From ef42bd39d878d9dea3236e1abb7a0628f24c9eda Mon Sep 17 00:00:00 2001 From: Nicholas Beydler Date: Thu, 19 Sep 2024 14:51:25 -1000 Subject: [PATCH] i #230 replace a notebook's paths to get functions In each notebook, the working directory is the vignettes/ directory, however, the getwd() command states that the working directory is the kaiaulu/ folder itself. This is because each R code chunk considers its directory to be the working directory. To test the functionality of the get functions, I edited the config file to reflect the relative directory of vignettes/, thus parent directory ../ file path changes were added to each function. --- R/config.R | 86 ++++++++++++------------ vignettes/blamed_line_types_showcase.Rmd | 17 ++--- 2 files changed, 52 insertions(+), 51 deletions(-) diff --git a/R/config.R b/R/config.R index 7c3eb872..8b1ad24f 100644 --- a/R/config.R +++ b/R/config.R @@ -11,7 +11,7 @@ #' @return the tools.yml file #' @export get_tools <- function() { - tool <- yaml::read_yaml("tools.yml") + tool <- yaml::read_yaml("../tools.yml") return(tool) } @@ -23,7 +23,7 @@ get_tools <- function() { #' @return the tool path from tools.yml #' @export get_tools_project <- function(tool_name) { - tool <- yaml::read_yaml("tools.yml") + tool <- yaml::read_yaml("../tools.yml") tool_path <- tool[[tool_name]] return(tool_path) } @@ -37,7 +37,7 @@ get_tools_project <- function(tool_name) { #' @export get_conf <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) if(is.null(conf)) { @@ -55,7 +55,7 @@ get_conf <- function(project_name) { #' @return the local git repo path #' @export get_git_repo_path <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) git_repo_path <- conf[["version_control"]][["log"]] @@ -76,7 +76,7 @@ get_git_repo_path <- function(project_name) { #' @export get_git_branches <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) git_branch <- conf[["version_control"]][["branch"]] @@ -97,7 +97,7 @@ get_git_branches <- function(project_name) { #' @export get_file_extensions <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) file_extensions <- conf[["filter"]][["keep_filepaths_ending_with"]] @@ -118,7 +118,7 @@ get_file_extensions <- function(project_name) { #' @export get_substring_filepath <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) substring_filepath <- conf[["filter"]][["remove_filepaths_containing"]] @@ -139,7 +139,7 @@ get_substring_filepath <- function(project_name) { #' @export get_filter_commit_size <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) filter_commit_size <- conf[["filter"]][["remove_filepaths_on_commit_size_greather_than"]] @@ -160,7 +160,7 @@ get_filter_commit_size <- function(project_name) { #' @export get_uctags_line_types <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) kinds <- conf[["tool"]][["uctags"]][["keep_lines_type"]] @@ -181,7 +181,7 @@ get_uctags_line_types <- function(project_name) { #' @export get_code_language <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) language <- conf[["tool"]][["depends"]][["code_language"]] @@ -202,7 +202,7 @@ get_code_language <- function(project_name) { #' @export get_keep_dependencies_type <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) keep_dependencies_type <- conf[["tool"]][["depends"]][["keep_dependencies_type"]] @@ -224,7 +224,7 @@ get_keep_dependencies_type <- function(project_name) { #' @export get_dv8_folder_path <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) project_path <- conf[["tool"]][["dv8"]][["folder_path"]] @@ -245,7 +245,7 @@ get_dv8_folder_path <- function(project_name) { #' @export get_dv8_flaws_params <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) flaws_params <- conf[["tool"]][["dv8"]][["architectural_flaws"]] @@ -266,7 +266,7 @@ get_dv8_flaws_params <- function(project_name) { #' @export get_issue_id_regex <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) issue_id_regex <- conf[["commit_message_id_regex"]][["issue_id"]] @@ -287,7 +287,7 @@ get_issue_id_regex <- function(project_name) { #' @export get_srcml_filepath <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) srcml_filepath <- conf[["tool"]][["srcml"]][["srcml_path"]] @@ -308,7 +308,7 @@ get_srcml_filepath <- function(project_name) { #' @export get_pattern4_folder_path <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) class_folder_path <- conf[["tool"]][["pattern4"]][["class_folder_path"]] @@ -329,7 +329,7 @@ get_pattern4_folder_path <- function(project_name) { #' @export get_pattern4_filepath <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) pattern4_output_filepath <- conf[["tool"]][["pattern4"]][["output_filepath"]] @@ -350,7 +350,7 @@ get_pattern4_filepath <- function(project_name) { #' @export get_topics <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) topics <- conf[["analysis"]][["topics"]] @@ -371,7 +371,7 @@ get_topics <- function(project_name) { #' @export get_mbox_key_indexes <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) mbox_keys <- conf[["mailing_list"]][["mod_mbox"]] @@ -393,7 +393,7 @@ get_mbox_key_indexes <- function(project_name) { #' @export get_mbox_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) mbox_path <- conf[["mailing_list"]][["mod_mbox"]][[project_key_index]][["mbox"]] @@ -415,7 +415,7 @@ get_mbox_path <- function(project_name, project_key_index) { #' @export get_mbox_domain <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) mbox_url <- conf[["mailing_list"]][["mod_mbox"]][[project_key_index]][["archive_url"]] @@ -437,7 +437,7 @@ get_mbox_domain <- function(project_name, project_key_index) { #' @export get_mbox_mailing_list <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) mailing_list <- conf[["mailing_list"]][["mod_mbox"]][[project_key_index]][["mailing_list"]] @@ -459,7 +459,7 @@ get_mbox_mailing_list <- function(project_name, project_key_index) { #' @export get_mbox_mailing_list <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) archive_type <- conf[["mailing_list"]][["mod_mbox"]][[project_key_index]][["archive_type"]] @@ -480,7 +480,7 @@ get_mbox_mailing_list <- function(project_name, project_key_index) { #' @export get_github_key_indexes <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) keys <- conf[["issue_tracker"]][["github"]] @@ -502,7 +502,7 @@ get_github_key_indexes <- function(project_name) { #' @export get_github_owner <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) owner <- conf[["issue_tracker"]][["github"]][[project_key_index]][["owner"]] @@ -524,7 +524,7 @@ get_github_owner <- function(project_name, project_key_index) { #' @export get_github_repo <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) repo <- conf[["issue_tracker"]][["github"]][[project_key_index]][["repo"]] @@ -546,7 +546,7 @@ get_github_repo <- function(project_name, project_key_index) { #' @export get_github_issue_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) issue_path <- conf[["issue_tracker"]][["github"]][[project_key_index]][["issue"]] @@ -568,7 +568,7 @@ get_github_issue_path <- function(project_name, project_key_index) { #' @export get_github_issue_or_pr_comment_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) issue_or_pr_comment_path <- conf[["issue_tracker"]][["github"]][[project_key_index]][["issue_or_pr_comment"]] @@ -590,7 +590,7 @@ get_github_issue_or_pr_comment_path <- function(project_name, project_key_index) #' @export get_github_issue_search_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) issue_search_path <- conf[["issue_tracker"]][["github"]][[project_key_index]][["issue_search"]] @@ -612,7 +612,7 @@ get_github_issue_search_path <- function(project_name, project_key_index) { #' @export get_github_pull_request_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) pull_request_path <- conf[["issue_tracker"]][["github"]][[project_key_index]][["pull_request"]] @@ -634,7 +634,7 @@ get_github_pull_request_path <- function(project_name, project_key_index) { #' @export get_github_commit_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) commit_path <- conf[["issue_tracker"]][["github"]][[project_key_index]][["commit"]] @@ -655,7 +655,7 @@ get_github_commit_path <- function(project_name, project_key_index) { #' @export