#!/bin/bash
# -*- coding: utf-8 -*-
# Test file for: process_tables.sh
THIS_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
ROOT_DIR="$(realpath "$THIS_DIR/../..")"
# Test counter
TESTS_RUN=0
TESTS_PASSED=0
TESTS_FAILED=0
# Colors
GREEN='\033[0;32m'
RED='\033[0;31m'
NC='\033[0m'
assert_success() {
local cmd="$1"
local desc="${2:-$cmd}"
((TESTS_RUN++))
if eval "$cmd" > /dev/null 2>&1; then
echo -e "${GREEN}✓${NC} $desc"
((TESTS_PASSED++))
else
echo -e "${RED}✗${NC} $desc"
((TESTS_FAILED++))
fi
}
assert_file_exists() {
local file="$1"
((TESTS_RUN++))
if [ -f "$file" ]; then
echo -e "${GREEN}✓${NC} File exists: $file"
((TESTS_PASSED++))
else
echo -e "${RED}✗${NC} File missing: $file"
((TESTS_FAILED++))
fi
}
# Add your tests here
test_placeholder() {
echo "TODO: Add tests for process_tables.sh"
}
# Run tests
main() {
echo "Testing: process_tables.sh"
echo "========================================"
test_placeholder
echo "========================================"
echo "Results: $TESTS_PASSED/$TESTS_RUN passed"
[ $TESTS_FAILED -gt 0 ] && exit 1
exit 0
}
main "$@"
