Issue 695: Upgrade script version of fixing container for sample files that have moved (#7365)

Author: labkey-susanh

experiment/resources/schemas/dbscripts/postgresql/exp-26.001-26.002.sql

@@ -0,0 +1 @@
+SELECT core.executeJavaUpgradeCode('fixContainerForMovedSampleFiles');

experiment/resources/schemas/dbscripts/sqlserver/exp-26.001-26.002.sql

@@ -0,0 +1 @@
+EXEC core.executeJavaUpgradeCode 'fixContainerForMovedSampleFiles';

experiment/src/org/labkey/experiment/ExperimentModule.java

@@ -205,7 +205,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.001;
+        return 26.002;
     }
 
     @Nullable

experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java

@@ -52,6 +52,7 @@
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.property.DomainUtil;
 import org.labkey.api.exp.property.PropertyService;
+import org.labkey.api.files.FileContentService;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.ontology.Unit;
@@ -484,4 +485,28 @@ else if (kind.getStorageSchemaName() == null)
 
         return new ProvisionedSampleTypeContext(domain, provisionedTable);
     }
+
+    /**
+     * Called from exp-26.001-26.002.sql
+     */
+    @SuppressWarnings("unused")
+    public static void fixContainerForMovedSampleFiles(ModuleContext context)
+    {
+        if (context.isNewInstall())
+            return;
+
+        try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction())
+        {
+            FileContentService service = FileContentService.get();
+            if (service == null)
+            {
+                LOG.error("No FileContentService found. Aborting.");
+                return;
+            }
+            LimitedUser admin = new LimitedUser(context.getUpgradeUser(), SiteAdminRole.class);
+            int numDuplicates = service.fixContainerForExpDataFiles(admin);
+            LOG.info("Fixed {} duplicate data files.", numDuplicates);
+        }
+    }
+
 }

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

@@ -7460,25 +7460,6 @@ public Object execute(Object o, BindException errors) throws Exception
         }
     }
 
-    @Marshal(Marshaller.Jackson)
-    @RequiresPermission(AdminPermission.class)
-    public static class RepairExpDataFilesAction extends MutatingApiAction<Object>
-    {
-        @Override
-        public Object execute(Object form, BindException errors)
-        {
-            FileContentService service = FileContentService.get();
-            if (service == null)
-            {
-                errors.reject(ERROR_GENERIC, "No FileContentService found");
-                return new SimpleResponse<>(false, "No FileContentService found");
-            }
-
-            int numDuplicates = service.fixContainerForExpDataFiles(getUser());
-            return success(Map.of("hadRepairs", numDuplicates > 0));
-        }
-    }
-
     @RequiresPermission(UpdatePermission.class)
     public static class UpdateMaterialQueryRowAction extends UserSchemaAction
     {

filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java

@@ -154,7 +154,8 @@ WHERE datafileurl IN (SELECT DataFileURL
                                                                                  FROM exp.data
                                                                                  WHERE DataFileURL IS NOT NULL
                                                                                  GROUP BY DataFileUrl) c
-                                                                           WHERE c.count > 1))""");
+                                                                           WHERE c.count > 1))
+                                                     AND datafileurl LIKE '%/sampletype/%'""");
         int count = new SqlExecutor(ExperimentService.get().getSchema().getScope()).execute(sql);
         _log.info("Deleted {} duplicate entries from exp.data", count);
         _log.info("Repopulating file data in exp.data.");
@@ -169,10 +170,7 @@ private void ensureFileDataInAllContainers(User user)
 
                     ExpDataTable expDataTable = ExperimentService.get().createDataTable("data", new ExpSchema(user, c), null);
                     if (expDataTable != null)
-                    {
-                        _log.info("Ensuring file data in container {}", c.getPath());
                         ensureFileDataUnsynchronized(expDataTable);
-                    }
                 }
         );
     }