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Primary Attribute for Score Set Ranges #532

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5667053
Add primary field to score range models and implement validation for …
bencap Oct 6, 2025
c11a1e7
Add Fayer score range models and integrate into score set ranges
bencap Oct 6, 2025
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111 changes: 111 additions & 0 deletions src/mavedb/view_models/score_range.py
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Original file line number Diff line number Diff line change
Expand Up @@ -148,10 +148,15 @@ class ScoreRangesCreate(ScoreRangesModify):
ranges: Sequence[ScoreRangeCreate]


class ScoreRangesAdminCreate(ScoreRangesCreate):
primary: bool = False


class SavedScoreRanges(ScoreRangesBase):
record_type: str = None # type: ignore

ranges: Sequence[SavedScoreRange]
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand Down Expand Up @@ -237,10 +242,15 @@ class BrnichScoreRangesCreate(ScoreRangesCreate, BrnichScoreRangesModify):
ranges: Sequence[BrnichScoreRangeCreate]


class BrnichScoreRangesAdminCreate(ScoreRangesAdminCreate, BrnichScoreRangesCreate):
pass


class SavedBrnichScoreRanges(SavedScoreRanges, BrnichScoreRangesBase):
record_type: str = None # type: ignore

ranges: Sequence[SavedBrnichScoreRange]
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand Down Expand Up @@ -290,11 +300,16 @@ class InvestigatorScoreRangesCreate(BrnichScoreRangesCreate, InvestigatorScoreRa
research_use_only: bool = False


class InvestigatorScoreRangesAdminCreate(ScoreRangesAdminCreate, InvestigatorScoreRangesCreate):
pass


class SavedInvestigatorScoreRanges(SavedBrnichScoreRanges, InvestigatorScoreRangesBase):
record_type: str = None # type: ignore

title: str = "Investigator-provided functional classes"
research_use_only: bool = False
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand Down Expand Up @@ -324,11 +339,16 @@ class ScottScoreRangesCreate(BrnichScoreRangesCreate, ScottScoreRangesModify):
research_use_only: bool = False


class ScottScoreRangesAdminCreate(ScoreRangesAdminCreate, ScottScoreRangesCreate):
pass


class SavedScottScoreRanges(SavedBrnichScoreRanges, ScottScoreRangesBase):
record_type: str = None # type: ignore

title: str = "Scott calibration"
research_use_only: bool = False
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand All @@ -338,6 +358,45 @@ class ScottScoreRanges(BrnichScoreRanges, SavedScottScoreRanges):
research_use_only: bool = False


##############################################################################################################
# Fayer score range models
##############################################################################################################


class FayerScoreRangesBase(BrnichScoreRangesBase):
title: str = "Fayer calibration"
research_use_only: bool = False


class FayerScoreRangesModify(BrnichScoreRangesModify, FayerScoreRangesBase):
title: str = "Fayer calibration"
research_use_only: bool = False


class FayerScoreRangesCreate(BrnichScoreRangesCreate, FayerScoreRangesModify):
title: str = "Fayer calibration"
research_use_only: bool = False


class FayerScoreRangesAdminCreate(ScoreRangesAdminCreate, FayerScoreRangesCreate):
pass


class SavedFayerScoreRanges(SavedBrnichScoreRanges, FayerScoreRangesBase):
record_type: str = None # type: ignore

title: str = "Fayer calibration"
research_use_only: bool = False
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)


class FayerScoreRanges(BrnichScoreRanges, SavedFayerScoreRanges):
title: str = "Fayer calibration"
research_use_only: bool = False


##############################################################################################################
# IGVF Coding Variant Focus Group (CVFG) range models
##############################################################################################################
Expand All @@ -364,13 +423,20 @@ class IGVFCodingVariantFocusGroupControlScoreRangesCreate(
research_use_only: bool = False


class IGVFCodingVariantFocusGroupControlScoreRangesAdminCreate(
ScoreRangesAdminCreate, IGVFCodingVariantFocusGroupControlScoreRangesCreate
):
pass


class SavedIGVFCodingVariantFocusGroupControlScoreRanges(
SavedBrnichScoreRanges, IGVFCodingVariantFocusGroupControlScoreRangesBase
):
record_type: str = None # type: ignore

title: str = "IGVF Coding Variant Focus Group -- Controls: All Variants"
research_use_only: bool = False
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand Down Expand Up @@ -404,13 +470,20 @@ class IGVFCodingVariantFocusGroupMissenseScoreRangesCreate(
research_use_only: bool = False


class IGVFCodingVariantFocusGroupMissenseScoreRangesAdminCreate(
ScoreRangesAdminCreate, IGVFCodingVariantFocusGroupMissenseScoreRangesCreate
):
pass


class SavedIGVFCodingVariantFocusGroupMissenseScoreRanges(
SavedBrnichScoreRanges, IGVFCodingVariantFocusGroupMissenseScoreRangesBase
):
record_type: str = None # type: ignore

title: str = "IGVF Coding Variant Focus Group -- Controls: Missense Variants Only"
research_use_only: bool = False
primary: bool = False

