From 77cad4218774c31d64cdf7f8d9bd4ceaedaffa59 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 12 Jun 2024 17:24:58 +0200
Subject: [PATCH] Fix issues with paths in snapshots

---
 .../extensions/util/PathConverterRaw.java     | 44 +++++++++++++++++++
 .../com/askimed/nf/test/util/ObjectUtil.java  |  5 ++-
 .../snapshot_transformer.nf.test.snap         |  4 +-
 3 files changed, 49 insertions(+), 4 deletions(-)
 create mode 100644 src/main/java/com/askimed/nf/test/lang/extensions/util/PathConverterRaw.java

diff --git a/src/main/java/com/askimed/nf/test/lang/extensions/util/PathConverterRaw.java b/src/main/java/com/askimed/nf/test/lang/extensions/util/PathConverterRaw.java
new file mode 100644
index 00000000..84e7fbb4
--- /dev/null
+++ b/src/main/java/com/askimed/nf/test/lang/extensions/util/PathConverterRaw.java
@@ -0,0 +1,44 @@
+package com.askimed.nf.test.lang.extensions.util;
+
+import com.askimed.nf.test.lang.extensions.PathExtension;
+import groovy.json.JsonGenerator.Converter;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.security.NoSuchAlgorithmException;
+import java.util.List;
+import java.util.Vector;
+
+public class PathConverterRaw implements Converter {
+
+	@Override
+	public boolean handles(Class<?> type) {
+		return true;
+	}
+
+	@Override
+	public Object convert(Object value, String key) {
+		Path path = null;
+		if (value instanceof Path) {
+			path = (Path) value;
+			if (!path.toFile().exists()) {
+				throw new RuntimeException("Path " + path.toString() + " not found.");
+			}
+		} else if (value instanceof File) {
+			path = ((File) value).toPath();
+			if (!path.toFile().exists()) {
+				throw new RuntimeException("Path " + path.toString() + " not found.");
+			}
+		} else {
+			path = new File(value.toString()).toPath();
+
+		}
+
+		if (path.toFile().exists()) {
+			return path.toFile().getAbsolutePath();
+		}
+		return value;
+	}
+
+}
\ No newline at end of file
diff --git a/src/main/java/com/askimed/nf/test/util/ObjectUtil.java b/src/main/java/com/askimed/nf/test/util/ObjectUtil.java
index fc516f52..c64bf644 100644
--- a/src/main/java/com/askimed/nf/test/util/ObjectUtil.java
+++ b/src/main/java/com/askimed/nf/test/util/ObjectUtil.java
@@ -2,6 +2,7 @@
 
 import com.askimed.nf.test.lang.extensions.SnapshotFile;
 import com.askimed.nf.test.lang.extensions.util.PathConverter;
+import com.askimed.nf.test.lang.extensions.util.PathConverterRaw;
 import groovy.json.JsonGenerator;
 import groovy.json.JsonOutput;
 import groovy.json.JsonSlurper;
@@ -60,10 +61,10 @@ public static JsonGenerator createJsonGenerator() {
     }
 
     public static JsonGenerator createJsonGeneratorRaw() {
-        return new JsonGenerator.Options().excludeFieldsByName("mapping").build();
+        return new JsonGenerator.Options().excludeFieldsByName("mapping")
+                .addConverter(new PathConverterRaw()).build();
     }
 
-
     public static Object toMap(Object object) {
         JsonGenerator jsonGenerator = createJsonGeneratorRaw();
         String json = jsonGenerator.toJson(object);
diff --git a/test-data/snapshots/snapshot_transformer.nf.test.snap b/test-data/snapshots/snapshot_transformer.nf.test.snap
index 2eb0f3da..aec87cc7 100644
--- a/test-data/snapshots/snapshot_transformer.nf.test.snap
+++ b/test-data/snapshots/snapshot_transformer.nf.test.snap
@@ -16,7 +16,7 @@
                     8,
                     9
                 ],
-                "value": "1,36",
+                "value": "1.36",
                 "files": [
                     [
                         "ID,Name,Quantity,Price",
@@ -49,6 +49,6 @@
             "nf-test": "0.9.0-rc2",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-06-11T16:48:22.553889"
+        "timestamp": "2024-06-12T17:08:37.459381"
     }
 }
\ No newline at end of file