From 62c8ae65023568ff64155003a127b25d312f12b1 Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Mon, 8 Jul 2024 15:03:02 -0400
Subject: [PATCH 1/8] start functionalizing make screenshots

---
 DESCRIPTION    |  3 ++-
 NAMESPACE      |  6 +++++
 R/screenshot.R | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+), 1 deletion(-)
 create mode 100644 R/screenshot.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 64a520ed..9921720e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,6 +40,7 @@ Imports:
     yaml
 Suggests:
     remotes,
+    cow,
     testthat,
     tibble,
     utils
@@ -48,4 +49,4 @@ VignetteBuilder:
 ByteCompile: true
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
index 68aaac30..9f8192a5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -56,6 +56,9 @@ export(set_up_leanpub)
 export(simple_references)
 export(unzip_pptx)
 export(xml_notes)
+import(bookdown_path)
+import(cow)
+import(dplyr)
 importFrom(fs,dir_copy)
 importFrom(httr,GET)
 importFrom(httr,accept_json)
@@ -68,10 +71,13 @@ importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(openssl,aes_cbc_decrypt)
 importFrom(readr,write_tsv)
+importFrom(rprojroot,find_root)
+importFrom(rprojroot,has_dir)
 importFrom(utils,download.file)
 importFrom(utils,installed.packages)
 importFrom(utils,menu)
 importFrom(utils,unzip)
+importFrom(webshot2,webshot)
 importFrom(xml2,read_xml)
 importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_text)
diff --git a/R/screenshot.R b/R/screenshot.R
new file mode 100644
index 00000000..d2a13d25
--- /dev/null
+++ b/R/screenshot.R
@@ -0,0 +1,60 @@
+#' A function to make screenshots from an OTTR bookdown website
+#' @description This function creates screenshots of course chapters that are stored in a created output directory 
+#' @param git_pat default is NULL; required argument; a Git secret
+#' @param repo default is NULL; required argument; GitHub repository name, e.g., jhudsl/OTTR_Template
+#' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored
+#' @param base_url default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url
+#' @import cow
+#' @import dplyr
+#' @importFrom webshot2 webshot
+#' @importFrom magrittr %>%
+#' @importFrom rprojroot find_root has_dir
+#' @author Candace Savonen
+make_screenshots <- function(git_pat = NULL, repo = NULL, output_dir = "resources/chapt_screen_images", base_url = NULL){
+  
+  # Find .git root directory
+  root_dir <- find_root(has_dir(".git"))
+  
+  output_folder <- file.path(output_dir)
+  if (!dir.exists(output_folder)) {
+    dir.create(output_folder, recursive = TRUE)
+  }
+  
+  if (is.null(base_url)){
+    base_url <- cow::get_pages_url(repo_name = repo, git_pat = git_pat) #what if these arguments are still NULL/not supplied?
+    base_url <- gsub("/$", "", base_url)
+  }
+  
+  # Collect all the chapter pages for the url given
+  chapt_df <- ottrpal::get_chapters(html_page = file.path(root_dir, "docs", "index.html"),
+                                    base_url = base_url)
+  
+  # Now take screenshots for each
+  file_names <- lapply(chapt_df$url, function(url){
+    file_name <- gsub(".html", 
+                      ".png", 
+                      file.path(output_folder, basename(url))
+                      )
+    
+    # Get rid of special characters because leanpub no like
+    file_name <- gsub(":|?|!|\\'",
+                      "",
+                      file_name
+                      )
+    
+    # Take the screenshot
+    webshot(url, file = file_name)
+    
+    return(file_name)
+  })
+  
+  # Save file of chapter urls and file_names
+  chapt_df <- chapt_df %>%
+    dplyr::mutate(img_path = unlist(file_names))
+  
+  chapt_df %>% 
+    readr::write_tsv(file.path(output_folder, "chapter_urls.tsv"))
+  
+  message(paste("Image Chapter key written to: ", file.path(output_folder, "chapter_urls.tsv")))
+  
+}
\ No newline at end of file

