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Replace kotlinx-cli with picocli #30

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ac660ac
Replace kotlinx with picocli
dfuchss Aug 6, 2025
4615ae6
cleanup code
dfuchss Aug 6, 2025
f53f654
Update cli/src/main/kotlin/edu/kit/kastel/mcse/ardoco/metrics/cli/com…
dfuchss Aug 6, 2025
16bcb70
Update cli/src/main/kotlin/edu/kit/kastel/mcse/ardoco/metrics/cli/com…
dfuchss Aug 6, 2025
059161c
make it compile
dfuchss Aug 6, 2025
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33 changes: 28 additions & 5 deletions cli/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<project.source.encoding>UTF-8</project.source.encoding>
<picocli.version>4.7.7</picocli.version>
</properties>

<dependencies>
Expand All @@ -27,16 +28,16 @@
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-kotlin</artifactId>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>${picocli.version}</version>
</dependency>
<dependency>
<groupId>io.github.ardoco</groupId>
<artifactId>metrics</artifactId>
<version>${revision}</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlinx</groupId>
<artifactId>kotlinx-cli-jvm</artifactId>
<version>0.3.6</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
Expand Down Expand Up @@ -81,6 +82,28 @@
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-maven-plugin</artifactId>
<version>${kotlin.version}</version>
<executions>
<execution>
<id>kapt</id>
<goals>
<goal>kapt</goal>
</goals>
<configuration combine.self="append">
<annotationProcessorPaths>
<annotationProcessorPath>
<groupId>info.picocli</groupId>
<artifactId>picocli-codegen</artifactId>
<version>${picocli.version}</version>
</annotationProcessorPath>
</annotationProcessorPaths>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
28 changes: 15 additions & 13 deletions cli/src/main/kotlin/edu/kit/kastel/mcse/ardoco/metrics/cli/App.kt
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Expand Up @@ -4,19 +4,21 @@ import edu.kit.kastel.mcse.ardoco.metrics.cli.commands.AggregationClassification
import edu.kit.kastel.mcse.ardoco.metrics.cli.commands.AggregationRankCommand
import edu.kit.kastel.mcse.ardoco.metrics.cli.commands.ClassificationCommand
import edu.kit.kastel.mcse.ardoco.metrics.cli.commands.RankCommand
import kotlinx.cli.ArgParser
import kotlinx.cli.ArgType
import kotlinx.cli.ExperimentalCli
import picocli.CommandLine

@OptIn(ExperimentalCli::class)
fun main(args: Array<String>) {
val parser = ArgParser("ArDoCo Metrics")

val outputFileOption = parser.option(ArgType.String, shortName = "o", description = "The output file", fullName = "output")
val classificationCommand = ClassificationCommand(outputFileOption)
val aggregationClassificationCommand = AggregationClassificationCommand(outputFileOption)
val rankCommand = RankCommand(outputFileOption)
val aggregationRankCommand = AggregationRankCommand(outputFileOption)
parser.subcommands(classificationCommand, aggregationClassificationCommand, rankCommand, aggregationRankCommand)
parser.parse(args)
val rootCommand = RootCommand()
CommandLine(rootCommand)
.addSubcommand("classification", ClassificationCommand())
.addSubcommand("aggCl", AggregationClassificationCommand())
.addSubcommand("rank", RankCommand())
.addSubcommand("aggRnk", AggregationRankCommand())
.execute(*args)
}

@CommandLine.Command(
name = "ArDoCo Metrics",
mixinStandardHelpOptions = true,
description = ["CLI for ArDoCo Metrics"]
)
class RootCommand
46 changes: 22 additions & 24 deletions ...otlin/edu/kit/kastel/mcse/ardoco/metrics/cli/commands/AggregationClassificationCommand.kt
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Expand Up @@ -6,28 +6,27 @@ import com.fasterxml.jackson.module.kotlin.readValue
import com.fasterxml.jackson.module.kotlin.registerKotlinModule
import edu.kit.kastel.mcse.ardoco.metrics.ClassificationMetricsCalculator
import edu.kit.kastel.mcse.ardoco.metrics.result.SingleClassificationResult
import kotlinx.cli.ArgType
import kotlinx.cli.ExperimentalCli
import kotlinx.cli.SingleNullableOption
import kotlinx.cli.Subcommand
import kotlinx.cli.required
import java.io.File
import picocli.CommandLine.Command
import picocli.CommandLine.Option
import java.util.concurrent.Callable

