Ensure consistent XML parser config

src/org/labkey/targetedms/datasource/PsiInstruments.java

@@ -21,6 +21,7 @@
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.resource.FileResource;
 import org.labkey.api.util.Path;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.targetedms.TargetedMSModule;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -29,7 +30,6 @@
 import org.xml.sax.SAXException;
 
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.File;
 import java.io.IOException;
@@ -75,12 +75,11 @@ public static List<PsiInstrument> getInstruments()
             LOG.error("File not found: psi-ms-PARSED.xml.");
             return Collections.emptyList();
         }
-        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
         DocumentBuilder db;
         Document document;
         try
         {
-            db = dbf.newDocumentBuilder();
+            db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
             document = db.parse(file);
         }
         catch (ParserConfigurationException | SAXException | IOException e)

src/org/labkey/targetedms/parser/SkylineDocumentParser.java

@@ -35,6 +35,7 @@
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.Tuple3;
 import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.targetedms.IrtPeptide;
 import org.labkey.targetedms.SkylineDocImporter.IProgressStatus;
 import org.labkey.targetedms.chromlib.ConnectionSource;
@@ -230,8 +231,7 @@ public SkylineDocumentParser(File file, Logger log, Container container, IProgre
         _progressStatus = progressStatus;
         _container = container;
         _inputStream = new ProgressInputStream(new FileInputStream(_file));
-        XMLInputFactory inputFactory = XMLInputFactory.newInstance();
-        _reader = inputFactory.createXMLStreamReader(_inputStream);
+        _reader = XmlBeansUtil.XML_INPUT_FACTORY.createXMLStreamReader(_inputStream);
         _log = log;
         readDocumentVersion(_reader);
     }

src/org/labkey/targetedms/parser/SpectrumFilter.java

@@ -18,10 +18,10 @@
 import com.google.protobuf.InvalidProtocolBufferException;
 import org.junit.Assert;
 import org.junit.Test;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass;
 import org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.FilterOperation;
 
-import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 import java.io.StringReader;
@@ -260,7 +260,7 @@ public void testParse() throws Exception
                     "        </spectrum_filter>",
                     "        <bibliospec_spectrum_info count_measured=\"1\" />",
                     "      </precursor>");
-            XMLStreamReader reader = XMLInputFactory.newInstance().createXMLStreamReader(new StringReader(xml));
+            XMLStreamReader reader = XmlBeansUtil.XML_INPUT_FACTORY.createXMLStreamReader(new StringReader(xml));
             int bibliospecSpectrumInfoCount = 0;
             List<FilterClause> clauses = new ArrayList<>();
             while (reader.hasNext())

src/org/labkey/targetedms/parser/TransitionChromInfoAndPrecursorTally.java

@@ -2,9 +2,9 @@
 
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.targetedms.parser.proto.SkylineDocument;
 
-import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 import java.io.File;
@@ -38,7 +38,7 @@ public boolean isWithinLimits(File file, Logger log) throws XMLStreamException,
         XMLStreamReader reader;
         try (FileInputStream inputStream = new FileInputStream(file))
         {
-            reader = XMLInputFactory.newInstance().createXMLStreamReader(inputStream);
+            reader = XmlBeansUtil.XML_INPUT_FACTORY.createXMLStreamReader(inputStream);
             try
             {
                 readCounts(reader);

src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogParser.java

@@ -26,12 +26,12 @@
 import org.labkey.api.resource.FileResource;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.Path;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.targetedms.TargetedMSModule;
 import org.labkey.targetedms.parser.XmlUtil;
 import org.xml.sax.SAXException;
 
 import javax.xml.XMLConstants;
-import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 import javax.xml.transform.stream.StreamSource;
@@ -44,7 +44,6 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.math.BigDecimal;
 import java.time.format.DateTimeParseException;
 import java.util.Collections;
@@ -124,7 +123,7 @@ private void validateXml() throws IOException, SAXException, AuditLogParsingExce
     }
 
     @NotNull
-    private InputStream openSchemaInputStream() throws AuditLogParsingException, FileNotFoundException, UnsupportedEncodingException
+    private InputStream openSchemaInputStream() throws AuditLogParsingException, FileNotFoundException
     {
         if (ModuleLoader.getInstance() != null)
         {   //if we are running web test
@@ -148,8 +147,7 @@ private InputStream openSchemaInputStream() throws AuditLogParsingException, Fil
     private void parseLogHeader() throws IOException, XMLStreamException
     {
         _fileStream = new FileInputStream(_file);
-        XMLInputFactory inputFactory = XMLInputFactory.newInstance();
-        _stream = inputFactory.createXMLStreamReader(_fileStream);
+        _stream = XmlBeansUtil.XML_INPUT_FACTORY.createXMLStreamReader(_fileStream);
 
         //Skipping most XML structure validation since the file passed the schema validation
         int evtType = _stream.nextTag();     //log root element read
@@ -305,8 +303,6 @@ public String getEnRootHash()
     //--------------------------------------------
     public static class TestCase extends Assert{
 
