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test: only check vrs ids on certain tests (#540)
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* We do not need to be checking VRS IDs on every single test. This
  reduces to making this check in one place where ga4gh_identify
function is called
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@korikuzma
korikuzma authored Mar 1, 2024
1 parent 32e1dc3 commit bc36816
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Showing 9 changed files with 73 additions and 495 deletions.
63 changes: 31 additions & 32 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
"""Create methods used throughout tests."""
import asyncio
import contextlib

import pytest
from cool_seq_tool.app import CoolSeqTool
Expand Down Expand Up @@ -93,7 +94,6 @@ def prpf8_ncbi_seq_loc():
},
"start": 1650628,
"end": 1684867,
"id": "ga4gh:SL.1i49iv3wcBq7SaOA14cs1Kz7SR6DkCw1",
"type": "SequenceLocation",
}

Expand Down Expand Up @@ -129,9 +129,7 @@ def braf_v600e(braf_600loc):
def vhl_reference_agree():
"""Create NP_000542.1:p.Pro61 fixture."""
params = {
"id": "ga4gh:VA.RMmwTvhrPVwfMZ6knsf5zMWQn_F1ukYh",
"location": {
"id": "ga4gh:SL.8TZYB8Oqqn93q07zrsNhvRW1JjNpaQXc",
"end": 61,
"start": 60,
"sequenceReference": {
Expand All @@ -150,9 +148,7 @@ def vhl_reference_agree():
def protein_insertion():
"""Create test fixture for NP protein insertion (CA645561585)."""
params = {
"id": "ga4gh:VA.AOCCh_BU5wKkdgoDNqkORF_x4GQwWh1T",
"location": {
"id": "ga4gh:SL.ciWb1ylkqUxiviU1djijiuYVZcgsnQnV",
"end": 770,
"start": 770,
"sequenceReference": {
Expand All @@ -173,9 +169,7 @@ def protein_deletion_np_range():
range for deletion.
"""
params = {
"id": "ga4gh:VA.3Rk_RElDfX820edkQOHsTTYRogr0EMEY",
"location": {
"id": "ga4gh:SL.kOTzy0aLlw0yqnmf29Zk8wh65zHQwere",
"end": 759,
"start": 754,
"sequenceReference": {
Expand All @@ -199,9 +193,7 @@ def protein_deletion_np_range():
def braf_v600e_genomic_sub():
"""Create test fixture for NC_000007.14:g.140753336A>T"""
params = {
"id": "ga4gh:VA.LX3ooHBAiZdKY4RfTXcliUmkj48mnD_M",
"location": {
"id": "ga4gh:SL.XutGzMvqbzN-vnxmPt2MJf7ehxmB0opi",
"end": 140753336,
"start": 140753335,
"sequenceReference": {
Expand Down Expand Up @@ -264,7 +256,6 @@ def genomic_dup1_38_cn(genomic_dup1_seq_loc_not_normalized):
def genomic_dup2_seq_loc_normalized():
"""Create genomic dup2 sequence location"""
return {
"id": "ga4gh:SL.rVXa8TXm6WTEw-_Lom6A347Q45SB7CON",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -280,7 +271,6 @@ def genomic_dup2_38_cn(genomic_dup2_seq_loc_normalized):
"""Create test fixture for copy number count dup2 on GRCh38"""
params = {
"type": "CopyNumberCount",
"id": "ga4gh:CN.C8WuNCba5AN1RoXK1enXgALlM1Qz6X6i",
"location": genomic_dup2_seq_loc_normalized,
"copies": 3,
}
Expand All @@ -291,7 +281,6 @@ def genomic_dup2_38_cn(genomic_dup2_seq_loc_normalized):
def genomic_del3_dup3_loc_not_normalized():
"""Create genomic del3 dup3 sequence location"""
return {
"id": "ga4gh:SL.-zCp7JBaKQ0niPDueJkuCgQhRIQ50hKw",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -306,7 +295,6 @@ def genomic_del3_dup3_loc_not_normalized():
def genomic_dup4_loc():
"""Create genomic dup4 sequence location"""
return {
"id": "ga4gh:SL.o8sCaAaW2a2f_HsNBTsHOCnWRvIyru0y",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.-A1QmD_MatoqxvgVxBLZTONHz9-c7nQo",
Expand All @@ -321,7 +309,6 @@ def genomic_dup4_loc():
def genomic_dup5_loc():
"""Create genomic dup5 sequence location"""
return {
"id": "ga4gh:SL.O__pyYq_u7R__2NUbI3koxxkeCBL7WXq",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -336,7 +323,6 @@ def genomic_dup5_loc():
def genomic_dup6_loc():
"""Create genomic dup6 sequence location"""
return {
"id": "ga4gh:SL.Ls2wfxI-2V2OdMY5HHttwlSwgbpNf_j2",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -351,7 +337,6 @@ def genomic_dup6_loc():