@OptIn(ExperimentalCli::class)
class AggregationClassificationCommand(
private val outputFileOption: SingleNullableOption<String>
) : Subcommand("aggCl", "Aggregate results of multiple classifications. I.e., Macro Average + WeightedAverage + Micro Average") {
private val directoryWithResultsOption by option(
ArgType.String,
shortName = "d",
description = "The directory with the classification results"
).required()
@Command(
name = "aggCl",
description = ["Aggregate results of multiple classifications. I.e., Macro Average + WeightedAverage + Micro Average"],
mixinStandardHelpOptions = true
)
class AggregationClassificationCommand : Callable<Int> {
@Option(names = ["-d", "--directory"], description = ["The directory with the classification results"], required = true)
lateinit var directoryWithResults: String

override fun execute() {
val directory = File(directoryWithResultsOption)
@Option(names = ["-o", "--output"], description = ["The output file"])
var outputFile: String? = null

override fun call(): Int {
val directory = java.io.File(directoryWithResults)
if (!directory.isDirectory) {
println("The provided path is not a directory")
return
return 1
}
val oom = ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT).registerKotlinModule()
val results: List<SingleClassificationResult<String>> =
Expand All @@ -38,16 +37,15 @@ class AggregationClassificationCommand(
} ?: emptyList()
if (results.isEmpty()) {
println("No classification results found")
return
return 1
}
val classificationMetrics = ClassificationMetricsCalculator.Instance
val average = classificationMetrics.calculateAverages(results)
average.forEach { it.prettyPrint() }

val output = outputFileOption.value
if (output != null) {
val outputFile = File(output)
oom.writeValue(outputFile, average)
outputFile?.let {
val outputFileObj = java.io.File(it)
oom.writeValue(outputFileObj, average)
}
return 0
}
}
46 changes: 22 additions & 24 deletions ...src/main/kotlin/edu/kit/kastel/mcse/ardoco/metrics/cli/commands/AggregationRankCommand.kt
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Expand Up @@ -6,28 +6,27 @@ import com.fasterxml.jackson.module.kotlin.readValue
import com.fasterxml.jackson.module.kotlin.registerKotlinModule
import edu.kit.kastel.mcse.ardoco.metrics.RankMetricsCalculator
import edu.kit.kastel.mcse.ardoco.metrics.result.SingleRankMetricsResult
import kotlinx.cli.ArgType
import kotlinx.cli.ExperimentalCli
import kotlinx.cli.SingleNullableOption
import kotlinx.cli.Subcommand
import kotlinx.cli.required
import java.io.File
import picocli.CommandLine.Command
import picocli.CommandLine.Option
import java.util.concurrent.Callable

@OptIn(ExperimentalCli::class)
class AggregationRankCommand(
private val outputFileOption: SingleNullableOption<String>
) : Subcommand("aggRnk", "Aggregate results of multiple rank metrics runs. I.e., Macro Average + WeightedAverage") {
private val directoryWithResultsOption by option(
ArgType.String,
shortName = "d",
description = "The directory with the rank results"
).required()
@Command(
name = "aggRnk",
description = ["Aggregate results of multiple rank metrics runs. I.e., Macro Average + WeightedAverage"],
mixinStandardHelpOptions = true
)
class AggregationRankCommand : Callable<Int> {
@Option(names = ["-d", "--directory"], description = ["The directory with the rank results"], required = true)
lateinit var directoryWithResults: String

override fun execute() {
val directory = File(directoryWithResultsOption)
@Option(names = ["-o", "--output"], description = ["The output file"])
var outputFile: String? = null

override fun call(): Int {
val directory = java.io.File(directoryWithResults)
if (!directory.isDirectory) {
println("The provided path is not a directory")
return
return 1
}
val oom = ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT).registerKotlinModule()
val results: List<SingleRankMetricsResult> =
Expand All @@ -38,16 +37,15 @@ class AggregationRankCommand(
} ?: emptyList()
if (results.isEmpty()) {
println("No classification results found")
return
return 1
}
val rankMetrics = RankMetricsCalculator.Instance
val average = rankMetrics.calculateAverages(results)
average.forEach { it.prettyPrint() }

