Extend list command by additional output formats (#105)

* Add option to list all available tags * Add json output format to list command * Add basic documentation for `list` command
askimed · Aug 30, 2023 · 1f97f4c · 1f97f4c
1 parent 1f30f70
commit 1f97f4c
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diff --git a/docs/docs/cli/list.md b/docs/docs/cli/list.md
@@ -10,6 +10,18 @@ nf-test list [<NEXTFLOW_FILES>|<SCRIPT_FOLDERS>]
 
 ### Optional Arguments
 
+#### `--tags`
+Print a list of all used tags.
+
+#### `--format json`
+Print the list of tests or tags as json object.
+
+#### `--format raw`
+Print the list of tests or tags as simple list without formatting.
+
+#### `--silent`
+Hide program version and header infos.
+
 #### `--debug`
 Show debugging infos.
 
@@ -28,3 +40,36 @@ Show debugging infos.
 
     nf-test list tests/modules tests/modules/bwa_index.nf.test
     ```
+
+* List of all testcases as json:
+
+```
+nf-test list --format json --silent
+["/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@69b98c67","/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@fdb6c1cc","/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@d1c219eb","/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@3c54e3cb",...]
+```
+
+* List of all testcases as unformatted ist:
+
+```
+nf-test list --format raw --silent
+/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@69b98c67
+/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@fdb6c1cc
+/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@d1c219eb
+/Users/lukfor/Development/git/nf-gwas/tests/main.nf.test@3c54e3cb
+...
+```
+
+* List of all tags as json:
+
+```
+nf-test list --tags --format json --silent
+["fastqc","snakemake"]
+```
+
+* List of all tags as unformatted list:
+
+```
+nf-test list --tags --format raw --silent
+fastqc
+snakemake
+```
diff --git a/src/main/java/com/askimed/nf/test/App.java b/src/main/java/com/askimed/nf/test/App.java
@@ -22,8 +22,6 @@ public class App {
 
 	public int run(String[] args) {
 
-		printHeader();
-
 		CommandLine commandLine = new CommandLine(new App());
 		commandLine.addSubcommand("clean", new CleanCommand());
 		commandLine.addSubcommand("init", new InitCommand());
@@ -38,16 +36,6 @@ public int run(String[] args) {
 
 	}
 
-	private void printHeader() {
-
-		System.out.println();
-		System.out.println(Emoji.ROCKET + AnsiText.bold(" " + App.NAME + " " + App.VERSION));
-		System.out.println("https://code.askimed.com/nf-test");
-		System.out.println("(c) 2021 - 2023 Lukas Forer and Sebastian Schoenherr");
-		System.out.println();
-
-	}
-
 	public static void main(String[] args) throws Exception {
 
 		App app = new App();

diff --git a/src/main/java/com/askimed/nf/test/commands/AbstractCommand.java b/src/main/java/com/askimed/nf/test/commands/AbstractCommand.java
@@ -0,0 +1,40 @@
+package com.askimed.nf.test.commands;
+
+import java.util.concurrent.Callable;
+
+import com.askimed.nf.test.App;
+import com.askimed.nf.test.util.AnsiText;
+import com.askimed.nf.test.util.Emoji;
+
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Help.Visibility;
+
+public abstract class AbstractCommand implements Callable<Integer> {
+
+	@Option(names = {
+			"--silent" }, description = "Hide header and program version", required = false, showDefaultValue = Visibility.ALWAYS)
+	private boolean silent = false;
+
+	@Override
+	public Integer call() throws Exception {
+
+		if (!silent) {
+			printHeader();
+		}
+
+		return execute();
+	}
+
+	public abstract Integer execute() throws Exception;
+
+	private void printHeader() {
+
+		System.out.println();
+		System.out.println(Emoji.ROCKET + AnsiText.bold(" " + App.NAME + " " + App.VERSION));
+		System.out.println("https://code.askimed.com/nf-test");
+		System.out.println("(c) 2021 - 2023 Lukas Forer and Sebastian Schoenherr");
+		System.out.println();
+
+	}
+
+}
diff --git a/src/main/java/com/askimed/nf/test/commands/CleanCommand.java b/src/main/java/com/askimed/nf/test/commands/CleanCommand.java
@@ -1,7 +1,6 @@
 package com.askimed.nf.test.commands;
 
 import java.io.File;
-import java.util.concurrent.Callable;
 
 import com.askimed.nf.test.config.Config;
 import com.askimed.nf.test.util.AnsiColors;
@@ -10,12 +9,12 @@
 import picocli.CommandLine.Command;
 
 @Command(name = "clean")
-public class CleanCommand implements Callable<Integer> {
+public class CleanCommand extends AbstractCommand {
 
 	public static String NF_DIRECTORY = ".nf-test";
 
