Preserve source subject/session labels (#10))

CHANGELOG.md

@@ -6,7 +6,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/)
 
 ---
 
-## [1.0.1-RC]
+## [1.1.0]
+
+### Added
+
+- **Preserve source labels on Reimport** ([#10](https://github.com/NrgXnat/batch-transfer-plugin/issues/10)) — the Reimport panel now offers two checkboxes (both on by default) to preserve the source **subject label** and/or **session label**. When enabled, those XNAT labels are passed to the DICOM importer as `SUBJECT_ID` / `EXPT_LABEL` overrides so the destination uses them instead of deriving labels from DICOM tags (e.g. `PatientName` / `PatientID`). 
+
+### Changed
+
+- Updated target XNAT version to 1.9.3.5
+
+---
+
+## [1.0.1]
 
 A performance and hardening release on top of the 1.0.0 rebrand: Reimport and Clone now run in parallel through JMS queues, mixed-operation batches route correctly, the listing query is parameterized, and workflow history is consistent across all three operations. The `/xapi/transfer` request format and the Java packages are unchanged from 1.0.0.
 

build.gradle

@@ -15,7 +15,7 @@ plugins {
 }
 
 group "org.nrg.xnatx.plugins"
-version "1.0.1"
+version "1.1.0-SNAPSHOT"
 description "XNAT Batch Transfer Plugin"
 
 sourceCompatibility = 1.8

docs/ROADMAP.md

@@ -1,15 +1,22 @@
 # Batch Transfer Plugin — Roadmap
 
-**Plugin Version**: 1.0.1-RC (rebranded from Batch Share Plugin 2.0.0-SNAPSHOT; version line reset at 1.0.0)
-**Target XNAT**: 1.9.3.3
-**Last Updated**: 2026-06-22
+**Plugin Version**: 1.1.0 (rebranded from Batch Share Plugin 2.0.0-SNAPSHOT; version line reset at 1.0.0)
+**Target XNAT**: 1.9.3.5
+**Last Updated**: 2026-06-29
 
 The Batch Transfer Plugin enables bulk data operations across XNAT projects. Users can Share, Clone, or Reimport subjects, sessions, and assessors in batch from a single interface. **Share** adds data into a destination project without copying (XNAT's standard sharing relationship); **Clone** duplicates data into the destination, producing an independent editable copy; **Reimport** re-ingests image sessions through the destination project's anonymization pipeline.
 
 ---
 
 ## Completed
 
+## [1.1.0]
+
+### Added
+
+- **Preserve source labels on Reimport** ([#10](https://github.com/NrgXnat/batch-transfer-plugin/issues/10)) — the Reimport panel now offers two checkboxes (both on by default) to preserve the source **subject label** and/or **session label**. When enabled, those XNAT labels are passed to the DICOM importer as `subject_ID` / `EXPT_LABEL` overrides so the destination uses them instead of deriving labels from DICOM tags (e.g. `PatientName` / `PatientID`).
+
+
 ## 1.0.1 — Performance & hardening
 - **Parallel processing via JMS queues** — Reimport (per session) and Clone (per subject) dispatched onto in-process (`vm://`) JMS queues instead of a single sequential loop; in-memory `BatchTransferMonitor` fan-in emits one terminal event per batch
 - **Admin-tunable queue concurrency** — site-admin settings + `GET`/`POST /xapi/batch_transfer/jms_queues`; defaults Reimport 4–8, Clone 1–2 (`min = max = 1` for serial)
@@ -63,7 +70,3 @@ The Batch Transfer Plugin enables bulk data operations across XNAT projects. Use
 - Extend PROJECT_SHARING_FEATURE and PROJECT_COPYING_FEATURE controls to include a separate PROJECT_IMPORTING_FEATURE (feature-flag naming intentionally deferred from the rebrand)
 - Per-experiment Reimport timeout to bound importer hangs. `BatchTransferServiceImpl.runImporter` invokes `DicomZipImporter.call()` synchronously, with no upper bound — a stuck prearchive write (wedged NFS mount, deadlocked rebuild queue, slow remote disk) parks the batch-loop thread indefinitely and blocks all subsequent requests in the batch. The 5-minute heartbeat logger makes a hang observable, but recovery still requires a Tomcat restart. Possible fix: wrap `importExperiment` in `Future.get(timeoutMs)` on a separate executor; on timeout, cancel the future, emit a Failed event, and let the batch loop continue with the next request. Caveats: `cancel(true)` cannot reliably stop uninterruptible I/O so the underlying thread leaks; the prearchive has no transactional rollback so a cancelled import may leave partial state; choosing a default timeout is environment-specific (large legitimate sessions can run 30+ min). Defer until a customer incident motivates it; if added, expose the timeout as a plugin config and document explicitly that it means "we gave up waiting", not "we cleaned up".
 
