for the events. 😆
Not wanting to be biased here, but I did see a peculiar user gender trend in the malformatted entries. 😂 We can always explain again, but I feel that with the pretty clear comment above, it would be best that manually entries are checked against our existing db entries. If we should allow manual input at all there? The submissions are brittle anyway, with little room for manual this-should-work-if-I-just-type-something-and-wish-for-it flair.

[dnil]

I'll clean up that submission, but lets fix.

[northwestwitch]

I'll clean up that submission, but lets fix.

Agreed