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Add medical action association table to UI (plus fixture & enum regen) #937

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Add medical action association table to UI (plus fixture & enum regen) #937

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f315267
Add medical action association tables (plus fixture & enum regen)
kevinschaper Jan 9, 2025
3982104
Add querying for disease_context_qualifier (+closure) to association …
kevinschaper Jan 9, 2025
9c66192
update multiple entity query test to expect disease_context_qualifier…
kevinschaper Jan 9, 2025
5e08d73
try setting the PYTHONPATH before running tests to get backend/tests …
kevinschaper Jan 9, 2025
e0307f3
try setting PYTHONPATH another way
kevinschaper Jan 9, 2025
90fa0eb
try setting PYTHONPATH another way
kevinschaper Jan 9, 2025
61bf967
trying a working dir change?
kevinschaper Jan 9, 2025
b898670
keep going with the working dir change
kevinschaper Jan 9, 2025
8a046f2
add subject & object specialization qualifiers to model, plus closure…
kevinschaper Jan 10, 2025
07d9acb
add original predicate to model
kevinschaper Jan 13, 2025
efccb45
use original_predicate for maxo_relation column in medical actions ta…
kevinschaper Jan 14, 2025
a716bdd
update fixtures with new kg
kevinschaper Jan 14, 2025
9ee736d
update association entity test to handle the case where the matched I…
kevinschaper Jan 14, 2025
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9 changes: 7 additions & 2 deletions .github/workflows/test-backend.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,9 @@ on:
pull_request:
workflow_dispatch:

env:
PYTHONPATH: ${{ github.workspace }}/backend

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fix for #935

# defaults:
# run:
# working-directory: ./backend
Expand Down Expand Up @@ -40,14 +43,16 @@ jobs:
# run pytest
#----------------------------------------------
- name: Run tests
run: poetry -C backend run pytest backend/tests
run: |
poetry -C backend run pytest tests
shell: bash

#----------------------------------------------
# coverage report
#----------------------------------------------
- name: Generate coverage results
run: |
poetry -C backend run coverage run -m pytest backend/tests
poetry -C backend run coverage run -m pytest tests
poetry -C backend run coverage xml
poetry -C backend run coverage report -m
shell: bash
Expand Down
116 changes: 32 additions & 84 deletions backend/src/monarch_py/datamodels/category_enums.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,119 +4,60 @@
class EntityCategory(Enum):
"""Entity categories"""