From 23f0fa5d74ae39c1ea16ab08e34ca189761783a5 Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Tue, 9 Jul 2024 11:52:10 -0400
Subject: [PATCH 2/8] Update R/screenshot.R

Co-authored-by: Candace Savonen <cansav09@gmail.com>
---
 R/screenshot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/screenshot.R b/R/screenshot.R
index d2a13d25..405cb631 100644
--- a/R/screenshot.R
+++ b/R/screenshot.R
@@ -2,7 +2,7 @@
 #' @description This function creates screenshots of course chapters that are stored in a created output directory 
 #' @param git_pat default is NULL; required argument; a Git secret
 #' @param repo default is NULL; required argument; GitHub repository name, e.g., jhudsl/OTTR_Template
-#' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored
+#' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored. For OTTR courses, don't change this unless you've changed the downstream functions accordingly. 
 #' @param base_url default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url
 #' @import cow
 #' @import dplyr

From 0aabec8daec4b20deb25f61f4e74cb2dd11cadb2 Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Tue, 9 Jul 2024 13:39:55 -0400
Subject: [PATCH 3/8] address quick suggestions

---
 R/screenshot.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/screenshot.R b/R/screenshot.R
index 405cb631..e1b7c39b 100644
--- a/R/screenshot.R
+++ b/R/screenshot.R
@@ -1,16 +1,22 @@
 #' A function to make screenshots from an OTTR bookdown website
 #' @description This function creates screenshots of course chapters that are stored in a created output directory 
-#' @param git_pat default is NULL; required argument; a Git secret
-#' @param repo default is NULL; required argument; GitHub repository name, e.g., jhudsl/OTTR_Template
+#' @param git_pat required argument; a Git secret -- see https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens for more info
+#' @param repo required argument; GitHub repository name, e.g., jhudsl/OTTR_Template
 #' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored. For OTTR courses, don't change this unless you've changed the downstream functions accordingly. 
 #' @param base_url default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url
+#' @return the file path for file where chapter urls are saved
 #' @import cow
 #' @import dplyr
 #' @importFrom webshot2 webshot
 #' @importFrom magrittr %>%
 #' @importFrom rprojroot find_root has_dir
 #' @author Candace Savonen
-make_screenshots <- function(git_pat = NULL, repo = NULL, output_dir = "resources/chapt_screen_images", base_url = NULL){
+#' @examples \dontrun{
+#' 
+#'  make_screenshots(Sys.getenv("secrets.GH_PAT"), "jhudsl/OTTR_Template")
+#'  
+#' }
+make_screenshots <- function(git_pat, repo, output_dir = "resources/chapt_screen_images", base_url = NULL){
   
   # Find .git root directory
   root_dir <- find_root(has_dir(".git"))
@@ -57,4 +63,6 @@ make_screenshots <- function(git_pat = NULL, repo = NULL, output_dir = "resource
   
   message(paste("Image Chapter key written to: ", file.path(output_folder, "chapter_urls.tsv")))
   
+  return(file.path(output_folder, "chapter_urls.tsv"))
+  
 }
\ No newline at end of file

From 4f85a8c9ca1cb474cdb7c360bb9abea5f45bda8a Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Tue, 9 Jul 2024 14:00:53 -0400
Subject: [PATCH 4/8] copy over cow function to ottrpal

