chore: rename Zeiberg calibrations to ExCALIBR across the codebase

src/mavedb/lib/annotation/agent.py

@@ -58,14 +58,14 @@ def mavedb_user_agent(user: User) -> Agent:
 
 
 # XXX: Ideally, this becomes versioned software.
-def zeiberg_calibration_agent() -> Agent:
+def excalibr_calibration_agent() -> Agent:
     """
     Create a [VA Agent](https://va-ga4gh.readthedocs.io/en/latest/core-information-model/entities/agent.html)
-    object for the Zeiberg calibration software.
+    object for the ExCALIBR calibration software.
     """
     return Agent(
-        name="Zeiberg Variant Calibrator",
+        name="ExCALIBR Variant Calibrator",
         agentType="Software",
         # XXX - version?
-        description="Zeiberg variant calibrator, see https://github.com/Dzeiberg/mave_calibration",
+        description="ExCALIBR variant calibrator, see https://github.com/Dzeiberg/mave_calibration",
     )

src/mavedb/lib/annotation/contribution.py

@@ -4,15 +4,15 @@
 from ga4gh.core.models import Extension
 from ga4gh.va_spec.base.core import Contribution
 
-from mavedb.models.mapped_variant import MappedVariant
-from mavedb.models.user import User
 from mavedb.lib.annotation.agent import (
+    excalibr_calibration_agent,
     mavedb_api_agent,
-    mavedb_vrs_agent,
     mavedb_user_agent,
-    zeiberg_calibration_agent,
+    mavedb_vrs_agent,
 )
 from mavedb.lib.types.annotation import ResourceWithCreationModificationDates
+from mavedb.models.mapped_variant import MappedVariant
+from mavedb.models.user import User
 
 logger = logging.getLogger(__name__)
 
@@ -46,15 +46,15 @@ def mavedb_vrs_contribution(mapped_variant: MappedVariant) -> Contribution:
     )
 
 
-def zeiberg_calibration_contribution() -> Contribution:
+def excalibr_calibration_contribution() -> Contribution:
     """
     Create a [VA Contribution](https://va-ga4gh.readthedocs.io/en/latest/core-information-model/entities/activities/contribution.html#contribution)
-    object for a sofware agent which performs calibrations on an arbitrary data set.
+    object for a software agent which performs calibrations on an arbitrary data set.
     """
     return Contribution(
-        name="Zeiberg Calibration",
-        description="Contribution from the Zeiberg Calibration software",
-        contributor=zeiberg_calibration_agent(),
+        name="ExCALIBR Calibration",
+        description="Contribution from the ExCALIBR Calibration software",
+        contributor=excalibr_calibration_agent(),
         activityType="variant specific calibration software",
     )
 

src/mavedb/lib/annotation/evidence_line.py

@@ -1,28 +1,28 @@
 from typing import Optional, Union
 
 from ga4gh.core.models import Coding, MappableConcept, iriReference
-from ga4gh.va_spec.base.enums import StrengthOfEvidenceProvided
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
 from ga4gh.va_spec.base.core import (
     Direction,
     EvidenceLine,
-    StudyResult,
     EvidenceLineType,
     StatementType,
+    StudyResult,
     VariantPathogenicityProposition,
 )
+from ga4gh.va_spec.base.enums import StrengthOfEvidenceProvided
 
 from mavedb.lib.annotation.classification import pathogenicity_classification_of_variant
 from mavedb.lib.annotation.contribution import (
+    excalibr_calibration_contribution,
     mavedb_api_contribution,
-    mavedb_vrs_contribution,
-    zeiberg_calibration_contribution,
     mavedb_creator_contribution,
     mavedb_modifier_contribution,
+    mavedb_vrs_contribution,
 )
 from mavedb.lib.annotation.document import score_set_to_document
 from mavedb.lib.annotation.method import (
-    zeiberg_calibration_method,
+    excalibr_calibration_method,
     publication_identifiers_to_method,
 )
 from mavedb.models.mapped_variant import MappedVariant
@@ -59,7 +59,7 @@ def acmg_evidence_line(
 
