R/yaml.debugger.R
In lborke/yamldebugger: YAML parser debugger according to the QuantNet style guide
#' Standard Quantlet keywords inherited from the older PHP based QuantNet.
#'
#' A character vector containing 594 standard Quantlet keywords.
#' Please use as many as possible of them to enable good text mining results for the D3 Visualization.
#'
#' @format A character vector with 594 keywords
#'
#' @source \url{http://quantlet.de/}
"allKeywords"
### STEP 1: initialize
#' YAML initialization function.
#'
#' @param RootPath current working directory with Qs for debugging
#'
#' @param show_keywords boolean trigger for showing / not showing the standard keywords
#'
#' @return The list with data needed in the further process.
#'
#' @examples
#' \dontrun{
#' d_init = yaml.debugger.init("c:/test", show_keywords = TRUE)
#' }
yaml.debugger.init = function(RootPath = "C:/r/test", show_keywords = FALSE) {
# specify the path where your quantlets are stored
allKeywords = tolower(allKeywords)
if (show_keywords) { print(allKeywords) }
res = list()
res$RootPath = RootPath
res$allKeywords = allKeywords
return(res)
}
### STEP 2: load list of Q folders
#' Loads the list of Q folders. RootPath is required where the Qs are located.
#'
#' @param RootPath current working directory with Qs for debugging
#'
#' @param show_qnames boolean trigger for showing / not showing the found Q folder names in the folder RootPath
#'
#' @return The list with Q folder names needed in the further process.
#'
#' @examples
#' \dontrun{
#' qnames = yaml.debugger.get.qnames(d_init$RootPath)
#' }
yaml.debugger.get.qnames = function(RootPath, show_qnames = TRUE) {
# define a pattern for the folder names containing quantlets
# pattern_qfolders = "[:alpha:]+"
# pattern_qfolders = "[^[:blank:]]" # no blank characters, i.e. space and tab.
pattern_qfolders = "[^\b|\\.git]" # no empty strings
listofQl = list.dirs(RootPath, full.names = FALSE, recursive = FALSE)
# no empty strings and no .git folder
listofQl = listofQl[grepl(pattern_qfolders, listofQl, ignore.case = TRUE)]
# no blanks in folder names
listofQl_ok = listofQl[!grepl("[[:blank:]]+", listofQl, ignore.case = TRUE)]
# bad folders
listofQl_bad = listofQl[grepl("[[:blank:]]+", listofQl, ignore.case = TRUE)]
if (show_qnames) {
print( paste(length(listofQl_ok), "Q folder(s) found:") )
print(listofQl_ok)
}
if (length(listofQl_bad) > 0) {
print( paste(length(listofQl_bad), "skipped Q folder(s) with blanks:") )
print(listofQl_bad)
print("The skipped Q folders need to be renamed! Otherwise no debugging is possible and no Style guide compliance!")
}
return(listofQl_ok)
}
### STEP 3: loop trough Q folders and extract YAML meta info
#' Main part of the YAML debugger. Loops trough the provided Q folders and extracts YAML meta info.
#' If errors occur, corresponding error handling is executed.
#'
#' @param qnames the list with Q folder names as provided by \code{yaml.debugger.get.qnames}
#'
#' @param init.obj as provided by \code{yaml.debugger.init}
#'
#' @return The summary data of the YAML debugger process. Possible YAML parser errors are also provided in this data structure
#'
#' @examples
#' \dontrun{
#' d_results = yaml.debugger.run(qnames, d_init)
#' }
yaml.debugger.run = function(qnames, init.obj) {
n = length(qnames)
# Initialize the lists for results
Metainfos <- QCodes <- QNames_meta <- Desc_stats <- KeywordsOK <- KeywordsToReplace <- as.list(rep(NA, n))
KeywordsOK_count <- KeywordsToReplace_count <- possible_pictures <- QDescription_words <- rep(0, n)
q_code_exist <- rep(TRUE, n)
wrong_quote_signs <- rep(FALSE, n)
Qbadnames <- SG_probs <- Metainfo_dnames <- Q_found_software <- rep("", n)
yaml_errors_v <- q_id_errors_v <- vector()
wrong_quote_signs_regex_pattern = "^‚|^‘"
sw_md_match = list("r" = "r", "m" = "matlab", "py" = "python", "sas" = "sas", "sh" = "shell")
accepted_sw = names(sw_md_match)
accepted_pict = c("png", "jpg")
possible_pict = c("pdf")
for (i in 1:n) {
# current name of quantlet folder
currentQfolder = qnames[i]
print(paste(i, ": ", currentQfolder, sep = ""))
qfolder = paste(init.obj$RootPath, currentQfolder, sep ="/")
q_files = list.files(qfolder, recursive = FALSE)
q_files_badnames = q_files[grepl("[[:blank:]]+", q_files, ignore.case = TRUE)]
if (length(q_files_badnames) > 0) {
print("This Q folder has at least one bad file name with blanks! All listed files must be renamed according to the Style guide.")
