From 41683daee5812536090eb0911f00ec52037540b4 Mon Sep 17 00:00:00 2001
From: Michael Innerberger <innerbergerm@hhmi.org>
Date: Wed, 21 Jun 2023 08:34:53 -0400
Subject: [PATCH] Add help command

This is mainly created for testing the conda installation
---
 install                          |  2 ++
 src/main/java/cmd/PrintHelp.java | 48 ++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 src/main/java/cmd/PrintHelp.java

diff --git a/install b/install
index 404a326..81d91a0 100755
--- a/install
+++ b/install
@@ -63,6 +63,7 @@ install_command st-add-annotations "cmd.AddAnnotations"
 install_command st-align-pairs "cmd.PairwiseSectionAligner"
 install_command st-align-pairs-view "cmd.ViewPairwiseAlignment"
 install_command st-align-global "cmd.GlobalOpt"
+install_command st-help "cmd.PrintHelp"
 
 if [ $(pwd) == "$INSTALL_DIR" ]; then
     echo "Installation directory equals current directory, we are done."
@@ -79,6 +80,7 @@ else
     mv st-align-pairs $INSTALL_DIR/
     mv st-align-pairs-view $INSTALL_DIR/
     mv st-align-global $INSTALL_DIR/
+    mv st-help $INSTALL_DIR/
 fi
 
 rm cp.txt
diff --git a/src/main/java/cmd/PrintHelp.java b/src/main/java/cmd/PrintHelp.java
new file mode 100644
index 0000000..ecabff1
--- /dev/null
+++ b/src/main/java/cmd/PrintHelp.java
@@ -0,0 +1,48 @@
+package cmd;
+
+import picocli.CommandLine;
+import picocli.CommandLine.Option;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.concurrent.Callable;
+
+public class PrintHelp implements Callable<Void> {
+
+	@Option(names = {"-v", "--version"}, required = false, description = "print version information")
+	private boolean version = false;
+
+	@Override
+	public Void call() throws Exception {
+
+		if (version) {
+			System.out.println("Spatial Transcriptomics as IMages project -- v0.2.0");
+			return null;
+		}
+
+		final Map<String, Callable<Void>> commands = new HashMap<>();
+		commands.put("st-explorer", new View());
+		commands.put("st-render", new RenderImage());
+		commands.put("st-bdv-view", new DisplayStackedSlides());
+		commands.put("st-resave", new Resave());
+		commands.put("st-add-slice", new AddDataset());
+		commands.put("st-normalize", new Normalize());
+		commands.put("st-add-annotations", new AddAnnotations());
+		commands.put("st-align-pairs", new PairwiseSectionAligner());
+		commands.put("st-align-pairs-view", new ViewPairwiseAlignment());
+		commands.put("st-align-global", new GlobalOpt());
+
+		for (final Entry<String, Callable<Void>> command : commands.entrySet()) {
+			System.out.println();
+			System.out.println("Usage for " + command.getKey() + ":");
+			CommandLine.usage(command.getValue(), System.out);
+		}
+
+		return null;
+	}
+
+	public static void main(final String[] args) {
+		CommandLine.call(new PrintHelp(), args);
+	}
+}