     return VariantPathogenicityEvidenceLine(
         description=f"Pathogenicity evidence line {mapped_variant.variant.urn}.",
-        specifiedBy=zeiberg_calibration_method(evidence_outcome),
+        specifiedBy=excalibr_calibration_method(evidence_outcome),
         evidenceOutcome={
             "primaryCoding": Coding(
                 code=evidence_outcome_code,
@@ -72,7 +72,7 @@ def acmg_evidence_line(
         contributions=[
             mavedb_api_contribution(),
             mavedb_vrs_contribution(mapped_variant),
-            zeiberg_calibration_contribution(),
+            excalibr_calibration_contribution(),
             mavedb_creator_contribution(mapped_variant.variant, mapped_variant.variant.score_set.created_by),
             mavedb_modifier_contribution(mapped_variant.variant, mapped_variant.variant.score_set.modified_by),
         ],

src/mavedb/lib/annotation/method.py

@@ -2,10 +2,11 @@
 from typing import Optional
 
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
-from ga4gh.va_spec.base.core import Method, iriReference as IRI
+from ga4gh.va_spec.base.core import Method
+from ga4gh.va_spec.base.core import iriReference as IRI
 
-from mavedb.models.publication_identifier import PublicationIdentifier
 from mavedb.lib.types.annotation import PublicationIdentifierAssociations
+from mavedb.models.publication_identifier import PublicationIdentifier
 
 logger = logging.getLogger(__name__)
 
@@ -86,22 +87,22 @@ def mavedb_vrs_as_method() -> Method:
     return Method(name="Software version", reportedIn=mavedb_vrs_releases_as_iri())
 
 
-def zeiberg_calibrations_as_iri() -> IRI:
+def excalibr_calibrations_as_iri() -> IRI:
     """
     Create an IRI as described in <https://datatracker.ietf.org/doc/html/rfc3986#section-4.1> for the software used to generate pillar project calibrations. Within
     the context of VA-Spec, this IRI can be used interchangeably with an equivalent method object for brevity.
     """
     return IRI("https://github.com/Dzeiberg/mave_calibration")
 
 
-def zeiberg_calibration_method(method: Optional[VariantPathogenicityEvidenceLine.Criterion]) -> Method:
+def excalibr_calibration_method(method: Optional[VariantPathogenicityEvidenceLine.Criterion]) -> Method:
     """
     Generate a [VA Method](https://va-ga4gh.readthedocs.io/en/latest/core-information-model/entities/information-entities/method.html#method)
     object for the pillar project calibration software distribution.
     """
     return Method(
         name="Software version",
-        reportedIn=zeiberg_calibrations_as_iri(),
+        reportedIn=excalibr_calibrations_as_iri(),
         methodType=method.value if method else None,
     )
 

src/mavedb/scripts/load_calibration_csv.py

@@ -275,7 +275,7 @@ def build_ranges(row: Dict[str, str], infer_strengths: bool = True) -> Tuple[Lis
         ranges.append(
             FunctionalClassificationCreate(
                 label=label,
-                classification=classification,
+                functional_classification=classification,
                 range=(lower, upper),
                 inclusive_lower_bound=incl_lower if lower is not None else False,
                 inclusive_upper_bound=incl_upper if upper is not None else False,

src/mavedb/scripts/load_pp_style_calibration.py

@@ -1,4 +1,4 @@
-"""Load an archive of Zeiberg calibration style calibrations into Score Sets.
+"""Load an archive of ExCALIBR calibration style calibrations into Score Sets.
 
 This script processes JSON calibration files from an archive directory and applies them
 to MaveDB Score Sets based on a dataset mapping file. The script iterates through all
@@ -9,7 +9,7 @@
 Args:
     archive_path (str): Path to directory containing calibration JSON files
     dataset_map (str): Path to JSON file mapping dataset names to Score Set URNs
-    overwrite (bool): Whether to overwrite existing "Zeiberg calibration" entries
+    overwrite (bool): Whether to overwrite existing "ExCALIBR calibration" entries
 
 Input File Formats:
 
@@ -56,8 +56,8 @@
    - Strength labels: Supporting (±1), Moderate (±2), Moderate+ (±3), Strong (±4-8)
 6. File Variants: Automatically detects and processes both regular and ClinVar 2018 variants
 7. Calibration Naming:
-   - Regular files: "Zeiberg calibration"
-   - ClinVar 2018 files: "Zeiberg calibration (ClinVar 2018)"
+   - Regular files: "ExCALIBR calibration"
+   - ClinVar 2018 files: "ExCALIBR calibration (ClinVar 2018)"
 
