Repair and prepare for further improvements.

Change visibility of two methods we need in some other projects.
Also set validation of documents to false because it is still very buggy.

Author: AndreG-P

src/main/java/com/formulasearchengine/mathmlquerygenerator/BasicXQueryGenerator.java

@@ -35,6 +35,9 @@ public static BasicXQueryGenerator getDefaultGenerator() {
                 .addFooter("}\n</result>");
     }
 
+    public BasicXQueryGenerator() {
+    }
+
     @Override
     public String generateQuery(Document document) {
         if (document == null) {

src/main/java/com/formulasearchengine/mathmlquerygenerator/XQueryGenerator.java

@@ -90,7 +90,7 @@ protected String getDefaultString() {
     }
 
 
-    Node getMainElement() {
+    public Node getMainElement() {
         return mainElement;
     }
 

src/main/java/com/formulasearchengine/mathmltools/mml/elements/MathDoc.java

@@ -11,12 +11,14 @@
 import com.formulasearchengine.mathmltools.xmlhelper.PartialLocalEntityResolver;
 import com.formulasearchengine.mathmltools.xmlhelper.XMLHelper;
 import com.formulasearchengine.mathmltools.xmlhelper.XmlDocumentReader;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.Source;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.stream.StreamSource;
 import javax.xml.validation.SchemaFactory;
+
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -35,9 +37,11 @@
 import org.xmlunit.validation.Validator;
 
 public class MathDoc {
-    private static final Logger log = LogManager.getLogger("Math");
-    private static final String DOCTYPE = "<!DOCTYPE math PUBLIC \"-//W3C//DTD MATHML 3.0 Transitional//EN\" \n"
-            + "     \"http://www.w3.org/Math/DTD/mathml3/mathml3.dtd\">\n";
+    private static final Logger log = LogManager.getLogger(MathDoc.class.getName());
+    private static final String DOCTYPE =
+            "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n"
+                    + "<!DOCTYPE math PUBLIC \"-//W3C//DTD MATHML 3.0 Transitional//EN\" \n"
+                    + "     \"http://www.w3.org/Math/DTD/mathml3/mathml3.dtd\">\n";
     private static final String MATHML3_XSD = "https://www.w3.org/Math/XMLSchema/mathml3/mathml3.xsd";
     private static final String APPLICATION_X_TEX = "application/x-tex";
     private static Validator v;
@@ -58,13 +62,15 @@ public MathDoc(String inputXMLString) throws ParserConfigurationException, SAXEx
         try {
             buildDom(inputXMLString, documentBuilder);
         } catch (Exception e) {
-            log.warn("Error parsing input \n{}\n. Adding MathML3 Document headers.", inputXMLString);
+            log.warn("Exception during parsing process. Adding MathML3 Document headers and try again.");
             inputXMLString = tryFixHeader(inputXMLString);
             try {
                 buildDom(inputXMLString, documentBuilder);
             } catch (SAXException | IOException e1) {
-                // Throw the exception caused by the original input, not by the corrected input.
-                throw e;
+                log.error(
+                        "Try to fix header but it didn't help. Still invalid document"
+                                + System.lineSeparator()
+                                + inputXMLString, e1);
             }
         }
     }

src/main/java/com/formulasearchengine/mathmltools/xmlhelper/XmlDocumentReader.java

@@ -1,17 +1,5 @@
 package com.formulasearchengine.mathmltools.xmlhelper;
 
-import static org.xmlunit.util.Convert.toInputSource;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Source;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.w3c.dom.Document;
@@ -21,6 +9,18 @@
 import org.xmlunit.builder.Input;
 import org.xmlunit.util.Convert;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Source;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import static org.xmlunit.util.Convert.toInputSource;
+
 /**
  * Helper class to format XML files to Document and Node types
  */
@@ -41,15 +41,13 @@ private XmlDocumentReader() {
 
     public static Document getDocumentFromXML(Path xmlF) {
         final Source source = Input.fromFile(xmlF.toAbsolutePath().toString()).build();
-        final InputSource is = toInputSource(source);
+        String orig = null;
         try {
-            return getDocument(is); //getDocument(is);
-        } catch (ParserConfigurationException | IOException | SAXException e) {
-            LOG.warn("Cannot parse XML file with grammar: " + xmlF.toString(), e);
+            orig = new String(Files.readAllBytes(xmlF));
+        } catch (IOException ioe) {
+            LOG.fatal("Cannot read xml file " + xmlF.toString());
         }
-        return oldgetDocumentFromXML(xmlF);
-
-
+        return getDocumentFromSource(source, orig);
     }
 
     private static Document getDocument(InputSource inputStream) throws ParserConfigurationException, IOException, SAXException {
@@ -97,18 +95,22 @@ public static Document oldgetDocumentFromXML(Path xmlF) {
 
     public static Document getDocumentFromXMLString(String xml) {
         Source source = Input.fromString(xml).build();
+        return getDocumentFromSource(source, xml);
+    }
+
+    private static Document getDocumentFromSource(Source source, String orig) {
         final InputSource is = toInputSource(source);
         try {
             return getDocument(is);
         } catch (ParserConfigurationException | IOException | SAXException e) {
-            e.printStackTrace();
+            LOG.warn("Cannot parse document directly '{}'.", e.getMessage());
         }
         try {
             return parse(source);
         } catch (ParserConfigurationException | IOException | SAXException e) {
-            e.printStackTrace();
+            LOG.warn("Cannot parse on second attempt '{}'.", e.getMessage());
         }
-        return oldgetDocumentFromXMLString(xml);
+        return oldgetDocumentFromXMLString(orig);
     }
 
     private static Document parse(Source s) throws ParserConfigurationException, IOException, SAXException {
@@ -131,7 +133,7 @@ public static DocumentBuilder getDocumentBuilder() throws ParserConfigurationExc
 
     private static DocumentBuilderFactory getDocumentBuilderFactory() throws ParserConfigurationException {
         DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-        dbf.setValidating(true);
+        dbf.setValidating(false);
         dbf.setFeature("http://xml.org/sax/features/validation", true);
         dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
         dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);