# --------------------------------------------------------------------------------
# Start of Source Code from: /home/ywatanabe/proj/scitex-writer/scripts/shell/modules/process_tables.sh
# --------------------------------------------------------------------------------
# #!/bin/bash
# # -*- coding: utf-8 -*-
# # Timestamp: "2025-09-28 19:49:15 (ywatanabe)"
# # File: ./paper/scripts/shell/modules/process_tables.sh
#
# # Quick check for --no_tables BEFORE expensive config loading
# NO_TABLES_ARG="${1:-false}"
# if [ "$NO_TABLES_ARG" = true ]; then
# echo -e "\033[0;90mINFO: Running $0 ...\033[0m"
# echo -e "\033[0;90mINFO: Skipping all table processing (--no_tables specified)\033[0m"
# exit 0
# fi
#
# ORIG_DIR="$(pwd)"
# THIS_DIR="$(cd $(dirname ${BASH_SOURCE[0]}) && pwd)"
# LOG_PATH="$THIS_DIR/.$(basename $0).log"
# echo > "$LOG_PATH"
#
# GIT_ROOT="$(git rev-parse --show-toplevel 2>/dev/null)"
#
# GRAY='\033[0;90m'
# GREEN='\033[0;32m'
# YELLOW='\033[0;33m'
# RED='\033[0;31m'
# NC='\033[0m' # No Color
#
# echo_info() { echo -e "${GRAY}INFO: $1${NC}"; }
# log_info() {
# if [ "${SCITEX_LOG_LEVEL:-1}" -ge 2 ]; then
# echo -e " \033[0;90m→ $1\033[0m"
# fi
# }
# echo_success() { echo -e "${GREEN}SUCC: $1${NC}"; }
# echo_warning() { echo -e "${YELLOW}WARN: $1${NC}"; }
# echo_error() { echo -e "${RED}ERRO: $1${NC}"; }
# echo_header() { echo_info "=== $1 ==="; }
# # ---------------------------------------
#
# # Timestamp tracking for table processing
# TABLE_STAGE_START=0
# log_table_stage_start() {
# TABLE_STAGE_START=$(date +%s)
# local timestamp=$(date '+%H:%M:%S')
# echo_info " [$timestamp] $1"
# }
#
# log_table_stage_end() {
# local end=$(date +%s)
# local elapsed=$((end - TABLE_STAGE_START))
# local timestamp=$(date '+%H:%M:%S')
# echo_success " [$timestamp] $1 (${elapsed}s)"
# }
# # ---------------------------------------
#
# # Configurations
# source ./config/load_config.sh $SCITEX_WRITER_DOC_TYPE
#
# # Logging
# touch "$LOG_PATH" >/dev/null 2>&1
# echo
# log_info "Running $0 ..."
#
# function init_tables() {
# # Cleanup and prepare directories
# rm -f "$SCITEX_WRITER_TABLE_COMPILED_DIR"/*.tex
# mkdir -p "$SCITEX_WRITER_TABLE_DIR" >/dev/null
# mkdir -p "$SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR" >/dev/null
# mkdir -p "$SCITEX_WRITER_TABLE_COMPILED_DIR" >/dev/null
# echo > "$SCITEX_WRITER_TABLE_COMPILED_FILE"
# }
#
# function xlsx2csv_convert() {
# # Convert Excel files to CSV if xlsx2csv is available
# if command -v xlsx2csv >/dev/null 2>&1; then
# for xlsx_file in "$SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR"/[0-9]*.{xlsx,xls}; do
# [ -e "$xlsx_file" ] || continue
#
# base_name=$(basename "$xlsx_file" | sed 's/\.\(xlsx\|xls\)$//')
# csv_file="${SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR}/${base_name}.csv"
#
# # Convert only if CSV doesn't exist or is older than Excel file
# if [ ! -f "$csv_file" ] || [ "$xlsx_file" -nt "$csv_file" ]; then
# echo_info " Converting $xlsx_file to CSV..."
# xlsx2csv "$xlsx_file" "$csv_file"
# if [ $? -eq 0 ]; then
# echo_success " Created $csv_file from Excel"
# else
# echo_warning " Failed to convert $xlsx_file"
# fi
# fi
# done
# fi
# }
#
# function ensure_caption() {
# # Create default captions for any table without one
# for csv_file in "$SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR"/[0-9]*.csv; do
# [ -e "$csv_file" ] || continue
# local base_name=$(basename "$csv_file" .csv)
# # Extract table number from filename like 01_seizure_count
# local table_number=""
# if [[ "$base_name" =~ ^([0-9]+)_ ]]; then
# table_number="${BASH_REMATCH[1]}"
# else
# table_number="$base_name"
# fi
# local caption_file="${SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR}/${base_name}.tex"
#
# if [ ! -f "$caption_file" ] && [ ! -L "$caption_file" ]; then
# echo_info " Creating default caption for table $base_name"
# mkdir -p $(dirname "$caption_file")
# cat > "$caption_file" << EOF
# \\caption{\\textbf{
# TABLE TITLE HERE
# }
# \\smallskip
# \\
# \\text{
# TABLE CAPTION HERE.
