Deprecate ancillary study feature (#6392)

api/src/org/labkey/api/qc/view/manageQCStates.jsp

@@ -27,7 +27,7 @@
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
-    JspView<AbstractManageQCStatesBean> me = (JspView<AbstractManageQCStatesBean>) HttpView.currentView();
+    JspView<AbstractManageQCStatesBean> me = HttpView.currentView();
 
     Container container = getContainer();
     AbstractManageQCStatesBean bean = me.getModelBean();

study/src/org/labkey/study/StudyModule.java

@@ -26,9 +26,11 @@
 import org.labkey.api.admin.notification.NotificationService;
 import org.labkey.api.attachments.AttachmentService;
 import org.labkey.api.audit.AuditLogService;
+import org.labkey.api.collections.LabKeyCollectors;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.PropertySchema;
+import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
@@ -53,6 +55,7 @@
 import org.labkey.api.qc.DataStateManager;
 import org.labkey.api.qc.export.DataStateImportExportHelper;
 import org.labkey.api.query.DefaultSchema;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.snapshot.QuerySnapshotService;
 import org.labkey.api.reports.ReportContentEmailManager;
@@ -95,8 +98,11 @@
 import org.labkey.api.study.security.permissions.ManageStudyPermission;
 import org.labkey.api.usageMetrics.UsageMetricsService;
 import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.HtmlStringBuilder;
 import org.labkey.api.util.JspTestCase;
+import org.labkey.api.util.Link;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.SystemMaintenance;
 import org.labkey.api.util.UsageReportingLevel;
 import org.labkey.api.view.ActionURL;
@@ -110,6 +116,9 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.api.view.WebPartView;
+import org.labkey.api.view.template.WarningProvider;
+import org.labkey.api.view.template.WarningService;
+import org.labkey.api.view.template.Warnings;
 import org.labkey.api.wiki.WikiRenderingService;
 import org.labkey.api.writer.ContainerUser;
 import org.labkey.study.assay.ExperimentListenerImpl;
@@ -133,7 +142,26 @@
 import org.labkey.study.dataset.DatasetSnapshotProvider;
 import org.labkey.study.dataset.DatasetViewProvider;
 import org.labkey.study.importer.StudyImporterFactory;
-import org.labkey.study.model.*;
+import org.labkey.study.model.CohortDomainKind;
+import org.labkey.study.model.ContinuousDatasetDomainKind;
+import org.labkey.study.model.DatasetDefinition;
+import org.labkey.study.model.DateDatasetDomainKind;
+import org.labkey.study.model.GroupSecurityType;
+import org.labkey.study.model.ImportHelperServiceImpl;
+import org.labkey.study.model.Participant;
+import org.labkey.study.model.ParticipantGroupManager;
+import org.labkey.study.model.ParticipantGroupServiceImpl;
+import org.labkey.study.model.ParticipantIdImportHelper;
+import org.labkey.study.model.ProtocolDocumentType;
+import org.labkey.study.model.SequenceNumImportHelper;
+import org.labkey.study.model.StudyDomainKind;
+import org.labkey.study.model.StudyImpl;
+import org.labkey.study.model.StudyLsidHandler;
+import org.labkey.study.model.StudyManager;
+import org.labkey.study.model.TestDatasetDomainKind;
+import org.labkey.study.model.TreatmentManager;
+import org.labkey.study.model.VisitDatasetDomainKind;
+import org.labkey.study.model.VisitImpl;
 import org.labkey.study.pipeline.StudyPipeline;
 import org.labkey.study.qc.StudyQCImportExportHelper;
 import org.labkey.study.qc.StudyQCStateHandler;
@@ -174,6 +202,7 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.stream.Collectors;
@@ -401,9 +430,15 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
             false, false, FeatureType.Deprecated));
 
         AdminConsole.addExperimentalFeatureFlag(DatasetQueryView.EXPERIMENTAL_QUERY_DATASETS,
-                "Allow query based dataset snapshots",
-                "Allow unprovisioned, query-based dataset snapshots to be created.",
-                false);
+            "Allow query based dataset snapshots",
+            "Allow unprovisioned, query-based dataset snapshots to be created.",
+            false);
+
+        AdminConsole.addOptionalFeatureFlag(new OptionalFeatureFlag(StudyManager.ENABLE_ANCILLARY_STUDIES,
+            "Restore ability to create ancillary studies",
+            "This option and all support for creating ancillary studies will be removed in LabKey Server v25.4.",
+            false, false, FeatureType.Deprecated
+        ));
 
         ReportAndDatasetChangeDigestProvider.get().addNotificationInfoProvider(new DatasetNotificationInfoProvider());
 
