feat: add notebook for submitting civic assertions via prod api

[korikuzma]

close #12

Probably didn't need a PR, but thought I'd save work.

[larrybabb]

I'm not sure what all this is. But I approve. 😁

[korikuzma]

@larrybabb @ahwagner SCV005045671 and SCV005045669 are now viewable on the ClinVar UI

[ahwagner]

Looking at this, it appears that there are some slight differences between the automated and manual submissions:

Primarily 1) links to the associated CIViC AID and EID records and 2) link to the appropriate method for each assertion type.

[ahwagner]

See #13 (comment)

[korikuzma]

Primarily 1) links to the associated CIViC AID and EID records

@ahwagner see this comment and the following comment. I had trouble submitting CIViC URLs

[korikuzma]

2. link to the appropriate method for each assertion type.

@ahwagner Hm. I will look into this later.

[korikuzma]

@ahwagner I am going to email the ClinVar team to see if there is a way to include this information using the API or if it's not supported yet.

[korikuzma]

@ahwagner I am going to email the ClinVar team to see if there is a way to include this information using the API or if it's not supported yet.

@ahwagner I emailed giving them examples of citations with URLs (including the germline test submission) with failures. They confirmed URLs are not working with the API but that the development team is discussing and will get back to us.

I’ve submitted an update to include guideline PMID and hoping it shows in the UI soon.

[korikuzma]

SCV005045669 link to guidelines has been updated (added assertionCriteria). Still waiting on onco to be updated.

[korikuzma]

@ahwagner I emailed giving them examples of citations with URLs (including the germline test submission) with failures. They confirmed URLs are not working with the API but that the development team is discussing and will get back to us.

They confirmed it is a bug and will let us know when it is fixed.