add table-converter utility

scripts/build.sh

@@ -4,10 +4,12 @@ set -o errexit
 set -o nounset
 set -o pipefail
 
-: "${BUILD_DIR:="build"}"
 
 script_dir="$(cd "$(dirname "${0}")" && pwd)"
 cd "${script_dir}/.."
+repo_root="$(pwd)"
+
+: "${BUILD_DIR:="${repo_root}/build"}"
 
 pkg_content_root() {
     local _pkg_name="${1}"
@@ -32,8 +34,9 @@ build_binary() {
     printf "## os='%s', arch='%s':\n" "${_os_go}" "${_arch_go}"
     env GOOS="${_os_go}" GOARCH="${_arch_go}" \
         go build \
+        -C "$(dirname "./${_go_name}")" \
         -o "${_pkg_root}/${_bin_name}${_ext}" \
-        "./${_go_name}"
+        "./$(basename "${_go_name}")"
 }
 
 additional_file() {
@@ -102,6 +105,8 @@ add_file() {
 
 rm -rf "${script_dir}/${BUILD_DIR}"
 
+build_binaries "table-converter" "table-converter/table-converter" "table-converter"
+
 build_binaries "runenv-java-stub" "dump-args.go" "bin/java"
 
 build_binaries "runenv-python-stub" "runenv-python-stub.go" "bin/python"

table-converter/.gitignore

@@ -0,0 +1 @@
+/table-converter/table-converter

table-converter/go.mod

@@ -0,0 +1,3 @@
+module github.com/milaboratory/small-binaries/table-converter
+
+go 1.22.3

table-converter/internal/config.go

@@ -0,0 +1,60 @@
+package converter
+
+import "errors"
+
+const (
+	DefaultSamplesColumnName = "Sample"
+	DefaultMetricColumnLabel = "Metric"
+	DefaultValueColumnLabel  = "Value"
+)
+
+type Config struct {
+	InputFileName      string
+	InputFileSeparator rune
+
+	OutputFileName      string
+	OutputFileSeparator rune
+
+	SampleColumnName string
+
+	MetricColumnLabel string
+	ValueColumnLabel  string
+}
+
+func (c *Config) LoadDefaults() {
+	if c.InputFileSeparator == 0 {
+		c.InputFileSeparator, _ = DetectTableSeparator(c.InputFileName)
+	}
+
+	if c.OutputFileSeparator == 0 {
+		if c.InputFileSeparator != 0 {
+			c.OutputFileSeparator = c.InputFileSeparator
+		} else {
+			c.OutputFileSeparator, _ = DetectTableSeparator(c.OutputFileName)
+		}
+	}
+
+	if c.MetricColumnLabel == "" {
+		c.MetricColumnLabel = DefaultMetricColumnLabel
+	}
+	if c.ValueColumnLabel == "" {
+		c.ValueColumnLabel = DefaultValueColumnLabel
+	}
+	if c.SampleColumnName == "" {
+		c.SampleColumnName = DefaultSamplesColumnName
+	}
+}
+
+func (c *Config) Validate() error {
+	var errs []error
+	if c.InputFileSeparator == 0 {
+		_, err := DetectTableSeparator(c.InputFileName)
+		errs = append(errs, Wrap(err, "[input]"))
+	}
+	if c.OutputFileSeparator == 0 {
+		_, err := DetectTableSeparator(c.OutputFileName)
+		errs = append(errs, Wrap(err, "[output]"))
+	}
+
+	return errors.Join(errs...)
+}

table-converter/internal/converter.go

@@ -0,0 +1,116 @@
+package converter
+
+import (
+	"encoding/csv"
+	"fmt"
+	"io"
+	"os"
+)
+
+const SampleColumnName = "Sample"
+
+type Converter struct {
+	config Config
+}
+
+func New(conf Config) *Converter {
+	conf.LoadDefaults()
+	return &Converter{config: conf}
+}
+
+func (c *Converter) parser(input io.Reader) *csv.Reader {
+	r := csv.NewReader(input)
+	r.Comma = c.config.InputFileSeparator
+	return r
+}
+
+func (c *Converter) formatter(output io.Writer) *csv.Writer {
+	w := csv.NewWriter(output)
+	w.Comma = c.config.OutputFileSeparator
+	return w
+}
+
+func (c *Converter) Convert(input io.Reader, output io.Writer) error {
+	reader := c.parser(input)
+	writer := c.formatter(output)
+	defer writer.Flush()
+
+	headers, err := reader.Read()
+	if err != nil {
+		return Wrap(err, "[input]: failed to read header")
+	}
+
+	sampleIndex, metricIndices := c.detectColumns(headers)
+	if sampleIndex == -1 {
+		return fmt.Errorf("sample name column %q not found in input header", c.config.SampleColumnName)
+	}
+
+	err = writer.Write([]string{SampleColumnName, c.config.MetricColumnLabel, c.config.ValueColumnLabel})
+	if err != nil {
+		return Wrap(err, "[output]: failed to write output header")
+	}
+
+	if len(metricIndices) == 0 {
+		return nil
+	}
+
+	for {
+		record, err := reader.Read()
+		if err == io.EOF {
+			break
+		}
+		if err != nil {
+			return Wrapf(err, "[input]")
+		}
+
+		sampleName := record[sampleIndex]
+		var metricI = 0
+		for _, metricIndex := range metricIndices {
+			metricI++
+			err = writer.Write([]string{sampleName, headers[metricIndex], record[metricIndex]})
+			if err != nil {
+				return Wrapf(err, "[output]: failed to write metric %d of sample %q", metricI, sampleName)
+			}
+		}
+	}
+
+	return nil
+}
+
+func (c *Converter) detectColumns(headers []string) (sampleIndex int, metricIndices []int) {
+	sampleIndex = -1
+	for i, header := range headers {
+		if header == c.config.SampleColumnName {
+			sampleIndex = i
+		} else {
+			metricIndices = append(metricIndices, i)
+		}
+	}
+	return
+}
+
+func (c *Converter) Run() error {
+	var input io.Reader = os.Stdin
+	if c.config.InputFileName != "-" {
+		inputFile, err := os.Open(c.config.InputFileName)
+		if err != nil {
+			return Wrapf(err, "[input]: failed to open input file %q", c.config.InputFileName)
+		}
+		defer inputFile.Close()
+
+		input = inputFile
+	}
+
+	var output io.Writer = os.Stdout
+	if c.config.OutputFileName != "-" {
+		outputFile, err := os.Create(c.config.OutputFileName)
+		if err != nil {
+			return Wrapf(err, "[output]: failed to open output file %q", c.config.OutputFileName)
+		}
+		defer outputFile.Close()
+
+		output = outputFile
+	}
+
+	return c.Convert(input, output)
+}