print(q_files_badnames)
#print("This Q will be excluded from the debugging process until all listed files are renamed according to the Style guide.")
Qbadnames[i] = paste("bad Q file names!:", paste(q_files_badnames, collapse = ", "))
#print("--------------------------------------------------------------------")
#next
}
t_vec = vector()
pic_vec = vector()
poss_pic_vec = vector()
found_software = vector()
for (qlet in q_files) {
f_ext = tolower(file_ext(qlet))
if (f_ext %in% accepted_sw) {
# clean file handling
q_full_path = paste(qfolder, qlet, sep ="/")
zz <- file(q_full_path, "r")
q_str = readChar(zz, file.info(q_full_path)$size)
close(zz)
# add code file text to the vector
t_vec[qlet] = q_str
# count this appearance of R/Matlab/etc. code
found_software = c(found_software, sw_md_match[[f_ext]])
}
if (f_ext %in% accepted_pict) {
pic_vec = c(pic_vec, qlet)
}
if (f_ext %in% possible_pict) {
poss_pic_vec = c(poss_pic_vec, qlet)
}
if( tolower(qlet) == "metainfo.txt" ){
q_full_path = paste(qfolder, qlet, sep ="/")
result = try( yaml_meta <- yaml.load_file(q_full_path), silent = FALSE )
if (class(result) == "try-error") {
print( paste("yaml parser error in: ", currentQfolder, sep = "") )
yaml_errors_v = c(yaml_errors_v, result)
q_id_errors_v = c(q_id_errors_v, i)
Metainfos[[i]] = "parser error"
QNames_meta[[i]] = "YAML error!"
} else {
# handle some trivial cases
if (is.null(yaml_meta)) {yaml_meta = ""}
Metainfos[[i]] = yaml_meta
QNames_meta[[i]] = yaml.getQField(yaml_meta, "q")
#Metainfo_dnames[i] = paste(names(yaml_meta), collapse = ", ")
Metainfo_dnames[i] = paste(yaml.Qdfields.from.meta(yaml_meta)$found_dnames, collapse = ", ")
sg_missingfields = vector()
# check Qname I
if (QNames_meta[[i]] == "") { sg_missingfields = c(sg_missingfields, "Name of Quantlet") }
# check Published II
if (yaml.getQField(yaml_meta, "p") == "") { sg_missingfields = c(sg_missingfields, "Published in") }
# check Author III
if (yaml.getQField(yaml_meta, "a") == "") { sg_missingfields = c(sg_missingfields, "Author") }
# check Desc IV + stats
QDescription = yaml.getQField(yaml_meta, "d")
print(QDescription)
if (QDescription == "") { sg_missingfields = c(sg_missingfields, "Description") }
# replace "%" making sure that words after "%" are counted
QDescription = gsub("%", " ", QDescription)
# replace "new lines" making sure that stri_stats_latex works
QDescription = gsub("\n", " ", QDescription)
desc_stat = stri_stats_latex(QDescription)
Desc_stats[[i]] = paste(desc_stat["Words"], " word(s), ", desc_stat["CharsWord"], " Character(s)", sep = "")
QDescription_words[i] = desc_stat["Words"]
# check Keywords V
QKeywords = yaml.getQField(yaml_meta, "k")
if (QKeywords == "") { sg_missingfields = c(sg_missingfields, "Keywords") } else {
# get all keywords from the current meta info file as array
keywords = unlist(strsplit(QKeywords, ","))
# standardize keywords
keywords = str_trim(tolower(keywords))