_record_type_factory = record_type_validator()(set_record_type)

Expand Down Expand Up @@ -507,11 +580,16 @@ class ZeibergCalibrationScoreRangesCreate(ScoreRangesCreate, ZeibergCalibrationS
ranges: Sequence[ZeibergCalibrationScoreRangeCreate]


class ZeibergCalibrationScoreRangesAdminCreate(ScoreRangesAdminCreate, ZeibergCalibrationScoreRangesCreate):
pass


class SavedZeibergCalibrationScoreRanges(SavedScoreRanges, ZeibergCalibrationScoreRangesBase):
record_type: str = None # type: ignore

title: str = "Zeiberg calibration"
research_use_only: bool = True
primary: bool = False
ranges: Sequence[SavedZeibergCalibrationScoreRange]

_record_type_factory = record_type_validator()(set_record_type)
Expand All @@ -535,6 +613,7 @@ class ZeibergCalibrationScoreRanges(ScoreRanges, SavedZeibergCalibrationScoreRan
class ScoreSetRangesBase(BaseModel):
investigator_provided: Optional[InvestigatorScoreRangesBase] = None
scott_calibration: Optional[ScottScoreRangesBase] = None
fayer_calibration: Optional[FayerScoreRangesBase] = None
zeiberg_calibration: Optional[ZeibergCalibrationScoreRangesBase] = None
cvfg_all_variants: Optional[IGVFCodingVariantFocusGroupControlScoreRangesBase] = None
cvfg_missense_variants: Optional[IGVFCodingVariantFocusGroupMissenseScoreRangesBase] = None
Expand All @@ -547,6 +626,7 @@ def score_range_labels_must_be_unique(self: "ScoreSetRangesBase") -> "ScoreSetRa
self.investigator_provided,
self.zeiberg_calibration,
self.scott_calibration,
self.fayer_calibration,
self.cvfg_all_variants,
self.cvfg_missense_variants,
):
Expand All @@ -571,6 +651,7 @@ def score_range_labels_must_be_unique(self: "ScoreSetRangesBase") -> "ScoreSetRa
class ScoreSetRangesModify(ScoreSetRangesBase):
investigator_provided: Optional[InvestigatorScoreRangesModify] = None
scott_calibration: Optional[ScottScoreRangesModify] = None
fayer_calibration: Optional[FayerScoreRangesModify] = None
zeiberg_calibration: Optional[ZeibergCalibrationScoreRangesModify] = None
cvfg_all_variants: Optional[IGVFCodingVariantFocusGroupControlScoreRangesModify] = None
cvfg_missense_variants: Optional[IGVFCodingVariantFocusGroupMissenseScoreRangesModify] = None
Expand All @@ -579,6 +660,7 @@ class ScoreSetRangesModify(ScoreSetRangesBase):
class ScoreSetRangesCreate(ScoreSetRangesModify):
investigator_provided: Optional[InvestigatorScoreRangesCreate] = None
scott_calibration: Optional[ScottScoreRangesCreate] = None
fayer_calibration: Optional[FayerScoreRangesCreate] = None
zeiberg_calibration: Optional[ZeibergCalibrationScoreRangesCreate] = None
cvfg_all_variants: Optional[IGVFCodingVariantFocusGroupControlScoreRangesCreate] = None
cvfg_missense_variants: Optional[IGVFCodingVariantFocusGroupMissenseScoreRangesCreate] = None
Expand All @@ -589,16 +671,45 @@ class SavedScoreSetRanges(ScoreSetRangesBase):

investigator_provided: Optional[SavedInvestigatorScoreRanges] = None
scott_calibration: Optional[SavedScottScoreRanges] = None
fayer_calibration: Optional[SavedFayerScoreRanges] = None
zeiberg_calibration: Optional[SavedZeibergCalibrationScoreRanges] = None
cvfg_all_variants: Optional[SavedIGVFCodingVariantFocusGroupControlScoreRanges] = None
cvfg_missense_variants: Optional[SavedIGVFCodingVariantFocusGroupMissenseScoreRanges] = None