# }}
# EOF
# fi
# done
# }
#
# # Function removed - no longer needed for new naming convention
#
# function check_csv_for_special_chars() {
# # Check CSV file for potential problematic characters
# local csv_file="$1"
# local problem_chars="[&%$#_{}^~\\|<>]"
# local problems=$(grep -n "$problem_chars" "$csv_file" 2>/dev/null || echo "")
# if [ -n "$problems" ]; then
# echo_warn " Potential LaTeX special characters found in $csv_file:"
# echo -e ${YELLOW}
# echo "$problems" | head -5
# echo "These may need proper LaTeX escaping."
# echo -e ${NC}
# fi
# }
#
# function csv2tex() {
# # Determine best method for CSV processing
# local use_method="fallback"
#
# # Check for csv2latex command (best option)
# if command -v csv2latex >/dev/null 2>&1; then
# use_method="csv2latex"
# echo_info " Using csv2latex for table processing"
# # Check if Python and pandas are available (second best)
# elif command -v python3 >/dev/null 2>&1 && python3 -c "import pandas" 2>/dev/null; then
# use_method="python"
# echo_info " Using Python with pandas for table processing"
# # Check if Python is available without pandas
# elif command -v python3 >/dev/null 2>&1; then
# use_method="python_basic"
# echo_info " Using Python (basic) for table processing"
# else
# echo_warning " Using fallback AWK processing for tables"
# fi
#
# # Process each CSV file
# for csv_file in "$SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR"/[0-9]*.csv; do
# [ -e "$csv_file" ] || continue
#
# base_name=$(basename "$csv_file" .csv)
# caption_file="${SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR}/${base_name}.tex"
# compiled_file="$SCITEX_WRITER_TABLE_COMPILED_DIR/${base_name}.tex"
#
# case "$use_method" in
# csv2latex)
# # Use csv2latex command - generate basic table structure
# # Note: csv2latex doesn't support captions or labels directly
# {
# echo "\\pdfbookmark[2]{Table ${base_name#0}}{table_${base_name}}"
# echo "\\begin{table}[htbp]"
# echo "\\centering"
# echo "\\footnotesize"
#
# # Generate the tabular environment using csv2latex
# csv2latex --nohead --separator comma "$csv_file" 2>/dev/null
#
# # Add caption if it exists
# if [ -f "$caption_file" ] || [ -L "$caption_file" ]; then
# cat "$caption_file"
# else
# echo "\\caption{Table ${base_name#0}: ${base_name#*_}}"
# fi
#
# # Add label
# echo "\\label{tab:${base_name}}"
# echo "\\end{table}"
# } > "$compiled_file"
#
# # Check if csv2latex succeeded (look for \begin{tabular} with single backslash)
# if [ -s "$compiled_file" ] && grep -q "\\\\begin{tabular}" "$compiled_file" 2>/dev/null; then
# echo_success " $compiled_file compiled (using csv2latex)"
# else
# echo_warning " csv2latex failed, trying fallback"
# csv2tex_single_fallback "$csv_file" "$compiled_file" "$caption_file"
# fi
# ;;
#
# python|python_basic)
# # Use our Python script
# local caption_arg=""
# if [ -f "$caption_file" ] || [ -L "$caption_file" ]; then
# temp_caption_file="/tmp/caption_${base_name}.txt"
# cat "$caption_file" > "$temp_caption_file"
# caption_arg="--caption-file $temp_caption_file"
# fi
#
# if [ -f "./scripts/python/csv_to_latex.py" ]; then
# python3 ./scripts/python/csv_to_latex.py "$csv_file" "$compiled_file" $caption_arg
# if [ $? -eq 0 ]; then
# echo_success " $compiled_file compiled (using Python)"
# else
# echo_warning " Python processing failed, trying fallback"
# csv2tex_single_fallback "$csv_file" "$compiled_file" "$caption_file"
# fi
# [ -f "$temp_caption_file" ] && rm -f "$temp_caption_file"
# else
# csv2tex_single_fallback "$csv_file" "$compiled_file" "$caption_file"
# fi
# ;;
#
# *)
# # Use fallback AWK processing
# csv2tex_single_fallback "$csv_file" "$compiled_file" "$caption_file"
# ;;
# esac
# done
# }
#
# function csv2tex_single_fallback() {
# # Basic CSV processing for a single file (fallback method)
# local csv_file="$1"
# local compiled_file="$2"
# local caption_file="$3"
#
# base_name=$(basename "$csv_file" .csv)
# # Extract table number from filename like 01_seizure_count
# if [[ "$base_name" =~ ^([0-9]+)_ ]]; then
