Add QC report

.github/workflows/main.yaml

@@ -21,6 +21,10 @@ jobs:
             r: 4.0.5
           - os: ubuntu-20.04
             r: 4.1.3
+          - os: ubuntu-20.04
+            r: 4.2.3
+          - os: ubuntu-20.04
+            r: 4.3.1
           - os: ubuntu-latest
             r: release
     env:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: review
 Title: QC Management and Helpers
-Version: 3.9.1
+Version: 3.9.1.9003
 Authors@R: 
     c(
     person(given = "Eric", family = "Anderson", email = "[email protected]", role = c("aut")),
@@ -9,12 +9,12 @@ Authors@R:
     )
 Description: Functions for managing logs of reviews of subversioned
         files (http://subversion.apache.org/).
-URL: https://github.com/metrumresearchgroup/review
+URL: https://github.com/metrumresearchgroup/review, https://metrumresearchgroup.github.io/review/
 BugReports: https://github.com/metrumresearchgroup/review/issues
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     dplyr,
     magrittr (>= 2.0.3),

NAMESPACE

@@ -8,13 +8,17 @@ export(diffFiles)
 export(diffPreviousRevisions)
 export(diffQced)
 export(dirSummary)
+export(fileSummary)
 export(getQcedRevision)
 export(logAccept)
 export(logAssign)
 export(logCreate)
 export(logPending)
+export(logRemove)
 export(logSummary)
+export(renderQCReport)
 export(renderQCSummary)
+export(repoHistory)
 export(svnExport)
 export(svnLog)
 export(with_demoRepo)

NEWS.md

@@ -1,3 +1,13 @@
+# review development
+
+## New features and changes
+
+- `logRemove` added to package to assist with removing files from the QC log. (#105)
+
+- `diffFiles` can now display the entire file that is being diffed. (#115)
+
+- Added `repoHistory` function to return history of all commits in the repository. (#116)
+
 # review 3.9.1
 
 ## New features and changes

R/buildCompare.R

@@ -80,8 +80,8 @@ buildCompare <- function(.dfpaths, .side_by_side, .headings, .show_on_load = TRU
 
     }
 
-    base_path.i <- .dfpaths$path2[i]
-    compare_path.i <- .dfpaths$path1[i]
+    base_path.i <- .dfpaths$path1[i]
+    compare_path.i <- .dfpaths$path2[i]
 
 
     # Unique IDs for HTML elements

R/diffFiles.R

@@ -14,6 +14,7 @@
 #' @param .banner_2 Header for second file in viewer
 #' @param .side_by_side Logical. Should diffs be displayed side by side?
 #' @param .ignore_white_space Logical. Should white space be ignored?
+#' @param .display_entire_file Logical. Should the entire file be displayed?
 #' @examples 
 #' with_demoRepo({
 #'  diffFiles(.file_1 = "script/data-assembly.R", 
@@ -26,7 +27,8 @@ diffFiles <- function(.file_1,
                       .banner_1 = NULL,
                       .banner_2 = NULL,
                       .side_by_side = TRUE,
-                      .ignore_white_space = FALSE) {
+                      .ignore_white_space = FALSE,
+                      .display_entire_file = FALSE) {
 
   if (is.null(.banner_1)) {
     .banner_1 = basename(.file_1)
@@ -43,7 +45,8 @@ diffFiles <- function(.file_1,
     mode = ifelse(.side_by_side, "sidebyside", "unified"),
     tar.banner = .banner_1,
     cur.banner = .banner_2,
-    ignore.white.space = .ignore_white_space
+    ignore.white.space = .ignore_white_space,
+    context = ifelse(.display_entire_file, -1, 2)
   )
 
 }

R/diffPreviousRevisions.R

@@ -10,6 +10,7 @@
 #' @param .current_revision current revision (defaults to local copy)
 #' @param .side_by_side Logical. Should diffs be displayed side by side?
 #' @param .ignore_white_space Logical. Should white space be ignored?
+#' @param .display_entire_file Logical. Should the entire file be displayed?
 #' 
 #' @examples 
 #' with_demoRepo({
@@ -22,7 +23,8 @@ diffPreviousRevisions <- function(.file,
                                   .previous_revision,
                                   .current_revision = NULL,
                                   .side_by_side = TRUE,
-                                  .ignore_white_space = FALSE){
+                                  .ignore_white_space = FALSE,
+                                  .display_entire_file = FALSE){
 
   previousCurrent <-
     getPreviousCurrent(
@@ -42,7 +44,8 @@ diffPreviousRevisions <- function(.file,
     .banner_1 = previousCurrent$.previous_revision_header,
     .banner_2 = previousCurrent$.current_revision_header, 
     .side_by_side = .side_by_side, 
-    .ignore_white_space = .ignore_white_space 
+    .ignore_white_space = .ignore_white_space,
+    .display_entire_file = .display_entire_file
   )
 
