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Environment

R version

## [1] "R version 4.0.5 (2021-03-31)"

Libraries initialisation

## Loading required package: dplyr
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:data.table':
## 
##     between, first, last
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Loading required package: DT
## Loading required package: stringr
## Loading required package: magrittr
## Loading required package: text2vec
## Loading required package: stopwords
## Loading required package: cld2
## Loading required package: cld3
## 
## Attaching package: 'cld3'
## The following objects are masked from 'package:cld2':
## 
##     detect_language, detect_language_mixed
## Loading required package: parallel

../000.core/00.01.libraries.R completed in 2.05 seconds

sourceTimeNeeded <- c( sourceTimeNeeded, timeNeeded)


source.starting.time <- proc.time()[3]


## Base functions

# ESCO skills
# @authors ds@eworx.gr
repository <- "/data/generic/"

getSourcePath <- function(filename, baseFolder = repository){
    return(paste(baseFolder, filename, sep = ""))
}

readData <- function(filename, colClasses = c(), baseFolder = repository, header = TRUE, sep = "\t", encoding = "UTF-8", stringsAsFactors = TRUE, na.strings = c("", "NULL"), verbose = FALSE){
    if(length(colClasses) == 0)
        return (data.table::fread(input = getSourcePath(filename, baseFolder), header = header, sep = sep, encoding = encoding, stringsAsFactors = stringsAsFactors, verbose = verbose, showProgress = TRUE, na.strings = na.strings ) )
    return (data.table::fread(input = getSourcePath(filename, baseFolder), colClasses = colClasses, header = header, sep = sep, encoding = encoding, verbose = verbose, showProgress = TRUE,   na.strings = na.strings )  )
}

#rds for small disk space & fst for fast load
saveBinary <- function(data, filename = filename, baseFolder = repository, format = "rds"){
  fileName <- getSourcePath(filename, baseFolder)
  dir.create(dirname(fileName), recursive = TRUE, showWarnings = FALSE)
  if(format == "rds") saveRDS(data, fileName)
  if(format == "fst") fst::write_fst(data, fileName)
}

#rds for small disk space & fst for fast load
loadBinary <- function(filename, baseFolder = repository, format = "rds", as.data.table = TRUE){
  if(format == "rds"){return(readRDS(getSourcePath(filename, baseFolder)))}
  if(format == "fst"){return(fst::read_fst(getSourcePath(filename, baseFolder), as.data.table = as.data.table))}
}

rowColumns <- function(data){
    return(paste( format(nrow(data),  big.mark=","), "Rows X ", ncol(data), "Columns"))
}

publishIncludeCss <- function(){
    sourceFile <- "/data/jobs/wp41.analysis/000.core/include.css"
    destinatinoFile <- "/data/tmpfs/results/include.css"
    if (!file.exists(destinatinoFile)) {
        return (file.copy(sourceFile, destinatinoFile))
    }else{
        return(TRUE);
    }

}
#as the mountstorage is on memory make sure the asset include.css is there.

summariseTable <- function(data){
    return(data.frame(unclass(summary(data)), check.names = FALSE, stringsAsFactors = FALSE))
    #return(do.call(cbind, lapply(data, summary)))
}

factoriseCharacterColumns <- function(data){
    for(name in names(data)){
        if( class(data[[name]]) =="character"){
            data[[name]] <- as.factor(data[[name]])
        }
    }
    return(data) 
}

codeBook <- function(dataset){

  out <- lapply(names(dataset), function(var_name) {
    knitr::knit_expand(text = readLines("../000.core/codeBook.template"))
  })
  
  cat(
    knitr::knit(
      text = unlist(paste(out, collapse = '\n')), 
      quiet = TRUE)
    )

}

fwrite_zip <- function(data, filename, quote = TRUE){
  dir.create(dirname(filename), recursive = TRUE, showWarnings = FALSE)
  filename_csv <- strsplit(filename, "/") %>% unlist %>% tail(1)
  filename_csv <- gsub(".zip", ".csv", filename_csv)
  fwrite(data, filename_csv, quote = quote)
  if(file.exists(filename))unlink(filename)
  zip(filename, filename_csv)
  unlink(filename_csv)
}

############################
# https://rstudio.github.io/DT/010-style.html
#https://rpubs.com/marschmi/RMarkdown

capitalise <- function(x) paste0(toupper(substring(x, 1, 1)), substring(x, 2, nchar(x)))


styliseDTNumericalColumn <- function(data, result, columnName, color, columnsName_original ){

    if(columnName%in% columnsName_original){
        result <- result %>%   formatStyle(
            columnName,
            background = styleColorBar(data[[columnName]], color),
            backgroundSize = '100% 90%',
            backgroundRepeat = 'no-repeat',
            backgroundPosition = 'center'
        )
    }
    return(result)

