Return Set<Class<?>> from Module "get test" methods

announcements/src/org/labkey/announcements/AnnouncementModule.java

@@ -200,8 +200,7 @@ public void startBackgroundThreads()
     }
 
     @Override
-    @NotNull
-    public Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return Set.of(
             AnnouncementManager.TestCase.class
@@ -228,7 +227,6 @@ public Collection<String> getSummary(Container c)
         return list;
     }
 
-
     @Override
     public void enumerateDocuments(SearchService.TaskIndexingQueue queue, final Date modifiedSince)
     {

api/src/org/labkey/api/ApiModule.java

@@ -361,7 +361,7 @@ public void registerServlets(ServletContext servletCtx)
     }
 
     @Override
-    public @NotNull Set<Class> getUnitTests()
+    public @NotNull Set<Class<?>> getUnitTests()
     {
         return Set.of(
             Aggregate.TestCase.class,
@@ -458,7 +458,7 @@ public void registerServlets(ServletContext servletCtx)
     }
 
     @Override
-    public @NotNull Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return Set.of(
             AbstractAuditDomainKind.TestCase.class,

api/src/org/labkey/api/audit/AbstractAuditTypeProvider.java

@@ -85,12 +85,6 @@ public abstract class AbstractAuditTypeProvider implements AuditTypeProvider
 
     private final AbstractAuditDomainKind _domainKind;
 
-    @Deprecated // Call the other constructor and stop overriding getDomainKind()
-    public AbstractAuditTypeProvider()
-    {
-        this(null);
-    }
-
     public AbstractAuditTypeProvider(@NotNull AbstractAuditDomainKind domainKind)
     {
         // TODO: consolidate domain kind initialization to this constructor and stop overriding getDomainKind()
@@ -99,7 +93,7 @@ public AbstractAuditTypeProvider(@NotNull AbstractAuditDomainKind domainKind)
         PropertyService.get().registerDomainKind(getDomainKind());
     }
 
-    protected AbstractAuditDomainKind getDomainKind()
+    protected final AbstractAuditDomainKind getDomainKind()
     {
         if (_domainKind == null)
             throw new IllegalStateException(String.format("The audit type : \"%s\" has a null domain kind", getLabel()));

api/src/org/labkey/api/data/NameGenerator.java

@@ -43,7 +43,6 @@
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
-import org.labkey.api.reader.TabLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.JunitUtil;
@@ -919,7 +918,7 @@ else if (ancestorPaths != null && !ancestorPaths.isEmpty())
                     dataTypes.add(sampleType);
             }
             else
-                dataTypes.addAll(SampleTypeService.get().getSampleTypes(_container, user, true));
+                dataTypes.addAll(SampleTypeService.get().getSampleTypes(_container, true));
         }
         if (isData)
         {
@@ -1122,7 +1121,7 @@ private void initialize(@Nullable Map<String, String> importAliasesMap)
             }
 
 
-            for (ExpSampleType sampleType : SampleTypeService.get().getSampleTypes(_container, user, true))
+            for (ExpSampleType sampleType : SampleTypeService.get().getSampleTypes(_container, true))
             {
                 sampleTypeLSIDs.put(sampleType.getName(), sampleType.getLSID());
                 sampleTypeNames.put(sampleType.getLSID(), sampleType.getName());

api/src/org/labkey/api/data/generator/DataGenerator.java

@@ -217,7 +217,7 @@ public List<? extends ExpSampleType> getSampleTypes(List<String> sampleTypeNames
         {
             SampleTypeService service = SampleTypeService.get();
             if (sampleTypeNames.isEmpty())
-                _sampleTypes.addAll(service.getSampleTypes(getContainer(), getUser(), false));
+                _sampleTypes.addAll(service.getSampleTypes(getContainer(), false));
             else
             {
                 for (String typeName : sampleTypeNames)
@@ -345,7 +345,7 @@ public void generateSamplesForAllTypes() throws SQLException, BatchValidationExc
         boolean hasParentTypes = !parentTypes.isEmpty();
         // Default to using all types in the container
         if (!hasParentTypes)
-            parentTypes.addAll(SampleTypeService.get().getSampleTypes(getContainer(), getUser(), false).stream().map(ExpSampleType::getName).toList());
+            parentTypes.addAll(SampleTypeService.get().getSampleTypes(getContainer(), false).stream().map(ExpSampleType::getName).toList());
         List<String> dataClassParents = new ArrayList<>(config.getDataClassParents());
         // Default to using all types in the container
         if (dataClassParents.isEmpty())

