Backport: Consolidate XML parsing initialization, remove some casts (#6976) (#6984)

Author: labkey-jeckels

api/src/org/labkey/api/cache/ehcache/EhSimpleCache.java

@@ -23,6 +23,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.cache.CacheType;
 import org.labkey.api.cache.SimpleCache;
+import org.labkey.api.util.IntegerUtils;
 
 import java.util.HashSet;
 import java.util.List;
@@ -51,7 +52,7 @@ public void put(@NotNull K key, V value)
     public void put(@NotNull K key, V value, long timeToLive)
     {
         Element element = new Element(key, value);
-        element.setTimeToLive((int)timeToLive / 1000);
+        element.setTimeToLive(IntegerUtils.asInteger(timeToLive / 1000)); // Convert from ms to sec
         _cache.put(element);
     }
 

api/src/org/labkey/api/data/Aggregate.java

@@ -567,13 +567,13 @@ public Result getResult(ResultSet rs, Map<FieldKey, ? extends ColumnInfo> column
         {
             o = rs.getObject(aggColName);
             // TODO: Handle BigDecimal values
-            if (o instanceof Number)
+            if (o instanceof Number n)
             {
-                double resultValue = ((Number)o).doubleValue();
+                double resultValue = n.doubleValue();
                 if (resultValue == Math.floor(resultValue))
-                    o = Long.valueOf((long) resultValue);
+                    o = n.longValue();
                 else
-                    o = Double.valueOf(resultValue);
+                    o = resultValue;
             }
         }
 

api/src/org/labkey/api/data/DbSchemaCache.java

@@ -42,7 +42,6 @@ public class DbSchemaCache
 
     // Ask the DbSchemaType how long to cache each schema
     private final CacheTimeChooser<String> SCHEMA_CACHE_TIME_CHOOSER = (key, argument) -> {
-        @SuppressWarnings({"unchecked"})
         SchemaDetails details = (SchemaDetails)argument;
         return details.getType().getCacheTimeToLive();
     };

api/src/org/labkey/api/data/DbSequence.java

@@ -139,11 +139,11 @@ public synchronized long next()
         }
 
         /* package */
-        synchronized long reserveSequentialBlock(int count)
+        synchronized long reserveSequentialBlock(long count)
         {
             if (null == _lastReservedValue || _currentValue+count > _lastReservedValue)
             {
-                Pair<Long, Long> reserved = DbSequenceManager.reserve(this, Math.max(count,_batchSize));
+                Pair<Long, Long> reserved = DbSequenceManager.reserve(this, Math.max(count, _batchSize));
                 _currentValue = reserved.first;
                 _lastReservedValue = reserved.second;
             }

api/src/org/labkey/api/data/DbSequenceManager.java

@@ -37,6 +37,7 @@
 import java.sql.Connection;
 import java.sql.SQLException;
 import java.util.Collection;
+import java.util.Objects;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 
@@ -106,8 +107,8 @@ public static DbSequence getPreallocatingSequence(Container c, String name, int
         return _sequences.computeIfAbsent(key, (k) -> new DbSequence.Preallocate(c, name, ensure(c, name, id), batchSize));
     }
 
-    /* This is not a recommended, but if you get stuck and need to reserve a block at once */
-    public static long reserveSequentialBlock(DbSequence seq, int count)
+    /* This is not recommended, but if you get stuck and need to reserve a block at once */
+    public static long reserveSequentialBlock(DbSequence seq, long count)
     {
         if (!(seq instanceof DbSequence.Preallocate))
             throw new IllegalStateException();
@@ -123,10 +124,7 @@ private static int ensure(Container c, String name, int id, boolean withUpdateLo
     {
         Integer rowId = getRowId(c, name, id, withUpdateLock);
 
-        if (null != rowId)
-            return rowId;
-        else
-            return create(c, name, id, withUpdateLock);
+        return Objects.requireNonNullElseGet(rowId, () -> create(c, name, id, withUpdateLock));
     }
 
     public static @Nullable Integer getRowId(Container c, String name, int id)
@@ -284,7 +282,7 @@ static long next(DbSequence sequence)
     // .first value returned is 'current', call to next() should return current+1
     // .second value is reserved for use by caller
     // in other words, next() should return values [pair.first+1, pair.second] inclusive
-    static Pair<Long,Long> reserve(DbSequence sequence, int count)
+    static Pair<Long,Long> reserve(DbSequence sequence, long count)
     {
         TableInfo tinfo = getTableInfo();
 

api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java

@@ -28,12 +28,13 @@
 import org.labkey.api.pipeline.PipelineProtocol;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.writer.PrintWriters;
 import org.xml.sax.InputSource;
 