# which keywords are in the global kw list ?
keywords_check = keywords %in% init.obj$allKeywords
# store "good" kw's
# KeywordsOK[[i]] = keywords[keywords_check]
KeywordsOK[[i]] = paste(keywords[keywords_check], collapse = ", ")
KeywordsOK_count[i] = length(keywords[keywords_check])
# save the array of "bad" keywords for later improvement in KeywordsToReplace
if(!all(keywords_check)) {
bad_keywords = keywords[!keywords_check]
bad_keywords_str = paste(bad_keywords, collapse = ", ")
print(paste("new/unknown keywords: ", bad_keywords_str, sep = ""))
KeywordsToReplace[[i]] = bad_keywords_str
KeywordsToReplace_count[i] = length(keywords[!keywords_check])
}
}
meta_df_text_v = c(QNames_meta[[i]], yaml.getQField(yaml_meta, "p"), yaml.getQField(yaml_meta, "a"), QDescription, QKeywords,
yaml.getQField(yaml_meta, "df"), yaml.getQField(yaml_meta, "e"), yaml.getQField(yaml_meta, "i"),
yaml.getQField(yaml_meta, "o"), yaml.getQField(yaml_meta, "s"), yaml.getQField(yaml_meta, "sa"))
wrong_quote_signs[i] = any(grepl(wrong_quote_signs_regex_pattern, meta_df_text_v))
if (wrong_quote_signs[i]) { print(paste("Wrong quote signs:", wrong_quote_signs[i])) }
SG_probs[i] = paste(sg_missingfields, collapse = ", ")
}
}
}
found_software = unique(found_software)
print(paste("Found_software: ", paste(found_software, collapse = ", ")))
print(paste("Number of code files: ", length(t_vec), " - ", paste(names(t_vec), collapse = ", ")) )
print(paste("Number of pictures: ", length(pic_vec), " - ", paste(pic_vec, collapse = ", ")) )
if ( length(poss_pic_vec) > 0 ) {
print(paste("Number of possible pictures: ", length(poss_pic_vec), " - ", paste(poss_pic_vec, collapse = ", ")) )
possible_pictures[i] = length(poss_pic_vec)
}
Q_found_software[i] = paste(found_software, collapse = ", ")
codename = tolower(QNames_meta[[i]])
fnames = tolower(file_path_sans_ext(names(t_vec)))
code_Q = t_vec[which(fnames == codename)]
if (length(code_Q) == 0) {
q_code_exist[i] = FALSE
print("No Quantlet CODE found !!!")
} else { QCodes[[i]] = code_Q }
# delimiter for text output
print("--------------------------------------------------------------------")
}
meta_names = unlist(sapply( Metainfos, function(y){ names(y) } ))
meta_names_distribution = sort(table(meta_names), decreasing = T)
res = list()
res$Metainfos = Metainfos
res$meta_names_distribution = meta_names_distribution
res$QNames_meta = QNames_meta
res$QCodes = QCodes
res$Metainfo_dnames = Metainfo_dnames
res$Desc_stats = Desc_stats
res$SG_probs = SG_probs
res$KeywordsOK = KeywordsOK
res$KeywordsOK_count = KeywordsOK_count
res$KeywordsToReplace = KeywordsToReplace
res$KeywordsToReplace_count = KeywordsToReplace_count
res$yaml_errors_v = yaml_errors_v
res$q_id_errors_v = q_id_errors_v
res$q_code_exist = q_code_exist
res$wrong_quote_signs = wrong_quote_signs
res$possible_pictures = possible_pictures
res$Qbadnames = Qbadnames
res$QDescription_words = QDescription_words
res$Q_found_software = Q_found_software
return(res)
}
### STEP 4: Overview of parser results
#' Overview of the parser results. If errors occured, the corresponding Q folder names and YAML errors are displayed.
