support stdin inputs, enable tests from gradle

Author: cwensel

README.md

@@ -55,7 +55,9 @@ To see the full results:
 
 ```shell
 ./gradlew installDist
-./build/install/subpop/bin/subpop --input src/test/resources/data/mushrooms.csv --min-ratio .4 --class-value EDIBLE
+./build/install/subpop/bin/subpop --input src/test/resources/data/mushrooms.csv --input-header --min-ratio .4 --class-value EDIBLE
+# or
+cat src/test/resources/data/mushrooms.csv | ./build/install/subpop/bin/subpop --input-header --min-ratio .4 --class-value EDIBLE 
 ```
 
 ## CLI Options

build.gradle.kts

@@ -11,7 +11,7 @@ import java.util.*
 
 plugins {
     id("com.github.johnrengelman.shadow") version "8.1.1"
-    id("io.micronaut.application") version "4.4.2"
+    id("io.micronaut.application") version "4.4.3"
 }
 
 val versionProperties = Properties().apply {
@@ -34,13 +34,13 @@ repositories {
 
 dependencies {
     annotationProcessor("info.picocli:picocli-codegen:4.7.6")
-    annotationProcessor("io.micronaut.serde:micronaut-serde-processor:2.11.0")
+    annotationProcessor("io.micronaut.serde:micronaut-serde-processor:2.11.1")
 
     implementation("org.jetbrains:annotations:24.1.0")
     implementation("info.picocli:picocli:4.7.6")
     implementation("com.opencsv:opencsv:5.9")
     implementation("io.micronaut.picocli:micronaut-picocli:5.5.0")
-    implementation("io.micronaut.serde:micronaut-serde-jackson:2.11.0")
+    implementation("io.micronaut.serde:micronaut-serde-jackson:2.11.1")
     implementation("com.google.guava:guava:33.2.1-jre")
     implementation("org.barfuin.texttree:text-tree:2.1.2")
 
@@ -59,7 +59,8 @@ java {
 }
 
 tasks.withType<Test> {
-    maxHeapSize = "2g" // Set the desired maximum heap size
+    useJUnitPlatform()
+    maxHeapSize = "5g" // Set the desired maximum heap size
 }
 
 tasks.named<ProcessResources>("processResources") {
@@ -70,6 +71,7 @@ tasks.named<ProcessResources>("processResources") {
 }
 
 micronaut {
+    version.set("4.6.0")
     testRuntime("junit5")
     processing {
         incremental(true)

settings.gradle.kts

@@ -9,6 +9,7 @@
 plugins {
     // Apply the foojay-resolver plugin to allow automatic download of JDKs
     id("org.gradle.toolchains.foojay-resolver-convention") version "0.4.0"
+    id("io.micronaut.platform.catalog") version "4.4.3"
 }
 
 rootProject.name = "subpop"

src/main/java/io/clusterless/subpop/Main.java

@@ -17,14 +17,16 @@
 import io.clusterless.subpop.options.OutputOptions;
 import io.clusterless.subpop.util.Verbosity;
 import io.clusterless.subpop.util.VersionProvider;
-import io.micronaut.configuration.picocli.PicocliRunner;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import picocli.CommandLine;
 import picocli.CommandLine.Command;
 
 import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.util.Arrays;
 import java.util.List;
+import java.util.concurrent.Callable;
 
 @Command(
         name = "subpop",
@@ -33,7 +35,7 @@
         versionProvider = VersionProvider.class,
         sortOptions = false
 )
-public class Main implements Runnable {
+public class Main implements Callable<Integer> {
     private static final Logger LOG = LoggerFactory.getLogger(Main.class);
 
     @CommandLine.Mixin
@@ -57,10 +59,50 @@ public class Main implements Runnable {
     protected Float supportRatio = null;
 
     public static void main(String[] args) throws Exception {
-        PicocliRunner.run(Main.class, args);
+        Main main = new Main();
+
+        CommandLine commandLine = new CommandLine(main);
+
+        try {
+            commandLine.parseArgs(args);
+        } catch (CommandLine.MissingParameterException | CommandLine.UnmatchedArgumentException e) {
+            System.err.println(e.getMessage());
+            commandLine.usage(System.out);
+            System.exit(-1);
+        }
+
+        if (commandLine.isUsageHelpRequested()) {
+            commandLine.usage(System.out);
+            return;
+        } else if (commandLine.isVersionHelpRequested()) {
+            commandLine.printVersionHelp(System.out);
+            return;
+        }
+
+        int exitCode = 0;
+
+        try {
+            exitCode = commandLine.execute(args);
+        } catch (Exception e) {
+            System.err.println(e.getMessage());
+
+            if (main.verbosity.isVerbose()) {
+                e.printStackTrace(System.err);
+            }
+
+            System.exit(-1); // get exit code from exception
+        }
+
+        System.exit(exitCode);
     }
 
-    public void run() {
+    @Override
+    public Integer call() throws Exception {
+        if (inputOptions.inputs().isEmpty() && hasStdIn() == 0) {
+            LOG.info("no input data");
+            throw new IllegalArgumentException("no input data");
+        }
+
         ItemStoreReader itemStoreReader = ItemStoreReader.builder()
                 .withSeparator(inputOptions.delimiter())
                 .withHasHeader(inputOptions.hasHeader())
@@ -75,10 +117,17 @@ public void run() {
                 .build();
 
         try {
-            ItemStore itemStore = itemStoreReader.read(inputOptions.inputs());
+            ItemStore itemStore;
+            if (inputOptions.inputs().isEmpty()) {
+                LOG.info("reading from stdin");
+                itemStore = itemStoreReader.read(System.in);
+            } else {
+                LOG.info("reading from files: {}", inputOptions.inputs());
+                itemStore = itemStoreReader.read(inputOptions.inputs());
+            }
 
-            if(!itemStore.containsAllClasses(classValue)) {
-                throw new IllegalArgumentException("class value not found");
+            if (!itemStore.containsAllClasses(classValue)) {
+                throw new IllegalArgumentException("class value not found: {}" + Arrays.toString(classValue));
             }
 
             CPTree cpTree = new CPTree(itemStore);
@@ -92,5 +141,15 @@ public void run() {
         } catch (CsvValidationException | IOException e) {
             throw new RuntimeException(e);
         }
+
+        return 0;
+    }
+
+    private static int hasStdIn() {
+        try {
+            return System.in.available();
+        } catch (IOException e) {
+            throw new UncheckedIOException(e.getMessage(), e);
+        }
     }
 }

src/test/java/io/clusterless/subpop/MainTest.java

@@ -16,8 +16,6 @@
 
 import java.io.*;
 
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
 public class MainTest {
 
     @Test
@@ -29,11 +27,13 @@ public void testWithCommandLineOption() throws Exception {
             String[] args = new String[]{
                     "--input", "src/test/resources/data/mushrooms.csv",
                     "--input-header",
+                    "--output-header",
                     "--class-col", "0",
                     "--class-value", "EDIBLE",
-                    "--min-ratio", ".4",
+                    "--min-ratio", ".4"
             };
-            PicocliRunner.run(Main.class, ctx, args);
+
+            PicocliRunner.call(Main.class, ctx, args);
 
             ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
             LineNumberReader lnr = new LineNumberReader(new InputStreamReader(bais));