}


reportTabularData <- function(data, anonymize=TRUE){

  if(anonymize)return()
    
    columnsName <- names(data)
    columnsName <- lapply(columnsName, capitalise)
    columnsName_original <- names(data)

    result <-
        DT::datatable(
            data,
            class = 'cell-border stripe',
            filter = 'top',
            rownames = FALSE,
            colnames = columnsName,
            extensions = 'Buttons',
            options = list(
                pageLength = 20,
                columnDefs = list(list(className = 'dt-left', targets = "_all")),
                dom = 'Bfrtip',
                buttons = c('copy', 'csv', 'excel', 'pdf'),
                searchHighlight = TRUE,
                initComplete = JS(
                    "function(settings, json) {",
                        "$(this.api().table().header()).css({'border': '1px solid'});",
                    "}"
                )
            )

        )


    result <- styliseDTNumericalColumn(data,result, "Count", 'steelblue', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "sourceTimeNeeded", '#808080', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "timeNeeded", '#808080', columnsName_original)
    #result <- styliseDTNumericalColumn(data,result, "percentMatch", '#5fba7d', columnsName_original)
    result <- styliseDTNumericalColumn(data,result, "percentMatch", '#4682b4', columnsName_original)

 
 

    return(result)
}

fonts <- list(
 sans = "DejaVu Serif",
  mono = "DejaVu Serif",
  `Times New Roman` = "DejaVu Serif"
)

#read_xml_to_list <- function(filepath, is.gz = FALSE){
#   if(is.gz){  
#       temp_data <- paste0(repository, "data/delete.me")
#       result <- xmlToList(xmlParse(gunzip(filepath, destname = temp_data, remove =FALSE)))
#       Sys.chmod(file.path(temp_data), "777", use_umask = FALSE)
#       unlink(temp_data)
#       result
#   }else{
#       xmlToList(xmlParse(filepath))
#   }
#}

#transpose_list_to_dt <- function(data_list){
#  dt <- t(as.data.table(data_list))
#  dt <- as.data.table(dt)
#  dt[, (names(dt)) := lapply(.SD, unlist), .SDcols = 1:ncol(dt)]
#  dt[, (names(dt)) := lapply(.SD, unlist), .SDcols = 1:ncol(dt)]
#  names(dt) <- names(data_list[[1]])
#  dt
#}

cleansingCorpus <- function(
    htmlString, rem.html =TRUE, rem.http = TRUE, rem.newline = TRUE,
    rem.nonalphanum = TRUE, rem.longwords = TRUE, rem.space = TRUE, 
    tolower = TRUE, add.space.to.numbers = TRUE, rem.country.begin = FALSE,
    rem.nonalphanum.begin = FALSE, rem.space.begin = FALSE
){
  if(rem.html){text <- gsub("<.*?>", " ", htmlString)} # removing html commands
  if(rem.http){text <- gsub(" ?(f|ht)tp(s?)://(.*)[.][a-z]+", " ", text)} #removing http destinations
  if(rem.newline){text <- gsub("[\r\n\t]", " ", text)} 
  if(rem.nonalphanum){text <- gsub("[^[:alpha:]]", " ", text)} #removing non-alphanumeric
  if(rem.longwords){text <- gsub("\\w{35,}", " ", text)} ##Removing words with more than 30 letters
  if(rem.space){text <- gsub("\\s+", " ", text)}  #removing excess space 
  if(tolower){text <- tolower(text)}
  if(add.space.to.numbers){    #add space between number and letters
    text <- gsub("([0-9])([[:alpha:]])", "\\1 \\2", text)
    text <- gsub("([[:alpha:]]|[.])([0-9])", "\\1 \\2", text)
  }
  if(rem.space.begin){text <- gsub("^[[:space:]]*", "", text)} 
  if(rem.country.begin){text <- gsub("^EU", "", text)} #remove country codes from the beginning of the text
  if(rem.nonalphanum.begin){text <- gsub("^[?–-]*", "", text)} #remove special characters identified in the beginning of text
  if(rem.space.begin){text <- gsub("^[[:space:]]*", "", text)}
  trimws(text)
}

cleansingEducationCorpus <- function(text) {
  text <- gsub("\\.", "", text) #removing periods
  text <- gsub("[[:punct:]]", " ", text) #removing other punctuation
  text <- gsub("\\s+", " ", text) #removing excess space
  text <- tolower(text) #changing case to lower
  #removing accent from Greek
  text <- gsub("ς", "σ", text)
  text <- gsub("ά", "α", text)
  text <- gsub("έ", "ε", text)
  text <- gsub("ή", "η", text)
  text <- gsub("ί", "ι", text)
  text <- gsub("ύ", "υ", text)
  text <- gsub("ό", "ο", text)
  text <- gsub("ώ", "ω", text)
  trimws(text) #trimming white-space
}