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -939,7 +939,7 @@ ExpRun derive(
     List<ObjectReferencer> getObjectReferencers();
 
     @NotNull
-    String getObjectReferenceDescription(Class referencedClass);
+    String getObjectReferenceDescription(Class<?> referencedClass);
 
     @Nullable ProtocolImplementation getProtocolImplementation(String name);
 

api/src/org/labkey/api/exp/api/ObjectReferencer.java

@@ -15,5 +15,5 @@ default Collection<Long> getItemsWithReferences(Collection<Long> referencedRowId
     @NotNull Collection<Long> getItemsWithReferences(Collection<Long> referencedRowIds, @NotNull String referencedSchemaName, @Nullable String referencedQueryName);
 
     @Nullable
-    String getObjectReferenceDescription(Class referencedClass);
+    String getObjectReferenceDescription(Class<?> referencedClass);
 }

api/src/org/labkey/api/exp/api/SampleTypeService.java

@@ -165,35 +165,40 @@ ExpSampleType createSampleType(Container c, User u, String name, String descript
     @Nullable
     DataState getSampleState(Container container, Long stateRowId);
 
-    void removeAutoLinkedStudy(@NotNull Container studyContainer, @Nullable User user);
+    void removeAutoLinkedStudy(@NotNull Container studyContainer);
 
     /**
      * @param includeOtherContainers whether sample types from the shared container or the container's project should be included
      */
-    // TODO: Remove user parameter (not used)
-    List<? extends ExpSampleType> getSampleTypes(@NotNull Container container, @Nullable User user, boolean includeOtherContainers);
+    List<? extends ExpSampleType> getSampleTypes(@NotNull Container container, boolean includeOtherContainers);
+
+    @Deprecated // Temporary just to keep code compiling during migration to new method
+    default List<? extends ExpSampleType> getSampleTypes(@NotNull Container container, User user, boolean includeOtherContainers)
+    {
+        return getSampleTypes(container, includeOtherContainers);
+    }
 
     /**
      * Get a SampleType by name within the definition container.
      */
     ExpSampleType getSampleType(@NotNull Container definitionContainer, @NotNull String sampleTypeName);
 
+    /**
+     * Get a SampleType by name within scope -- current, project, and shared.
+     * Requires a user to check for container read permission.
+     */
+    // TODO: Remove user parameter (not used)
+    ExpSampleType getSampleType(@NotNull Container scope, @NotNull User user, @NotNull String sampleTypeName);
+
     /** Get the sample type with name at a specific time */
     @Nullable
-    // TODO: Remove user parameter (not used)
-    ExpSampleType getEffectiveSampleType(@NotNull Container definitionContainer, @NotNull User user, @NotNull String sampleTypeName, @NotNull Date effectDate, @Nullable ContainerFilter cf);
+    ExpSampleType getEffectiveSampleType(@NotNull Container definitionContainer, @NotNull String sampleTypeName, @NotNull Date effectDate, @Nullable ContainerFilter cf);
 
     /**
      * Return the sample type for this LSID, optionally pass Container hint for performance
      */
     ExpSampleType getSampleTypeByType(@NotNull String lsid, Container hint);
 
-    /**
-     * Get a SampleType by name within scope -- current, project, and shared.
-     * Requires a user to check for container read permission.
-     */
-    ExpSampleType getSampleType(@NotNull Container scope, @NotNull User user, @NotNull String sampleTypeName);
-
     /**
      * Get a SampleType by rowId within the definition container.
      */

api/src/org/labkey/api/exp/query/SamplesSchema.java

@@ -77,7 +77,7 @@ static private Map<String, ExpSampleType> getSampleTypeMap(Container container,
     {
         Map<String, ExpSampleType> map = new CaseInsensitiveTreeMap<>();
         // User can be null if we're running in a background thread, such as doing a study export
-        for (ExpSampleType st : SampleTypeService.get().getSampleTypes(container, user, user != null))
+        for (ExpSampleType st : SampleTypeService.get().getSampleTypes(container, user != null))
         {
             map.put(st.getName(), st);
         }

api/src/org/labkey/api/module/DefaultModule.java

@@ -494,15 +494,13 @@ protected void addWebPart(String name, Container c, @Nullable String location, i
     }
 