 }

R/diffQced.R

@@ -8,14 +8,18 @@
 #' @param .file file path from working directory
 #' @param .side_by_side Logical. Should diffs be displayed side by side?
 #' @param .ignore_white_space Logical. Should white space be ignored?
+#' @param .display_entire_file Logical. Should the entire file be displayed?
 #' 
 #' @examples 
 #' with_demoRepo({
 #'   diffQced("script/data-assembly.R")
 #' })
 #' 
 #' @export
-diffQced <- function(.file, .side_by_side = TRUE, .ignore_white_space = FALSE){
+diffQced <- function(.file,
+                     .side_by_side = TRUE,
+                     .ignore_white_space = FALSE,
+                     .display_entire_file = FALSE){
 
   up_to_date <-
     tryCatch(
@@ -38,26 +42,16 @@ diffQced <- function(.file, .side_by_side = TRUE, .ignore_white_space = FALSE){
   file_log <- svnLog(.file)
   file_info <- file_log %>% dplyr::slice(1)
 
-  authors_last_qc <-
-    file_log %>% 
-    dplyr::filter(rev > qced_revision) %>% 
-    dplyr::pull(author)
-
   cli::cli_h2(glue::glue("QC diff for: ", .file))
   cli::cli_inform(glue::glue("Last QCed Revision: ", qced_revision))
   cli::cli_inform(glue::glue("Last Author: ", file_info$author))
 
-  this_user <- Sys.info()[["user"]]
-
-  if (this_user %in% authors_last_qc) {
-    cli::cli_alert_warning(glue::glue("'{this_user}' has modified '{basename(.file)}' since last QC"))
-  }
-
   diffPreviousRevisions(
     .file = .file, 
     .previous_revision = qced_revision,
     .side_by_side = .side_by_side, 
-    .ignore_white_space = .ignore_white_space
+    .ignore_white_space = .ignore_white_space,
+    .display_entire_file = .display_entire_file
   )
 