 Skipping Behavior:
 - Files with no mapping entry or empty/invalid URNs (N/A, #VALUE!, empty string)
@@ -84,7 +84,7 @@
 from sqlalchemy.orm import Session
 
 from mavedb.lib.score_calibrations import create_score_calibration_in_score_set
-from mavedb.models.enums.functional_classification import FunctionalClassification as FunctionalClassifcationOptions
+from mavedb.models.enums.functional_classification import FunctionalClassification as FunctionalClassificationOptions
 from mavedb.models.score_calibration import ScoreCalibration
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.user import User
@@ -103,16 +103,16 @@
 }
 
 ALL_POINT_LABEL_MAPPINGS = {**POINT_LABEL_MAPPINGS, **{k * -1: v for k, v in POINT_LABEL_MAPPINGS.items()}}
-ZEIBERG_CALIBRATION_CITATION = {"identifier": "2025.04.29.651326", "db_name": "bioRxiv"}
+EXCALIBR_CALIBRATION_CITATION = {"identifier": "2025.04.29.651326", "db_name": "bioRxiv"}
 
 
 @click.command()
 @with_database_session
 @click.argument("archive_path", type=click.Path(exists=True, file_okay=False))
 @click.argument("dataset_map", type=click.Path(exists=True, dir_okay=False))
-@click.option("--overwrite", is_flag=True, default=False, help="Overwrite existing `Zeiberg calibration` in score set")
+@click.option("--overwrite", is_flag=True, default=False, help="Overwrite existing `ExCALIBR calibration` in score set")
 def main(db: Session, archive_path: str, dataset_map: str, overwrite: bool) -> None:
-    """Load an archive of Zeiberg calibration style calibrations into Score Sets"""
+    """Load an archive of ExCALIBR calibration style calibrations into Score Sets"""
     with open(dataset_map, "r") as f:
         dataset_mapping: Dict[str, str] = json.load(f)
 
@@ -165,16 +165,18 @@ def main(db: Session, archive_path: str, dataset_map: str, overwrite: bool) -> N
 
             # Determine calibration name based on file name
             if "_clinvar_2018" in json_file:
-                calibration_name = "Zeiberg calibration (ClinVar 2018)"
+                calibration_name = "ExCALIBR calibration (ClinVar 2018)"
+                legacy_name = "Zeiberg calibration (ClinVar 2018)"  # --- IGNORE ---
             else:
-                calibration_name = "Zeiberg calibration"
+                calibration_name = "ExCALIBR calibration"
+                legacy_name = "Zeiberg calibration"  # --- IGNORE ---
 
             existing_calibration = None
             if overwrite:
                 existing_calibration = (
                     db.query(ScoreCalibration)
                     .filter(ScoreCalibration.score_set_id == score_set.id)
-                    .filter(ScoreCalibration.title == calibration_name)
+                    .filter(ScoreCalibration.title.in_([calibration_name, legacy_name]))
                     .one_or_none()
                 )
 
@@ -215,9 +217,9 @@ def main(db: Session, archive_path: str, dataset_map: str, overwrite: bool) -> N
 
                 functional_range = score_calibration.FunctionalClassificationCreate(
                     label=f"{ps_or_bs} {strength_label} ({points})",
-                    classification=FunctionalClassifcationOptions.abnormal
+                    functional_classification=FunctionalClassificationOptions.abnormal
                     if points > 0
-                    else FunctionalClassifcationOptions.normal,
+                    else FunctionalClassificationOptions.normal,
                     range=range_data,
                     acmg_classification=acmg_classification.ACMGClassificationCreate(
                         points=int(points),
@@ -233,9 +235,9 @@ def main(db: Session, archive_path: str, dataset_map: str, overwrite: bool) -> N
                 research_use_only=True,
                 score_set_urn=score_set.urn,
                 calibration_metadata={"prior_probability_pathogenicity": calibration_data.get("prior", None)},
-                method_sources=[ZEIBERG_CALIBRATION_CITATION],
                 threshold_sources=[],
                 classification_sources=[],
+                method_sources=[EXCALIBR_CALIBRATION_CITATION],
             )
 
             new_calibration_object = asyncio.run(

tests/lib/annotation/test_agent.py

@@ -1,14 +1,13 @@
 from unittest import mock
 
 from mavedb import __version__
-from mavedb.models.user import User
 from mavedb.lib.annotation.agent import (
+    excalibr_calibration_agent,
     mavedb_api_agent,
-    mavedb_vrs_agent,
     mavedb_user_agent,
-    zeiberg_calibration_agent,
+    mavedb_vrs_agent,
 )
-
+from mavedb.models.user import User
 from tests.helpers.constants import TEST_USER
 
 
@@ -45,9 +44,9 @@ def test_mavedb_user_agent():
     assert agent.agentType == "Person"
 
