Fix sax content handler to handle all the things.

src/main/kotlin/xml/SAXContentHandler.kt

@@ -20,6 +20,7 @@ package org.memobase.xml
 
 import ch.memobase.reporting.Report
 import ch.memobase.reporting.ReportStatus
+import com.beust.klaxon.JsonArray
 import com.beust.klaxon.JsonObject
 import java.io.StringWriter
 import org.apache.logging.log4j.LogManager
@@ -158,15 +159,25 @@ class SAXContentHandler(
 
         when {
             currentElementTag == localName -> {
+                // extract the identifier value based on the given field name from configuration.
+                // this is used for the message key
                 if (currentElementTag == identifierFieldName) {
                     identifier = currentElementContent
                 }
                 if (innerElements.isEmpty()) {
                     if (currentElementContent.isNotEmpty()) {
-                        jsonResult[currentElementTag] = currentElementContent
+                        when (val item = jsonResult[currentElementTag]){
+                            null -> jsonResult[currentElementTag] = currentElementContent
+                            is JsonArray<*> -> item + currentElementContent
+                            else -> jsonResult[currentElementTag] = JsonArray(item, currentElementContent)
+                        }
                     }
                 } else {
-                    jsonResult[currentElementTag] = innerElements.toMap()
+                    when (val item = jsonResult[currentElementTag]) {
+                        null -> jsonResult[currentElementTag] = innerElements.toMap()
+                        is JsonArray<*> -> item + innerElements.toMap()
+                        else -> jsonResult[currentElementTag] = JsonArray(item, innerElements.toMap())
+                    }
                     innerElements.clear()
                 }
                 currentElementTag = ""

src/test/kotlin/LocalTestRun.kt

+/*
+ * XML Data Transform
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+package org.memobase.test
+
+import ch.memobase.settings.HeaderMetadata
+import com.beust.klaxon.Klaxon
+import java.io.File
+import java.io.FileOutputStream
+import org.junit.jupiter.api.Disabled
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.TestInstance
+import org.memobase.models.Message
+import org.memobase.xml.XMLTransformer
+
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@Disabled
+class LocalTestRun {
+
+    private val headerMetadata = HeaderMetadata(
+        "snp-001",
+        "1",
+        "snp",
+        false,
+        "record",
+        "identifierMain",
+        0, 0, 0, 0
+    )
+
+    @Test
+    @Disabled
+    fun `test local folder`() {
+        val folder = "/home/jonas/memobase/data/snp-001"
+        val inputFolder = "/home/jonas/memobase/data/test/step-1"
+        val outputFolder = "/home/jonas/memobase/data/test/step-2"
+        val transformFile = "/config/transform.xslt"
+        val xslt = File(folder + transformFile).readBytes()
+        val transformer = XMLTransformer()
+        File(inputFolder)
+            .walk(FileWalkDirection.TOP_DOWN)
+            .maxDepth(1)
+            .filter { it.isFile }
+            .map { Pair(it.name, it) }
+            .map {
+                Pair(it.first, Message.fromJson(it.second.readText())[0])
+            }
+            .map {
+                transformer.applyXSLT(
+                    it.first,
+                    headerMetadata,
+                    File(it.second.path).inputStream(),
+                    xslt
+                )
+            }
+            .forEach { result ->
+                FileOutputStream(File(outputFolder + "/" + result.second.identifier)).use {
+                    it.bufferedWriter().use { writer ->
+                        writer.write(result.second.output.toString())
+                    }
+                }
+            }
+    }
+}