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bioentity-variant.feature
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Feature: Variant association queries that return a list of associations
## Variant to Case associations
Scenario: User queries for cases associated with a variant
Given a path "/bioentity/variant/dbSNP:rs766529116/cases"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "MONARCH:c000017"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "case"
## Variant to Disease associations
Scenario: User queries for diseases associated with a variant
Given a path "/bioentity/variant/ClinVarVariant:14925/diseases"
then the JSON should have some JSONPath "associations[*].subject.label" with "string" "HSPG2, 9-BP DEL"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "MONDO:0009717"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "disease"
## Variant to Gene associations
Scenario: User queries for genes associated with a variant
Given a path "/bioentity/variant/ClinVarVariant:39783/genes"
then the JSON should have some JSONPath "associations[*].subject.label" containing "string" "Gly34Val"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "HGNC:10896"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "gene"
## Variant to Genotype associations
Scenario: User queries for genotypes associated with a variant
Given a path "/bioentity/variant/ZFIN:ZDB-ALT-010427-8/genotypes"
then the JSON should have some JSONPath "associations[*].subject.label" with "string" "tbx392"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "ZFIN:ZDB-FISH-150901-24810"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "genotype"
## Variant to Model associations
Scenario: User queries for models associated with a variant
Given a path "/bioentity/variant/dbSNP:rs5030868/models"
then the JSON should have some JSONPath "associations[*].subject.label" with "string" "rs5030868-A"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "Coriell:GM01165"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "model"
## Variant to Phenotype associations
# https://github.com/monarch-initiative/monarch-ui/issues/189
# TODO replace with gwas catalog association
#Scenario: User queries for phenotypes associated with a variant
# Given a path "/bioentity/variant/ClinVarVariant:39783/phenotypes"
# then the JSON should have some JSONPath "associations[*].subject.label" containing "string" "p.Gly34Val"
# then the JSON should have some JSONPath "associations[*].object.label" with "string" "Craniosynostosis"
# then the JSON should have some JSONPath "associations[*].object.category" containing "string" "phenotype"
## Variant to Publication associations
Scenario: User queries for publications associated with a variant
Given a path "/bioentity/variant/ClinVarVariant:39783/publications"
then the JSON should have some JSONPath "associations[*].object.id" with "string" "PMID:23103230"
then the JSON should have some JSONPath "associations[*].object.category" containing "string" "publication"