def genomic_del1_seq_loc():
"""Create genomic del1 sequence location"""
return {
"id": "ga4gh:SL.zMba5wGtQWQmdFd70yEqMYszGoRaYX25",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.Zu7h9AggXxhTaGVsy7h_EZSChSZGcmgX",
Expand All @@ -367,7 +352,6 @@ def genomic_del1_lse(genomic_del1_seq_loc):
"""Create a test fixture for genomic del LSE."""
params = {
"type": "Allele",
"id": "ga4gh:VA.gztc0BFS6p5V1_QVnEYIJ6DwzZQeDCd2",
"location": genomic_del1_seq_loc,
"state": {
"length": 0,
Expand All @@ -384,7 +368,6 @@ def genomic_del1_38_cn(genomic_del1_seq_loc):
"""Create test fixture for copy number count del1 on GRCh38"""
params = {
"type": "CopyNumberCount",
"id": "ga4gh:CN.wRj3ZKNriLtPDVj0VlPaTCQfklj2ocGU",
"location": genomic_del1_seq_loc,
"copies": 1,
}
Expand All @@ -395,7 +378,6 @@ def genomic_del1_38_cn(genomic_del1_seq_loc):
def genomic_del2_seq_loc():
"""Create genomic del2 sequence location"""
return {
"id": "ga4gh:SL.usVkXRvjfX0cEXLvP87Oi8eJJGyizjQF",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.Zu7h9AggXxhTaGVsy7h_EZSChSZGcmgX",
Expand All @@ -411,7 +393,6 @@ def genomic_del2_lse(genomic_del2_seq_loc):
"""Create a test fixture for genomic del LSE."""
params = {
"type": "Allele",
"id": "ga4gh:VA.9NmH0sRYerurt-CE6WlF9UaxZiujByIE",
"location": genomic_del2_seq_loc,
"state": {
"type": "ReferenceLengthExpression",
Expand All @@ -428,7 +409,6 @@ def genomic_del2_38_cn(genomic_del2_seq_loc):
"""Create test fixture for copy number count del1 on GRCh38"""
params = {
"type": "CopyNumberCount",
"id": "ga4gh:CN.i7HRf9gge1HJKzazgvtinosa0bE3gHJu",
"location": genomic_del2_seq_loc,
"copies": 1,
}
Expand All @@ -439,7 +419,6 @@ def genomic_del2_38_cn(genomic_del2_seq_loc):
def genomic_del4_seq_loc():
"""Create genomic del4 sequence location"""
return {
"id": "ga4gh:SL.bWbNmdT__ptImBwTAIYdyNfazhwvEtXD",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -454,7 +433,6 @@ def genomic_del4_seq_loc():
def genomic_del5_seq_loc():
"""Create genomic del5 sequence location"""
return {
"id": "ga4gh:SL.WDxMzftZLrwp2eQJrlasKuY4ns99wG0v",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
Expand All @@ -469,7 +447,6 @@ def genomic_del5_seq_loc():
def genomic_del6_seq_loc():
"""Create genomic del6 sequence location"""
return {
"id": "ga4gh:SL.TKIwU5OzGgOWIpnzAHfkCLB7vrKupKhD",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV",
Expand All @@ -484,7 +461,6 @@ def genomic_del6_seq_loc():
def grch38_genomic_insertion_seq_loc():
"""Create test fixture for GRCh38 genomic insertion seq location"""
return {
"id": "ga4gh:SL.oVzSkGhh3QJ0FAgihm-kNr9CJbF_7Ln2",
"end": 39724743,
"start": 39724731,
"sequenceReference": {
Expand All @@ -499,7 +475,6 @@ def grch38_genomic_insertion_seq_loc():
def grch38_genomic_insertion_variation(grch38_genomic_insertion_seq_loc):
"""Create a test fixture for NC_000017.10:g.37880993_37880994insGCTTACGTGATG"""
params = {
"id": "ga4gh:VA.eorsJMgis9uDdRRPVd3srYofdPaM_xn2",
"location": grch38_genomic_insertion_seq_loc,
"state": {
"length": 24,
Expand Down Expand Up @@ -528,7 +503,6 @@ def braf_amplification(braf_ncbi_seq_loc):
def prpf8_amplification(prpf8_ncbi_seq_loc):
"""Create test fixture for PRPF8 Amplification"""
params = {
"id": "ga4gh:CX.KH_rYvTqg5Hq0ysqbrh8JR20oeLYa7bk",
"location": prpf8_ncbi_seq_loc,
"copyChange": "efo:0030072",
"type": "CopyNumberChange",
Expand All @@ -541,28 +515,53 @@ def genomic_del3_dup3_cn_38(genomic_del3_dup3_loc_not_normalized):
"""Create test fixture copy number variation for del/dup 3 on GRCh38"""
params = {
"type": "CopyNumberCount",
"id": "ga4gh:CN.rPsK0krAHgmXhDZEw4fqymR0iDQa3UCJ",
"location": genomic_del3_dup3_loc_not_normalized,
"copies": 2,
}
return models.CopyNumberCount(**params)