SEQUENCE_VARIANT = "biolink:SequenceVariant"
GENE = "biolink:Gene"
GENOTYPE = "biolink:Genotype"
PHENOTYPIC_FEATURE = "biolink:PhenotypicFeature"
BIOLOGICAL_PROCESS_OR_ACTIVITY = "biolink:BiologicalProcessOrActivity"
DISEASE = "biolink:Disease"
GROSS_ANATOMICAL_STRUCTURE = "biolink:GrossAnatomicalStructure"
CELL = "biolink:Cell"
PATHWAY = "biolink:Pathway"
NAMED_THING = "biolink:NamedThing"
GENOTYPE = "biolink:Genotype"
ANATOMICAL_ENTITY = "biolink:AnatomicalEntity"
CELLULAR_COMPONENT = "biolink:CellularComponent"
MOLECULAR_ENTITY = "biolink:MolecularEntity"
BIOLOGICAL_PROCESS = "biolink:BiologicalProcess"
MACROMOLECULAR_COMPLEX = "biolink:MacromolecularComplex"
MOLECULAR_ACTIVITY = "biolink:MolecularActivity"
DISEASE = "biolink:Disease"
NAMED_THING = "biolink:NamedThing"
PATHWAY = "biolink:Pathway"
PROTEIN = "biolink:Protein"
CELLULAR_ORGANISM = "biolink:CellularOrganism"
VERTEBRATE = "biolink:Vertebrate"
VIRUS = "biolink:Virus"
BEHAVIORAL_FEATURE = "biolink:BehavioralFeature"
CHEMICAL_ENTITY = "biolink:ChemicalEntity"
LIFE_STAGE = "biolink:LifeStage"
PATHOLOGICAL_PROCESS = "biolink:PathologicalProcess"
DRUG = "biolink:Drug"
SMALL_MOLECULE = "biolink:SmallMolecule"
SEQUENCE_VARIANT = "biolink:SequenceVariant"
MOLECULAR_ACTIVITY = "biolink:MolecularActivity"
CELLULAR_COMPONENT = "biolink:CellularComponent"
CELL = "biolink:Cell"
ORGANISM_TAXON = "biolink:OrganismTaxon"
INFORMATION_CONTENT_ENTITY = "biolink:InformationContentEntity"
NUCLEIC_ACID_ENTITY = "biolink:NucleicAcidEntity"
EVIDENCE_TYPE = "biolink:EvidenceType"
RNAPRODUCT = "biolink:RNAProduct"
TRANSCRIPT = "biolink:Transcript"
FUNGUS = "biolink:Fungus"
PLANT = "biolink:Plant"
PROCESSED_MATERIAL = "biolink:ProcessedMaterial"
ACTIVITY = "biolink:Activity"
AGENT = "biolink:Agent"
CONFIDENCE_LEVEL = "biolink:ConfidenceLevel"
DATASET = "biolink:Dataset"
ENVIRONMENTAL_FEATURE = "biolink:EnvironmentalFeature"
GENETIC_INHERITANCE = "biolink:GeneticInheritance"
HAPLOTYPE = "biolink:Haplotype"
INVERTEBRATE = "biolink:Invertebrate"
MAMMAL = "biolink:Mammal"
POPULATION_OF_INDIVIDUAL_ORGANISMS = "biolink:PopulationOfIndividualOrganisms"
PROTEIN_FAMILY = "biolink:ProteinFamily"
PUBLICATION = "biolink:Publication"
ACCESSIBLE_DNA_REGION = "biolink:AccessibleDnaRegion"
BACTERIUM = "biolink:Bacterium"
BIOLOGICAL_SEX = "biolink:BiologicalSex"
CELL_LINE = "biolink:CellLine"
CHEMICAL_EXPOSURE = "biolink:ChemicalExposure"
CHEMICAL_MIXTURE = "biolink:ChemicalMixture"
DATASET_DISTRIBUTION = "biolink:DatasetDistribution"
DIAGNOSTIC_AID = "biolink:DiagnosticAid"
DRUG_EXPOSURE = "biolink:DrugExposure"
ENVIRONMENTAL_PROCESS = "biolink:EnvironmentalProcess"
EVENT = "biolink:Event"
EXON = "biolink:Exon"
GENOME = "biolink:Genome"
GENOTYPIC_SEX = "biolink:GenotypicSex"
HUMAN = "biolink:Human"
INDIVIDUAL_ORGANISM = "biolink:IndividualOrganism"
MATERIAL_SAMPLE = "biolink:MaterialSample"
MICRO_RNA = "biolink:MicroRNA"
ORGANISMAL_ENTITY = "biolink:OrganismalEntity"
PATENT = "biolink:Patent"
PHENOTYPIC_SEX = "biolink:PhenotypicSex"
POLYPEPTIDE = "biolink:Polypeptide"
PROTEIN_DOMAIN = "biolink:ProteinDomain"
REAGENT_TARGETED_GENE = "biolink:ReagentTargetedGene"
REGULATORY_REGION = "biolink:RegulatoryRegion"
SI_RNA = "biolink:SiRNA"
SNV = "biolink:Snv"
STUDY = "biolink:Study"
STUDY_VARIABLE = "biolink:StudyVariable"
TRANSCRIPTION_FACTOR_BINDING_SITE = "biolink:TranscriptionFactorBindingSite"
TREATMENT = "biolink:Treatment"
WEB_PAGE = "biolink:WebPage"
ZYGOSITY = "biolink:Zygosity"
MOLECULAR_ENTITY = "biolink:MolecularEntity"
LIFE_STAGE = "biolink:LifeStage"
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I'm going to presume that all of these deletions and additions make sense, although I admit I didn't check to make sure we don't need these.



class AssociationCategory(Enum):
"""Association categories"""

PAIRWISE_GENE_TO_GENE_INTERACTION = "biolink:PairwiseGeneToGeneInteraction"
GENE_TO_EXPRESSION_SITE_ASSOCIATION = "biolink:GeneToExpressionSiteAssociation"
VARIANT_TO_GENE_ASSOCIATION = "biolink:VariantToGeneAssociation"
MACROMOLECULAR_MACHINE_TO_BIOLOGICAL_PROCESS_ASSOCIATION = (
"biolink:MacromolecularMachineToBiologicalProcessAssociation"
)
GENE_TO_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:GeneToPhenotypicFeatureAssociation"
ASSOCIATION = "biolink:Association"
MACROMOLECULAR_MACHINE_TO_MOLECULAR_ACTIVITY_ASSOCIATION = (
"biolink:MacromolecularMachineToMolecularActivityAssociation"
)
MACROMOLECULAR_MACHINE_TO_CELLULAR_COMPONENT_ASSOCIATION = (
"biolink:MacromolecularMachineToCellularComponentAssociation"
)
ASSOCIATION = "biolink:Association"
GENE_TO_GENE_HOMOLOGY_ASSOCIATION = "biolink:GeneToGeneHomologyAssociation"
GENOTYPE_TO_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:GenotypeToPhenotypicFeatureAssociation"
DISEASE_TO_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:DiseaseToPhenotypicFeatureAssociation"
GENE_TO_PATHWAY_ASSOCIATION = "biolink:GeneToPathwayAssociation"
DISEASE_OR_PHENOTYPIC_FEATURE_TO_LOCATION_ASSOCIATION = "biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"
CHEMICAL_TO_PATHWAY_ASSOCIATION = "biolink:ChemicalToPathwayAssociation"
VARIANT_TO_GENE_ASSOCIATION = "biolink:VariantToGeneAssociation"
VARIANT_TO_DISEASE_ASSOCIATION = "biolink:VariantToDiseaseAssociation"
GENOTYPE_TO_DISEASE_ASSOCIATION = "biolink:GenotypeToDiseaseAssociation"
CORRELATED_GENE_TO_DISEASE_ASSOCIATION = "biolink:CorrelatedGeneToDiseaseAssociation"
CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"
DISEASE_OR_PHENOTYPIC_FEATURE_TO_GENETIC_INHERITANCE_ASSOCIATION = (
"biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"
)
VARIANT_TO_DISEASE_ASSOCIATION = "biolink:VariantToDiseaseAssociation"
CAUSAL_GENE_TO_DISEASE_ASSOCIATION = "biolink:CausalGeneToDiseaseAssociation"
CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"
DISEASE_OR_PHENOTYPIC_FEATURE_TO_LOCATION_ASSOCIATION = "biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"
CHEMICAL_OR_DRUG_OR_TREATMENT_TO_DISEASE_OR_PHENOTYPIC_FEATURE_ASSOCIATION = (
"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"
)
VARIANT_TO_PHENOTYPIC_FEATURE_ASSOCIATION = "biolink:VariantToPhenotypicFeatureAssociation"
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Again, I'll presume your reorganization is for improving readability or logical consistency.