@@ -429,6 +464,9 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
                 metric.put("linkedAssayDatasetCount", new SqlSelector(StudySchema.getInstance().getSchema(), "SELECT COUNT(PublishSourceType) FROM study.dataset WHERE PublishSourceType = 'Assay'").getObject(Long.class));
 
                 metric.put("redcapCount", new SqlSelector(PropertySchema.getInstance().getSchema(), "SELECT COUNT(*) FROM prop.PropertySets WHERE Category = 'RedcapConfigurationSettings'").getObject(Long.class));
+
+                // Note: study.StudySnapshot maintains a rows for deleted child studies (allowing re-creation of those child studies).
+                // In that case, Destination is set to null. COUNT(DISTINCT) skips these null values, so this returns the count of existing child studies.
                 metric.put("publishStudyCount", new SqlSelector(PropertySchema.getInstance().getSchema(), "SELECT COUNT(DISTINCT destination) FROM study.StudySnapshot WHERE Type = 'publish'").getObject(Long.class));
                 metric.put("ancillaryStudyCount", new SqlSelector(PropertySchema.getInstance().getSchema(), "SELECT COUNT(DISTINCT destination) FROM study.StudySnapshot WHERE Type = 'ancillary'").getObject(Long.class));
 
@@ -504,6 +542,40 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
 
         AdminConsole.addLink(AdminConsole.SettingsLinkType.Premium, "Master Patient Index", new ActionURL(StudyController.MasterPatientProviderAction.class, ContainerManager.getRoot()), AdminPermission.class);
         DataStateImportExportHelper.registerProvider(new StudyQCImportExportHelper());
+
+        WarningService.get().register(new WarningProvider()
+        {
+            @Override
+            public void addStaticWarnings(@NotNull Warnings warnings, boolean showAllWarnings)
+            {
+                MutableInt count = new MutableInt(0);
+                HtmlString links = getAncillaryStudies(count);
+                if (showAllWarnings || !links.isEmpty())
+                {
+                    HtmlStringBuilder builder = HtmlStringBuilder.of(
+                        "Support for ancillary studies will be removed in the next release of LabKey Server. This " +
+                        "server has " + StringUtilsLabKey.pluralize(count.getValue(), "ancillary study",
+                        "ancillary studies") + ": [")
+                        .append(links)
+                        .append("]. Contact your LabKey Account Manager if you have any concerns about this change.");
+                    warnings.add(builder);
+                }
+            }
+
+            private HtmlString getAncillaryStudies(MutableInt count)
+            {
+                StudyUrls urls = PageFlowUtil.urlProvider(StudyUrls.class);
+                TableInfo studySnapshot = StudySchema.getInstance().getTableInfoStudySnapshot();
+                FieldKey type = studySnapshot.getColumn("Type").getFieldKey();
+                return new TableSelector(studySnapshot, Collections.singleton("Destination"), new SimpleFilter(type, "ancillary"), null).stream(String.class)
+                    .filter(Objects::nonNull)
+                    .map(ContainerManager::getForId)
+                    .filter(Objects::nonNull)
+                    .map(c -> new Link.LinkBuilder(c.getPath()).href(urls.getBeginURL(c)).clearClasses().build().getHtmlString())
+                    .peek(h -> count.increment())
+                    .collect(LabKeyCollectors.joining(HtmlString.of(", ")));
+            }
+        });
     }
 
     @Override

study/src/org/labkey/study/controllers/StudyController.java

@@ -3573,6 +3573,11 @@ public void setShowPrivateDataByDefault(boolean showPrivateDataByDefault)
         }
     }
 
+    public static ActionURL getManageQCStatesURL(Container c, @NotNull ActionURL returnUrl)
+    {
+        return new ActionURL(ManageQCStatesAction.class, c).addReturnURL(returnUrl);
+    }
+
     @RequiresPermission(AdminPermission.class)
     public class ManageQCStatesAction extends AbstractManageQCStatesAction<ManageQCStatesForm>
     {

study/src/org/labkey/study/model/StudyManager.java

@@ -73,7 +73,6 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.UpdateableTableInfo;
-import org.labkey.api.data.UpgradeCode;
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.dataiterator.BeanDataIterator;
 import org.labkey.api.dataiterator.DataIteratorBuilder;
@@ -103,7 +102,6 @@
 import org.labkey.api.exp.property.SystemProperty;
 import org.labkey.api.gwt.client.AuditBehaviorType;
 import org.labkey.api.module.Module;
-import org.labkey.api.module.ModuleContext;
 import org.labkey.api.module.ModuleHtmlView;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.portal.ProjectUrls;
@@ -234,6 +232,7 @@ public class StudyManager
 {
     public static final SearchService.SearchCategory datasetCategory = new SearchService.SearchCategory("dataset", "Study Datasets");
     public static final SearchService.SearchCategory subjectCategory = new SearchService.SearchCategory("subject", "Study Subjects");
+    public static final String ENABLE_ANCILLARY_STUDIES = "enableAncillaryStudies";
 