_record_type_factory = record_type_validator()(set_record_type)

@model_validator(mode="after")
def one_and_only_one_primary_score_range_set(self: "SavedScoreSetRanges") -> "SavedScoreSetRanges":
primary_count = 0
for container in (
self.investigator_provided,
self.zeiberg_calibration,
self.scott_calibration,
self.cvfg_all_variants,
self.cvfg_missense_variants,
):
if container is None:
continue
if getattr(container, "primary", False):
primary_count += 1

# Set the investigator provided score ranges as primary if no other primary is set.
if primary_count == 0 and self.investigator_provided is not None:
self.investigator_provided.primary = True
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@jstone-dev jstone-dev Oct 8, 2025

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Are there other cases where we use validators that have side-effects? Seems like it would be good to separate this logic from the actual validation, though I don't have a good idea about it at the moment.


elif primary_count > 1:
raise ValidationError(
f"A maximum of one score range set must be marked as primary, but {primary_count} were.",
custom_loc=["body", "scoreRanges"],
)

return self


class ScoreSetRanges(SavedScoreSetRanges):
investigator_provided: Optional[InvestigatorScoreRanges] = None
scott_calibration: Optional[ScottScoreRanges] = None
fayer_calibration: Optional[FayerScoreRanges] = None
zeiberg_calibration: Optional[ZeibergCalibrationScoreRanges] = None
cvfg_all_variants: Optional[IGVFCodingVariantFocusGroupControlScoreRanges] = None
cvfg_missense_variants: Optional[IGVFCodingVariantFocusGroupMissenseScoreRanges] = None
9 changes: 9 additions & 0 deletions tests/helpers/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1614,6 +1614,7 @@
],
"research_use_only": False,
"title": "Test Base Ranges with Source",
"primary": False,
"source": [{"identifier": TEST_PUBMED_IDENTIFIER, "db_name": "PubMed"}],
}

Expand Down Expand Up @@ -1666,6 +1667,7 @@
],
"research_use_only": False,
"title": "Test Brnich Functional Ranges",
"primary": False,
"odds_path_source": [{"identifier": TEST_PUBMED_IDENTIFIER, "db_name": "PubMed"}],
"source": None,
}
Expand All @@ -1681,6 +1683,7 @@
],
"researchUseOnly": False,
"title": "Test Brnich Functional Ranges",
"primary": False,
"oddsPathSource": [{"identifier": TEST_PUBMED_IDENTIFIER, "dbName": "PubMed"}],
"source": None,
}
Expand Down Expand Up @@ -1745,6 +1748,7 @@
],
"research_use_only": False,
"title": "Test Scott Functional Ranges",
"primary": False,
"odds_path_source": [{"identifier": TEST_PUBMED_IDENTIFIER, "db_name": "PubMed"}],
"source": None,
}
Expand All @@ -1760,6 +1764,7 @@
],
"researchUseOnly": False,
"title": "Test Scott Functional Ranges",
"primary": False,
"oddsPathSource": [{"identifier": TEST_PUBMED_IDENTIFIER, "dbName": "PubMed"}],
"source": None,
}
Expand Down Expand Up @@ -1824,6 +1829,7 @@
],
"research_use_only": False,
"title": "Test Investigator-provided Functional Ranges",
"primary": True,
"odds_path_source": [{"identifier": TEST_PUBMED_IDENTIFIER, "db_name": "PubMed"}],
"source": None,
}
Expand All @@ -1839,6 +1845,7 @@
],
"researchUseOnly": False,
"title": "Test Investigator-provided Functional Ranges",
"primary": True,
"oddsPathSource": [{"identifier": TEST_PUBMED_IDENTIFIER, "dbName": "PubMed"}],
"source": None,
}
Expand Down Expand Up @@ -2039,6 +2046,7 @@
],
"research_use_only": True,
"title": "Test Zeiberg Calibration",
"primary": False,
"parameter_sets": TEST_ZEIBERG_CALIBRATION_PARAMETER_SETS,
"prior_probability_pathogenicity": 0.20,
"source": None,
Expand All @@ -2059,6 +2067,7 @@
],
"researchUseOnly": True,
"title": "Test Zeiberg Calibration",
"primary": False,
"parameterSets": TEST_SAVED_ZEIBERG_CALIBRATION_PARAMETER_SETS,
"priorProbabilityPathogenicity": 0.20,
}
Expand Down
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