From 130faa58ffc1e9b8f6c83de014004c06676261bd Mon Sep 17 00:00:00 2001
From: Toby Dylan Hocking <toby.dylan.hocking@usherbrooke.ca>
Date: Wed, 18 Dec 2024 09:32:09 -0500
Subject: [PATCH] capture first glob test and doc

---
 R/capture_first_glob.R          |  4 +--
 man/capture_first_glob.Rd       |  4 +--
 tests/testthat/test-CRAN-glob.R | 49 +++++++++++++++++++++++++++------
 3 files changed, 45 insertions(+), 12 deletions(-)

diff --git a/R/capture_first_glob.R b/R/capture_first_glob.R
index f6d2e6f..13f4aae 100644
--- a/R/capture_first_glob.R
+++ b/R/capture_first_glob.R
@@ -4,8 +4,8 @@ capture_first_glob <- structure(function
 (glob, 
 ### string: glob specifying files to read.
   ..., 
-### pattern passed to capture_first_vec, used to get meta-data from
-### file names.
+### passed to capture_first_vec, should include pattern used on vector
+### of file names to get meta-data.
   READ=fread
 ### function of one argument (file name) which returns a data table,
 ### default data.table::fread.
diff --git a/man/capture_first_glob.Rd b/man/capture_first_glob.Rd
index 07124be..e09a79a 100644
--- a/man/capture_first_glob.Rd
+++ b/man/capture_first_glob.Rd
@@ -7,8 +7,8 @@ file name, and combine with contents of each file.}
     ..., READ = fread)}
 \arguments{
   \item{glob}{string: \code{glob} specifying files to read.}
-  \item{\dots}{pattern passed to \code{\link{capture_first_vec}}, used to get meta-data from
-file names.}
+  \item{\dots}{passed to \code{\link{capture_first_vec}}, should include pattern used on vector
+of file names to get meta-data.}
   \item{READ}{function of one argument (file name) which returns a data table,
 default \code{\link[data.table]{fread}}.}
 }
diff --git a/tests/testthat/test-CRAN-glob.R b/tests/testthat/test-CRAN-glob.R
index 4b19fee..6c310f6 100644
--- a/tests/testthat/test-CRAN-glob.R
+++ b/tests/testthat/test-CRAN-glob.R
@@ -7,11 +7,44 @@ db <- system.file("extdata/chip-seq-chunk-db", package="nc", mustWork=TRUE)
 glob <- paste0(db, "/*/*/counts/*")
 read.bedGraph <- function(f)data.table::fread(
   f, skip=1, col.names = c("chrom","start", "end", "count"))
-data.chunk.pattern <- list(
-  data="H.*?",
-  "/",
-  chunk="[0-9]+", as.integer)
-if(requireNamespace("R.utils"))test_engines("capture_first_glob returns expected columns", {
-  count.dt <- nc::capture_first_glob(glob, data.chunk.pattern, READ=read.bedGraph)
-  expect_identical(names(count.dt), c("data", "chunk", "chrom", "start", "end", "count"))
-})
+
+if(requireNamespace("R.utils")){
+
+  test_engines("capture_first_glob returns expected columns", {
+    count.dt <- nc::capture_first_glob(
+      glob,
+      data="H.*?",
+      "/",
+      chunk="[0-9]+", as.integer,
+      READ=read.bedGraph)
+    computed.cls <- sapply(count.dt, class)
+    expected.cls <- c(
+      data = "character",
+      chunk = "integer",
+      chrom = "character",
+      start = "integer",
+      end = "integer",
+      count = "integer")
+    expect_identical(computed.cls, expected.cls)
+  })
+
+  test_engines("capture_first_glob(type.convert) works", {
+    count.dt <- nc::capture_first_glob(
+      glob,
+      data="H.*?",
+      "/",
+      chunk="[0-9]+",
+      READ=read.bedGraph,
+      type.convert=TRUE)
+    computed.cls <- sapply(count.dt, class)
+    expected.cls <- c(
+      data = "character",
+      chunk = "integer",
+      chrom = "character",
+      start = "integer",
+      end = "integer",
+      count = "integer")
+    expect_identical(computed.cls, expected.cls)
+  })
+
+}