---
 NAMESPACE               |  4 +-
 R/get_pages_url.R       | 81 +++++++++++++++++++++++++++++++++++++++++
 R/screenshot.R          |  3 +-
 man/get_pages_url.Rd    | 36 ++++++++++++++++++
 man/make_screenshots.Rd | 38 +++++++++++++++++++
 5 files changed, 157 insertions(+), 5 deletions(-)
 create mode 100644 R/get_pages_url.R
 create mode 100644 man/get_pages_url.Rd
 create mode 100644 man/make_screenshots.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 37fec0f6..a97a304b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,6 +23,7 @@ export(get_gs_pptx)
 export(get_image_from_slide)
 export(get_image_link_from_slide)
 export(get_object_id_notes)
+export(get_pages_url)
 export(get_slide_id)
 export(get_slide_page)
 export(get_yaml_spec)
@@ -46,10 +47,7 @@ export(set_up_leanpub)
 export(unzip_pptx)
 export(website_to_embed_leanpub)
 export(xml_notes)
-import(bookdown_path)
-import(cow)
 import(dplyr)
-importFrom(fs,dir_copy)
 importFrom(httr,GET)
 importFrom(httr,accept_json)
 importFrom(httr,config)
diff --git a/R/get_pages_url.R b/R/get_pages_url.R
new file mode 100644
index 00000000..d65f0829
--- /dev/null
+++ b/R/get_pages_url.R
@@ -0,0 +1,81 @@
+#' Retrieve pages url for a repo
+#'
+#' Given an repository on GitHub, retrieve the pages URL for it.
+#'
+#' @param repo_name The full name of the repo to get bookdown chapters from.
+#' e.g. "jhudsl/OTTR_Template"
+#' @param git_pat If private repositories are to be retrieved, a github personal
+#' access token needs to be supplied. If none is supplied, then this will attempt to
+#' grab from a git pat set in the environment with usethis::create_github_token().
+#' Authorization handled by \link[cow]{get_git_auth}
+#' @param verbose TRUE/FALSE do you want more progress messages?
+#' @param keep_json verbose TRUE/FALSE keep the json file locally?
+#'
+#' @return a data frame with the repository with the following columns:
+#' data_level, data_path, chapt_name, url, repository name
+#'
+#' @importFrom magrittr %>%
+#' @import dplyr
+#'
+#' @export
+#'
+#' @examples \dontrun{
+#'
+#' usethis::create_github_token()
+#'
+#' get_chapters("jhudsl/Documentation_and_Usability")
+#' }
+get_pages_url <- function(repo_name,
+                          git_pat = NULL,
+                          verbose = FALSE,
+                          keep_json = FALSE) {
+  page_url <- NA
+
+  # Try to get credentials other way
+  auth_arg <- get_git_auth(git_pat = git_pat, quiet = !verbose)
+
+  git_pat <- try(auth_arg$password, silent = TRUE)
+
+  if (grepl("Error", git_pat[1])) {
+    warning("Cannot retrieve page info without GitHub credentials. Passing an NA.")
+  }
+
+  # We can only retrieve pages if we have the credentials
+  if (!grepl("Error", git_pat[1])) {
+    exists <- check_git_repo(
+      repo_name = repo_name,
+      git_pat = git_pat,
+      verbose = FALSE
+    )
+
+    if (exists) {
+      # Get repo info
+      repo_info <- get_repo_info(
+        repo_name = repo_name,
+        git_pat = git_pat
+      )
+
+      # Declare URL
+      url <- paste0("https://api.github.com/repos/", repo_name, "/pages")
+
+      # Github api get
+      response <- httr::GET(
+        url,
+        httr::add_headers(Authorization = paste0("token ", auth_arg$password)),
+        httr::accept_json()
+      )
+
+      if (httr::http_error(response)) {
+        if (verbose) {
+          warning(paste0("url: ", url, " failed"))
+        }
+      } else {
+        # Get content as JSON
+        page_info <- httr::content(response, as = "parsed")
+
+        page_url <- page_info$html_url
+      }
+    }
+  }
+  return(page_url)
+}
diff --git a/R/screenshot.R b/R/screenshot.R
index e1b7c39b..5315a772 100644
--- a/R/screenshot.R
+++ b/R/screenshot.R
@@ -5,7 +5,6 @@
 #' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored. For OTTR courses, don't change this unless you've changed the downstream functions accordingly. 
 #' @param base_url default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url
 #' @return the file path for file where chapter urls are saved
-#' @import cow
 #' @import dplyr
 #' @importFrom webshot2 webshot
 #' @importFrom magrittr %>%
@@ -27,7 +26,7 @@ make_screenshots <- function(git_pat, repo, output_dir = "resources/chapt_screen
   }
   
