Test fix

samtools · Aug 1, 2023 · 500cffd · 500cffd
1 parent 662c827
commit 500cffd
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/src/main/java/htsjdk/beta/io/bundle/BundleJSON.java b/src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
@@ -108,19 +108,19 @@ public static <T extends IOPath> Bundle toBundle(
             }
 
             // validate the schema name
-            final String schemaName = jsonDocument.optString(JSON_PROPERTY_SCHEMA_NAME, null);
+            final String schemaName = getRequiredPropertyAsString(jsonDocument, JSON_PROPERTY_SCHEMA_NAME);
             if (!schemaName.equals(JSON_SCHEMA_NAME)) {
                 throw new IllegalArgumentException(
                         String.format("Expected bundle schema name %s but found %s", JSON_SCHEMA_NAME, schemaName));
             }
 
             // validate the schema version
-            final String schemaVersion = jsonDocument.optString(JSON_PROPERTY_SCHEMA_VERSION, null);
+            final String schemaVersion = getRequiredPropertyAsString(jsonDocument, JSON_PROPERTY_SCHEMA_VERSION);
             if (!schemaVersion.equals(JSON_SCHEMA_VERSION)) {
                 throw new IllegalArgumentException(String.format("Expected bundle schema version %s but found %s",
                         JSON_SCHEMA_VERSION, schemaVersion));
             }
-            primaryContentType = jsonDocument.optString(JSON_PROPERTY_PRIMARY, null);
+            primaryContentType = getRequiredPropertyAsString(jsonDocument, JSON_PROPERTY_PRIMARY);
 
             jsonDocument.keySet().forEach((String contentType) -> {
                 if (! (jsonDocument.get(contentType) instanceof JSONObject jsonDoc)) {
@@ -130,7 +130,7 @@ public static <T extends IOPath> Bundle toBundle(
                 if (!TOP_LEVEL_PROPERTIES.contains(contentType)) {
                     final String format = jsonDoc.optString(JSON_PROPERTY_FORMAT, null);
                     final IOPathResource ioPathResource = new IOPathResource(
-                            ioPathConstructor.apply(jsonDoc.optString(JSON_PROPERTY_PATH, null)),
+                            ioPathConstructor.apply(getRequiredPropertyAsString(jsonDoc, JSON_PROPERTY_PATH)),
                             contentType,
                             format == null ?
                                     null :
@@ -147,4 +147,16 @@ public static <T extends IOPath> Bundle toBundle(
 
         return new Bundle(primaryContentType, resources);
     }
+
+    private static String getRequiredPropertyAsString(JSONObject jsonDocument, String propertyName) {
+        final String propertyValue = jsonDocument.optString(propertyName, null);
+        if (propertyValue == null) {
+            throw new IllegalArgumentException(
+                    String.format("JSON bundle is missing the required property %s (%s)",
+                            propertyName,
+                            jsonDocument));
+        }
+
+        return propertyValue;
+    }
 }
diff --git a/src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java b/src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java
@@ -3,6 +3,7 @@
 import htsjdk.HtsjdkTest;
 import htsjdk.io.HtsPath;
 import htsjdk.io.IOPath;
+import org.json.JSONObject;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -157,7 +158,7 @@ public Object[][] getRoundTripJSON() {
     public void testRoundTripJSON(final String jsonString, final String primaryKey, final List<BundleResource> resources) {
         final Bundle bundleFromResources = new Bundle(primaryKey, resources);
         final String actualJSONString = BundleJSON.toJSON(bundleFromResources);
-        Assert.assertEquals(actualJSONString, jsonString);
+        Assert.assertEquals(actualJSONString, new JSONObject(jsonString).toString(1));
 
         // now recreate the bundle from JSON
         final Bundle bundleFromJSON = BundleJSON.toBundle(jsonString);
@@ -227,7 +228,7 @@ public Object[][] getInvalidBundleJSON() {
                 // syntax error (missing quote in before schemaName
                 { "{\"schemaVersion\":\"0.1.0\",schemaName\":\"htsbundle\",\"ALIGNED_READS\":{\"path\":\"myreads" +
                         ".bam\",\"format\":\"BAM\"},\"primary\":\"ALIGNED_READS\"}",
-                        "Invalid JSON near position: 25" },
+                        "Expected a ':' after a key at 36" },
                 // no enclosing {} -> UnsupportedOperationException (no text message)
                 {"\"schemaName\":\"htsbundle\", \"schemaVersion\":\"0.1.0\"",
                         "", },