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Create annotation to track UtilityActions and Admin Console page to list them
1 parent 5db8f70 commit 167faa4

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5 files changed

+288
-1
lines changed

5 files changed

+288
-1
lines changed

‎SequenceAnalysis/build.gradle‎

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@@ -44,6 +44,7 @@ dependencies {
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BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "apiJarFile")
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BuildUtils.addExternalDependency(
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project,
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new ExternalDependency(

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java‎

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@@ -72,6 +72,7 @@
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import org.labkey.api.data.Table;
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import org.labkey.api.data.TableInfo;
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import org.labkey.api.data.TableSelector;
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import org.labkey.api.discvrcore.annotation.UtilityAction;
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import org.labkey.api.exceptions.OptimisticConflictException;
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import org.labkey.api.exp.ExperimentException;
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import org.labkey.api.exp.api.DataType;
@@ -501,6 +502,7 @@ public void export(ConvertTextToFileForm form, HttpServletResponse response, Bin
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}
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}
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@UtilityAction(label = "Find Orphan Files", description = "This will start a pipeline job that will inspect all files in this folder to identify potential orphan or otherwise unnecessary files")
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@RequiresPermission(ReadPermission.class)
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public static class FindOrphanFilesAction extends ConfirmAction<Object>
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{
@@ -5065,6 +5067,7 @@ public void setOutputFileIds(Integer[] outputFileIds)
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}
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}
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@UtilityAction(label = "Update ExpData Path", description = "This will update the DataFileUrl on the selected ExpData to the path provided")
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@RequiresSiteAdmin
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public static class UpdateExpDataPathAction extends ConfirmAction<UpdateExpDataPathForm>
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{

‎discvrcore/api-src/org/labkey/api/discvrcore/annotation/UtilityAction.java‎

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@@ -0,0 +1,16 @@
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package org.labkey.api.discvrcore.annotation;
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import org.jetbrains.annotations.Nullable;
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import java.lang.annotation.ElementType;
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import java.lang.annotation.Retention;
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import java.lang.annotation.RetentionPolicy;
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import java.lang.annotation.Target;
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@Retention(RetentionPolicy.RUNTIME) @Target(ElementType.TYPE)
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public @interface UtilityAction
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{
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String description();
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String label();
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}