def assertion_checks(normalize_response, test_variation):
def _delete_id(vrs_obj_dict):
"""Delete ID property from VRS object"""
with contextlib.suppress(KeyError):
# Some fixtures have IDs for other tests
del vrs_obj_dict["id"]


def assertion_checks(normalize_response, test_variation, check_vrs_id=False):
"""Check that normalize_response and test_variation are equal."""
actual = normalize_response.variation.model_dump(exclude_none=True)
expected = test_variation.model_dump(exclude_none=True)
if not check_vrs_id:
assert actual.pop("id").startswith(("ga4gh:VA.", "ga4gh:CX", "ga4gh:CN."))
assert actual["location"].pop("id").startswith("ga4gh:SL.")

expected = test_variation.copy().model_dump(exclude_none=True)
if not check_vrs_id:
_delete_id(expected)
_delete_id(expected["location"])

assert actual == expected, "variation"


def cnv_assertion_checks(resp, test_fixture):
def cnv_assertion_checks(resp, test_fixture, check_vrs_id=False):
"""Check that actual response for to copy number matches expected"""
try:
cnc = resp.copy_number_count
except AttributeError:
actual = resp.copy_number_change.model_dump(exclude_none=True)
prefix = "ga4gh:CX."
else:
actual = cnc.model_dump(exclude_none=True)
expected = test_fixture.model_dump(exclude_none=True)
prefix = "ga4gh:CN."

if not check_vrs_id:
assert actual.pop("id").startswith(prefix)
assert actual["location"].pop("id").startswith("ga4gh:SL.")

expected = test_fixture.copy().model_dump(exclude_none=True)
if not check_vrs_id:
_delete_id(expected)
_delete_id(expected["location"])

assert actual == expected
assert resp.warnings == []
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