#'
#' @param qfolders the list with Q folder names as provided by \code{yaml.debugger.get.qnames}
#'
#' @param results as provided by \code{yaml.debugger.run}
#'
#' @param showErrors boolean trigger for showing / not showing the parser errors
#'
#' @param showOverView boolean trigger for showing / not showing the total \code{Overview}
#'
#' @param summaryType [mini/compact/full] controls the details and extent of the \code{Overview} output
#'
#' @return The summary overview as data frame for further inspection
#'
#' @examples
#' \dontrun{
#' OverView = yaml.debugger.summary(qfolders, d_results, summaryType = "mini")
#' }
yaml.debugger.summary = function(qfolders, results, showErrors = TRUE, showOverView = TRUE, summaryType = "full") {
if (showErrors && length(results$q_id_errors_v) > 0) {
for (i in 1:length(results$q_id_errors_v)) {
print(qfolders[results$q_id_errors_v[i]])
print(results$yaml_errors_v[i])
print("--------------------------------------------------------------------")
}
}
n = length(qfolders)
#Qfolders = as.vector(qfolders)
YAML_Ranking = rep("A", n)
Keywords_count = results$KeywordsOK_count
newKeywords_count = results$KeywordsToReplace_count
# additional calculation of statistics
kw_total = Keywords_count + newKeywords_count
kw_stats = paste(kw_total, ": ", Keywords_count, " (standard), ", newKeywords_count, " (new)", sep ="")
YAML_Ranking[kw_total < 5] = "B"
YAML_Ranking[results$QDescription_words < 10] = "B"
PossPicts = results$possible_pictures
YAML_Ranking[PossPicts > 0] = "B"
PossPicts[PossPicts == 0] = ""
PossPicts[PossPicts > 0] = "If PDF is a picture PNG or JPG required!"
QExist = results$q_code_exist
YAML_Ranking[QExist == FALSE] = "C"
QExist[QExist == TRUE] = "ok"
QExist[QExist == FALSE] = "NOT FOUND"
WrongSigns = results$wrong_quote_signs
YAML_Ranking[WrongSigns == TRUE]= "C"
WrongSigns[WrongSigns == TRUE] = "Wrong quotes!"
WrongSigns[WrongSigns == FALSE] = ""
Q_Bad_names = results$Qbadnames
YAML_Ranking[Q_Bad_names != ""] = "C"
SG_probs = results$SG_probs
YAML_Ranking[SG_probs != ""]= "C"
Qnames = as.vector(results$QNames_meta)
YAML_Ranking[is.na(Qnames)] = "N"
YAML_Ranking[Qnames == "YAML error!"] = "D"
Qnames[is.na(Qnames)] = "No metainfo found!"
Qnames = as.character(Qnames)
Meta_DNames = results$Metainfo_dnames
Q_found_software = results$Q_found_software
Desc_stats = as.character(as.vector(results$Desc_stats))
Keywords = as.character(as.vector(results$KeywordsOK))
newKeywords = as.character(as.vector(results$KeywordsToReplace))
# create OverView of metainfos and errors retrieved by the yaml parser
if (summaryType == "mini") {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats")
} else if (summaryType == "compact") {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats, Q_found_software, Meta_DNames)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats", "Found SW", "Meta Info data fields")
} else {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats, Meta_DNames, Keywords, newKeywords)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats", "Meta Info data fields", "Keywords", "new Keywords")
}
if (length(QExist[QExist == "NOT FOUND"]) > 0) {
OverView = cbind(OverView, QExist)
OverViewLabels = c(OverViewLabels, "Q Code")
}
if (length(SG_probs[SG_probs != ""]) > 0) {
OverView = cbind(OverView, SG_probs)
OverViewLabels = c(OverViewLabels, "Missing Style Guide fields")
}
if (length(WrongSigns[WrongSigns != ""]) > 0) {
OverView = cbind(OverView, WrongSigns)
OverViewLabels = c(OverViewLabels, "Quote signs")
}
if (length(Q_Bad_names[Q_Bad_names != ""]) > 0) {
OverView = cbind(OverView, Q_Bad_names)
OverViewLabels = c(OverViewLabels, "Bad file names")
}
if (length(PossPicts[PossPicts != ""]) > 0) {
OverView = cbind(OverView, PossPicts)
OverViewLabels = c(OverViewLabels, "PDF files")
}
names(OverView) = OverViewLabels
if (showOverView) { View(OverView) }
return(OverView)
}
lborke/yamldebugger documentation built on May 20, 2019, 10:24 p.m.