   if (is.null(base_url)){
-    base_url <- cow::get_pages_url(repo_name = repo, git_pat = git_pat) #what if these arguments are still NULL/not supplied?
+    base_url <- ottrpal::get_pages_url(repo_name = repo, git_pat = git_pat) #what if these arguments are still NULL/not supplied?
     base_url <- gsub("/$", "", base_url)
   }
   
diff --git a/man/get_pages_url.Rd b/man/get_pages_url.Rd
new file mode 100644
index 00000000..3ee5765b
--- /dev/null
+++ b/man/get_pages_url.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_pages_url.R
+\name{get_pages_url}
+\alias{get_pages_url}
+\title{Retrieve pages url for a repo}
+\usage{
+get_pages_url(repo_name, git_pat = NULL, verbose = FALSE, keep_json = FALSE)
+}
+\arguments{
+\item{repo_name}{The full name of the repo to get bookdown chapters from.
+e.g. "jhudsl/OTTR_Template"}
+
+\item{git_pat}{If private repositories are to be retrieved, a github personal
+access token needs to be supplied. If none is supplied, then this will attempt to
+grab from a git pat set in the environment with usethis::create_github_token().
+Authorization handled by \link[cow]{get_git_auth}}
+
+\item{verbose}{TRUE/FALSE do you want more progress messages?}
+
+\item{keep_json}{verbose TRUE/FALSE keep the json file locally?}
+}
+\value{
+a data frame with the repository with the following columns:
+data_level, data_path, chapt_name, url, repository name
+}
+\description{
+Given an repository on GitHub, retrieve the pages URL for it.
+}
+\examples{
+\dontrun{
+
+usethis::create_github_token()
+
+get_chapters("jhudsl/Documentation_and_Usability")
+}
+}
diff --git a/man/make_screenshots.Rd b/man/make_screenshots.Rd
new file mode 100644
index 00000000..d3d4c9dd
--- /dev/null
+++ b/man/make_screenshots.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/screenshot.R
+\name{make_screenshots}
+\alias{make_screenshots}
+\title{A function to make screenshots from an OTTR bookdown website}
+\usage{
+make_screenshots(
+  git_pat,
+  repo,
+  output_dir = "resources/chapt_screen_images",
+  base_url = NULL
+)
+}
+\arguments{
+\item{git_pat}{required argument; a Git secret -- see https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens for more info}
+
+\item{repo}{required argument; GitHub repository name, e.g., jhudsl/OTTR_Template}
+
+\item{output_dir}{default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored. For OTTR courses, don't change this unless you've changed the downstream functions accordingly.}
+
+\item{base_url}{default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url}
+}
+\value{
+the file path for file where chapter urls are saved
+}
+\description{
+This function creates screenshots of course chapters that are stored in a created output directory
+}
+\examples{
+\dontrun{
+
+ make_screenshots(Sys.getenv("secrets.GH_PAT"), "jhudsl/OTTR_Template")
+ 
+}
+}
+\author{
+Candace Savonen
+}

From edddb94ed17bd1d6a7fb491cad5943dac05f3610 Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Tue, 9 Jul 2024 14:36:25 -0400
Subject: [PATCH 5/8] update example for get pages and add export to screenshot

