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fix: ensure all filters work for retrieving interactions by gene #49

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Merged
jsstevenson merged 1 commit into from
Oct 7, 2026
Merged

fix: ensure all filters work for retrieving interactions by gene #49

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36 changes: 33 additions & 3 deletions R/dgidb.R
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,35 @@ getGenes <- function(terms, apiUrl = NULL) {
)
}

.filterInteractions <- function(nodes, source = NULL, approved = NULL) {
lapply(nodes, function(node) {
interactions <- node$interactions
if (!is.null(approved)) {
interactions <- Filter(
function(interaction) {
identical(interaction$drug$approved, approved)
},
interactions
)
}
if (!is.null(source)) {
interactions <- Filter(
function(interaction) {
sources <- vapply(
interaction$interactionClaims,
function(claim) claim$source$sourceDbName,
character(1)
)
source %in% sources
},
interactions
)
}
node$interactions <- interactions
node
})
}

#' Get Interactions
#'
#' Performs an interaction lookup for drugs or genes of interest.
Expand All @@ -183,10 +212,10 @@ getGenes <- function(terms, apiUrl = NULL) {
#' @param search Either `"genes"` or `"drugs"`.
#' @param immunotherapy Optionally filter drug searches by immunotherapy use.
#' @param antineoplastic Optionally filter drug searches by antineoplastic use.
#' @param source Optionally filter by source database name.
#' @param source Optionally filter interactions by source database name.
#' @param pmid Optionally filter by PubMed identifier.
#' @param interactionType Optionally filter by interaction type.
#' @param approved Optionally filter drug searches by approval status.
#' @param approved Optionally filter interactions by drug approval status.
#' @param apiUrl DGIdb GraphQL endpoint; defaults to `DGIDB_API_URL`.
#'
#' @return A data frame of interaction records. Multi-valued fields are
Expand Down Expand Up @@ -220,10 +249,10 @@ getInteractions <- function(
) {
search <- match.arg(search, c("genes", "drugs"))
params <- list(names = terms)
if (!is.null(source)) params$sourceDbName <- source
if (!is.null(pmid)) params$pmid <- pmid
if (!is.null(interactionType)) params$interactionType <- interactionType
if (search == "drugs") {
if (!is.null(source)) params$sourceDbName <- source
if (!is.null(immunotherapy)) params$immunotherapy <- immunotherapy
if (!is.null(antineoplastic)) params$antineoplastic <- antineoplastic
if (!is.null(approved)) params$approved <- approved
Expand All @@ -234,6 +263,7 @@ getInteractions <- function(
"queries/get_interactions_by_drug.graphql"
}
results <- .postQuery(apiUrl, queryFile, params)[[search]]$nodes
results <- .filterInteractions(results, source, approved)
.interactionOutput(results)
}

Expand Down
4 changes: 2 additions & 2 deletions man/getInteractions.Rd
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74 changes: 74 additions & 0 deletions tests/testthat/test-dgidb.R
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,80 @@ test_that("getInteractions() applies filters by search type", {
expect_true(params$approved)
})

test_that("getInteractions() locally filters interactions returned for genes", {
local_mocked_bindings(
.postQuery = function(apiUrl, queryFile, variables) {
expect_equal(queryFile, "queries/get_interactions_by_gene.graphql")
expect_equal(variables, list(names = "KRAS"))
list(genes = list(nodes = list(list(interactions = list(
list(
gene = list(
name = "KRAS", conceptId = "hgnc:6407",
longName = "KRAS proto-oncogene"
),
drug = list(
name = "Approved ChEMBL drug", conceptId = "drug:1",
approved = TRUE
),
interactionScore = 1,
interactionAttributes = list(),
interactionClaims = list(list(
publications = list(),
source = list(sourceDbName = "ChEMBL")
))
),
list(
gene = list(
name = "KRAS", conceptId = "hgnc:6407",
longName = "KRAS proto-oncogene"
),
drug = list(
name = "Unapproved drug", conceptId = "drug:2",
approved = FALSE
),
interactionScore = 1,
interactionAttributes = list(),
interactionClaims = list(list(
publications = list(),
source = list(sourceDbName = "DrugBank")
))
),
list(
gene = list(
name = "KRAS", conceptId = "hgnc:6407",
longName = "KRAS proto-oncogene"
),
drug = list(
name = "Approved non-ChEMBL drug", conceptId = "drug:3",
approved = TRUE
),
interactionScore = 1,
interactionAttributes = list(),
interactionClaims = list(list(
publications = list(),
source = list(sourceDbName = "DrugBank")
))
)
)))))
}
)

approved <- getInteractions("KRAS", approved = TRUE)
expect_true(all(approved$drug_approved))
expect_setequal(
approved$drug_name,
c("Approved ChEMBL drug", "Approved non-ChEMBL drug")
)

chembl <- getInteractions("KRAS", source = "ChEMBL")
expect_equal(chembl$drug_name, "Approved ChEMBL drug")
expect_true(all(vapply(
chembl$interaction_sources,
function(sources) "ChEMBL" %in% sources,
logical(1)
)))
})

test_that("getInteractionTypes() returns all interaction claim types", {
local_mocked_bindings(
.postQuery = function(apiUrl, queryFile, variables) {
Expand Down
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