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Fix for ConcurrentMod Exception seen in DatasetsIT test #12128

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Fix for ConcurrentMod Exception seen in DatasetsIT test #12128

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e64a9e2
Add synchronization, avoid sharing list across fmds, copy prov
qqmyers Jan 30, 2026
435031c
make sure fmd is associated with correct version
qqmyers Jan 30, 2026
f1ea924
make test use new method
qqmyers Jan 30, 2026
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18 changes: 1 addition & 17 deletions src/main/java/edu/harvard/iq/dataverse/Dataset.java
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Original file line number Diff line number Diff line change
Expand Up @@ -406,21 +406,7 @@ private DatasetVersion createNewDatasetVersion(Template template, FileMetadata f
in a pre-save validation SEK 12/6/2021
*/
for (FileMetadata fm : latestVersion.getFileMetadatas()) {
FileMetadata newFm = new FileMetadata();
// TODO:
// the "category" will be removed, shortly.
// (replaced by multiple, tag-like categories of
// type DataFileCategory) -- L.A. beta 10
//newFm.setCategory(fm.getCategory());
// yep, these are the new categories:
newFm.setCategories(fm.getCategories());
newFm.setDescription(fm.getDescription());
newFm.setLabel(fm.getLabel());
newFm.setDirectoryLabel(fm.getDirectoryLabel());
newFm.setRestricted(fm.isRestricted());
newFm.setDataFile(fm.getDataFile());
newFm.setDatasetVersion(dsv);
newFm.setProvFreeForm(fm.getProvFreeForm());
FileMetadata newFm = fm.createCopyInVersion(dsv);
newFm.setInPriorVersion(true);

//fmVarMet would be updated in DCT
Expand All @@ -432,8 +418,6 @@ private DatasetVersion createNewDatasetVersion(Template template, FileMetadata f
newFm.copyVarGroups(fm.getVarGroups());
}
}

dsv.getFileMetadatas().add(newFm);
}

if (latestVersion.getTermsOfUseAndAccess()!= null){
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18 changes: 1 addition & 17 deletions src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
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Expand Up @@ -706,23 +706,7 @@ public DatasetVersion cloneDatasetVersion(){
*/

for (FileMetadata fm : this.getFileMetadatas()) {
FileMetadata newFm = new FileMetadata();
// TODO:
// the "category" will be removed, shortly.
// (replaced by multiple, tag-like categories of
// type DataFileCategory) -- L.A. beta 10
//newFm.setCategory(fm.getCategory());
// yep, these are the new categories:
newFm.setCategories(fm.getCategories());
newFm.setDescription(fm.getDescription());
newFm.setLabel(fm.getLabel());
newFm.setDirectoryLabel(fm.getDirectoryLabel());
newFm.setRestricted(fm.isRestricted());
newFm.setDataFile(fm.getDataFile());
newFm.setDatasetVersion(dsv);
newFm.setProvFreeForm(fm.getProvFreeForm());

dsv.getFileMetadatas().add(newFm);
fm.createCopyInVersion(dsv);
}

if (this.getTermsOfUseAndAccess()!= null){
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40 changes: 14 additions & 26 deletions src/main/java/edu/harvard/iq/dataverse/FileMetadata.java
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Expand Up @@ -154,21 +154,21 @@ public class FileMetadata implements Serializable {
private Collection<VariableMetadata> variableMetadatas;

/**
* Creates a copy of {@code this}, with identical business logic fields.
* E.g., {@link #label} would be duplicated; {@link #version} will not.
* Creates a copy of {@code this}, with identical business logic fields, making the bi-drectional connections to the specified version.
*
* @return A copy of {@code this}, except for the DB-related data.
* @return A copy of {@code this}
*/
public FileMetadata createCopy() {
public FileMetadata createCopyInVersion(DatasetVersion dsv) {
FileMetadata fmd = new FileMetadata();
fmd.setCategories(new LinkedList<>(getCategories()) );
fmd.setDataFile( getDataFile() );
fmd.setDatasetVersion( getDatasetVersion() );
fmd.setDatasetVersion( dsv );
fmd.setDescription( getDescription() );
fmd.setLabel( getLabel() );
fmd.setRestricted( isRestricted() );
fmd.setDirectoryLabel(getDirectoryLabel());

fmd.setProvFreeForm(getProvFreeForm());
dsv.getFileMetadatas().add(fmd);
return fmd;
}