#This function removes dates that are "relics" from the xml parsing
removeDates <- function(text){
  days <-  "(Sunday,|Monday,|Tuesday,|Wednesday,|Thursday,|Friday,|Saturday,)"
  months <- "(January|February|March|April|May|June|July|August|September|October|November|December|Months)"
  date_form1 <- paste(days, months, "([0-9]|[0-9][0-9]), [0-9][0-9][0-9][0-9]")
  date_form2 <- "\\?[0-9][0-9][0-9][0-9]"
  text <- gsub(date_form1, " ", text)
  gsub(date_form2, " ", text)
}

xmlToDataTable <- function(xmlData, itemNames){
  itemList <- lapply(itemNames,
    function(x){
      xml_text(xml_find_all(xmlData, paste0(".//item/", x)))
    }
  )
  names(itemList) <- xmlItems
  as.data.table(itemList)
}

cleanCorpusHtml <- function(text){
  unlist(lapply(text, function(x){
    if(nchar(x) > 0){
        # because nodes were starting with tag keywords in li, we relocate at the end so the information remains and the description 
        # starts with the main content
        html <- gsub(">","> ", x) # add spaces after html tags so these aren't concatenated 
        xml <- read_xml(html, as_html = TRUE)
        lis <- xml_find_all(xml, ".//li")
        xml_remove(lis)
        text <- paste( paste(xml_text(xml), collapse ="") , paste(xml_text(lis) , collapse =""), collapse ="")
        text <- gsub("\\s+"," ",  text)

    }else {""}
  }))
}

#Split equally a vector into chunks of number n_chunks
equal_split <- function(vct, n_chunks) {
  lim <- length(vct)
  fstep <- lim%/%n_chunks
  idx_list <- list()
  for(i in seq(n_chunks - 1)){
    idx_list[[i]] <- vct[((i-1)*fstep + 1):(i*(fstep))]
  }
  idx_list[[n_chunks]] <- vct[((n_chunks - 1)*fstep + 1):(lim)]
  return(idx_list)
}

#Function that takes a vector, and returns thresholded first 10 sorted indexes
getThresholdOrderRwmd <- function(vct, idVec, threshold = 1e-6, numHead = 10){
    vct <- ifelse(vct > threshold, vct, Inf)
    indexVec <- head(order(vct), numHead)
    idVec[indexVec]
}


#Function to read xml nodes in description
maintainElements <- function(nodes, elementType = "a", attribute = "href"){
    xml_attr(xml_find_all(nodes, paste0(".//", elementType)), attribute)
}

#Function to add results to datatable
elementsToDataTable <- function(result, elementType){
    if(length(result) > 0)
        data.table(elementType = elementType, attributeValue = result)
    else
        data.table()
}

#Function to retrieve urls from text
keepHtmlElements <- function(feedItem){
    nodes <- read_xml(paste0("<div>",  feedItem, "</div>"), as_html = TRUE)
    rbind(
        elementsToDataTable(maintainElements(nodes, "a", "href"), "link"),
        elementsToDataTable(maintainElements(nodes, "img", "src"), "image"),
        elementsToDataTable(maintainElements(nodes, "img-src", "src"), "image")
        #All "img-src" are NA
    )
}

#retrieve list of parameters in a http request query
getQueryParams <- function(url){
  query <- httr::parse_url(url)$query
  queryValues <- unlist(query)
  queryNames <- names(query)
  dat <- data.table(varName = queryNames, value = queryValues)
  dat[queryValues != ""]
}

keepCountryName <- function(string){
  string <- gsub(".*_", "", string)
  gsub("\\..*", "", string)
}

keepNTokens <- function(string, num){
    tokenList <- strsplit(string, split = " ")
    sapply(tokenList, function(tokens){
        tokens <- sort(tokens)
        tokensShift <- shift(tokens, -num, fill = FALSE)
        paste(tokens[tokens != tokensShift], collapse = " ")    
    })
}

findTFIDF <- function(corpus, stopwords, normalize = "double", min_char = 1) {

  tokensList <- strsplit(corpus[, text], " ")
  names(tokensList) <- corpus[, code]