 
-def test_zeiberg_calibration_agent():
-    agent = zeiberg_calibration_agent()
+def test_excalibr_calibration_agent():
+    agent = excalibr_calibration_agent()
 
-    assert agent.name == "Zeiberg Variant Calibrator"
-    assert agent.description == "Zeiberg variant calibrator, see https://github.com/Dzeiberg/mave_calibration"
+    assert agent.name == "ExCALIBR Variant Calibrator"
+    assert agent.description == "ExCALIBR variant calibrator, see https://github.com/Dzeiberg/mave_calibration"
     assert agent.agentType == "Software"

tests/lib/annotation/test_contribution.py

@@ -1,14 +1,14 @@
 from datetime import datetime
-import pytest
 
+import pytest
 from ga4gh.va_spec.base import Contribution
 
 from mavedb.lib.annotation.contribution import (
+    excalibr_calibration_contribution,
     mavedb_api_contribution,
-    mavedb_vrs_contribution,
-    zeiberg_calibration_contribution,
     mavedb_creator_contribution,
     mavedb_modifier_contribution,
+    mavedb_vrs_contribution,
 )
 
 
@@ -32,12 +32,12 @@ def test_mavedb_vrs_contribution(mock_mapped_variant):
     assert contribution.date.strftime("%Y-%m-%d") == mock_mapped_variant.mapped_date.strftime("%Y-%m-%d")
 
 
-def test_zeiberg_calibration_contribution():
-    contribution = zeiberg_calibration_contribution()
+def test_excalibr_calibration_contribution():
+    contribution = excalibr_calibration_contribution()
     assert isinstance(contribution, Contribution)
     assert contribution.activityType == "variant specific calibration software"
-    assert contribution.name == "Zeiberg Calibration"
-    assert contribution.description == "Contribution from the Zeiberg Calibration software"
+    assert contribution.name == "ExCALIBR Calibration"
+    assert contribution.description == "Contribution from the ExCALIBR Calibration software"
     assert contribution.contributor is not None
 
 

tests/lib/annotation/test_method.py

@@ -1,21 +1,22 @@
 from unittest.mock import Mock
-from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
+
 import pytest
+from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
 
-from mavedb.models.score_set_publication_identifier import ScoreSetPublicationIdentifierAssociation
 from mavedb.lib.annotation.method import (
+    excalibr_calibration_method,
+    excalibr_calibrations_as_iri,
+    mavedb_api_as_method,
+    mavedb_api_releases_as_iri,
+    mavedb_vrs_as_method,
+    mavedb_vrs_releases_as_iri,
     publication_as_iri,
     publication_identifier_to_method,
     publication_identifiers_to_method,
-    mavedb_api_releases_as_iri,
-    mavedb_api_as_method,
-    mavedb_vrs_releases_as_iri,
-    mavedb_vrs_as_method,
-    zeiberg_calibrations_as_iri,
-    zeiberg_calibration_method,
     variant_interpretation_functional_guideline_as_iri,
     variant_interpretation_functional_guideline_method,
 )
+from mavedb.models.score_set_publication_identifier import ScoreSetPublicationIdentifierAssociation
 
 MAVEDB_API_RELEASES_URL = "https://github.com/VariantEffect/mavedb-api/releases"
 MAVEDB_MAPPER_RELEASES_URL = "https://github.com/VariantEffect/dcd_mapping2/releases"
@@ -93,15 +94,15 @@ def test_mavedb_vrs_as_method():
     assert method.reportedIn.root == MAVEDB_MAPPER_RELEASES_URL
 
 
-def test_zeiberg_calibrations_as_iri():
-    assert zeiberg_calibrations_as_iri().root == MAVEDB_CALIBRATION_URL
+def test_excalibr_calibrations_as_iri():
+    assert excalibr_calibrations_as_iri().root == MAVEDB_CALIBRATION_URL
 
 
 @pytest.mark.parametrize(
     "evidence_outcome", [VariantPathogenicityEvidenceLine.Criterion.BS3, VariantPathogenicityEvidenceLine.Criterion.PS3]
 )
-def test_zeiberg_calibration_method(evidence_outcome):
-    method = zeiberg_calibration_method(evidence_outcome)
+def test_excalibr_calibration_method(evidence_outcome):
+    method = excalibr_calibration_method(evidence_outcome)
     assert method.name == "Software version"
     assert method.reportedIn.root == MAVEDB_CALIBRATION_URL
     assert method.methodType == evidence_outcome.value