rework the schema forward migration

for run documents, there is a lot more variation in how the schema is declared, so we have to do a more generous replacement

Author: jeanetteclark

src/main/java/edu/ucsb/nceas/mdqengine/serialize/XmlMarshaller.java

@@ -2,20 +2,25 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringEscapeUtils;
+import org.w3c.dom.Document;
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import javax.xml.XMLConstants;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
 import javax.xml.bind.Unmarshaller;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.stream.StreamSource;
 import javax.xml.validation.Schema;
 import javax.xml.validation.SchemaFactory;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.util.Map;
 
@@ -133,4 +138,22 @@ public static String normalizeNamespace(String xml) {
 		return result;
 	}
 
+	/**
+	 * Extracts the root namespace URI from an XML string.
+	 * 
+	 * @param xml the XML string from which the root namespace will be extracted
+	 * @return the root namespace URI of the XML document
+	 * @throws ParserConfigurationException
+	 * @throws SAXException
+	 * @throws IOException
+	 */
+	public static String getRootNamespace(String xml) throws ParserConfigurationException, SAXException, IOException {
+		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+		dbf.setNamespaceAware(true);
+		DocumentBuilder db = dbf.newDocumentBuilder();
+		Document doc = db.parse(new InputSource(new StringReader(xml)));
+
+		return doc.getDocumentElement().getNamespaceURI();
+	}
+
 }

src/main/java/edu/ucsb/nceas/mdqengine/store/DatabaseStore.java

@@ -32,6 +32,8 @@
 import java.time.Instant;
 import java.util.*;
 import java.util.Date;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Persistent storage for quality runs.
@@ -184,9 +186,15 @@ public Run getRun(String metadataId, String suiteId) throws MetadigStoreExceptio
                     // Convert the returned run xml document to a 'run' object.
 
                     // first migrate the schema forward
-
-                    resultStr = resultStr.replace("https://nceas.ucsb.edu/mdqe/v1", "https://nceas.ucsb.edu/mdqe/v1.2");
-                    resultStr = resultStr.replace("https://nceas.ucsb.edu/mdqe/v1.1","https://nceas.ucsb.edu/mdqe/v1.2");
+                    String ns = XmlMarshaller.getRootNamespace(resultStr);
+
+                    if ("https://nceas.ucsb.edu/mdqe/v1".equals(ns) || "https://nceas.ucsb.edu/mdqe/v1.1".equals(ns)) {
+                        // Replace known older namespaces with v1.2
+                        resultStr = resultStr.replace("https://nceas.ucsb.edu/mdqe/v1",
+                                "https://nceas.ucsb.edu/mdqe/v1.2");
+                        resultStr = resultStr.replace("https://nceas.ucsb.edu/mdqe/v1.1",
+                                "https://nceas.ucsb.edu/mdqe/v1.2");
+                    }
 
                     InputStream is = new ByteArrayInputStream(resultStr.getBytes());
                     run = TypeMarshaller.unmarshalTypeFromStream(Run.class, is);