Ensure consistent XML parser config (#605)

labkey-jeckels · web-flow · commit f1977199a973 · 2026-02-20T09:48:07.000-08:00
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataImporter.java
@@ -9,6 +9,7 @@
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.writer.VirtualFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -17,7 +18,6 @@
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -72,7 +72,7 @@ private void readXmlAndImport(Container container, VirtualFile vf, FileContentSe
                 return;
             }
 
-            Document document = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(is));
+            Document document = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder().parse(new InputSource(is));
             NodeList nodes = document.getElementsByTagName(FilesMetadataWriter.FILE);
             for(int i = 0; i < nodes.getLength(); i++)
             {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/FilesMetadataWriter.java
@@ -11,12 +11,12 @@
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.security.User;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.writer.FileSystemFile;
 import org.labkey.api.writer.VirtualFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
@@ -76,7 +76,7 @@ private void writeFilesMetadata(VirtualFile vf, Container container, boolean inc
     private void writeFilesXml(Container container, ExperimentService expSvc, FileContentService fcs, PrintWriter writer, Logger log)
             throws ParserConfigurationException, TransformerException
     {
-        Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
+        Document doc = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder().newDocument();
 
         List<? extends ExpData> expDatasWithComments = getExpDatasWithComments(container, expSvc);
 
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
@@ -23,6 +23,7 @@
 import org.labkey.api.collections.IntHashMap;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.AjaxCompletion;
 import org.w3c.dom.CharacterData;
@@ -33,7 +34,6 @@
 import org.xml.sax.SAXException;
 
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -43,7 +43,6 @@
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Matcher;
@@ -134,8 +133,7 @@ public static Map<Integer, String> getScientificNames(List<Integer> taxIds) thro
 
             if (status == HttpURLConnection.HTTP_OK)
             {
-                DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-                DocumentBuilder builder = factory.newDocumentBuilder();
+                DocumentBuilder builder = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
                 Document doc = builder.parse(conn.getInputStream());
 
                 NodeList nodes = doc.getElementsByTagName("DocSum");
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PsiInstrumentParser.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PsiInstrumentParser.java
@@ -22,6 +22,7 @@
 import org.labkey.api.resource.FileResource;
 import org.labkey.api.targetedms.TargetedMSService;
 import org.labkey.api.util.Path;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.util.logging.LogHelper;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -30,7 +31,6 @@
 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;
@@ -94,12 +94,11 @@ public static List<PsiInstrument> getInstruments() throws PxException
         {
             throw new PxException("File not found: psi-ms-PARSED.xml.");
         }
-        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)
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/UnimodParser.java
@@ -20,6 +20,7 @@
 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.panoramapublic.PanoramaPublicModule;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -28,7 +29,6 @@
 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;
@@ -77,13 +77,11 @@ private void parse(File unimodXml, UnimodModifications uMods, boolean isPrimaryX
         {
             throw new PxException("UNIMOD xml file does not exist: " + unimodXml);
         }
-        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-        dbf.setNamespaceAware(true);
         DocumentBuilder db;
         Document document;
         try
         {
-            db = dbf.newDocumentBuilder();
+            db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
             document = db.parse(unimodXml);
         }
         catch (ParserConfigurationException | SAXException | IOException e)
@@ -122,7 +120,7 @@ private void readAminoAcids(Element root, UnimodModifications uMods) throws PxEx
     private void parseAminoAcid(Element aaEl, UnimodModifications uMods) throws PxException
     {
         String title = aaEl.getAttribute("title");
-        if(title == null || title.length() > 1 || !Character.isUpperCase(title.charAt(0)))
+        if(title.length() > 1 || !Character.isUpperCase(title.charAt(0)))
         {
             return;
         }
diff --git a/testresults/src/org/labkey/testresults/TestResultsController.java b/testresults/src/org/labkey/testresults/TestResultsController.java
@@ -56,6 +56,7 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.MimeMap;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.ViewContext;
@@ -93,7 +94,6 @@
 
 import javax.management.modelmbean.XMLParseException;
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
 import java.io.ByteArrayOutputStream;
 import java.io.DataOutputStream;
 import java.io.File;
@@ -1381,8 +1381,7 @@ private static void ParseAndStoreXML(String xml, Container c) throws Exception
                 "\\[(\\d\\d):(\\d\\d)]\\s+(\\d+)\\.\\d+\\s+([A-Za-z]\\w*)\\s+\\(([A-Za-z]+)\\)");
 
             try (DbScope.Transaction transaction = TestResultsSchema.getSchema().getScope().ensureTransaction()) {
-                DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
-                DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+                DocumentBuilder dBuilder = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
                 InputSource is = new InputSource();
                 is.setCharacterStream(new StringReader(xml));
                 Document doc = dBuilder.parse(is);

Original file line number	Diff line number	Diff line change
`@@ -20,6 +20,7 @@`
`20`	`20`	`import org.labkey.api.module.ModuleLoader;`
`21`	`21`	`import org.labkey.api.resource.FileResource;`
`22`	`22`	`import org.labkey.api.util.Path;`
	`23`	`+import org.labkey.api.util.XmlBeansUtil;`
`23`	`24`	`import org.labkey.panoramapublic.PanoramaPublicModule;`
`24`	`25`	`import org.w3c.dom.Document;`
`25`	`26`	`import org.w3c.dom.Element;`
`@@ -28,7 +29,6 @@`
`28`	`29`	`import org.xml.sax.SAXException;`
`29`	`30`
`30`	`31`	`import javax.xml.parsers.DocumentBuilder;`
`31`		`-import javax.xml.parsers.DocumentBuilderFactory;`
`32`	`32`	`import javax.xml.parsers.ParserConfigurationException;`
`33`	`33`	`import java.io.File;`
`34`	`34`	`import java.io.IOException;`
`@@ -77,13 +77,11 @@ private void parse(File unimodXml, UnimodModifications uMods, boolean isPrimaryX`
`77`	`77`	`{`
`78`	`78`	`throw new PxException("UNIMOD xml file does not exist: " + unimodXml);`
`79`	`79`	`}`
`80`		`- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();`
`81`		`- dbf.setNamespaceAware(true);`
`82`	`80`	`DocumentBuilder db;`
`83`	`81`	`Document document;`
`84`	`82`	`try`
`85`	`83`	`{`
`86`		`- db = dbf.newDocumentBuilder();`
	`84`	`+ db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();`
`87`	`85`	`document = db.parse(unimodXml);`
`88`	`86`	`}`
`89`	`87`	`catch (ParserConfigurationException \| SAXException \| IOException e)`
`@@ -122,7 +120,7 @@ private void readAminoAcids(Element root, UnimodModifications uMods) throws PxEx`
`122`	`120`	`private void parseAminoAcid(Element aaEl, UnimodModifications uMods) throws PxException`
`123`	`121`	`{`
`124`	`122`	`String title = aaEl.getAttribute("title");`
`125`		`- if(title == null \|\| title.length() > 1 \|\| !Character.isUpperCase(title.charAt(0)))`
	`123`	`+ if(title.length() > 1 \|\| !Character.isUpperCase(title.charAt(0)))`
`126`	`124`	`{`
`127`	`125`	`return;`
`128`	`126`	`}`