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fix: update consequences to match mehari 0.43.2 (#2630) #2633

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fix: update consequences to match mehari 0.43.2 (#2630) #2633

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bdd5c1c
fix: update consequences to match mehari 0.43.2 (#2630)
stolpeo May 15, 2026
bb2c808
fixed js tests
stolpeo May 15, 2026
9d4127c
add missing SO terms.
stolpeo May 15, 2026
69e2cd2
clarify npm test counting effects
stolpeo May 18, 2026
9afc617
added UTR variants to noncoding effect group.
stolpeo May 19, 2026
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2 changes: 1 addition & 1 deletion backend/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ gen-api-schema:
.PHONY: protos-build
protos-build:
PYTHONPATH=. \
protoc \
pipenv run python -m grpc_tools.protoc \
-Iprotos \
--python_out=. \
--mypy_out=. \
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3 changes: 2 additions & 1 deletion backend/Pipfile
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Expand Up @@ -80,7 +80,6 @@ flake8-pyproject = "*"
freezegun = "~=1.5"
isort = "~=7.0"
jsonmatch = "*"
mypy-protobuf = "*"
openpyxl = "~=3.1"
parameterized = "~=0.9.0"
protolint-bin = "*"
Expand All @@ -96,6 +95,8 @@ watchdog = "*"
werkzeug = "~=3.1.6"
uritemplate = "*"
django-types = "*"
grpcio-tools = "==1.68.1"
mypy-protobuf = "==3.6.0"

[ldap-packages]
# Dependencies for enabling LDAP support. You will need the system library
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143 changes: 136 additions & 7 deletions backend/Pipfile.lock
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16 changes: 16 additions & 0 deletions backend/protos/seqvars/protos/query.proto
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Expand Up @@ -216,6 +216,14 @@ enum Consequence {
CONSEQUENCE_RARE_AMINO_ACID_VARIANT = 45;
// Protein altering variant
CONSEQUENCE_PROTEIN_ALTERING_VARIANT = 46;
// Inframe deletion
CONSEQUENCE_INFRAME_DELETION = 49;
// Inframe insertion
CONSEQUENCE_INFRAME_INSERTION = 50;
// Selenocysteine gain
CONSEQUENCE_SELENOCYSTEINE_GAIN = 51;
// Selenocysteine loss
CONSEQUENCE_SELENOCYSTEINE_LOSS = 52;
/*
* low impact
*/
Expand All @@ -235,6 +243,8 @@ enum Consequence {
CONSEQUENCE_STOP_RETAINED_VARIANT = 22;
// Synonymous variant.
CONSEQUENCE_SYNONYMOUS_VARIANT = 23;
// Incomplete terminal codon variant
CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT = 53;
/*
* modifier
*/
Expand All @@ -246,14 +256,20 @@ enum Consequence {
CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 26;
// 5' UTR intron variant.
CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 27;
// 5' UTR variant.
CONSEQUENCE_FIVE_PRIME_UTR_VARIANT = 54;
// 3' UTR exon variant.
CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 28;
// 3' UTR intron variant.
CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 29;
// 3' UTR variant.
CONSEQUENCE_THREE_PRIME_UTR_VARIANT = 55;
// Non-coding transcript exon variant.
CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 30;
// Non-coding transcript intron variant.
CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 31;
// Non-coding transcript variant.
CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT = 56;
// Coding transcript intron variant.
CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT = 48;
// Upstream gene variant.
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