James Stevenson jsstevenson

`uv` notes

uv is a Python tool for managing dependencies, builds, and runtimes. Inspired by major players in other languages like cargo and npm. It should further simplify the hassle of dealing with Python runtimes and environments and I would strongly recommend switching over to it.

installation

Cleanup

Get rid of pyenv

get DictReader for interactions TSV:

import csv
with open("~/Downloads/interactions.tsv") as f:
    next(f)  # skip header rows
    next(f)
    lines = list(csv.DictReader(f, delimiter="\t"))

misc notes

Dependencies on intake form seem incomplete -- OBI, Uberon?
treatment of 'history' is weird. BFO history (process) is imported but unreferenced. "smoking history" is defined as a "quality" but not as a subclass of "medical history".

Criteria

1. Ontology scope

notes

Each kind of response is slightly different, but this tries to make them more consistent in a few ways:

No more gene vs normalized gene object. Everything is a GA4GH core Gene. This means no more associated_with vs xref, so one less kind of MatchType.
The outermost level includes the query, additional parameters passed to the API endpoint (I think (...?) this is good practice to include) and service information
The outermost level also includes a match key that points to what the individual Python QueryHandler methods would return. IMO it makes more sense to move this stuff into the REST API response because these are things that you don't otherwise typically include in Python-to-Python methods (e.g. another class doesn't need to know what version of Gene Normalizer is running, it's literally sharing the environment).
match objects include source metadata and warnings. In some of the responses, we have previously included source metadata closer to the actual source matches, b

	[
	{
	"n": {
	"identity": 1625,
	"labels": [
	"Strength"
	],
	"properties": {
	"mappings": "[{\"id\":null,\"extensions\":null,\"coding\":{\"id\":null,\"extensions\":null,\"name\":\"preclinical evidence\",\"system\":\"https://go.osu.edu/evidence-codes\",\"systemVersion\":null,\"code\":\"e000009\",\"iris\":null},\"relation\":\"exactMatch\"}]",
	"primary_coding": "{\"id\":null,\"extensions\":null,\"name\":null,\"system\":\"https://civic.readthedocs.io/en/latest/model/evidence/level.html\",\"systemVersion\":null,\"code\":\"D\",\"iris\":null}",

	# This file is autogenerated by maturin v1.7.6
	# To update, run
	#
	# maturin generate-ci github -o tmp.yaml
	#
	name: CI

	on:
	push:
	branches:

	name \| name \| score \| gene_specificity \| drug_specificity \| evidence_score
	------+------------------------------------------------------------+----------------------+---------------------+----------------------+----------------
	BCL2 \| BORTEZOMIB \| 0.007488459062167905 \| 0.17546867625942625 \| 0.042676899500264064 \| 1
	BCL2 \| CARBOPLATIN \| 0.00757760738433657 \| 0.17546867625942625 \| 0.04318495782764816 \| 1
	BCL2 \| DOCETAXEL ANHYDROUS \| 0.007668903858846649 \| 0.17546867625942625 \| 0.04370525852436681 \| 1
	BCL2 \| VINCRISTINE \| 0.007858259509682369 \| 0.17546867625942625 \| 0.044784400710153646 \| 1
	BCL2 \| DOXORUBICIN HYDROCHLORIDE \| 0.008601608382219891 \| 0.17546867625942625

	{
	"pre_mapped": {
	"id": "ga4gh:VA.FLe4-pSUs7vjdVtVD4TmUNL4JhrBbqTd",
	"type": "Allele",
	"extensions": [
	{
	"name": "vrs_ref_allele_seq",
	"value": "Y"
	}
	],

	{
	"schemaVersion": 1,
	"label": "QC",
	"message": "N/A",
	"color": "white",
	"logoSvg": "<svg id=\"Layer_1\" data-name=\"Layer 1\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 135.54 133.3\"><defs><style>.cls-1{fill:#fff;}.cls-2{fill:#231f20;}</style></defs><path class=\"cls-1\" d=\"M85.31,20.58l-4-16.64s0,0,0,0c-1.11-.14-2.21-.26-3.33-.35s-2.24-.15-3.36-.18-2.26,0-3.4,0c-.82,0-1.66.06-2.49.11L63.21,19.66c-.22,0-.43.11-.65.15l0,.11c-1.58.3-3.13.68-4.65,1.12s-3,1-4.45,1.53L40.52,11.64c-.58.32-1.17.63-1.74,1-1,.56-1.91,1.14-2.83,1.74s-1.84,1.23-2.73,1.88-1.77,1.31-2.63,2l-.73.6L34.72,35c-.15.16-.28.33-.42.48v0c-1.12,1.18-2.17,2.42-3.17,3.7s-1.95,2.59-2.84,4h-.06v0l-16.83-1c-.31.62-.62,1.23-.91,1.85-.46,1-.88,2-1.29,3.07-.28.69-.53,1.39-.79,2.09-.12.35-.26.7-.38,1.05-.36,1-.69,2.1-1,3.17-.1.33-.17.68-.26,1l13.4,10.13a54.29,54.29,0,0,0-.56,10.73L5.25,84.54c.09.52.16,1,.26,1.55.21,1.08.44,2.16.7,3.23s.54,2.14.85,3.2.65,2.12,1,3.16c.14.42.31.82.46,1.24h0L25.22,97l0,0h.13a51.6,51.6,0,0,0,5.88,9

	{
	"oboscore": {
	"dashboard_score_max_impact": {
	"dashboard": 1,
	"impact": 1,
	"impact_external": 3,
	"no_base": 5,
	"overall_error": 20,
	"overall_info": 5,
	"overall_warning": 10,