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerFactory;
@@ -105,7 +106,7 @@ public void setXml(String xml)
             String line;
             while ((line = reader.readLine()) != null)
                 stripped.append(line.trim());
-            DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+            DocumentBuilder db = XmlBeansUtil.DOCUMENT_BUILDER_FACTORY.newDocumentBuilder();
             DOMSource xmlInput = new DOMSource(db.parse(new InputSource(new StringReader(stripped.toString()))));
             StreamResult xmlOutput = new StreamResult(new StringWriter());
             Transformer transformer = TransformerFactory.newInstance().newTransformer();
@@ -254,7 +255,15 @@ protected void save(Path file, Map<String, String> addParams, Map<String, String
     protected ParamParser parse()
     {
         ParamParser parser = getFactory().createParamParser();
-        parser.parse(new ReaderInputStream(new StringReader(xml), Charset.defaultCharset()));
+        try
+        {
+            parser.parse(new ReaderInputStream.Builder().setReader(new StringReader(xml)).setCharset(Charset.defaultCharset()).get());
+        }
+        catch (IOException e)
+        {
+            // Shouldn't happen since we already had the content in-memory as a String
+            throw UnexpectedException.wrap(e);
+        }
         return parser;
     }
 
@@ -277,7 +286,7 @@ public FileType findInputType(Path file)
     public abstract List<FileType> getInputTypes();
 
     @Override
-    public abstract AbstractFileAnalysisProtocolFactory getFactory();
+    public abstract AbstractFileAnalysisProtocolFactory<?> getFactory();
 
     public abstract JOB createPipelineJob(ViewBackgroundInfo info,
                                           PipeRoot root, List<Path> filesInput,

api/src/org/labkey/api/reports/report/RedirectReport.java

@@ -21,8 +21,10 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
+import org.labkey.api.view.RedirectException;
 import org.labkey.api.view.ViewContext;
 
 import java.net.MalformedURLException;
@@ -35,7 +37,7 @@
  */
 public abstract class RedirectReport extends AbstractReport
 {
-    private static final Logger LOG = LogManager.getLogger(RedirectReport.class);
+    private static final Logger LOG = LogHelper.getLogger(RedirectReport.class, "Reports that send the user to some other URL");
 
     public static final String REDIRECT_URL = ReportDescriptor.Prop.redirectUrl.name();
     public static final String TARGET = "target";
@@ -45,15 +47,15 @@ public RedirectReport()
     }
 
     @Override
-    public HttpView renderReport(ViewContext context)
+    public HttpView<?> renderReport(ViewContext context)
     {
         String url = getUrl(context.getContainer());
 
         // When rendering in a portal webpart, render the redirect link and thumbnail
         if (context.get(renderParam.reportWebPart.name()) != null)
             return new JspView<>("/org/labkey/api/reports/report/view/redirectReportWebPart.jsp", this);
 
-        return HttpView.redirect(url);
+        throw new RedirectException(url);
     }
 
     @Override

api/src/org/labkey/api/search/AbstractXMLDocumentParser.java

@@ -15,14 +15,14 @@
  */
 package org.labkey.api.search;
 
+import org.labkey.api.util.XmlBeansUtil;
 import org.xml.sax.Attributes;
 import org.xml.sax.ContentHandler;
 import org.xml.sax.SAXException;
 import org.xml.sax.helpers.DefaultHandler;
 
 import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.HashSet;
@@ -40,13 +40,9 @@ public abstract class AbstractXMLDocumentParser extends AbstractDocumentParser
     @Override
     public void parseContent(InputStream stream, ContentHandler handler) throws IOException, SAXException
     {
-        try
+        try (BufferedInputStream buffered = new BufferedInputStream(stream))
         {
-            SAXParser parser = SAXParserFactory.newInstance().newSAXParser();
-            parser.getXMLReader().setFeature("http://xml.org/sax/features/validation", false);
-            parser.getXMLReader().setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
-            parser.getXMLReader().setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
-            parser.parse(stream, createSAXHandler(handler));
+            XmlBeansUtil.SAX_PARSER_FACTORY.newSAXParser().parse(buffered, createSAXHandler(handler));
         }
         catch (ParserConfigurationException e)
         {

api/src/org/labkey/api/util/HttpsUtil.java

@@ -62,7 +62,7 @@ public static void disableValidation(HttpsURLConnection sslConnection)
 
 
     /** Attempts a connection to the testURL, returning null on success and a Pair with error message and (possibly null) response code on failure */
-    public static @Nullable Pair<String, Integer> testSslUrl(URL testURL, String advice)
+    public static @Nullable Pair<String, Integer> testHttpsUrl(URL testURL, String advice)
     {
         try
         {
@@ -152,7 +152,7 @@ public static void checkSslRedirectConfiguration(HttpServletRequest request, int
 
                 // Now switch to a URL, since that's what testSslUrl() requires
                 URL testURL = new URL(helper.getURIString());
-                Pair<String, Integer> sslResult = HttpsUtil.testSslUrl(testURL,
+                Pair<String, Integer> sslResult = HttpsUtil.testHttpsUrl(testURL,
                     "This LabKey Server instance is configured to require secure connections on port " + redirectPort + ", but it does not appear to be responding " +
                     "to HTTPS requests at " + testURL + ". Please see " + new HelpTopic("stagingServerTips").getHelpTopicHref() + " for " +
                     "details about how to turn off the SSL redirect settings in the database.");