fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle pro…

tests/testthat/test-annotateProteinInfoFromIndra.R

@@ -128,3 +128,220 @@ test_that("annotateProteinInfoFromIndra works correctly with HGNC name", {
     expect_type(annotated_df$IsPhosphatase, "logical")
 
 })
+
+# ----- Protein groups: ";"-joined identifiers are grounded member by member,
+# then pooled into the semicolon-joined Entity* columns that
+# getSubnetworkFromIndra already fans out. Mocked, so no network access. -----
+
+test_that(".splitProteinGroup splits, trims and drops empty members", {
+    expect_equal(MSstatsBioNet:::.splitProteinGroup("P13747;P23132"),
+                 c("P13747", "P23132"))
+    expect_equal(MSstatsBioNet:::.splitProteinGroup("P13747"), "P13747")
+    expect_equal(MSstatsBioNet:::.splitProteinGroup(" P13747 ; P23132 "),
+                 c("P13747", "P23132"))
+    expect_equal(MSstatsBioNet:::.splitProteinGroup(";P13747;;"), "P13747")
+    expect_equal(MSstatsBioNet:::.splitProteinGroup(NA), character(0))
+    expect_equal(MSstatsBioNet:::.splitProteinGroup(""), character(0))
+})
+
+test_that(".joinProteinGroup round-trips and returns NA when empty", {
+    expect_equal(MSstatsBioNet:::.joinProteinGroup(c("P13747", "P23132")),
+                 "P13747;P23132")
+    expect_equal(MSstatsBioNet:::.joinProteinGroup("P13747"), "P13747")
+    expect_true(is.na(MSstatsBioNet:::.joinProteinGroup(character(0))))
+})
+
+test_that(".stripPtmSite removes only the site suffix", {
+    expect_equal(MSstatsBioNet:::.stripPtmSite(c("P13747_S148", "P23132")),
+                 c("P13747", "P23132"))
+    expect_equal(MSstatsBioNet:::.stripPtmSite("CLH1_HUMAN"), "CLH1_HUMAN")
+})
+
+test_that("PTM site suffixes are stripped from every protein group member", {
+    df <- data.frame(Protein = c("P13747_S148;P23132_T20", "P13747_S148"),
+                     stringsAsFactors = FALSE)
+    out <- MSstatsBioNet:::.populateUniprotIdsInDataFrame(df, "Uniprot")
+
+    expect_equal(out$GlobalProtein, c("P13747;P23132", "P13747"))
+    expect_equal(out$UniprotId,     c("P13747;P23132", "P13747"))
+})
+
+test_that("annotateProteinInfoFromIndra grounds each Uniprot protein group member", {
+    df <- data.frame(Protein = c("P13747;P23132", "Q00610"),
+                     stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGetHgncIdsFromUniprotIdsApi = function(uniprotIds) {
+            list(P13747 = "4931", P23132 = "10012", Q00610 = "2092")
+        },
+        .callGetHgncNamesFromHgncIdsApi = function(hgncIds) {
+            list(`4931` = "HLA-E", `10012` = "RAD23A", `2092` = "CLTC")
+        },
+        .callIsTranscriptionFactorApi = function(genes) list(CLTC = FALSE),
+        .callIsKinaseApi = function(genes) list(CLTC = FALSE),
+        .callIsPhosphataseApi = function(genes) list(CLTC = FALSE)
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot")
+
+    group_row <- annotated_df[annotated_df$Protein == "P13747;P23132", ]
+    expect_equal(group_row$UniprotId,       "P13747;P23132")
+    expect_equal(group_row$EntityNamespace, "HGNC;HGNC")
+    expect_equal(group_row$EntityId,        "4931;10012")
+    expect_equal(group_row$EntityName,      "HLA-E;RAD23A")
+    # Gene-only flags stay NA while the row carries more than one grounding
+    expect_true(is.na(group_row$IsTranscriptionFactor))
+    expect_true(is.na(group_row$IsKinase))
+    expect_true(is.na(group_row$IsPhosphatase))
+
+    # A single-identifier row is unaffected by the split
+    single_row <- annotated_df[annotated_df$Protein == "Q00610", ]