     @Override
-    @NotNull
-    public Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return Collections.emptySet();
     }
 
     @Override
-    @NotNull
-    public Set<Class> getUnitTests()
+    public @NotNull Set<Class<?>> getUnitTests()
     {
         return Collections.emptySet();
     }

api/src/org/labkey/api/module/MockModule.java

@@ -232,15 +232,13 @@ public TabDisplayMode getTabDisplayMode()
     }
 
     @Override
-    @NotNull
-    public Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return Collections.emptySet();
     }
 
     @Override
-    @NotNull
-    public Set<Class> getUnitTests()
+    public @NotNull Set<Class<?>> getUnitTests()
     {
         return Collections.emptySet();
     }

api/src/org/labkey/api/module/Module.java

@@ -236,11 +236,12 @@ default void startBackgroundThreads()
      * Modules can provide JUnit tests that must be run inside the server
      * VM. These tests will be executed as part of the DRT. These are not true unit tests, and may rely on external
      * resources such as a database connection or services provided by other modules.
+     *
      * @return the integration tests that this module provides
      */
-    @NotNull
     @JsonIgnore
-    Set<Class> getIntegrationTests();
+    @NotNull
+    Set<Class<?>> getIntegrationTests();
 
     /**
      * Modules can provide JUnit tests that must be run inside the server
@@ -258,11 +259,12 @@ default void startBackgroundThreads()
     /**
      * Modules can provide JUnit tests that can be run independent of the server VM. Satisfies the requirements for a
      * traditional unit test.
+     *
      * @return the unit tests that this module provides
      */
-    @NotNull
     @JsonIgnore
-    Set<Class> getUnitTests();
+    @NotNull
+    Set<Class<?>> getUnitTests();
 
     /**
      * Returns a set of schemas that the module wants tested. The DbSchema junit test calls this and ensures that the

api/src/org/labkey/api/module/SimpleWebPartFactory.java

@@ -183,15 +183,15 @@ public String getViewName()
 
 
     @Override
-    public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart) throws WebPartConfigurationException
+    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart) throws WebPartConfigurationException
     {
         if (null != _loadException)
             throw new WebPartConfigurationException(this, "Error thrown during load", _loadException);
 
         if (null == getViewName())
             throw new WebPartConfigurationException(this, "No view name specified for the module web part defined in " + _resourceName);
 
-        WebPartView ret = ModuleHtmlView.get(getModule(), ModuleHtmlView.getStandardPath(getViewName()), webPart);
+        WebPartView<?> ret = ModuleHtmlView.get(getModule(), ModuleHtmlView.getStandardPath(getViewName()), webPart);
         if (null != _webPartDef && null != _webPartDef.getView())
         {
             if (null != _webPartDef.getView().getFrame())

api/src/org/labkey/api/study/security/SecurityEscalationAuditProvider.java

@@ -50,11 +50,6 @@
  */
 public abstract class SecurityEscalationAuditProvider extends AbstractAuditTypeProvider implements AuditTypeProvider
 {
-    protected SecurityEscalationAuditProvider()
-    {
-        super();
-    }
-
     protected SecurityEscalationAuditProvider(AbstractAuditDomainKind dk)
     {
         super(dk);

api/src/org/labkey/api/study/security/StudySecurityEscalationAuditProvider.java

@@ -25,6 +25,11 @@ public class StudySecurityEscalationAuditProvider extends SecurityEscalationAudi
     public static String EVENT_TYPE = StudySecurityEscalationEvent.class.getSimpleName();
     public static String AUDIT_LOG_TITLE = "Study Security Escalations";
 
+    public StudySecurityEscalationAuditProvider()
+    {
+        super(new StudySecurityEscalationDomainKind());
+    }
+
     @Override
     public String getDescription() {
         return "This audits all uses of the Study Security Escalation";
@@ -45,11 +50,6 @@ public String getAuditLogTitle() {
         return AUDIT_LOG_TITLE;
     }
 