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#' Standard Quantlet keywords inherited from the older PHP based QuantNet.
#'
#' A character vector containing 594 standard Quantlet keywords.
#' Please use as many as possible of them to enable good text mining results for the D3 Visualization.
#'
#' @format A character vector with 594 keywords
#'
#' @source \url{http://quantlet.de/}
"allKeywords"
### STEP 1: initialize
#' YAML initialization function.
#'
#' @param RootPath current working directory with Qs for debugging
#'
#' @param show_keywords boolean trigger for showing / not showing the standard keywords
#'
#' @return The list with data needed in the further process.
#'
#' @examples
#' \dontrun{
#' d_init = yaml.debugger.init("c:/test", show_keywords = TRUE)
#' }
yaml.debugger.init = function(RootPath = "C:/r/test", show_keywords = FALSE) {
# specify the path where your quantlets are stored
allKeywords = tolower(allKeywords)
if (show_keywords) { print(allKeywords) }
res = list()
res$RootPath = RootPath
res$allKeywords = allKeywords
return(res)
}
### STEP 2: load list of Q folders
#' Loads the list of Q folders. RootPath is required where the Qs are located.
#'
#' @param RootPath current working directory with Qs for debugging
#'
#' @param show_qnames boolean trigger for showing / not showing the found Q folder names in the folder RootPath
#'
#' @return The list with Q folder names needed in the further process.
#'
#' @examples
#' \dontrun{
#' qnames = yaml.debugger.get.qnames(d_init$RootPath)
#' }
yaml.debugger.get.qnames = function(RootPath, show_qnames = TRUE) {
# define a pattern for the folder names containing quantlets
# pattern_qfolders = "[:alpha:]+"
# pattern_qfolders = "[^[:blank:]]" # no blank characters, i.e. space and tab.
pattern_qfolders = "[^\b|\\.git]" # no empty strings
listofQl = list.dirs(RootPath, full.names = FALSE, recursive = FALSE)
# no empty strings and no .git folder
listofQl = listofQl[grepl(pattern_qfolders, listofQl, ignore.case = TRUE)]
# no blanks in folder names
listofQl_ok = listofQl[!grepl("[[:blank:]]+", listofQl, ignore.case = TRUE)]
# bad folders
listofQl_bad = listofQl[grepl("[[:blank:]]+", listofQl, ignore.case = TRUE)]
if (show_qnames) {
print( paste(length(listofQl_ok), "Q folder(s) found:") )
print(listofQl_ok)
}
if (length(listofQl_bad) > 0) {
print( paste(length(listofQl_bad), "skipped Q folder(s) with blanks:") )
print(listofQl_bad)
print("The skipped Q folders need to be renamed! Otherwise no debugging is possible and no Style guide compliance!")
}
return(listofQl_ok)
}
### STEP 3: loop trough Q folders and extract YAML meta info
#' Main part of the YAML debugger. Loops trough the provided Q folders and extracts YAML meta info.
#' If errors occur, corresponding error handling is executed.
#'
#' @param qnames the list with Q folder names as provided by \code{yaml.debugger.get.qnames}
#'
#' @param init.obj as provided by \code{yaml.debugger.init}
#'
#' @return The summary data of the YAML debugger process. Possible YAML parser errors are also provided in this data structure
#'
#' @examples
#' \dontrun{
#' d_results = yaml.debugger.run(qnames, d_init)
#' }
yaml.debugger.run = function(qnames, init.obj) {
n = length(qnames)
# Initialize the lists for results
Metainfos <- QCodes <- QNames_meta <- Desc_stats <- KeywordsOK <- KeywordsToReplace <- as.list(rep(NA, n))
KeywordsOK_count <- KeywordsToReplace_count <- possible_pictures <- QDescription_words <- rep(0, n)
q_code_exist <- rep(TRUE, n)
wrong_quote_signs <- rep(FALSE, n)
Qbadnames <- SG_probs <- Metainfo_dnames <- Q_found_software <- rep("", n)
yaml_errors_v <- q_id_errors_v <- vector()
wrong_quote_signs_regex_pattern = "^‚|^‘"
sw_md_match = list("r" = "r", "m" = "matlab", "py" = "python", "sas" = "sas", "sh" = "shell")
accepted_sw = names(sw_md_match)
accepted_pict = c("png", "jpg")
possible_pict = c("pdf")
for (i in 1:n) {
# current name of quantlet folder
currentQfolder = qnames[i]
print(paste(i, ": ", currentQfolder, sep = ""))
qfolder = paste(init.obj$RootPath, currentQfolder, sep ="/")
q_files = list.files(qfolder, recursive = FALSE)
q_files_badnames = q_files[grepl("[[:blank:]]+", q_files, ignore.case = TRUE)]
if (length(q_files_badnames) > 0) {
print("This Q folder has at least one bad file name with blanks! All listed files must be renamed according to the Style guide.")