+    expect_equal(single_row$EntityNamespace, "HGNC")
+    expect_equal(single_row$EntityId,        "2092")
+    expect_equal(single_row$EntityName,      "CLTC")
+    expect_equal(single_row$IsKinase,        FALSE)
+})
+
+test_that("a protein group whose members share a gene collapses to one grounding", {
+    df <- data.frame(Protein = "P13747;P13747-2", stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGetHgncIdsFromUniprotIdsApi = function(uniprotIds) {
+            list(P13747 = "4931", `P13747-2` = "4931")
+        },
+        .callGetHgncNamesFromHgncIdsApi = function(hgncIds) list(`4931` = "HLA-E"),
+        .callIsTranscriptionFactorApi = function(genes) list(`HLA-E` = FALSE),
+        .callIsKinaseApi = function(genes) list(`HLA-E` = FALSE),
+        .callIsPhosphataseApi = function(genes) list(`HLA-E` = TRUE)
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot")
+
+    expect_equal(annotated_df$EntityNamespace, "HGNC")
+    expect_equal(annotated_df$EntityId,        "4931")
+    expect_equal(annotated_df$EntityName,      "HLA-E")
+    # Collapsed to a single grounding, so the gene-only flags are populated
+    expect_equal(annotated_df$IsTranscriptionFactor, FALSE)
+    expect_equal(annotated_df$IsPhosphatase,         TRUE)
+})
+
+test_that("unresolvable protein group members are dropped, not carried as NA", {
+    df <- data.frame(Protein = c("P13747;NOTANID", "NOTANID;ALSONOT"),
+                     stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGetHgncIdsFromUniprotIdsApi = function(uniprotIds) list(P13747 = "4931"),
+        .callGetHgncNamesFromHgncIdsApi = function(hgncIds) list(`4931` = "HLA-E"),
+        .callIsTranscriptionFactorApi = function(genes) list(`HLA-E` = FALSE),
+        .callIsKinaseApi = function(genes) list(`HLA-E` = FALSE),
+        .callIsPhosphataseApi = function(genes) list(`HLA-E` = FALSE)
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot")
+
+    # Partially resolved group keeps only the member that grounded, and so is
+    # single-grounded and does get the gene-only flags
+    expect_equal(annotated_df$EntityId[1],   "4931")
+    expect_equal(annotated_df$EntityName[1], "HLA-E")
+    expect_equal(annotated_df$IsKinase[1],   FALSE)
+
+    # Fully unresolved group stays NA across the Entity columns, and its
+    # presence alongside a resolved row must not break the flag lookups
+    expect_true(is.na(annotated_df$EntityNamespace[2]))
+    expect_true(is.na(annotated_df$EntityId[2]))
+    expect_true(is.na(annotated_df$EntityName[2]))
+    expect_true(is.na(annotated_df$IsKinase[2]))
+})
+
+test_that("Uniprot_Mnemonic groups map each member to its own UniProt id", {
+    df <- data.frame(Protein = c("CLH1_HUMAN;HLAE_HUMAN", "CLH1_HUMAN;NOPE_HUMAN"),
+                     stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGetUniprotIdsFromUniprotMnemonicIdsApi = function(uniprotMnemonicIds) {
+            list(CLH1_HUMAN = "Q00610", HLAE_HUMAN = "P13747")
+        },
+        .callGetHgncIdsFromUniprotIdsApi = function(uniprotIds) {
+            list(Q00610 = "2092", P13747 = "4931")
+        },
+        .callGetHgncNamesFromHgncIdsApi = function(hgncIds) {
+            list(`2092` = "CLTC", `4931` = "HLA-E")
+        },
+        .callIsTranscriptionFactorApi = function(genes) list(CLTC = FALSE),
+        .callIsKinaseApi = function(genes) list(CLTC = FALSE),
+        .callIsPhosphataseApi = function(genes) list(CLTC = FALSE)
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot_Mnemonic")
+
+    expect_equal(annotated_df$UniprotId[1],       "Q00610;P13747")