get_jira_key_indexes <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) keys <- conf[["issue_tracker"]][["jira"]] @@ -677,7 +677,7 @@ get_jira_key_indexes <- function(project_name) { #' @export get_jira_domain <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) domain <- conf[["issue_tracker"]][["jira"]][[project_key_index]][["domain"]] @@ -699,7 +699,7 @@ get_jira_domain <- function(project_name, project_key_index) { #' @export get_jira_project_key_name <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) name <- conf[["issue_tracker"]][["jira"]][[project_key_index]][["project_key"]] @@ -721,7 +721,7 @@ get_jira_project_key_name <- function(project_name, project_key_index) { #' @export get_jira_issues_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) jira_issues_path <- conf[["issue_tracker"]][["jira"]][[project_key_index]][["issues"]] @@ -743,7 +743,7 @@ get_jira_issues_path <- function(project_name, project_key_index) { #' @export get_jira_issues_comments_path <- function(project_name, project_key_index) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) jira_issue_comments_path <- conf[["issue_tracker"]][["jira"]][[project_key_index]][["issue_comments"]] @@ -764,7 +764,7 @@ get_jira_issues_comments_path <- function(project_name, project_key_index) { #' @export get_bugzilla_project_key <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) key <- conf[["issue_tracker"]][["bugzilla"]][["project_key_index"]][["project_key"]] @@ -785,7 +785,7 @@ get_bugzilla_project_key <- function(project_name) { #' @export get_nvdfeed_folder_path <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) nvdfeed_folder_path <- conf[["vulnerabilities"]][["nvd_feed"]] @@ -806,7 +806,7 @@ get_nvdfeed_folder_path <- function(project_name) { #' @export get_cveid_regex <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) cveid_regex <- conf[["commit_message_id_regex"]][["cve_id"]] @@ -827,7 +827,7 @@ get_cveid_regex <- function(project_name) { #' @export get_enumeration_commits <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) commit <- conf[["analysis"]][["enumeration"]][["commit"]] @@ -848,7 +848,7 @@ get_enumeration_commits <- function(project_name) { #' @export get_window_start_commit <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) start_commit <- conf[["analysis"]][["window"]][["start_commit"]] @@ -869,7 +869,7 @@ get_window_start_commit <- function(project_name) { #' @export get_window_end_commit <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) end_commit <- conf[["analysis"]][["window"]][["end_commit"]] @@ -890,7 +890,7 @@ get_window_end_commit <- function(project_name) { #' @export get_window_size <- function(project_name) { - conf_path <- paste0("conf/", project_name, ".yml") + conf_path <- paste0("../conf/", project_name, ".yml") conf <- yaml::read_yaml(conf_path) window_size <- conf[["analysis"]][["window"]][["size_days"]] diff --git a/vignettes/blamed_line_types_showcase.Rmd b/vignettes/blamed_line_types_showcase.Rmd index 3f12eb05..82f54a04 100644 --- a/vignettes/blamed_line_types_showcase.Rmd +++ b/vignettes/blamed_line_types_showcase.Rmd @@ -84,22 +84,23 @@ filter: We load the above various sections of the single .yaml project configuration file as follows: ```{r} -tool <- yaml::read_yaml("../tools.yml") -conf <- yaml::read_yaml("../conf/apr.yml") +source("../R/config.R") +tool <- get_tools() +conf <- get_conf("apr") # 3rd Party Tools -perceval_path <- tool[["perceval"]] -utags_path <- tool[["utags"]] +perceval_path <- get_tools_project("perceval") +utags_path <- get_tools_project("utags") # Ctags Line Types -kinds <- conf[["tool"]][["uctags"]][["keep_lines_type"]] +kinds <- get_uctags_line_types("apr") # Local Git Repo Folder Path -git_repo_path <- conf[["version_control"]][["log"]] +git_repo_path <- get_git_repo_path("apr") # File Filters -file_extensions <- conf[["filter"]][["keep_filepaths_ending_with"]] -substring_filepath <- conf[["filter"]][["remove_filepaths_containing"]] +file_extensions <- get_file_extensions("apr") +substring_filepath <- get_substring_filepath("apr") ```