  tokensDT <- lapply(tokensList, as.data.table) %>% 
    rbindlist(idcol = TRUE) %>%
        setnames(c("class", "term"))

  tokensDT <- tokensDT[!term %in% stopwords][nchar(term) > min_char]
    #inverse document frequency smooth  
    idfDT <- tokensDT[!duplicated(tokensDT)][, .(docFreq = .N), by = "term"]
    idfDT[, idf :=  log(length(unique(tokensDT$class)) / (docFreq + 1)) + 1]    

  tfDT <- tokensDT[, .(term_count = .N), by = c("class", "term")]

  if(normalize == "double")tfDT[, tf := 0.5 + 0.5 * term_count / max(term_count)]
  if(normalize == "log")tfDT[, tf := log(1 +term_count)]
  
  merge(tfDT, idfDT, on = "term")[, tfIdf := tf*idf ][, .(term, class, tfIdf)]
    
}

tidyJsonData <- function(jsonList){
    if(length(jsonList) == 0)return(NULL)
    unlistOccupations <- jsonList %>% unlist
    codesMaleFemale <- names(unlistOccupations)
    epasMapping <- data.table(unlistOccupations)
    epasMapping[ , code := gsub("\\.[[:alpha:]]$", "", codesMaleFemale)]
    uniqueMappingBoolean <- epasMapping[ , unlistOccupations != c(unlistOccupations[-1], F), by = code]$V1
    codesEpasDB <- epasMapping[uniqueMappingBoolean]
    names(codesEpasDB) <- c("title", "code")
    codesEpasDB[ , title := cleansingCorpus(title)]
}

findNGrams <- function(corpus, min_n, max_n = min_n, stopWords = NA_character_) {
  ngrams <- itoken(corpus, tokenizer = word_tokenizer, progressbar = FALSE) %>%
    create_vocabulary(stopwords = stopWords, c(min_n, max_n), sep_ngram = " ") %>%
    as.data.table()
  ngrams[order(-doc_count)][, .(term, count = doc_count)]
}

`%W>%` <- function(lhs,rhs){
  w <- options()$warn
  on.exit(options(warn=w))
  options(warn=-1)
  eval.parent(substitute(lhs %>% rhs))
}

getStopwords <- function(locale) { 
  stopwordsLocale <- c(stopwords_getlanguages(source = "misc"), stopwords_getlanguages(source = "snowball")) 
  stopWords <- ""
  if (locale %in% stopwordsLocale) 
    stopWords <- locale %W>% stopwords
  stopWords  
}

###################################################################################################
# Text translation
###################################################################################################

translateText <- function(sourceText, sourceLang, translationLang, batchSize = 4800) {
  if (length(sourceText) == 0) {
    return ("")
  } else if (length(sourceText) == 1) {
    return (requestTranslation(sourceText, sourceLang, translationLang))
  } else if (length(sourceText) > 4800) {
    return (NA)
  }

  sourceQueries <- gsub("$", "\n >", sourceText)
  sourceQueries <- gsub("^", "< \n", sourceQueries)
  queries <- data.table(query = sourceQueries, size = nchar(sourceQueries), batch = nchar(sourceQueries))
  for (row in seq(nrow(queries) - 1)) {
    cumulativeSum <- queries[row, batch] + queries[row + 1, batch] + 3
    queries[row + 1, batch := ifelse(cumulativeSum > batchSize, batch, cumulativeSum)]
  }
  batchStarts <- which(queries[, size] == queries[, batch])
  batchFins <- c(batchStarts[-1] - 1, nrow(queries))
  batches <- lapply(seq_along(batchStarts), function(i) batchStarts[i]:batchFins[i])
  pastedQueries <- lapply(batches, function(batch) paste0(queries[batch, query], collapse = "\n")) %>% unlist()

  translatedText <- lapply(pastedQueries, requestTranslation, sourceLang, translationLang) %>% 
    unlist() %>%
    paste0(collapse = " ")
  translatedText <- gsub("\\s?<", "", translatedText)
  gsub(">$", "", translatedText) %>% 
    space_tokenizer(sep = ">") %>% 
    unlist() %>% 
    trimws()
}

requestTranslation <- function(sourceText, sourceLang, translationLang) { 
  googleTranslateURL <- paste0(
    "https://translate.google.com/m",
    "?hl=", sourceLang,
    "&sl=", sourceLang,
    "&tl=", translationLang,
    "&ie=UTF-8&prev=_m&q=", URLencode(sourceText, reserved = TRUE)
  )
  GET(googleTranslateURL, add_headers("user-agent" = "Mozilla/5.0")) %>%
    read_html() %>% 
    xml_child(2) %>%
    xml_child(5) %>%
    xml_text() %>%
    unlist()
}