-        private File _logFile;
-        private SkylineAuditLogParser _parser;
         private static final Logger _logger = LogManager.getLogger(TestCase.class);
         public final static String SYS_PROPERTY_CWD = "user.dir";
         public final static String SKYLINE_LOG_EXTENSION = "skyl";
@@ -325,49 +321,55 @@ public void testLogParser()  throws XMLStreamException, AuditLogException, Audit
             List<AuditLogEntry> entries = new LinkedList<>();
 
             File fZip = UnitTestUtil.getSampleDataFile("AuditLogFiles/MethodEdit_v6.2.zip");
-            _logFile = UnitTestUtil.extractLogFromZip(fZip, _logger);
-            _parser = new SkylineAuditLogParser(_logFile, _logger);
-            Assert.assertNotNull(_parser.getEnRootHash());
+            File logFile = UnitTestUtil.extractLogFromZip(fZip, _logger);
+            try (SkylineAuditLogParser parser = new SkylineAuditLogParser(logFile, _logger))
+            {
+                Assert.assertNotNull(parser.getEnRootHash());
 
-            AuditLogEntry prevEntry = null;
+                AuditLogEntry prevEntry = null;
 
-            while(_parser.hasNextEntry())
-            {
-                AuditLogEntry ent = _parser.parseLogEntry();
-                ent.setDocumentGUID(_docGUID);
-                if(prevEntry != null)
-                    ent.setParentEntryHash(prevEntry.getEntryHash());
-                entries.add(ent);
-                _logger.debug(ent.toString());
-                //all messages in this file should have expanded text
-                //ent.persist();
-
-                for(AuditLogMessage msg : ent.getAllInfoMessage())
+                while (parser.hasNextEntry())
                 {
-                    Assert.assertNotNull(msg.getEnText());
+                    AuditLogEntry ent = parser.parseLogEntry();
+                    ent.setDocumentGUID(_docGUID);
+                    if (prevEntry != null)
+                        ent.setParentEntryHash(prevEntry.getEntryHash());
+                    entries.add(ent);
+                    _logger.debug(ent.toString());
+                    //all messages in this file should have expanded text
+                    //ent.persist();
+
+                    for (AuditLogMessage msg : ent.getAllInfoMessage())
+                    {
+                        Assert.assertNotNull(msg.getEnText());
+                    }
+                    prevEntry = ent;
                 }
-                prevEntry = ent;
-            }
 
-            Assert.assertNotNull(entries.get(2).getExtraInfo());
-            Assert.assertNull(entries.get(1).getExtraInfo());
+                Assert.assertNotNull(entries.get(2).getExtraInfo());
+                Assert.assertNull(entries.get(1).getExtraInfo());
 
-            Assert.assertEquals(11, entries.size());
-            Assert.assertEquals(6, entries.get(5).getAllInfoMessage().size());
-            Assert.assertTrue(entries.get(0).canBeHashed());
+                Assert.assertEquals(11, entries.size());
+                Assert.assertEquals(6, entries.get(5).getAllInfoMessage().size());
+                Assert.assertTrue(entries.get(0).canBeHashed());
+            }
         }
 
         @Test
         public void testInvalidXmlFile() throws IOException
         {
+            SkylineAuditLogParser parser = null;
             try
             {
                 File logFile = UnitTestUtil.getSampleDataFile("AuditLogFiles/InvalidSchemaTest.skyl");
-                SkylineAuditLogParser parser = new SkylineAuditLogParser(logFile, _logger);
+                parser = new SkylineAuditLogParser(logFile, _logger);
                 Assert.fail("Expected file validation failure but it succeeded.");
             }
-            catch (AuditLogException ignored)
+            catch (AuditLogException _) {}
+            finally
             {
+                if (parser != null)
+                    parser.close();
             }
         }
 

webapp/TargetedMS/js/LinkVersionsDialog.js

@@ -208,7 +208,7 @@ Ext4.define('LABKEY.targetedms.LinkedVersions', {
     removeColumnCellClick : function(grid, td, cellIndex, record, tr, rowIndex, e) {
         // 'Remove' column listener to remove a record from an existing method chain
         if (cellIndex == 0 && e.target.className.indexOf('remove-link-version') > 0) {
-            Ext4.Msg.confirm('Remove Confirmation', 'Are you sure you want to remove <b>' + record.get('File/FileName')
+            Ext4.Msg.confirm('Remove Confirmation', 'Are you sure you want to remove <b>' + LABKEY.Utils.encodeHtml(record.get('File/FileName'))
                     + '</b> from its existing method chain?',
                 function(btnId) {
                     if (btnId == 'yes') {

webapp/passport/js/beforeAfter/protein.js

@@ -86,7 +86,7 @@ protein =
 
                     var label = document.createElement('Label');
                     label.setAttribute("for",checkbox.id);
-                    label.innerHTML = capitalizeFirstLetter(type);
+                    label.innerText = capitalizeFirstLetter(type);
                     label.setAttribute("style", "padding-left: 5px; border-left: 5px solid "+protein.UI.features.colors[featureId] +";");
 
                     var listItem = document.createElement("li");