     private static final Logger _log = LogManager.getLogger(StudyManager.class);
     private static final StudyManager _instance = new StudyManager();

study/src/org/labkey/study/query/DatasetQueryView.java

@@ -612,8 +612,7 @@ private MenuButton createQCStateButton()
         {
             if (!addSeparator)
                 button.addSeparator();
-            button.addMenuItem("Manage states", new ActionURL(StudyController.ManageQCStatesAction.class,
-                    getContainer()).addReturnURL(getViewContext().getActionURL()));
+            button.addMenuItem("Manage states", StudyController.getManageQCStatesURL(getContainer(), getViewContext().getActionURL()));
         }
         return button;
     }

study/src/org/labkey/study/view/manageStudy.jsp

@@ -27,6 +27,7 @@
 <%@ page import="org.labkey.api.security.User" %>
 <%@ page import="org.labkey.api.security.permissions.AdminPermission" %>
 <%@ page import="org.labkey.api.security.permissions.ReadPermission" %>
+<%@ page import="org.labkey.api.settings.OptionalFeatureService" %>
 <%@ page import="org.labkey.api.study.Dataset" %>
 <%@ page import="org.labkey.api.study.FolderArchiveSource" %>
 <%@ page import="org.labkey.api.study.Study" %>
@@ -36,19 +37,20 @@
 <%@ page import="org.labkey.api.study.TimepointType" %>
 <%@ page import="org.labkey.api.study.Visit" %>
 <%@ page import="org.labkey.api.study.model.ParticipantGroup" %>
+<%@ page import="org.labkey.api.util.HtmlString" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.study.StudyInternalServiceImpl" %>
 <%@ page import="org.labkey.study.controllers.CohortController.ManageCohortsAction" %>
+<%@ page import="org.labkey.study.controllers.StudyController" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ConfigureMasterPatientSettingsAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.DeleteStudyAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.DemoModeAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageExternalReloadAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageLocationsAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageParticipantCategoriesAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageParticipantsAction" %>
-<%@ page import="org.labkey.study.controllers.StudyController.ManageQCStatesAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageStudyPropertiesAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageTypesAction" %>
 <%@ page import="org.labkey.study.controllers.StudyController.ManageVisitsAction" %>
@@ -251,7 +253,7 @@
                     <tr>
                         <td class="lk-study-prop-label">Quality Control States</td>
                         <td class="lk-study-prop-desc">Manage QC states for datasets in this study</td>
-                        <td><%=link("Manage Dataset QC States", ManageQCStatesAction.class) %></td>
+                        <td><%=link("Manage Dataset QC States", StudyController.getManageQCStatesURL(getContainer(), getActionURL())) %></td>
                     </tr>
                     <tr>
                         <td class="lk-study-prop-label">Study Products</td>
@@ -338,7 +340,7 @@
     if (study.allowExport(getUser()))
     {
 %>
-        <%= button("Create Ancillary Study").onClick("showCreateStudyWizard('ancillary'); return false;") %>
+        <%= OptionalFeatureService.get().isFeatureEnabled(StudyManager.ENABLE_ANCILLARY_STUDIES) ? button("Create Ancillary Study").onClick("showCreateStudyWizard('ancillary'); return false;") : HtmlString.EMPTY_STRING%>
         <%= button("Publish Study").onClick("showCreateStudyWizard('publish'); return false;") %>
 <%
     }

study/test/src/org/labkey/test/tests/study/AncillaryStudyTest.java

@@ -23,6 +23,7 @@
 import org.labkey.test.categories.Daily;
 import org.labkey.test.tests.StudyBaseTest;
 import org.labkey.test.util.DataRegionTable;
+import org.labkey.test.util.OptionalFeatureHelper;
 import org.labkey.test.util.StudyHelper;
 import org.labkey.test.util.WikiHelper;
 
@@ -75,6 +76,7 @@ public void doCleanup(boolean afterTest) throws TestTimeoutException
     {
         _containerHelper.deleteProject(getProjectName(), afterTest);
         TestFileUtils.deleteDir(new File(StudyHelper.getStudySubfolderPath(), "export"));
+        OptionalFeatureHelper.disableOptionalFeature(createDefaultConnection(), "enableAncillaryStudies");
     }
 
     @Override
@@ -101,6 +103,7 @@ public void doCreateSteps()
 
     private void createAncillaryStudy()
     {
+        OptionalFeatureHelper.enableOptionalFeature(createDefaultConnection(), "enableAncillaryStudies");
         navigateToFolder(PROJECT_NAME, getFolderName());
         clickTab("Manage");