-### Testing & Release
-- Test admin/owner/member permissions
-- Testing for Share/Clone/Reimport operations with assessors
-- Scale testing on large project

src/main/java/org/nrg/xnatx/plugins/transfer/jms/listeners/TransferReimportListener.java

@@ -69,7 +69,8 @@ public void onRequest(final TransferItemRequest request) {
         try {
             eventService.triggerEvent(BatchTransferEvent.progress(request.getRequestingUserId(),
                     monitor.currentPercent(trackingId), trackingId, "Reimporting " + itemId + " to " + request.getDestinationProject()));
-            service.processItem(new TransferRequest(request.getDestinationProject(), itemId, TransferMode.REIMPORT),
+            service.processItem(new TransferRequest(request.getDestinationProject(), itemId, TransferMode.REIMPORT,
+                            request.getPreserveSubjectLabel(), request.getPreserveSessionLabel()),
                     user, new EventInfo(trackingId, monitor.currentPercent(trackingId)));
         } catch (Exception e) {
             log.error("Reimport {} failed", itemId, e);

src/main/java/org/nrg/xnatx/plugins/transfer/jms/requests/TransferItemRequest.java

@@ -29,4 +29,6 @@ public class TransferItemRequest implements Serializable {
     private final String  destinationProject;
     private final String  username;
     private final Integer requestingUserId;
+    private final Boolean preserveSubjectLabel;
+    private final Boolean preserveSessionLabel;
 }

src/main/java/org/nrg/xnatx/plugins/transfer/model/TransferRequest.java

@@ -16,4 +16,13 @@ public class TransferRequest {
     private String destinationProject;
     private String id;
     private TransferMode mode;
+    // Reimport only: preserve the source subject's XNAT label by passing it to the importer
+    private Boolean preserveSubjectLabel;
+    // Reimport only: preserve the source session's XNAT label by passing it to the importer
+    private Boolean preserveSessionLabel;
+
+    //  Retain no-preserve-flag default constructor
+    public TransferRequest(String destinationProject, String id, TransferMode mode) {
+        this(destinationProject, id, mode, null, null);
+    }
 }

src/main/java/org/nrg/xnatx/plugins/transfer/service/impl/BatchTransferServiceImpl.java

@@ -153,7 +153,8 @@ private void enqueueReimport(final String trackingId, final List<TransferRequest
         for (final TransferRequest request : requests) {
             try {
                 XDAT.sendJmsRequest(new TransferItemRequest(trackingId, request.getId(),
-                        request.getDestinationProject(), user.getUsername(), user.getID()));
+                        request.getDestinationProject(), user.getUsername(), user.getID(),
+                        request.getPreserveSubjectLabel(), request.getPreserveSessionLabel()));
             } catch (Exception e) {
                 // Couldn't enqueue this item — report it as a failed completion so the batch still finishes.
                 log.error("Failed to queue reimport for {}", request.getId(), e);
@@ -311,7 +312,9 @@ public void processItem(final TransferRequest request, final UserI user, final E
             } else if (request.getMode().equals(TransferMode.CLONE)) {
                 getOrCopyExperimentOrAssessor(sourceExperiment, existingExperiment, destinationProjectData, user, eventInfo);
             } else if (request.getMode().equals(TransferMode.REIMPORT)) {
-                importExperiment(sourceExperiment, destinationProjectData, user, eventInfo);
+                importExperiment(sourceExperiment, destinationProjectData, user, eventInfo,
+                        request.getPreserveSubjectLabel(),
+                        request.getPreserveSessionLabel());
             } else {
                 throw new Exception(String.format("Unsupported mode %s", request.getMode()));
             }
@@ -336,7 +339,8 @@ private void shareSubject(XnatSubjectdata sourceSubject, XnatSubjectdata existin
         }
     }
 
-    private void importExperiment(XnatExperimentdata sourceExperiment, XnatProjectdata destinationProjectData, UserI user, EventInfo eventInfo) throws Exception {
+    private void importExperiment(XnatExperimentdata sourceExperiment, XnatProjectdata destinationProjectData, UserI user, EventInfo eventInfo,
+                                  Boolean preserveSubjectLabel, Boolean preserveSessionLabel) throws Exception {
         if (sourceExperiment instanceof XnatImageassessordata) {
             throw new Exception("Reimport operation is not supported for assessors.");
         }
@@ -346,6 +350,27 @@ private void importExperiment(XnatExperimentdata sourceExperiment, XnatProjectda
         params.put("rename", "true");
         params.put("project", destinationProjectData.getId());
 