print(q_files_badnames)
#print("This Q will be excluded from the debugging process until all listed files are renamed according to the Style guide.")
Qbadnames[i] = paste("bad Q file names!:", paste(q_files_badnames, collapse = ", "))
#print("--------------------------------------------------------------------")
#next
}
t_vec = vector()
pic_vec = vector()
poss_pic_vec = vector()
found_software = vector()
for (qlet in q_files) {
f_ext = tolower(file_ext(qlet))
if (f_ext %in% accepted_sw) {
# clean file handling
q_full_path = paste(qfolder, qlet, sep ="/")
zz <- file(q_full_path, "r")
q_str = readChar(zz, file.info(q_full_path)$size)
close(zz)
# add code file text to the vector
t_vec[qlet] = q_str
# count this appearance of R/Matlab/etc. code
found_software = c(found_software, sw_md_match[[f_ext]])
}
if (f_ext %in% accepted_pict) {
pic_vec = c(pic_vec, qlet)
}
if (f_ext %in% possible_pict) {
poss_pic_vec = c(poss_pic_vec, qlet)
}
if( tolower(qlet) == "metainfo.txt" ){
q_full_path = paste(qfolder, qlet, sep ="/")
result = try( yaml_meta <- yaml.load_file(q_full_path), silent = FALSE )
if (class(result) == "try-error") {
print( paste("yaml parser error in: ", currentQfolder, sep = "") )
yaml_errors_v = c(yaml_errors_v, result)
q_id_errors_v = c(q_id_errors_v, i)
Metainfos[[i]] = "parser error"
QNames_meta[[i]] = "YAML error!"
} else {
# handle some trivial cases
if (is.null(yaml_meta)) {yaml_meta = ""}
Metainfos[[i]] = yaml_meta
QNames_meta[[i]] = yaml.getQField(yaml_meta, "q")
#Metainfo_dnames[i] = paste(names(yaml_meta), collapse = ", ")
Metainfo_dnames[i] = paste(yaml.Qdfields.from.meta(yaml_meta)$found_dnames, collapse = ", ")
sg_missingfields = vector()
# check Qname I
if (QNames_meta[[i]] == "") { sg_missingfields = c(sg_missingfields, "Name of Quantlet") }
# check Published II
if (yaml.getQField(yaml_meta, "p") == "") { sg_missingfields = c(sg_missingfields, "Published in") }
# check Author III
if (yaml.getQField(yaml_meta, "a") == "") { sg_missingfields = c(sg_missingfields, "Author") }
# check Desc IV + stats
QDescription = yaml.getQField(yaml_meta, "d")
print(QDescription)
if (QDescription == "") { sg_missingfields = c(sg_missingfields, "Description") }
# replace "%" making sure that words after "%" are counted
QDescription = gsub("%", " ", QDescription)
# replace "new lines" making sure that stri_stats_latex works
QDescription = gsub("\n", " ", QDescription)
desc_stat = stri_stats_latex(QDescription)
Desc_stats[[i]] = paste(desc_stat["Words"], " word(s), ", desc_stat["CharsWord"], " Character(s)", sep = "")
QDescription_words[i] = desc_stat["Words"]
# check Keywords V
QKeywords = yaml.getQField(yaml_meta, "k")
if (QKeywords == "") { sg_missingfields = c(sg_missingfields, "Keywords") } else {
# get all keywords from the current meta info file as array
keywords = unlist(strsplit(QKeywords, ","))
# standardize keywords
keywords = str_trim(tolower(keywords))