class AssociationPredicate(Enum):
Expand All @@ -125,33 +66,40 @@ class AssociationPredicate(Enum):
INTERACTS_WITH = "biolink:interacts_with"
EXPRESSED_IN = "biolink:expressed_in"
HAS_PHENOTYPE = "biolink:has_phenotype"
IS_SEQUENCE_VARIANT_OF = "biolink:is_sequence_variant_of"
ENABLES = "biolink:enables"
ACTIVELY_INVOLVED_IN = "biolink:actively_involved_in"
ORTHOLOGOUS_TO = "biolink:orthologous_to"
LOCATED_IN = "biolink:located_in"
SUBCLASS_OF = "biolink:subclass_of"
LOCATED_IN = "biolink:located_in"
RELATED_TO = "biolink:related_to"
PARTICIPATES_IN = "biolink:participates_in"
ACTS_UPSTREAM_OF_OR_WITHIN = "biolink:acts_upstream_of_or_within"
ACTIVE_IN = "biolink:active_in"
IS_ACTIVE_IN = "biolink:is_active_in"
PART_OF = "biolink:part_of"
MODEL_OF = "biolink:model_of"
CAUSES = "biolink:causes"
IS_SEQUENCE_VARIANT_OF = "biolink:is_sequence_variant_of"
MODEL_OF = "biolink:model_of"
ACTS_UPSTREAM_OF = "biolink:acts_upstream_of"
TREATS_OR_APPLIED_OR_STUDIED_TO_TREAT = "biolink:treats_or_applied_or_studied_to_treat"
HAS_MODE_OF_INHERITANCE = "biolink:has_mode_of_inheritance"
CONTRIBUTES_TO = "biolink:contributes_to"
GENE_ASSOCIATED_WITH_CONDITION = "biolink:gene_associated_with_condition"
TREATS_OR_APPLIED_OR_STUDIED_TO_TREAT = "biolink:treats_or_applied_or_studied_to_treat"
CONTRIBUTES_TO = "biolink:contributes_to"
ASSOCIATED_WITH_INCREASED_LIKELIHOOD_OF = "biolink:associated_with_increased_likelihood_of"
COLOCALIZES_WITH = "biolink:colocalizes_with"
GENETICALLY_ASSOCIATED_WITH = "biolink:genetically_associated_with"
DISEASE_HAS_LOCATION = "biolink:disease_has_location"
ACTS_UPSTREAM_OF_POSITIVE_EFFECT = "biolink:acts_upstream_of_positive_effect"
ACTS_UPSTREAM_OF_OR_WITHIN_POSITIVE_EFFECT = "biolink:acts_upstream_of_or_within_positive_effect"
AMELIORATES_CONDITION = "biolink:ameliorates_condition"
ACTS_UPSTREAM_OF_NEGATIVE_EFFECT = "biolink:acts_upstream_of_negative_effect"
ACTS_UPSTREAM_OF_OR_WITHIN_NEGATIVE_EFFECT = "biolink:acts_upstream_of_or_within_negative_effect"
PREVENTATIVE_FOR_CONDITION = "biolink:preventative_for_condition"
CONTRAINDICATED_IN = "biolink:contraindicated_in"


class MappingPredicate(Enum):
"""Mapping predicates"""

EXACT_MATCH = "skos:exactMatch"
CLOSE_MATCH = "skos:closeMatch"
BROAD_MATCH = "skos:broadMatch"
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