-    public StudySecurityEscalationAuditProvider()
-    {
-        super(new StudySecurityEscalationDomainKind());
-    }
-
     public static class StudySecurityEscalationEvent extends SecurityEscalationEvent
     {
         /** Important for reflection-based instantiation */

api/src/org/labkey/api/view/DefaultWebPartFactory.java

@@ -43,7 +43,7 @@ public DefaultWebPartFactory(String name, Class<? extends WebPartView> cls, @Not
     }
 
     @Override
-    public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
+    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
     {
         if (!portalCtx.hasPermission(ReadPermission.class))
             return new HtmlView("Not Authorized", HtmlString.of(portalCtx.getUser().isGuest() ? "Please log in to see this data." : "You do not have permission to see this data"));

api/src/org/labkey/api/view/SimpleWebPartFactory.java

@@ -131,7 +131,7 @@ ModelAndView newInstance(ViewContext portalCtx, Portal.WebPart wp, Object form,
 
 
     @Override
-    public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
+    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
     {
         Object form = null;
         BindException errors = null;
@@ -154,7 +154,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta
         if (view instanceof HttpView && _formClass != null)
             ((HttpView)view).setModelBean(form);
         if (view instanceof WebPartView)
-            return (WebPartView)view;
+            return (WebPartView<?>)view;
         VBox v = new VBox(view);
         v.setTitle(getName());
         return v;

assay/src/org/labkey/assay/AssayModule.java

@@ -327,7 +327,7 @@ public Set<String> getProvisionedSchemaNames()
     }
 
     @Override
-    public @NotNull Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return Set.of(
             ModuleAssayCache.TestCase.class,
@@ -345,7 +345,7 @@ public Set<String> getProvisionedSchemaNames()
     }
 
     @Override
-    public @NotNull Set<Class> getUnitTests()
+    public @NotNull Set<Class<?>> getUnitTests()
     {
         return Set.of(
             TsvAssayProvider.TestCase.class,

assay/src/org/labkey/assay/view/AssayBaseWebPartFactory.java

@@ -87,7 +87,7 @@ public static Long getProtocolId(Portal.WebPart webPart)
 //    }
 
     @Override
-    public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
+    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
     {
         Long protocolId = getProtocolId(webPart);
         ProtocolIdForm protocolIdForm = new ProtocolIdForm();
@@ -97,7 +97,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta
 
         boolean showButtons = Boolean.parseBoolean(webPart.getPropertyMap().get(SHOW_BUTTONS_KEY));
         ExpProtocol protocol;
-        WebPartView view;
+        WebPartView<?> view;
         try
         {
             protocol = protocolIdForm.getProtocol(true);
@@ -113,7 +113,7 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta
         return view;
     }
 
-    public abstract WebPartView getWebPartView(ViewContext portalCtx, Portal.WebPart webPart, ExpProtocol protocol, boolean showButtons);
+    public abstract WebPartView<?> getWebPartView(ViewContext portalCtx, Portal.WebPart webPart, ExpProtocol protocol, boolean showButtons);
 
     public abstract String getDescription();
 
@@ -124,7 +124,7 @@ public static class EditViewBean
     }
 
     @Override
-    public HttpView getEditView(Portal.WebPart webPart, ViewContext context)
+    public HttpView<?> getEditView(Portal.WebPart webPart, ViewContext context)
     {
         EditViewBean bean = new EditViewBean();
         bean.description = getDescription();

assay/src/org/labkey/assay/view/AssayListWebPartFactory.java

@@ -37,9 +37,9 @@ public AssayListWebPartFactory()
     }
 
     @Override
-    public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
+    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
     {
-        WebPartView listView = AssayService.get().createAssayListView(portalCtx, true, null);
+        WebPartView<?> listView = AssayService.get().createAssayListView(portalCtx, true, null);
         ActionURL url = PageFlowUtil.urlProvider(AssayUrls.class).getBeginURL(portalCtx.getContainer());
         listView.setTitle("Assay List");
         listView.setTitleHref(url);