###########################################################################################################

Libraries version

Session info

## R version 4.0.5 (2021-03-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] cld3_1.4.1        cld2_1.2.1        stopwords_2.2     text2vec_0.6     
##  [5] magrittr_2.0.1    stringr_1.4.0     DT_0.18           dplyr_1.0.6      
##  [9] rmarkdown_2.8     data.table_1.14.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.6           pillar_1.6.0         bslib_0.2.5         
##  [4] compiler_4.0.5       jquerylib_0.1.4      highr_0.9           
##  [7] tools_4.0.5          digest_0.6.27        jsonlite_1.7.2      
## [10] evaluate_0.14        lifecycle_1.0.0      tibble_3.1.1        
## [13] lattice_0.20-41      pkgconfig_2.0.3      rlang_0.4.11        
## [16] Matrix_1.3-2         mlapi_0.1.0          RhpcBLASctl_0.20-137
## [19] yaml_2.2.1           xfun_0.23            knitr_1.33          
## [22] generics_0.1.0       vctrs_0.3.8          sass_0.4.0          
## [25] htmlwidgets_1.5.3    grid_4.0.5           tidyselect_1.1.1    
## [28] glue_1.4.2           R6_2.5.0             fansi_0.4.2         
## [31] lgr_0.4.2            purrr_0.3.4          ellipsis_0.3.2      
## [34] htmltools_0.5.1.1    float_0.2-4          rsparse_0.4.0       
## [37] utf8_1.2.1           stringi_1.6.2        crayon_1.4.1

../000.core/00.02.base.functions.R completed in 0.11 seconds

Data loading

Loading stratified Demograph data

  • Type of data: data.table, data.frame.

  • Dimensions: 353518, 20.

  • Column Names: id, locale, creationDate, lastUpdate, postalcode, country, gender, birthdate, nationality, work_years, num_work, min_work_years, max_work_years, mean_work_years, is_employed, eqf_level, eqf_previous, is_student, headline_type, headline_isco.

Loading stratified Education data

  • Type of data: data.table, data.frame.

  • Dimensions: 1766160, 26.

  • Column Names: index, id, locale, country, nationality, birthYear, age, final_level, institution_name, institution_short, numQual, title, organisation, organisationCountry, from, to, status, fromAge, toAge, studyAge, length, cumLength, eqf_level, eqf_group, edu_level, edu_field.

Loading stratified Work data

  • Type of data: data.table, data.frame.

  • Dimensions: 1303728, 35.

  • Column Names: id, URI, from, to, label, employer, code, occupationTitle, iscoCode1, iscoCode2, iscoCode3, iscoCode4, iscoLabel1, iscoLabel2, iscoLabel3, iscoLabel4, locale, creationDate, lastUpdate, postalcode, country, gender, birthdate, nationality, work_years, num_work, min_work_years, max_work_years, mean_work_years, is_employed, eqf_level, eqf_previous, is_student, headline_type, headline_isco.

Loading stratified Work data

  • Type of data: data.table, data.frame.

  • Dimensions: 1139016, 24.

  • Column Names: id, locale, creationDate, lastUpdate, postalcode, country, gender, birthdate, nationality, work_years, num_work, min_work_years, max_work_years, mean_work_years, is_employed, eqf_level, eqf_previous, is_student, headline_type, headline_isco, skillCode, type, category, skillTitle.

1.load.data.R completed in 19.9 seconds

Data processing

Preparation

  • Making column names more descriptive.
  • Making modifications to some columns.
  • Adding some required additional columns.

2.process.data.R completed in 9.82 seconds

Data persistance

  • fst format

Datasource : /data/generic/jobsOutput/code_book/aggregations/qualifications_aggregate.fst of 24,675,921 bytes.

Datasource : /data/generic/jobsOutput/code_book/aggregations/education_fields_aggregate.fst of 87,192,592 bytes.

  • csv format

Datasource : /data/tmpfs/results/survey_data/csv/qualifications_aggregate.zip of 4,020,416 bytes.

Datasource : /data/tmpfs/results/survey_data/csv/education_fields_aggregate.zip of 17,458,908 bytes.

5.save.data.R completed in 34.37 seconds

Computation metrics

Computational report

Completed in 73.6 seconds.

Subpart metrics

## NULL

End of report

Reports index

Eworx S.A. DSENSE report for EPAS.

– end of report –