Merge 25.7 to develop

Author: labkey-teamcity

api/src/org/labkey/api/query/AbstractQueryImportAction.java

@@ -609,7 +609,7 @@ else if (!dataFileDir.exists())
             //di = wrap(di, ve);
             //importData(di, ve);
 
-            configureLoader(loader);
+            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases(), getOptionParamsMap());
 
             TransactionAuditProvider.TransactionAuditEvent auditEvent = null;
             if (isCrossTypeImport || (behaviorType != null && behaviorType != AuditBehaviorType.NONE))
@@ -650,13 +650,12 @@ else if (!dataFileDir.exists())
 
     }
 
-    protected void configureLoader(DataLoader loader) throws IOException
+    public static void configureLoader(DataLoader loader, @Nullable TableInfo target, @Nullable Map<String, String> renamedColumns, boolean allowLineageColumns, @Nullable Set<String> lineageAliasNames, @Nullable Map<Params, Boolean> optionParamsMap) throws IOException
     {
-        configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), null);
-    }
+        // Issue 53804: When updating or adding samples across different sample types, the strings 'Yes' and 'No' are converted to their boolean values
+        if (loader != null && optionParamsMap != null && optionParamsMap.getOrDefault(Params.crossTypeImport, false))
+            loader.setInferTypes(false);
 
-    public static void configureLoader(DataLoader loader, @Nullable TableInfo target, @Nullable Map<String, String> renamedColumns, boolean allowLineageColumns, @Nullable Set<String> lineageAliasNames) throws IOException
-    {
         //apply known columns so loader can do better type conversion
         if (loader != null && target != null)
             loader.setKnownColumns(target.getColumns());

api/src/org/labkey/api/query/QueryImportPipelineJob.java

@@ -294,7 +294,7 @@ public void run()
 
             loader = DataLoader.get().createLoader(_importContextBuilder.getPrimaryFile(), _importContextBuilder.getFileContentType(), _importContextBuilder.isHasColumnHeaders(), null, null);
 
-            AbstractQueryImportAction.configureLoader(loader, target, _importContextBuilder.getRenamedColumns(), _importContextBuilder.allowLineageColumns(), _importContextBuilder.getLineageImportAliases());
+            AbstractQueryImportAction.configureLoader(loader, target, _importContextBuilder.getRenamedColumns(), _importContextBuilder.allowLineageColumns(), _importContextBuilder.getLineageImportAliases(), _importContextBuilder.getOptionParamsMap());
 
             DataIteratorContext diContext = createDataIteratorContext(ve, getContainer());
 

experiment/src/org/labkey/experiment/ExpDataIterators.java

@@ -2527,7 +2527,7 @@ private int _importSplitFile(TypeData typeData, File splitFile, Container dataCo
                 else
                     aliasNames = new CaseInsensitiveHashSet(((ExpDataClass) typeData.dataType).getImportAliases().keySet());
                 // We do not need to configure the loader for renamed columns as that has been taken care of when writing the file.
-                configureLoader(loader, dataTable, null, true, aliasNames);
+                configureLoader(loader, dataTable, null, true, aliasNames, null /* Not needed since partition is not a cross type import*/);
                 if (loader instanceof TabLoader tabLoader)
                     tabLoader.setIncludeComments(true); // don't skip lines that starts with "#" (if the original file is Excel)
                 QueryService.get().setEnvironment(QueryService.Environment.CONTAINER, dataContainer);

experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java

@@ -4507,13 +4507,6 @@ protected JSONObject createSuccessResponse(int rowCount)
             return json;
         }
 
-        @Override
-        protected void configureLoader(DataLoader loader) throws IOException
-        {
-            if (getOptionParamValue(Params.crossTypeImport))
-                loader.setInferTypes(false);
-            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases());
-        }
     }
 
     public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction<QueryForm>
@@ -4671,12 +4664,6 @@ public void addNavTrail(NavTree root)
             root.addChild("Import Data");
         }
 
-        @Override
-        protected void configureLoader(DataLoader loader) throws IOException
-        {
-            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases());
-        }
-
     }
 
     @RequiresPermission(UpdatePermission.class)

issues/src/org/labkey/issue/IssueServiceImpl.java

@@ -140,7 +140,8 @@ public Issue saveIssue(ViewContext context, Issue issue, Issue.action action, Li
                     for (int curIssueId : prevIssues)
                     {
                         IssueObject relatedIssue = ChangeSummary.relatedIssueCommentHandler(issueObject.getIssueId(), curIssueId, user, true);
-                        IssueManager.saveIssue(getRelatedIssueUser(container, user, relatedIssue), container, relatedIssue);
+                        if (null != relatedIssue)
+                            IssueManager.saveIssue(getRelatedIssueUser(container, user, relatedIssue), container, relatedIssue);
                     }
                 }
 

issues/src/org/labkey/issue/actions/IssueValidation.java

@@ -235,13 +235,18 @@ public static void relatedIssueHandler(IssueObject issue, User user, Errors erro
                 }
             }
 
-            // Issue 40178: Related Issues need to be in synch when related issues are deleted
+            // Issue 40178: Related Issues need to be in sync when related issues are deleted
             for (Integer originalRelatedId : originalRelatedIssues)
             {
                 if (!newRelatedIssues.contains(originalRelatedId))
                 {
                     IssueObject related = IssueManager.getIssue(null, user, originalRelatedId);
-                    if (null != related)
+                    if (related == null || !related.lookupContainer().hasPermission(user, ReadPermission.class))
+                    {
+                        errors.reject(SpringActionController.ERROR_MSG, "User does not have Read Permission for related issue '" + originalRelatedId + "'");
+                        return;
+                    }
+                    else
                     {
                       related = ChangeSummary.relatedIssueCommentHandler(originalIssue.getIssueId(), related.getIssueId(), user, true );
                       IssueManager.saveIssue(user, related.lookupContainer(), related);

query/api-src/org/labkey/remoteapi/SelectRowsStreamHack.java

@@ -195,17 +195,13 @@ public void testFileDeletion() throws Exception
                 DataIteratorContext dic = new DataIteratorContext();
 
                 DataIterator di = dib.getDataIterator(dic);
-
-                // This should create the file:
-                Set<String> actualTempFiles = getMatchingTempFileNames();
-                assertEquals("Temp file not created", preexistingTempFiles.size() + 1, actualTempFiles.size());
-
+                
                 // This should iterate and close the stream:
                 long actualCount = di.stream().count();
                 assertEquals("Incorrect row count", expectedRows, actualCount);
 
                 // The file should be deleted now:
-                actualTempFiles = getMatchingTempFileNames();
+                Set<String> actualTempFiles = getMatchingTempFileNames();
                 actualTempFiles.removeAll(preexistingTempFiles);
                 assertEquals("Temp files were not deleted, found: " + actualTempFiles.size(), 0, actualTempFiles.size());