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Merged
labkey-jeckels merged 3 commits into from
Feb 28, 2026
+10 −383
Merged

Ensure consistent XML parser config #983

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39f7147
Ensure consistent XML parser config
labkey-jeckels Feb 20, 2026
506d0e6
Merge branch 'develop' into fb_xmlConfig
labkey-jeckels Feb 27, 2026
a997b4f
Flow needs DocType
labkey-jeckels Feb 28, 2026
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4 changes: 4 additions & 0 deletions flow/enginesrc/org/labkey/flow/analysis/model/FlowJoWorkspace.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,13 @@
package org.labkey.flow.analysis.model;

import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.junit.Assert;
import org.junit.Test;
import org.labkey.api.util.JunitUtil;
import org.labkey.api.util.VersionNumber;
import org.labkey.api.util.logging.LogHelper;
import org.labkey.flow.analysis.web.FCSAnalyzer;
import org.labkey.flow.analysis.web.GraphSpec;
import org.labkey.flow.analysis.web.StatisticSpec;
Expand All @@ -44,6 +46,8 @@

abstract public class FlowJoWorkspace extends Workspace
{
public static final Logger LOG = LogHelper.getLogger(FlowJoWorkspace.class, "FlowJo workspace parsing");

static Map<String, StatisticSpec.STAT> STATS = new HashMap<>();
static
{
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12 changes: 5 additions & 7 deletions flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java
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Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.flow.analysis.model;

import org.apache.logging.log4j.LogManager;
import org.apache.xerces.impl.Constants;
import org.apache.xerces.parsers.DOMParser;
import org.apache.xerces.util.SymbolTable;
Expand All @@ -24,6 +23,7 @@
import org.apache.xerces.xni.QName;
import org.apache.xerces.xni.XMLLocator;
import org.apache.xerces.xni.XNIException;
import org.labkey.api.util.XmlBeansUtil;
import org.w3c.dom.Attr;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
Expand All @@ -41,7 +41,6 @@
import org.xml.sax.helpers.DefaultHandler;

import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
Expand Down Expand Up @@ -135,13 +134,14 @@ static public boolean isFlowJoWorkspace(File file)
WorkspaceRecognizer recognizer = new WorkspaceRecognizer();
try
{
SAXParser parser = SAXParserFactory.newInstance().newSAXParser();
SAXParser parser = XmlBeansUtil.SAX_PARSER_FACTORY_ALLOWING_DOCTYPE.newSAXParser();

parser.parse(file, recognizer);
}
catch (Exception e)
{
// suppress
FlowJoWorkspace.LOG.debug("Unexpected error", e);
}
return recognizer.isWorkspace();
}
Expand Down Expand Up @@ -371,7 +371,6 @@ public void fatalError(SAXParseException exception) throws SAXException
static class FJParseFilter implements LSParserFilter
{
SymbolTable fSymbolTable = new SymbolTable();
Set<String> rejected = new HashSet<>();

@Override
public short startElement(Element element)
Expand All @@ -385,7 +384,6 @@ public short startElement(Element element)
else if (nsURI != null && (GATINGML_1_5_NAMESPACES.contains(nsURI) || FJ_GATINGML_1_5_NAMEPSACE_FIXUP.containsKey(nsURI) || GATINGML_2_0_NAMESPACES.contains(nsURI)))
filter = FILTER_ACCEPT;

// if (filter != FILTER_ACCEPT && rejected.add(element.getNodeName())) System.err.println((filter == FILTER_SKIP ? "SKIPPED: " : "REJECTED: ") + element.getNodeName());
return filter;
}

Expand Down Expand Up @@ -457,7 +455,7 @@ static FJDOMParser create()
{
super(st);
fSymbolTable = st;
fSkippedElemStack = new Stack();
fSkippedElemStack = new Stack<>();
fDOMFilter = new FJParseFilter();
try
{
Expand Down Expand Up @@ -516,7 +514,7 @@ public void parse(InputSource inputSource) throws SAXException, IOException
}
catch (RuntimeException x)
{
LogManager.getLogger(FlowJoWorkspace.class).error("Unexpected error", x);
FlowJoWorkspace.LOG.error("Unexpected error", x);
throw x;
}
}
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1 change: 0 additions & 1 deletion ms2/src/org/labkey/ms2/reader/Q3AnalysisSummary.java
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Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.ms2.reader;

import org.labkey.ms2.reader.SimpleXMLEventRewriter;
import org.labkey.api.reader.SimpleXMLStreamReader;

import org.apache.logging.log4j.Logger;
Expand Down
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