# table_number="${BASH_REMATCH[1]}"
# table_clean_name="${base_name#*_}"
# else
# table_number="$base_name"
# table_clean_name="$base_name"
# fi
#
# # Pre-check CSV for problematic characters
# check_csv_for_special_chars "$csv_file"
#
# # Basic AWK processing (existing code)
# num_columns=$(head -n 1 "$csv_file" | awk -F, '{print NF}')
# num_rows=$(wc -l < "$csv_file")
# max_rows=30
#
# # Use standard font size for tables
# # Standard academic paper convention: \footnotesize (8pt) for tables
# fontsize="\\footnotesize"
#
# # Check if truncation needed
# truncated=false
# if [ $num_rows -gt $((max_rows + 1)) ]; then # +1 for header
# truncated=true
# rows_omitted=$((num_rows - max_rows - 1))
# fi
#
# {
# echo "\\pdfbookmark[2]{Table ${table_number#0}}{table_${base_name}}"
# echo "\\begin{table}[htbp]"
# echo "\\centering"
# echo "$fontsize"
#
# # Adjust tabcolsep based on number of columns to fit width
# if [ $num_columns -gt 8 ]; then
# echo "\\setlength{\\tabcolsep}{2pt}" # Very tight for many columns
# elif [ $num_columns -gt 6 ]; then
# echo "\\setlength{\\tabcolsep}{3pt}" # Tight spacing
# elif [ $num_columns -gt 4 ]; then
# echo "\\setlength{\\tabcolsep}{4pt}" # Medium spacing
# else
# echo "\\setlength{\\tabcolsep}{6pt}" # Normal spacing
# fi
#
# # Use resizebox to ensure table fits within text width
# echo "\\resizebox{\\textwidth}{!}{%"
# echo "\\begin{tabular}{*{$num_columns}{l}}"
# echo "\\toprule"
#
# # Simple header processing
# head -n 1 "$csv_file" | awk -F, '{
# for (ii=1; ii<=NF; ii++) {
# val = $ii
# gsub(/[_]/, "\\\\_", val)
# printf("\\textbf{%s}", val)
# if (ii < NF) printf(" & ")
# }
# print "\\\\"
# }'
#
# echo "\\midrule"
#
# # Process data with potential truncation
# if [ "$truncated" = true ]; then
# # Show first max_rows-2 rows
# tail -n +2 "$csv_file" | head -n $((max_rows - 2)) | awk -F, '{
# for (i=1; i<=NF; i++) {
# val = $i
# gsub(/[_]/, "\\\\_", val)
# printf("%s", val)
# if (i < NF) printf(" & ")
# }
# print "\\\\"
# }'
#
# # Add truncation indicator
# echo "\\midrule"
# echo "\\multicolumn{$num_columns}{c}{\\textit{... $rows_omitted rows omitted ...}} \\\\"
# echo "\\midrule"
#
# # Show last 2 rows
# tail -n 2 "$csv_file" | awk -F, '{
# for (i=1; i<=NF; i++) {
# val = $i
# gsub(/[_]/, "\\\\_", val)
# printf("%s", val)
# if (i < NF) printf(" & ")
# }
# print "\\\\"
# }'
# else
# # Simple data processing without truncation
# tail -n +2 "$csv_file" | awk -F, '{
# for (i=1; i<=NF; i++) {
# val = $i
# gsub(/[_]/, "\\\\_", val)
# printf("%s", val)
# if (i < NF) printf(" & ")
# }
# print "\\\\"
# }'
# fi
#
# echo "\\bottomrule"
# echo "\\end{tabular}"
# echo "}" # Close resizebox
#
# if [ -f "$caption_file" ] || [ -L "$caption_file" ]; then
# if [ "$truncated" = true ]; then
# # Add truncation note to caption
# cat "$caption_file" | sed 's/}$//'
# echo "\\textit{Note: Table truncated to $max_rows rows from $num_rows total rows for display purposes.}}"
# else
# cat "$caption_file"
# fi
# else
# echo "\\caption{Table ${table_number#0}: ${table_clean_name//_/ }"
# if [ "$truncated" = true ]; then
# echo "\\textit{Note: Table truncated to $max_rows rows from $num_rows total rows for display purposes.}"
# fi
# echo "}"
# fi
#
# echo "\\label{tab:${base_name}}"
# echo "\\end{table}"
# } > "$compiled_file"
#
# echo_info " $compiled_file compiled (using fallback)"
# }
#
# function csv2tex_fallback() {
# # Process all CSV files with fallback method
# for csv_file in "$SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR"/[0-9]*.csv; do
# [ -e "$csv_file" ] || continue
# base_name=$(basename "$csv_file" .csv)
# caption_file="${SCITEX_WRITER_TABLE_CAPTION_MEDIA_DIR}/${base_name}.tex"
# compiled_file="$SCITEX_WRITER_TABLE_COMPILED_DIR/${base_name}.tex"
# csv2tex_single_fallback "$csv_file" "$compiled_file" "$caption_file"
# done
# }
#
# function create_table_header() {
# # Create a header/template table when no real tables exist
# local header_file="$SCITEX_WRITER_TABLE_COMPILED_DIR/00_Tables_Header.tex"
#
# cat > "$header_file" << 'EOF'
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# %% TABLES