# which keywords are in the global kw list ?
keywords_check = keywords %in% init.obj$allKeywords
# store "good" kw's
# KeywordsOK[[i]] = keywords[keywords_check]
KeywordsOK[[i]] = paste(keywords[keywords_check], collapse = ", ")
KeywordsOK_count[i] = length(keywords[keywords_check])
# save the array of "bad" keywords for later improvement in KeywordsToReplace
if(!all(keywords_check)) {
bad_keywords = keywords[!keywords_check]
bad_keywords_str = paste(bad_keywords, collapse = ", ")
print(paste("new/unknown keywords: ", bad_keywords_str, sep = ""))
KeywordsToReplace[[i]] = bad_keywords_str
KeywordsToReplace_count[i] = length(keywords[!keywords_check])
}
}
meta_df_text_v = c(QNames_meta[[i]], yaml.getQField(yaml_meta, "p"), yaml.getQField(yaml_meta, "a"), QDescription, QKeywords,
yaml.getQField(yaml_meta, "df"), yaml.getQField(yaml_meta, "e"), yaml.getQField(yaml_meta, "i"),
yaml.getQField(yaml_meta, "o"), yaml.getQField(yaml_meta, "s"), yaml.getQField(yaml_meta, "sa"))
wrong_quote_signs[i] = any(grepl(wrong_quote_signs_regex_pattern, meta_df_text_v))
if (wrong_quote_signs[i]) { print(paste("Wrong quote signs:", wrong_quote_signs[i])) }
SG_probs[i] = paste(sg_missingfields, collapse = ", ")
}
}
}
found_software = unique(found_software)
print(paste("Found_software: ", paste(found_software, collapse = ", ")))
print(paste("Number of code files: ", length(t_vec), " - ", paste(names(t_vec), collapse = ", ")) )
print(paste("Number of pictures: ", length(pic_vec), " - ", paste(pic_vec, collapse = ", ")) )
if ( length(poss_pic_vec) > 0 ) {
print(paste("Number of possible pictures: ", length(poss_pic_vec), " - ", paste(poss_pic_vec, collapse = ", ")) )
possible_pictures[i] = length(poss_pic_vec)
}
Q_found_software[i] = paste(found_software, collapse = ", ")
codename = tolower(QNames_meta[[i]])
fnames = tolower(file_path_sans_ext(names(t_vec)))
code_Q = t_vec[which(fnames == codename)]
if (length(code_Q) == 0) {
q_code_exist[i] = FALSE
print("No Quantlet CODE found !!!")
} else { QCodes[[i]] = code_Q }
# delimiter for text output
print("--------------------------------------------------------------------")
}
meta_names = unlist(sapply( Metainfos, function(y){ names(y) } ))
meta_names_distribution = sort(table(meta_names), decreasing = T)
res = list()
res$Metainfos = Metainfos
res$meta_names_distribution = meta_names_distribution
res$QNames_meta = QNames_meta
res$QCodes = QCodes
res$Metainfo_dnames = Metainfo_dnames
res$Desc_stats = Desc_stats
res$SG_probs = SG_probs
res$KeywordsOK = KeywordsOK
res$KeywordsOK_count = KeywordsOK_count
res$KeywordsToReplace = KeywordsToReplace
res$KeywordsToReplace_count = KeywordsToReplace_count
res$yaml_errors_v = yaml_errors_v
res$q_id_errors_v = q_id_errors_v
res$q_code_exist = q_code_exist
res$wrong_quote_signs = wrong_quote_signs
res$possible_pictures = possible_pictures
res$Qbadnames = Qbadnames
res$QDescription_words = QDescription_words
res$Q_found_software = Q_found_software
return(res)
}
### STEP 4: Overview of parser results
#' Overview of the parser results. If errors occured, the corresponding Q folder names and YAML errors are displayed.