+    expect_equal(annotated_df$EntityNamespace[1], "HGNC;HGNC")
+    expect_equal(annotated_df$EntityId[1],        "2092;4931")
+    expect_equal(annotated_df$EntityName[1],      "CLTC;HLA-E")
+
+    # Only one member resolves, so the row degrades to that single grounding
+    expect_equal(annotated_df$UniprotId[2],  "Q00610")
+    expect_equal(annotated_df$EntityName[2], "CLTC")
+    expect_equal(annotated_df$IsKinase[2],   FALSE)
+})
+
+test_that("Hgnc_Name groups pool and deduplicate Gilda groundings", {
+    df <- data.frame(Protein = c("EGFR;ERBB2", "EGFR;EGFR"),
+                     stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGroundEntitiesFromGildaApi = function(textInputs, keep_only = NULL, organisms = NULL) {
+            list(EGFR  = list(ns = "HGNC", id = "3236", name = "EGFR"),
+                 ERBB2 = list(ns = "HGNC", id = "3430", name = "ERBB2"))
+        },
+        .callIsTranscriptionFactorApi = function(genes) list(EGFR = FALSE),
+        .callIsKinaseApi = function(genes) list(EGFR = TRUE),
+        .callIsPhosphataseApi = function(genes) list(EGFR = FALSE)
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Hgnc_Name")
+
+    expect_equal(annotated_df$EntityNamespace[1], "HGNC;HGNC")
+    expect_equal(annotated_df$EntityId[1],        "3236;3430")
+    expect_equal(annotated_df$EntityName[1],      "EGFR;ERBB2")
+
+    # A repeated member contributes its grounding once
+    expect_equal(annotated_df$EntityId[2],   "3236")
+    expect_equal(annotated_df$EntityName[2], "EGFR")
+    expect_equal(annotated_df$IsKinase[2],   TRUE)
+})
+
+test_that("Metabolite groups keep every namespace Gilda returns per member", {
+    df <- data.frame(Protein = "glucose;citrate", stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGroundEntitiesFromGildaApi = function(textInputs, keep_only = NULL, organisms = NULL) {
+            list(glucose = list(ns   = c("CHEBI", "MESH"),
+                                id   = c("17234", "D005947"),
+                                name = c("glucose", "Glucose")),
+                 citrate = list(ns = "CHEBI", id = "133748", name = "citrate"))
+        }
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Metabolite")
+
+    expect_equal(annotated_df$EntityNamespace, "CHEBI;MESH;CHEBI")
+    expect_equal(annotated_df$EntityId,        "17234;D005947;133748")
+    expect_equal(annotated_df$EntityName,      "glucose;Glucose;citrate")
+    expect_true(is.na(annotated_df$UniprotId))
+    expect_true(is.na(annotated_df$IsKinase))
+})
+
+test_that("a protein group's groundings fan out into separate query nodes", {
+    df <- data.frame(Protein = "P13747;P23132", stringsAsFactors = FALSE)
+    local_mocked_bindings(
+        .callGetHgncIdsFromUniprotIdsApi = function(uniprotIds) {
+            list(P13747 = "4931", P23132 = "10012")
+        },
+        .callGetHgncNamesFromHgncIdsApi = function(hgncIds) {
+            list(`4931` = "HLA-E", `10012` = "RAD23A")
+        },
+        .callIsTranscriptionFactorApi = function(genes) list(),
+        .callIsKinaseApi = function(genes) list(),
+        .callIsPhosphataseApi = function(genes) list()
+    )
+    annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot")
+
+    pairs <- MSstatsBioNet:::.buildCogexGroundings(
+        namespaces = annotated_df$EntityNamespace,
+        ids        = annotated_df$EntityId,
+        force_include_other = NULL
+    )
+    expect_setequal(
+        vapply(pairs, function(p) paste(p[[1]], p[[2]], sep = ":"), character(1)),
+        c("HGNC:4931", "HGNC:10012")
+    )
+})