Remove data only used for testing

llrs · Sep 27, 2023 · 0aec4ab · 0aec4ab
1 parent 181633f
commit 0aec4ab
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Showing 2 changed files with 68 additions and 22 deletions.
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/tests/testthat/test_pathSim.R b/tests/testthat/test_pathSim.R
@@ -1,22 +1,68 @@
-library("BioCor")
-context("Testing pathSim")
-
-test_that("pathSim", {
-    test <- pathSim("194840", "156580", info)
-    expect_equal(test, 0.4)
-    expect_error(pathSim(NULL, "156580", info), "several")
-    expect_error(pathSim(1, "156580", info), "characters")
-    expect_error(pathSim("1", "156580", "a"), "list")
-    expect_true(is.na(pathSim("1", "156580", info)))
-    expect_equal(pathSim("109582", "114608", info), 1)
-})
-
-test_that("pathSim with GSC", {
-    test <- pathSim("194840", "156580", Info)
-    expect_equal(test, 0.4)
-    expect_error(pathSim(NULL, "156580", Info), "several")
-    expect_error(pathSim(1, "156580", Info), "characters")
-    expect_error(pathSim("1", "156580", "a"), "list")
-    expect_true(is.na(pathSim("1", "156580", Info)))
-    expect_true(is.na(pathSim("109582", "114608", Info)))
-})
+library("BioCor")
+context("Testing pathSim")
+
+test_that("pathSim", {
+  test <- pathSim("194840", "156580", info)
+  expect_equal(test, 0.4)
+  expect_error(pathSim(NULL, "156580", info), "several")
+  expect_error(pathSim(1, "156580", info), "characters")
+  expect_error(pathSim("1", "156580", "a"), "list")
+  expect_true(is.na(pathSim("1", "156580", info)))
+  expect_equal(pathSim("109582", "114608", info), 1)
+})
+
+test_that("pathSim with GSC", {
+  Info <- new("GeneSetCollection",
+              .Data = list(
+                new("GeneSet",
+                    geneIdType = new("NullIdentifier", type = "Null", annotation = ""),
+                    geneIds = c("10", "9"),
+                    setName = "1430728",
+                    setIdentifier = "linux:7312:Fri Mar 30 13:41:18 2018:36",
+                    shortDescription = "", longDescription = "", organism = "",
+                    pubMedIds = character(0), urls = character(0),
+                    contributor = character(0),
+                    creationDate = character(0),
+                    collectionType = new("NullCollection", type = "Null")),
+                new("GeneSet",
+                    geneIdType = new("NullIdentifier", type = "Null", annotation = ""),
+                    geneIds = c("10", "3", "9"), setName = "156580",
+                    setIdentifier = "linux:7312:Fri Mar 30 13:41:18 2018:37",
+                    shortDescription = "", longDescription = "", organism = "",
+                    pubMedIds = character(0), urls = character(0),
+                    contributor = character(0), creationDate = character(0),
+                    collectionType = new("NullCollection", type = "Null")),
+                new("GeneSet",
+                    geneIdType = new("NullIdentifier", type = "Null", annotation = ""),
+                    geneIds = c("10", "9"), setName = "156582",
+                    setIdentifier = "linux:7312:Fri Mar 30 13:41:18 2018:38",
+                    shortDescription = "", longDescription = "", organism = "",
+                    pubMedIds = character(0), urls = character(0),
+                    contributor = character(0),
+
+                    collectionType = new("NullCollection", type = "Null")),
+                new("GeneSet",
+                    geneIdType = new("NullIdentifier", type = "Null", annotation = ""),
+                    geneIds = c("2", "3"), setName = "194840",
+                    setIdentifier = "linux:7312:Fri Mar 30 13:41:18 2018:39",
+                    shortDescription = "", longDescription = "", organism = "",
+                    pubMedIds = character(0), urls = character(0),
+                    contributor = character(0),  creationDate = character(0),
+                    collectionType = new("NullCollection", type = "Null")),
+                new("GeneSet",
+                    geneIdType = new("NullIdentifier", type = "Null", annotation = ""),
+                    geneIds = c("10", "9"), setName = "211859",
+                    setIdentifier = "linux:7312:Fri Mar 30 13:41:18 2018:40",
+                    shortDescription = "", longDescription = "", organism = "",
+                    pubMedIds = character(0), urls = character(0),
+                    contributor = character(0),
+                    creationDate = character(0),
+                    collectionType = new("NullCollection", type = "Null"))))
+  test <- pathSim("194840", "156580", Info)
+  expect_equal(test, 0.4)
+  expect_error(pathSim(NULL, "156580", Info), "several")
+  expect_error(pathSim(1, "156580", Info), "characters")
+  expect_error(pathSim("1", "156580", "a"), "list")
+  expect_true(is.na(pathSim("1", "156580", Info)))
+  expect_true(is.na(pathSim("109582", "114608", Info)))
+})