#'
#' @param qfolders the list with Q folder names as provided by \code{yaml.debugger.get.qnames}
#'
#' @param results as provided by \code{yaml.debugger.run}
#'
#' @param showErrors boolean trigger for showing / not showing the parser errors
#'
#' @param showOverView boolean trigger for showing / not showing the total \code{Overview}
#'
#' @param summaryType [mini/compact/full] controls the details and extent of the \code{Overview} output
#'
#' @return The summary overview as data frame for further inspection
#'
#' @examples
#' \dontrun{
#' OverView = yaml.debugger.summary(qfolders, d_results, summaryType = "mini")
#' }
yaml.debugger.summary = function(qfolders, results, showErrors = TRUE, showOverView = TRUE, summaryType = "full") {
if (showErrors && length(results$q_id_errors_v) > 0) {
for (i in 1:length(results$q_id_errors_v)) {
print(qfolders[results$q_id_errors_v[i]])
print(results$yaml_errors_v[i])
print("--------------------------------------------------------------------")
}
}
n = length(qfolders)
#Qfolders = as.vector(qfolders)
YAML_Ranking = rep("A", n)
Keywords_count = results$KeywordsOK_count
newKeywords_count = results$KeywordsToReplace_count
# additional calculation of statistics
kw_total = Keywords_count + newKeywords_count
kw_stats = paste(kw_total, ": ", Keywords_count, " (standard), ", newKeywords_count, " (new)", sep ="")
YAML_Ranking[kw_total < 5] = "B"
YAML_Ranking[results$QDescription_words < 10] = "B"
PossPicts = results$possible_pictures
YAML_Ranking[PossPicts > 0] = "B"
PossPicts[PossPicts == 0] = ""
PossPicts[PossPicts > 0] = "If PDF is a picture PNG or JPG required!"
QExist = results$q_code_exist
YAML_Ranking[QExist == FALSE] = "C"
QExist[QExist == TRUE] = "ok"
QExist[QExist == FALSE] = "NOT FOUND"
WrongSigns = results$wrong_quote_signs
YAML_Ranking[WrongSigns == TRUE]= "C"
WrongSigns[WrongSigns == TRUE] = "Wrong quotes!"
WrongSigns[WrongSigns == FALSE] = ""
Q_Bad_names = results$Qbadnames
YAML_Ranking[Q_Bad_names != ""] = "C"
SG_probs = results$SG_probs
YAML_Ranking[SG_probs != ""]= "C"
Qnames = as.vector(results$QNames_meta)
YAML_Ranking[is.na(Qnames)] = "N"
YAML_Ranking[Qnames == "YAML error!"] = "D"
Qnames[is.na(Qnames)] = "No metainfo found!"
Qnames = as.character(Qnames)
Meta_DNames = results$Metainfo_dnames
Q_found_software = results$Q_found_software
Desc_stats = as.character(as.vector(results$Desc_stats))
Keywords = as.character(as.vector(results$KeywordsOK))
newKeywords = as.character(as.vector(results$KeywordsToReplace))
# create OverView of metainfos and errors retrieved by the yaml parser
if (summaryType == "mini") {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats")
} else if (summaryType == "compact") {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats, Q_found_software, Meta_DNames)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats", "Found SW", "Meta Info data fields")
} else {
OverView = data.frame(YAML_Ranking, qfolders, Qnames, Desc_stats, kw_stats, Meta_DNames, Keywords, newKeywords)
OverViewLabels = c("Q-Quali", "Q folders", "Q Names", "Descriptions stats", "Keywords stats", "Meta Info data fields", "Keywords", "new Keywords")
}
if (length(QExist[QExist == "NOT FOUND"]) > 0) {
OverView = cbind(OverView, QExist)
OverViewLabels = c(OverViewLabels, "Q Code")
}
if (length(SG_probs[SG_probs != ""]) > 0) {
OverView = cbind(OverView, SG_probs)
OverViewLabels = c(OverViewLabels, "Missing Style Guide fields")
}
if (length(WrongSigns[WrongSigns != ""]) > 0) {
OverView = cbind(OverView, WrongSigns)
OverViewLabels = c(OverViewLabels, "Quote signs")
}
if (length(Q_Bad_names[Q_Bad_names != ""]) > 0) {
OverView = cbind(OverView, Q_Bad_names)
OverViewLabels = c(OverViewLabels, "Bad file names")
}
if (length(PossPicts[PossPicts != ""]) > 0) {
OverView = cbind(OverView, PossPicts)
OverViewLabels = c(OverViewLabels, "PDF files")
}
names(OverView) = OverViewLabels
if (showOverView) { View(OverView) }
return(OverView)
}
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