+        // Preserve the source XNAT labels instead of letting the destination derive them from DICOM
+        // tags. If the user asked to preserve a label but it is blank or missing, there is nothing
+        // usable to override with, so fail the item rather than silently skipping the substitution.
+        if (Boolean.TRUE.equals(preserveSubjectLabel)) {
+            final XnatSubjectdata sourceSubject = XnatUtils.getSubject((String) sourceExperiment.getProperty("subject_ID"), user);
+            final String subjectLabel = sourceSubject.getLabel();
+            if (StringUtils.isBlank(subjectLabel)) {
+                throw new Exception("Cannot preserve the source subject label for " + sourceExperiment.getId()
+                        + ": the source subject label is blank or missing.");
+            }
+            params.put("subject", subjectLabel);
+        }
+        if (Boolean.TRUE.equals(preserveSessionLabel)) {
+            final String sessionLabel = sourceExperiment.getLabel();
+            if (StringUtils.isBlank(sessionLabel)) {
+                throw new Exception("Cannot preserve the source session label for " + sourceExperiment.getId()
+                        + ": the source session label is blank or missing.");
+            }
+            params.put("session", sessionLabel);
+        }
+
         final StreamingZipFileWriter wrapper = new StreamingZipFileWriter(sourcePath, sourceExperiment.getId() + ".zip");
         final AtomicReference<List<String>> uriRef = new AtomicReference<>();
         XnatUtils.doActionWithWorkflow(user, sourceExperiment,

src/main/resources/META-INF/resources/scripts/xnat/plugin/batchTransfer/batchTransfer.js

@@ -191,6 +191,8 @@ var XNAT = getObject(XNAT || {});
 
     function updateOperationDetail() {
         $('#bt-op-detail-desc').text(operationDetails[selectedOp] || '');
+        // The preserve-source-label checkboxes only apply to Reimport.
+        $('#bt-reimport-label-option').toggle(selectedOp === 'Reimport');
     }
 
     // ── Operation Selection ──
@@ -672,15 +674,25 @@ var XNAT = getObject(XNAT || {});
             return false;
         }
 
+        // Reimport only: whether to preserve the source XNAT subject/session labels (server resolves
+        // the actual label values). Ignored for Share/Clone.
+        var preserveSubjectLabel = (selectedOp === 'Reimport') && $('#bt-preserve-subject-label').is(':checked');
+        var preserveSessionLabel = (selectedOp === 'Reimport') && $('#bt-preserve-session-label').is(':checked');
+
         var items = [];
         $selected.each(function() {
             var id = $(this).data('id');
             if (id) {
-                items.push({
+                var item = {
                     id: id,
                     mode: selectedOp,
                     destination_project: selectedProject
-                });
+                };
+                if (selectedOp === 'Reimport') {
+                    item.preserve_subject_label = preserveSubjectLabel;
+                    item.preserve_session_label = preserveSessionLabel;
+                }
+                items.push(item);
             }
         });
 

src/main/resources/META-INF/resources/style/xnat/plugin/batchTransfer/batchTransfer.css

@@ -1008,3 +1008,42 @@ tr.bt-import-disabled[data-type="subject"]:hover {
 .bt-proj-locked-name {
     font-weight: 600;
 }
+
+/* Reimport: preserve-source-label checkboxes, laid out side by side (Subject | Session). */
+.bt-label-options {
+    margin-top: 12px;
+    padding-top: 12px;
+    border-top: 1px solid #e8eaed;
+}
+
+.bt-label-options-title {
+    font-size: 14px;
+    font-weight: 500;
+    color: #202124;
+    margin-bottom: 3px;
+}
+
+.bt-label-options-help {
+    font-size: 12px;
+    color: #5f6368;
+    line-height: 1.45;
+    margin: 0 0 10px;
+}
+
+.bt-label-checks {
+    display: flex;
+    gap: 20px;
+}
+
+.bt-label-checks label {
+    display: inline-flex;
+    align-items: center;
+    font-size: 13px;
+    color: #3c4043;
+    cursor: pointer;
+}
+
+.bt-label-checks input[type="checkbox"] {
+    margin: 0 6px 0 0;
+    vertical-align: middle;
+}

src/main/resources/META-INF/resources/templates/screens/XDATScreen_batch_transfer.vm

@@ -82,6 +82,16 @@
                     <div class="bt-op-desc">Re-anonymize image sessions</div>
                 </div>
             </div>
+            <!-- Reimport only: preserve source XNAT labels instead of deriving them from DICOM tags. -->
+            <div id="bt-reimport-label-option" class="bt-label-options" style="display:none;">
+                <div class="bt-label-options-title">Preserve source labels</div>
+                <p class="bt-label-options-help">Use the source's XNAT labels instead of deriving them from DICOM tags.</p>
+                <div class="bt-label-checks">
+                    <label><input type="checkbox" id="bt-preserve-subject-label" checked /> Subject</label>
+                    <label><input type="checkbox" id="bt-preserve-session-label" checked /> Session</label>
+                </div>
+            </div>
+
         </div>
 
         <!-- About this transfer (operation description + anon status) -->