Fix #28 - _id type

[dnil]

This PR adds | fixes:

• issue retrieving SV vars from the API - See #28.

How to test:

• test a local curl for a SV variant on cg-vm1
• check that scout-stage can reach SV variants

Review:

• [ ] Code approved by
• [ ] Tests executed by

This version is a:

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

[dnil]

Hm, apparently not enough with 'Any' (nor missing). A validator it is then?!

Mar 01 10:42:15 cg-vm1.scilifelab.se conmon[1906892]:   File "/usr/local/lib/python3.9/site-packages/fastapi/encoders.py", line 139, in jsonable_encoder
Mar 01 10:42:15 cg-vm1.scilifelab.se conmon[1906892]:     raise ValueError(errors)
Mar 01 10:42:15 cg-vm1.scilifelab.se conmon[1906892]: ValueError: [TypeError("'ObjectId' object is not iterable"), TypeError('vars() argument must have __dict__ attribute')]

[dnil]

Ok, tested on cg-vm1. BUT needs testing with more scenarios and scout interaction before merging.

[hiseq.clinical@cg-vm1 ~]$ systemctl --user stop loqusdbapi.target
[hiseq.clinical@cg-vm1 ~]$ systemctl --user start loqusdbapi-rd@fix_broken_svs
[hiseq.clinical@cg-vm1 ~]$  curl -X GET "http://cg-vm1.scilifelab.se:7079/svs/?chrom=X&end_chrom=X&pos=65549568&end=88119178&sv_type=DEL"
{"chrom":"X","observations":1228,"families":["choiceracer","tightdoe","briefglider","primeasp","livingpup","topghost","tidygull","caringhound","neatkodiak","fluentsnake","trueroughy","movingbengal","superbhyena","growncrane","novelfilly","awareliger","frankswan","greatosprey","activehyena","mintlocust","suitedakita","subtlestag","poeticraptor","validmoose","intentboar","normallion","vocalrodent","gamegoblin","crackkodiak","moralmidge","actualfeline","squarequail","betterturtle","loyaloryx","onechimp","robustsnipe","happyrobin","busyloon","viableparrot","socialbream","truedeer","frankloon","neatmole","honestparrot","livingmarmot","freeelk","gladurchin","caringskunk","pumpedquail"],"_id":"5d0929a66202ae53c63bfff1","end_chrom":"X","end_left":88116180,"end_right":88122180,"end_sum":108210353266,"sv_type":"DEL","length":22569593,"pos_left":65546587,"pos_right":65552587,"pos_sum":80494892915,"total":5323}

[dnil]

Scout(-stage) interaction works.

[northwestwitch]

Deployed on stage:

Observations are present now!