Expand Down Expand Up @@ -245,38 +245,26 @@ public void setVarGroups(List<VarGroup> varGroups) {

public List<DataFileCategory> getCategories() {
if (fileCategories != null) {
/*
* fileCategories can sometimes be an
* org.eclipse.persistence.indirection.IndirectList When that happens, the
* comparator in the Collections.sort below is not called, possibly due to
* https://bugs.eclipse.org/bugs/show_bug.cgi?id=446236 which is Java 1.8+
* specific Converting to an ArrayList solves the problem, but the longer term
* solution may be in avoiding the IndirectList or moving to a new version of
* the jar it is in.
*/
if (!(fileCategories instanceof ArrayList)) {
List<DataFileCategory> newDFCs = new ArrayList<DataFileCategory>();
for (DataFileCategory fdc : fileCategories) {
newDFCs.add(fdc);
synchronized (this) {
if (!(fileCategories instanceof ArrayList)) {
fileCategories = new ArrayList<>(fileCategories);
}
setCategories(newDFCs);
Collections.sort(fileCategories, FileMetadata.compareByNameWithSortCategories);
}
Collections.sort(fileCategories, FileMetadata.compareByNameWithSortCategories);
}
return fileCategories;
}
public void setCategories(List<DataFileCategory> fileCategories) {

public synchronized void setCategories(List<DataFileCategory> fileCategories) {
this.fileCategories = fileCategories;
}
public void addCategory(DataFileCategory category) {

public synchronized void addCategory(DataFileCategory category) {
if (fileCategories == null) {
fileCategories = new ArrayList<>();
}
fileCategories.add(category);
}

/**
* Retrieve categories
* @return
Expand Down
10 changes: 4 additions & 6 deletions src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateDatasetVersionCommand.java
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Expand Up @@ -61,13 +61,11 @@ public DatasetVersion execute(CommandContext ctxt) throws CommandException {

registerExternalVocabValuesIfAny(ctxt, newVersion);

List<FileMetadata> newVersionMetadatum = new ArrayList<>(latest.getFileMetadatas().size());
for ( FileMetadata fmd : latest.getFileMetadatas() ) {
FileMetadata fmdCopy = fmd.createCopy();
fmdCopy.setDatasetVersion(newVersion);
newVersionMetadatum.add( fmdCopy );
List<FileMetadata> latestVersionMetadata = latest.getFileMetadatas();
newVersion.setFileMetadatas(new ArrayList<>(latest.getFileMetadatas().size()));
for ( FileMetadata fmd : latestVersionMetadata ) {
fmd.createCopyInVersion(newVersion);
}
newVersion.setFileMetadatas(newVersionMetadatum);

//moving prepare Dataset here
//because it includes validation and we need the validation
Expand Down
15 changes: 7 additions & 8 deletions src/test/java/edu/harvard/iq/dataverse/DatasetVersionDifferenceTest.java
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Expand Up @@ -76,7 +76,8 @@ public void testDifferencing() {
datasetVersion2.setVersionState(DatasetVersion.VersionState.DRAFT);
datasetVersion2.setTermsOfUseAndAccess(new TermsOfUseAndAccess());
datasetVersion2.getTermsOfUseAndAccess().setLicense(license);

datasetVersion.setFileMetadatas(new ArrayList<>());

// Published version's two files
DataFile dataFile = new DataFile();
dataFile.setId(1L);
Expand All @@ -88,19 +89,17 @@ public void testDifferencing() {

FileMetadata fileMetadata2 = createFileMetadata(20L, datasetVersion, dataFile2, "file2.txt");

List<FileMetadata> fileMetadatas = new ArrayList<>(Arrays.asList(fileMetadata1, fileMetadata2));
datasetVersion.setFileMetadatas(fileMetadatas);

// Draft version - same two files with one label change
FileMetadata fileMetadata3 = fileMetadata1.createCopy();
FileMetadata fileMetadata3 = fileMetadata1.createCopyInVersion(datasetVersion2);
fileMetadata3.setId(30L);

FileMetadata fileMetadata4 = fileMetadata2.createCopy();
FileMetadata fileMetadata4 = fileMetadata2.createCopyInVersion(datasetVersion2);
fileMetadata4.setLabel("file3.txt");
fileMetadata4.setId(40L);

List<FileMetadata> fileMetadatas = new ArrayList<>(Arrays.asList(fileMetadata1, fileMetadata2));
datasetVersion.setFileMetadatas(fileMetadatas);
List<FileMetadata> fileMetadatas2 = new ArrayList<>(Arrays.asList(fileMetadata3, fileMetadata4));
datasetVersion2.setFileMetadatas(fileMetadatas2);

SimpleDateFormat dateFmt = new SimpleDateFormat("yyyyMMdd");
Date publicationDate;
try {
Expand Down