‎discvrcore/src/org/labkey/discvrcore/DiscvrCoreController.java‎

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@@ -16,15 +16,279 @@
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package org.labkey.discvrcore;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.Logger;
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import org.jetbrains.annotations.NotNull;
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import org.labkey.api.action.ConfirmAction;
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import org.labkey.api.action.SimpleErrorView;
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import org.labkey.api.action.SimpleRedirectAction;
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import org.labkey.api.action.SimpleViewAction;
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import org.labkey.api.action.SpringActionController;
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import org.labkey.api.audit.AuditLogService;
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import org.labkey.api.data.Container;
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import org.labkey.api.data.ContainerManager;
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import org.labkey.api.data.CoreSchema;
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import org.labkey.api.data.DbSequenceManager;
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import org.labkey.api.data.SqlExecutor;
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import org.labkey.api.data.TableInfo;
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import org.labkey.api.discvrcore.annotation.UtilityAction;
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import org.labkey.api.module.Module;
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import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.pipeline.PipelineUrls;
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import org.labkey.api.query.DetailsURL;
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import org.labkey.api.query.UserSchema;
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import org.labkey.api.security.RequiresPermission;
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import org.labkey.api.security.permissions.AdminPermission;
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import org.labkey.api.util.DOM;
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import org.labkey.api.util.GUID;
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import org.labkey.api.util.Link;
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.api.util.URLHelper;
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import org.labkey.api.util.logging.LogHelper;
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import org.labkey.api.view.ActionURL;
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import org.labkey.api.view.HtmlView;
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import org.labkey.api.view.NavTree;
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import org.springframework.validation.BindException;
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import org.springframework.validation.Errors;
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import org.springframework.web.servlet.ModelAndView;
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import org.springframework.web.servlet.mvc.Controller;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Map;
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import java.util.TreeMap;
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import static javax.swing.Spring.width;
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import static org.labkey.api.util.DOM.Attribute.valign;
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import static org.labkey.api.util.DOM.at;
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import static org.labkey.api.util.DOM.cl;
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public class DiscvrCoreController extends SpringActionController
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{
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private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(DiscvrCoreController.class);
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public static final String NAME = "discvrcore";
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private static final Logger _log = LogHelper.getLogger(DiscvrCoreController.class, "Messages from DISCVR Core Controller");
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public DiscvrCoreController()
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{
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setActionResolver(_actionResolver);
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}
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@UtilityAction(label = "Truncate Query Audit Log", description = "Provides a mechanism to truncate the query and dataset audit tables for a container")
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@RequiresPermission(AdminPermission.class)
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public static class TruncateQueryAuditLogAction extends ConfirmAction<Object>
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{
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@Override
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public ModelAndView getConfirmView(Object o, BindException errors) throws Exception
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{
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setTitle("Truncate Query/Dataset Audit Logs");
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return HtmlView.of("This will truncate the query and dataset audit logs for this container. Do you want to continue?");
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}
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@Override
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public boolean handlePost(Object o, BindException errors) throws Exception
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{
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UserSchema us = AuditLogService.getAuditLogSchema(getUser(), getContainer());
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for (String tableName : Arrays.asList("DatasetAuditEvent", "QueryUpdateAuditEvent"))
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{
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TableInfo ti = us.getTable(tableName);
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ti.getUpdateService().truncateRows(getUser(), getContainer(), null, null);
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}
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return true;
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}
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@Override
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public void validateCommand(Object o, Errors errors)
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{
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}
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@NotNull
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@Override
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public URLHelper getSuccessURL(Object o)
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{
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return PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
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}
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}
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@RequiresPermission(AdminPermission.class)
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public static class ShowUtilityActionsAction extends SimpleViewAction<Object>
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{
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@Override
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public ModelAndView getView(Object form, BindException errors)
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{
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Map<String, DOM.Renderable> items = new TreeMap<>();
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Collection<Module> modules = getContainer().isRoot() ? ModuleLoader.getInstance().getModules() : getContainer().getActiveModules();
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for (Module m : modules)
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{
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m.getControllerNameToClass().forEach((key, controllerCls) -> {
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Arrays.stream(controllerCls.getDeclaredClasses()).filter(x -> x.isAnnotationPresent(UtilityAction.class)).forEach(x -> {
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if (Controller.class.isAssignableFrom(x))
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{
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UtilityAction annot = x.getAnnotation(UtilityAction.class);
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Class<? extends Controller> actionClass = (Class<? extends Controller>)x;
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items.put(annot.label(), DOM.TR(
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DOM.TD(at(valign,"top"), new Link.LinkBuilder(annot.label()).href(new ActionURL(actionClass, getContainer())).build()),
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DOM.TD(at(valign,"top"), annot.description())
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));
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}
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});
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});
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}
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return new HtmlView(DOM.TABLE(cl("labkey-data-region-legacy","labkey-show-borders"), items.values()));
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}
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@Override
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public void addNavTrail(NavTree root)
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{
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root.addChild("Utility & Management Actions");
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}
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}
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@UtilityAction(label = "Move Workbook", description = "This will move this workbook to the selected folder, renaming this workbook to match the series in that container. Note: there are many reasons this can be problematic, so please do this with great care")
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@RequiresPermission(AdminPermission.class)
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public static class MoveWorkbookAction extends ConfirmAction<MoveWorkbookForm>
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{
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private Container _movedWb = null;
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@Override
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public void validateCommand(MoveWorkbookForm form, Errors errors)
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{