val output = outputFileOption.value
if (output != null) {
val outputFile = File(output)
oom.writeValue(outputFile, average)
outputFile?.let {
val outputFileObj = java.io.File(it)
oom.writeValue(outputFileObj, average)
}
return 0
}
}
72 changes: 41 additions & 31 deletions cli/src/main/kotlin/edu/kit/kastel/mcse/ardoco/metrics/cli/commands/ClassificationCommand.kt
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Expand Up @@ -3,50 +3,60 @@ package edu.kit.kastel.mcse.ardoco.metrics.cli.commands
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.databind.SerializationFeature
import com.fasterxml.jackson.module.kotlin.registerKotlinModule
import edu.kit.kastel.mcse.ardoco.metrics.ClassificationMetricsCalculator
import kotlinx.cli.ArgType
import kotlinx.cli.ExperimentalCli
import kotlinx.cli.SingleNullableOption
import kotlinx.cli.Subcommand
import kotlinx.cli.default
import kotlinx.cli.required
import java.io.File
import picocli.CommandLine.Command
import picocli.CommandLine.Option
import java.util.concurrent.Callable

@OptIn(ExperimentalCli::class)
class ClassificationCommand(private val outputFileOption: SingleNullableOption<String>) : Subcommand("classification", "Calculates classification metrics") {
private val classificationFileOption by option(ArgType.String, shortName = "c", description = "The classification file", fullName = "classification").required()
private val groundTruthFileOption by option(ArgType.String, shortName = "g", description = "The ground truth file", fullName = "ground-truth").required()
private val fileHeaderOption by option(ArgType.Boolean, description = "Whether the files have a header", fullName = "header").default(false)
private val confusionMatrixSumOption by option(ArgType.Int, shortName = "s", description = "The sum of the confusion matrix", fullName = "sum").default(-1)
@Command(name = "classification", description = ["Calculates classification metrics"], mixinStandardHelpOptions = true)
class ClassificationCommand : Callable<Int> {
@Option(names = ["-c", "--classification"], description = ["The classification file"], required = true)
lateinit var classificationFile: String

override fun execute() {
println("Calculating classification metrics")
val classificationFile = File(classificationFileOption)
val groundTruthFile = File(groundTruthFileOption)
@Option(names = ["-g", "--ground-truth"], description = ["The ground truth file"], required = true)
lateinit var groundTruthFile: String

if (!classificationFile.exists() || !groundTruthFile.exists()) {
println("Classification file or ground truth file does not exist")
return
}
@Option(names = ["--header"], description = ["Whether the files have a header"])
var fileHeader: Boolean = false

val classification = classificationFile.readLines().filter { it.isNotBlank() }.drop(if (fileHeaderOption) 1 else 0).toSet()
val groundTruth = groundTruthFile.readLines().filter { it.isNotBlank() }.drop(if (fileHeaderOption) 1 else 0).toSet()
@Option(names = ["-s", "--sum"], description = ["The sum of the confusion matrix"])
var confusionMatrixSum: Int = -1

val classificationMetrics = ClassificationMetricsCalculator.Instance
@Option(names = ["-o", "--output"], description = ["The output file"])
var outputFile: String? = null

override fun call(): Int {
println("Calculating classification metrics")
val classificationFileObj = java.io.File(classificationFile)
val groundTruthFileObj = java.io.File(groundTruthFile)
if (!classificationFileObj.exists() || !groundTruthFileObj.exists()) {
println("Classification file or ground truth file does not exist")
return 1
}
val classification =
classificationFileObj
.readLines()
.filter { it.isNotBlank() }
.drop(if (fileHeader) 1 else 0)
.toSet()
val groundTruth =
groundTruthFileObj
.readLines()
.filter { it.isNotBlank() }
.drop(if (fileHeader) 1 else 0)
.toSet()
val classificationMetrics = edu.kit.kastel.mcse.ardoco.metrics.ClassificationMetricsCalculator.Instance
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Copilot AI Aug 6, 2025

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The fully qualified class name is unnecessarily verbose. Since ClassificationMetricsCalculator is already imported, you can use 'ClassificationMetricsCalculator.Instance' instead.

Suggested change
val classificationMetrics = edu.kit.kastel.mcse.ardoco.metrics.ClassificationMetricsCalculator.Instance
val classificationMetrics = ClassificationMetricsCalculator.Instance

Copilot uses AI. Check for mistakes.

val result =
classificationMetrics.calculateMetrics(
classification,
groundTruth,
if (confusionMatrixSumOption < 0) null else confusionMatrixSumOption
if (confusionMatrixSum < 0) null else confusionMatrixSum
)
result.prettyPrint()

val output = outputFileOption.value
if (output != null) {
val outputFile = File(output)
outputFile?.let {
val outputFileObj = java.io.File(it)
val oom = ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT).registerKotlinModule()
oom.writeValue(outputFile, result)
oom.writeValue(outputFileObj, result)
}
return 0
}
}
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