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
 
 		File workDir = new File(NF_DIRECTORY);
 

diff --git a/src/main/java/com/askimed/nf/test/commands/InitCommand.java b/src/main/java/com/askimed/nf/test/commands/InitCommand.java
@@ -1,7 +1,6 @@
 package com.askimed.nf.test.commands;
 
 import java.io.File;
-import java.util.concurrent.Callable;
 
 import com.askimed.nf.test.App;
 import com.askimed.nf.test.commands.init.InitTemplates;
@@ -11,10 +10,10 @@
 import picocli.CommandLine.Command;
 
 @Command(name = "init")
-public class InitCommand implements Callable<Integer> {
+public class InitCommand extends AbstractCommand {
 
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
 
 		try {
 

diff --git a/src/main/java/com/askimed/nf/test/commands/ListTestsCommand.java b/src/main/java/com/askimed/nf/test/commands/ListTestsCommand.java
@@ -3,19 +3,19 @@
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.concurrent.Callable;
 
 import com.askimed.nf.test.config.Config;
 import com.askimed.nf.test.core.TestExecutionEngine;
 import com.askimed.nf.test.util.AnsiColors;
+import com.askimed.nf.test.util.OutputFormat;
 
 import picocli.CommandLine.Command;
+import picocli.CommandLine.Help.Visibility;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
-import picocli.CommandLine.Help.Visibility;
 
 @Command(name = "list")
-public class ListTestsCommand implements Callable<Integer> {
+public class ListTestsCommand extends AbstractCommand {
 
 	@Parameters(description = "list all tests")
 	private List<File> testPaths = new ArrayList<File>();
@@ -24,8 +24,16 @@ public class ListTestsCommand implements Callable<Integer> {
 			"--debug" }, description = "Show debugging infos", required = false, showDefaultValue = Visibility.ALWAYS)
 	private boolean debug = false;
 
+	@Option(names = {
+			"--tags" }, description = "Show all available tags", required = false, showDefaultValue = Visibility.ALWAYS)
+	private boolean tags = false;
+
+	@Option(names = {
+			"--format" }, description = "Output format", required = false, showDefaultValue = Visibility.ALWAYS)
+	private OutputFormat format = OutputFormat.PRETTY;
+
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
 
 		try {
 
@@ -65,7 +73,11 @@ public Integer call() throws Exception {
 
 			TestExecutionEngine engine = new TestExecutionEngine();
 			engine.setScripts(scripts);
-			return engine.listTests();
+			if (tags) {
+				return engine.listTags(format);
+			} else {
+				return engine.listTests(format);
+			}
 
 		} catch (Throwable e) {
 

diff --git a/src/main/java/com/askimed/nf/test/commands/RunTestsCommand.java b/src/main/java/com/askimed/nf/test/commands/RunTestsCommand.java
@@ -8,7 +8,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
-import java.util.concurrent.Callable;
 import java.util.function.Consumer;
 
 import com.askimed.nf.test.config.Config;
@@ -28,7 +27,7 @@
 import picocli.CommandLine.Parameters;
 
 @Command(name = "test")
-public class RunTestsCommand implements Callable<Integer> {
+public class RunTestsCommand extends AbstractCommand {
 
 	@Parameters(description = "test files")
 	private List<File> testPaths = new ArrayList<File>();
@@ -69,7 +68,8 @@ public class RunTestsCommand implements Callable<Integer> {
 	private List<String> tags = new Vector<String>();
 
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
+
 		List<File> scripts = new ArrayList<File>();
 		PluginManager manager = new PluginManager(false);
 

diff --git a/src/main/java/com/askimed/nf/test/commands/UpdatePluginsCommand.java b/src/main/java/com/askimed/nf/test/commands/UpdatePluginsCommand.java
@@ -1,7 +1,6 @@
 package com.askimed.nf.test.commands;
 
 import java.io.File;
-import java.util.concurrent.Callable;
 
 import com.askimed.nf.test.config.Config;
 import com.askimed.nf.test.plugins.PluginManager;
@@ -10,10 +9,10 @@
 import picocli.CommandLine.Command;
 
 @Command(name = "update-plugins")
-public class UpdatePluginsCommand implements Callable<Integer> {
+public class UpdatePluginsCommand extends AbstractCommand {
 
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
 
 		File configFile = new File(Config.FILENAME);
 

diff --git a/src/main/java/com/askimed/nf/test/commands/VersionCommand.java b/src/main/java/com/askimed/nf/test/commands/VersionCommand.java
@@ -1,17 +1,15 @@
 package com.askimed.nf.test.commands;
 
-import java.util.concurrent.Callable;
-
 import com.askimed.nf.test.nextflow.NextflowCommand;
 import com.askimed.nf.test.util.AnsiColors;
 
 import picocli.CommandLine.Command;
 
 @Command(name = "version")
-public class VersionCommand implements Callable<Integer> {
+public class VersionCommand extends AbstractCommand {
 
 	@Override
-	public Integer call() throws Exception {
+	public Integer execute() throws Exception {
 
 		try {