Clinical-Genomics / scout / 8366

84%

push

travis-ci

Improved OMIM diagnosis handling (#1707)

* work in progress

* autocomplete omim diagnoses works

* autocomplete works for diagnoses and genes

* some more work in progress

* fix bug blocking partial causatives for cases with only OMIM diagnosis and not HPO terms

* fix partial causative message

* display number of genes alogside OMIM diagnosis

* created code to handle diagnoses

* fixed error when removing OMIM terms from case

* fix potential bug

* blacked all and renamed a class

* fix pytest.ini

* added tests for the frontend (server) code

* added backend tests

* reformat 2 tests

* revert pytest.ini

* renamed a template

* add genes and link to omim page also in diagn phenotypes

* better code and unblack stuff to be consistent with unchanged files

* update a test

* blacked one file

* prevent error when users type nonsense in omim form and allow them to input numeric omim ids only

* add a page for showing all available diagnoses

* template fix

* some html fixes

* make table sortable

* go back to all OMIM terms from a specific term

* typo

* query diagnosis by gene

* query by gene hgncid

* revert query

* remove conflict leftovers

* black some files

* Delete madeline.svg

* prevent crash when case diseases corespond to missing omim terms

* prevent crash when case diseases corespond to missing omim terms

* update pytest dependency

* More user friendly placeholders in form

* remove redundant text due to previous conflict fix

* black one file

* typo

Co-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>

52 of 52 new or added lines in 7 files covered. (100.0%)

10325 of 13167 relevant lines covered (78.42%)

0.78 hits per line