 }

R/fileSummary.R

@@ -0,0 +1,144 @@
+#' Summarize revision and QC history for a file
+#'
+#' @description
+#' Generates a comprehensive summary of the revision and quality control (QC) history
+#' for a file. The function reports:
+#' * QC status (up to date, needs QC, or not assigned)
+#' * Presence in the QC log
+#' * Historical information about previous authors
+#' * Historical information about previous QC reviewers
+#'
+#' @param .file File path.
+#'
+#' @details
+#' The function prints a formatted summary to the console and invisibly returns
+#' the data for programmatic use. Non-existent files generate warnings and are
+#' skipped. Files not found in the repository history are also skipped.
+#'
+#' QC status can be:
+#' * "QC up to date" - Latest revision has been QC'd
+#' * "Needs QC" - New changes need review
+#' * "Not assigned" - File not in QC system
+#'
+#' @examples
+#' \dontrun{
+#' # Analyze a single script file
+#' fileSummary("script/data-assembly/study-101.R")
+#'
+#' # Process all files in a directory
+#' purrr::walk(list.files("script/data-assembly", full.names = TRUE), ~ fileSummary(.file = .x))
+#' }
+#'
+#' @export
+fileSummary <- function(.file) {
+  if (length(.file) != 1) {
+    stop("'.file' must be a single file path")
+  }
+
+  if (!file.exists(.file)) {
+    warning(paste0(.file, " does not exist"))
+    return(invisible(NULL))
+  }
+
+  # Initialize output list
+  out <- list()
+  out$qclog <- cli::col_red("No")
+  out$qcstatus <- cli::col_magenta("Not assigned")
+  out$prevQC <- "No previous QC"
+
+  # Get repo history and QC log
+
+  # Get repo commit history for the file
+  script_history <- svnLog(.file)
+  script_history$date <- as.Date(script_history$datetime)
+
+  qc_log <- logRead()
+
+  if (nrow(script_history) == 0) {
+    warning(paste0(.file, " has no svn history"))
+    return(invisible(NULL))
+  }
+
+  # Get last revision of the file
+  last_rev <- as.numeric(script_history$rev[1])
+
+  # Filter QC log to file of interest
+  qc_file <- qc_log[qc_log$file == .file, ]
+
+  # Check if file is in QC log
+  if (nrow(qc_file) > 0) {
+
+    out$qclog <- cli::col_green("Yes")
+
+    # Process QC history
+    qc_file_filtered <- qc_file %>% dplyr::filter(revf != 0)
+
+    # For cases where no QC has been previously completed
+    if (nrow(qc_file_filtered) == 0) {
+
+      out$qcstatus <- cli::col_red("Needs QC")
+
+    } else {
+
+      qc_rev <- 
+        qc_file_filtered %>%
+        dplyr::arrange(-as.numeric(revf)) %>%
+        dplyr::slice(1) %>%
+        dplyr::pull(revf) %>%
+        as.numeric()
+
+      out$prevQC <- 
+        qc_file_filtered %>%
+        dplyr::arrange(-as.numeric(revf)) %>%
+        dplyr::group_by(reviewer) %>%
+        dplyr::slice(1) %>%
+        dplyr::ungroup() %>%
+        dplyr::transmute(VALUE = paste0(
+          reviewer, ", ",
+          as.numeric(difftime(Sys.Date(), as.Date(time), units = "days")),
+          " days ago"
+        )) %>%
+        dplyr::pull()
+
+      out$qcstatus <- 
+        ifelse(
+          last_rev > qc_rev,
+          cli::col_red("Needs QC"), 
+          cli::col_green("QC up to date")
+        )
+
+    }
+
+  } 
+
+  # Process author history
+  out$authors <- 
+    script_history %>%
+    dplyr::group_by(author) %>%
+    dplyr::slice(1) %>%
+    dplyr::ungroup() %>%
+    dplyr::arrange(-as.numeric(rev)) %>%
+    dplyr::transmute(VALUE = paste0(
+      author, ", ",
+      as.numeric(difftime(Sys.Date(), date, units = "days")),
+      " days ago"
+    )) %>%
+    dplyr::pull()
+
+  # Print summary
+  cli::cli_h2(glue::glue(.file, " summary"))
+  cli::cli_inform(glue::glue("In QC log: ", out$qclog))
+  cli::cli_inform(glue::glue("QC status: ", out$qcstatus))
+
+  cli::cli_verbatim("") # line break
+  cli::cli_inform("Previous QCer(s): ")
+  names(out$prevQC) <- rep(">", length(out$prevQC))
+  cli::cli_bullets(out$prevQC)
+
+  cli::cli_verbatim("") # line break
+  cli::cli_inform("Previous author(s): ")
+  names(out$authors) <- rep(">", length(out$authors))
+  cli::cli_bullets(out$authors)
+
+  return(invisible(out))
+}

R/findAuthorsQcers.R

@@ -0,0 +1,27 @@
+#' @noRd
+findAuthorsQcers <- function(.repoHistory, .qcLog) {
+
+  qclog <- 
+    .qcLog %>% 
+    dplyr::transmute(file, rev = as.character(revf), reviewer) %>% 
+    dplyr::filter(rev != "0") %>% 
+    dplyr::distinct()
+
+  rH_qclog <-
+    .repoHistory %>%
+    dplyr::left_join(qclog, by = c("file", "rev")) %>%
+    dplyr::arrange(file, -as.numeric(rev)) %>% 
+    dplyr::group_by(file) %>% 
+    tidyr::fill(reviewer, .direction = "down") %>%
+    dplyr::ungroup()
+
+  out <- list()
+
+  out$authors <- rH_qclog %>% dplyr::filter(is.na(reviewer) | author != reviewer)
+
+  out$qcers <- rH_qclog %>% dplyr::filter(author == reviewer)
+
+  stopifnot(nrow(.repoHistory) == nrow(out$authors) + nrow(out$qcers))
+
+  return(out)
+}

R/logRemove.R

@@ -0,0 +1,24 @@
+#' Remove file from QClog
+#' 
+#' @description 
+#' This function facilitates deleting a file from the QClog.csv file. 
+#' When run, all rows associated with the file will be deleted and 
+#' removed from the QC log.
+#' 
+#' @param .filepath current file path of file to be removed
+#' 
+#' @export
+logRemove <- function(.filepath) {
+
+  qclog <- logRead()
+  qclog2 <- qclog[qclog$file != .filepath, ]
+
+  # Check current file path exists
+  if(nrow(qclog) == nrow(qclog2)) {
+    stop(paste0(.filepath, " does not exist in QClog.csv"))
+  }
+
+  cli::cli_alert_info(glue::glue("Deleted '{.filepath}' from QClog.csv"))
+
+  logWrite(qclog2, file = "QClog.csv")
+}