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}
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@Override
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public ModelAndView getConfirmView(MoveWorkbookForm form, BindException errors) throws Exception
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{
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if (!getContainer().isWorkbook())
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{
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errors.reject(ERROR_MSG, "This is only supported for workbooks");
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return new SimpleErrorView(errors);
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}
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String sb = "This will move this workbook to the selected folder, renaming this workbook to match the series in that container. Note: there are many reasons this can be problematic, so please do this with great care<p>" +
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"<input name=\"targetContainer\" type=\"text\"></input>";
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return new HtmlView(sb);
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}
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@Override
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public boolean handlePost(MoveWorkbookForm form, BindException errors) throws Exception
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{
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Container toMove = getContainer();
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if (!toMove.isWorkbook())
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{
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errors.reject(ERROR_MSG, "This is only supported for workbooks");
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return false;
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}
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if (StringUtils.trimToNull(form.getTargetContainer()) == null)
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{
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errors.reject(ERROR_MSG, "Must provide target container");
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return false;
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}
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Container target = ContainerManager.getForPath(StringUtils.trimToNull(form.getTargetContainer()));
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if (target == null)
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{
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target = ContainerManager.getForId(StringUtils.trimToNull(form.getTargetContainer()));
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}
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if (target == null)
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{
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errors.reject(ERROR_MSG, "Unknown container: " + form.getTargetContainer());
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return false;
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}
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if (target.isWorkbook())
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{
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errors.reject(ERROR_MSG, "Target cannot be a workbook: " + form.getTargetContainer());
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return false;
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}
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if (ContainerManager.isSystemContainer(target))
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{
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errors.reject(ERROR_MSG, "Cannot move to system containers: " + form.getTargetContainer());
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return false;
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}
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if (target.equals(toMove.getParent()))
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{
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errors.reject(ERROR_MSG, "Cannot move the workbook to its current parent: " + form.getTargetContainer());
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return false;
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}
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//NOTE: transaction causing problems for larger sites?
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//try (DbScope.Transaction transaction = CoreSchema.getInstance().getSchema().getScope().ensureTransaction())
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//{
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//first rename workbook to make unique
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String tempName = new GUID().toString();
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int sortOrder = (int) DbSequenceManager.get(target, ContainerManager.WORKBOOK_DBSEQUENCE_NAME).next();
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_log.info("renaming workbook to in preparation for move from: " + toMove.getPath() + " to: " + tempName);
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ContainerManager.rename(toMove, getUser(), tempName);
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toMove = ContainerManager.getForId(toMove.getId());
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//then move parent
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_log.info("moving workbook from: " + toMove.getPath() + " to: " + target.getPath());
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ContainerManager.move(toMove, target, getUser());
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toMove = ContainerManager.getForId(toMove.getId());
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//finally move to correct name
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_log.info("renaming workbook from: " + toMove.getPath() + " to: " + sortOrder);
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ContainerManager.rename(toMove, getUser(), String.valueOf(sortOrder));
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toMove.setSortOrder(sortOrder);
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new SqlExecutor(CoreSchema.getInstance().getSchema()).execute("UPDATE core.containers SET SortOrder = ? WHERE EntityId = ?", toMove.getSortOrder(), toMove.getId());
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toMove = ContainerManager.getForId(toMove.getId());
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//transaction.commit();
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_log.info("workbook move finished");
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_movedWb = toMove;
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//}
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return true;
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}
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@NotNull
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@Override
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public URLHelper getSuccessURL(MoveWorkbookForm moveWorkbookForm)
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{
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if (_movedWb == null)
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return getContainer().getStartURL(getUser());
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else
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return _movedWb.getStartURL(getUser());
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}
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}
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public static class MoveWorkbookForm
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{
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private String _targetContainer;
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public String getTargetContainer()
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{
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return _targetContainer;
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}
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public void setTargetContainer(String targetContainer)
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{
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_targetContainer = targetContainer;
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}
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}
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// This allows registration of this action without creating a dependency between laboratory and discvrcore
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@UtilityAction(label = "Set Table Increment Value", description = "This allows you to reset the current value for an auto-incrementing table")
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@RequiresPermission(AdminPermission.class)
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public class SetTableIncrementValueAction extends SimpleRedirectAction<Object>
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{
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@Override
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public URLHelper getRedirectURL(Object o) throws Exception
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{
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return DetailsURL.fromString("laboratory/setTableIncrementValue.view", getContainer()).getActionURL();
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}
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}
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}

‎discvrcore/src/org/labkey/discvrcore/DiscvrCoreModule.java‎

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@@ -18,8 +18,11 @@
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import org.jetbrains.annotations.NotNull;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.data.ContainerManager;
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import org.labkey.api.module.DefaultModule;
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import org.labkey.api.module.ModuleContext;
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import org.labkey.api.query.DetailsURL;
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import org.labkey.api.settings.AdminConsole;
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.api.view.WebPartFactory;
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@@ -66,7 +69,7 @@ protected void init()
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@Override
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public void doStartup(ModuleContext moduleContext)
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{
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AdminConsole.addLink(AdminConsole.SettingsLinkType.Management, "site utility actions", DetailsURL.fromString("discvrcore/showUtilityActions.view", ContainerManager.getRoot()).getActionURL());
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}
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@Override

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