Conversation
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #99 +/- ##
===========================================
+ Coverage 83.05% 83.09% +0.03%
===========================================
Files 18 18
Lines 2461 2466 +5
===========================================
+ Hits 2044 2049 +5
Misses 417 417
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
| # Matching disease RIDs from GraphKB using term tree | ||
| # (Will raise uncatched error if no match) | ||
| disease_matches: list[str] = get_kb_disease_matches(graphkb_conn, kb_disease_match) | ||
| disease_match_records: [list[str], list[str]] = get_kb_disease_matches( |
There was a problem hiding this comment.
technically returns a tuple[list[str], list[str]]
| return disease_matches | ||
| disease_match_rids = [item['@rid'] for item in disease_matches] | ||
| disease_match_names = [item['name'] for item in disease_matches] | ||
| return (disease_match_rids, disease_match_names) |
There was a problem hiding this comment.
I'm curious, why returning 2 seperate lists instead of a list of dict like
[
{"@rid":"#123:45", "name":"disease 1"},
{"@rid":"#123:46", "name":"disease 2"},
...
]
There was a problem hiding this comment.
Went back and forth on this, it's just a question of whether the work gets done in this func or in main. I'm happy to move it.
There was a problem hiding this comment.
I find it easier for get_kb_disease_matches() reusability, but non-blocking.
| disease_match_records: [list[str], list[str]] = get_kb_disease_matches( | ||
| graphkb_conn, kb_disease_match | ||
| ) | ||
| disease_match_rids: list[str] = disease_match_records[0] |
There was a problem hiding this comment.
You can have it all in one go::
disease_match_rids, disease_match_names = get_kb_disease_matches(
graphkb_conn,
kb_disease_match,
)
3 participants
When generating analyst summary text from IPR prepared variant text, does disease matching using same the list of matching disease terms from graphkb that are used to set matched_cancer on kb statements.