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# %% \clearpage
# \section*{Tables}
# \label{tables}
# \pdfbookmark[1]{Tables}{tables}
#
# % Template table when no actual tables are present
# \begin{table}[htbp]
# \centering
# \caption{\textbf{Table 0: Placeholder}\\
# \smallskip
# To add tables to your manuscript:\\
# 1. Place CSV files in \texttt{caption\_and\_media/} with format \texttt{XX\_description.csv}\\
# 2. Create matching caption files \texttt{XX\_description.tex}\\
# 3. Reference in text using \texttt{Table\textasciitilde\textbackslash ref\{tab:XX\_description\}}\\
# \smallskip
# Example: \texttt{01\_seizure\_count.csv} with \texttt{01\_seizure\_count.tex}
# }
# \label{tab:0_Tables_Header}
# \begin{tabular}{p{0.3\textwidth}p{0.6\textwidth}}
# \toprule
# \textbf{Step} & \textbf{Instructions} \\
# \midrule
# 1. Add CSV & Place file like \texttt{01\_data.csv} in \texttt{caption\_and\_media/} \\
# 2. Add Caption & Create \texttt{01\_data.tex} with table caption \\
# 3. Compile & Run \texttt{./compile -m} to process tables \\
# 4. Reference & Use \texttt{\textbackslash ref\{tab:01\_data\}} in manuscript \\
# \bottomrule
# \end{tabular}
# \end{table}
# EOF
# echo_info " Created table header template with instructions"
# }
#
# function gather_table_tex_files() {
# # Gather all table tex files into the final compiled file
# output_file="${SCITEX_WRITER_TABLE_COMPILED_FILE}"
# rm -f "$output_file" > /dev/null 2>&1
# echo "% Auto-generated file containing all table inputs" > "$output_file"
# echo "% Generated by gather_table_tex_files()" >> "$output_file"
# echo "" >> "$output_file"
#
# # First check if there are any real table files
# local table_files=($(find "$SCITEX_WRITER_TABLE_COMPILED_DIR" -maxdepth 1 -name "[0-9]*.tex" 2>/dev/null | grep -v "00_Tables_Header.tex" | sort))
# local has_real_tables=false
# if [ ${#table_files[@]} -gt 0 ]; then
# has_real_tables=true
# # Don't add anything here - base.tex handles the section header and spacing
# fi
#
# # If no real tables, create the header/template
# if [ "$has_real_tables" = false ]; then
# create_table_header
# fi
#
# # Count available tables
# table_count=0
# for table_tex in $(find "$SCITEX_WRITER_TABLE_COMPILED_DIR" -name "[0-9]*.tex" 2>/dev/null | sort); do
# if [ -f "$table_tex" ] || [ -L "$table_tex" ]; then
# # Skip header if we have real tables
# local basename=$(basename "$table_tex")
# if [[ "$basename" == "00_Tables_Header.tex" ]] && [ "$has_real_tables" = true ]; then
# continue
# fi
#
# # For header template when no real tables exist
# if [[ "$basename" == "00_Tables_Header.tex" ]] && [ "$has_real_tables" = false ]; then
# echo "\\input{$table_tex}" >> "$output_file"
# else
# # For real tables, input them directly
# echo "% Table from: $basename" >> "$output_file"
# echo "\\input{$table_tex}" >> "$output_file"
# fi
# echo "" >> "$output_file"
# table_count=$((table_count + 1))
# fi
# done
#
# if [ $table_count -eq 0 ]; then
# echo_warning " No tables were found to compile."
# else
# echo_success " $table_count tables compiled"
# fi
# }
#
# # Main execution
# log_table_stage_start "Initializing tables"
# init_tables
# log_table_stage_end "Initializing tables"
#
# log_table_stage_start "Converting XLSX to CSV"
# xlsx2csv_convert # Convert Excel files to CSV first
# log_table_stage_end "Converting XLSX to CSV"
#
# log_table_stage_start "Ensuring captions exist"
# ensure_caption
# log_table_stage_end "Ensuring captions exist"
#
# log_table_stage_start "Converting CSV to LaTeX"
# csv2tex
# log_table_stage_end "Converting CSV to LaTeX"
#
# log_table_stage_start "Gathering table files"
# gather_table_tex_files
# log_table_stage_end "Gathering table files"
#
# # EOF
# --------------------------------------------------------------------------------
# End of Source Code from: /home/ywatanabe/proj/scitex-writer/scripts/shell/modules/process_tables.sh
# --------------------------------------------------------------------------------
/