---
 NAMESPACE            | 1 +
 R/get_pages_url.R    | 2 +-
 R/screenshot.R       | 7 +++++++
 man/get_pages_url.Rd | 2 +-
 4 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index a97a304b..aa7ad95d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,6 +33,7 @@ export(gs_png_download)
 export(gs_png_url)
 export(include_slide)
 export(make_embed_markdown)
+export(make_screenshots)
 export(output_destination)
 export(parse_q_tag)
 export(parse_quiz)
diff --git a/R/get_pages_url.R b/R/get_pages_url.R
index d65f0829..14471259 100644
--- a/R/get_pages_url.R
+++ b/R/get_pages_url.R
@@ -23,7 +23,7 @@
 #'
 #' usethis::create_github_token()
 #'
-#' get_chapters("jhudsl/Documentation_and_Usability")
+#' get_pages_url("jhudsl/Documentation_and_Usability")
 #' }
 get_pages_url <- function(repo_name,
                           git_pat = NULL,
diff --git a/R/screenshot.R b/R/screenshot.R
index 5315a772..50e30842 100644
--- a/R/screenshot.R
+++ b/R/screenshot.R
@@ -1,15 +1,22 @@
 #' A function to make screenshots from an OTTR bookdown website
 #' @description This function creates screenshots of course chapters that are stored in a created output directory 
+#'
 #' @param git_pat required argument; a Git secret -- see https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens for more info
 #' @param repo required argument; GitHub repository name, e.g., jhudsl/OTTR_Template
 #' @param output_dir default is "resources/chapt_screen_images"; Output directory where the chapter's screen images should be stored. For OTTR courses, don't change this unless you've changed the downstream functions accordingly. 
 #' @param base_url default is NULL; rendered bookdown URL where screenshots are taken from, if NULL, the function will use the repo_name and and git_pat to find the base_url
+#'
 #' @return the file path for file where chapter urls are saved
+#'
 #' @import dplyr
 #' @importFrom webshot2 webshot
 #' @importFrom magrittr %>%
 #' @importFrom rprojroot find_root has_dir
+#' 
 #' @author Candace Savonen
+#'
+#' @export
+#'
 #' @examples \dontrun{
 #' 
 #'  make_screenshots(Sys.getenv("secrets.GH_PAT"), "jhudsl/OTTR_Template")
diff --git a/man/get_pages_url.Rd b/man/get_pages_url.Rd
index 3ee5765b..8f45facc 100644
--- a/man/get_pages_url.Rd
+++ b/man/get_pages_url.Rd
@@ -31,6 +31,6 @@ Given an repository on GitHub, retrieve the pages URL for it.
 
 usethis::create_github_token()
 
-get_chapters("jhudsl/Documentation_and_Usability")
+get_pages_url("jhudsl/Documentation_and_Usability")
 }
 }

From 8dd642db7de50f2f1b22067c4fdef3e8bded8777 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 10 Jul 2024 14:45:13 -0400
Subject: [PATCH 6/8] Update R-CMD-check.yaml

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 091012fd..ffca4661 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -36,7 +36,7 @@ jobs:
           rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
         shell: Rscript {0}
         env:
-          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+          GH_PAT: ${{ secrets.GH_PAT }}
 
       - name: Check testthat
         id: check_check

From d8f16227fca061e0f5e08b67ddc3fa4952f7579d Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:49:21 -0400
Subject: [PATCH 7/8] Update DESCRIPTION

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 593fccc8..0f4b8a9a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -35,6 +35,7 @@ Imports:
     rprojroot,
     rvest,
     stringr,
+    webshot2,
     xml2,
     yaml
 Suggests:

From 55005af8eea005a062180ca978991c749315b41d Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 19 Jul 2024 12:06:40 -0400
Subject: [PATCH 8/8] Fix description file for cow dependency

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0f4b8a9a..6d0fe56f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,11 +39,11 @@ Imports:
     xml2,
     yaml
 Suggests:
-    remotes,
-    cow,
     testthat (>= 3.0.0),
     tibble,
     utils
+Remotes: 
+    jhudsl/cow
 VignetteBuilder: 
     knitr
 ByteCompile: true