Remove unused User parameters from service methods

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

@@ -28,16 +28,14 @@
 public interface AuditTypeProvider
 {
     /**
-     * The audit event name associated with this audit provider. Must be
-     * unique within the system.
+     * The audit event name associated with this audit provider. Must be unique within the system.
      */
     String getEventName();
     String getLabel();
     String getDescription();
 
     /**
-     * Perform any initialization of the provider at registration time such as
-     * domain creation.
+     * Perform any initialization of the provider at registration time such as domain creation.
      * @param user User used when saving the backing Domain.
      */
     void initializeProvider(User user);

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

@@ -852,14 +852,14 @@ public static boolean isParentInputWithDataType(String[] parts, @Nullable String
 
         if (isMaterial || isInput)
         {
-            if (SampleTypeService.get().getSampleType(container, user, dataType) != null)
+            if (SampleTypeService.get().getSampleType(container, dataType, true) != null)
                 return true;
 
             if (isMaterial)
                 return false;
         }
 
-        return ExperimentService.get().getDataClass(container, user, dataType) != null;
+        return ExperimentService.get().getDataClass(container, dataType, true) != null;
     }
 
     private Object getParentLookupTokenPreview(String currentDataType, FieldKey fkTok, String inputPrefix, @Nullable String inputDataType, @Nullable NameExpressionAncestorPartOption ancestorPartOption, String lookupField, User user, Map<String, String> dataClassNames, Map<String, String> sampleTypeNames)
@@ -913,7 +913,7 @@ else if (ancestorPaths != null && !ancestorPaths.isEmpty())
         {
             if (!StringUtils.isEmpty(inputDataType))
             {
-                ExpSampleType sampleType = SampleTypeService.get().getSampleType(_container, user, inputDataType);
+                ExpSampleType sampleType = SampleTypeService.get().getSampleType(_container, inputDataType, true);
                 if (sampleType != null)
                     dataTypes.add(sampleType);
             }
@@ -924,12 +924,12 @@ else if (ancestorPaths != null && !ancestorPaths.isEmpty())
         {
             if (!StringUtils.isEmpty(inputDataType))
             {
-                ExpDataClass dataClass = ExperimentService.get().getDataClass(_container, user, inputDataType);
+                ExpDataClass dataClass = ExperimentService.get().getDataClass(_container, inputDataType, true);
                 if (dataClass != null)
                     dataTypes.add(dataClass);
             }
             else
-                dataTypes.addAll(ExperimentService.get().getDataClasses(_container, user, true));
+                dataTypes.addAll(ExperimentService.get().getDataClasses(_container, true));
         }
 
         boolean isCurrentDataType = inputDataType != null && inputDataType.equals(currentDataType);
@@ -1114,7 +1114,7 @@ private void initialize(@Nullable Map<String, String> importAliasesMap)
 
         if (_container != null)
         {
-            for (ExpDataClass dataClass : ExperimentService.get().getDataClasses(_container, user, true))
+            for (ExpDataClass dataClass : ExperimentService.get().getDataClasses(_container, true))
             {
                 dataClassLSIDs.put(dataClass.getName(), dataClass.getLSID());
                 dataClassNames.put(dataClass.getLSID(), dataClass.getName());

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

@@ -539,8 +539,8 @@ else if (expParentLookupFields.containsKey(FieldKey.fromParts(ExpData.DATA_INPUT
         Map<String, ExpSampleType> sampleTypes = getSampleTypes();
         Map<String, ExpDataClass> dataClasses = getDataClasses();
         ExpObject parentObjectType = isMaterialParent ?
-                sampleTypes.computeIfAbsent(parentTypeName, (name) -> SampleTypeService.get().getSampleType(_container, _user, name))
-                : dataClasses.computeIfAbsent(parentTypeName, (name) -> ExperimentService.get().getDataClass(_container, _user, name));
+                sampleTypes.computeIfAbsent(parentTypeName, (name) -> SampleTypeService.get().getSampleType(_container, name, true))
+                : dataClasses.computeIfAbsent(parentTypeName, (name) -> ExperimentService.get().getDataClass(_container, name, true));
         if (parentObjectType == null)
             throw new RuntimeValidationException("Invalid parent type: " + parentTypeName);
 

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

@@ -222,7 +222,7 @@ public List<? extends ExpSampleType> getSampleTypes(List<String> sampleTypeNames
             {
                 for (String typeName : sampleTypeNames)
                 {
-                    ExpSampleType sampleType = service.getSampleType(getContainer(), getUser(), typeName);
+                    ExpSampleType sampleType = service.getSampleType(getContainer(), typeName, true);
                     if (sampleType == null)
                         _log.warn(String.format("Unable to resolve sample type by name '%s'.", typeName));
                     else
@@ -302,7 +302,7 @@ public void generateSampleTypes(String namePrefix, String namingPatternPrefix) t
                 typeIndex++;
                 sampleTypeName = namePrefix + typeIndex;
             }
-            while (service.getSampleType(_container, _user, sampleTypeName) != null);
+            while (service.getSampleType(_container, sampleTypeName, true) != null);
             String prefixWithIndex = namingPatternPrefix + typeIndex + "_";
             String namingPattern = prefixWithIndex + "${genId}";
             ExpSampleType sampleType = generateSampleType(sampleTypeName, namingPattern, numFields);
@@ -349,7 +349,7 @@ public void generateSamplesForAllTypes() throws SQLException, BatchValidationExc
         List<String> dataClassParents = new ArrayList<>(config.getDataClassParents());
         // Default to using all types in the container
         if (dataClassParents.isEmpty())
-            dataClassParents.addAll(ExperimentService.get().getDataClasses(getContainer(), getUser(), false).stream().map(ExpDataClass::getName).toList());
+            dataClassParents.addAll(ExperimentService.get().getDataClasses(getContainer(), false).stream().map(ExpDataClass::getName).toList());
         for (ExpSampleType sampleType : getSampleTypes(_config.getSampleTypeNames()))
         {
             _log.info(String.format("Generating %d samples for sample type '%s'.", numSamples, sampleType.getName()));
@@ -702,7 +702,7 @@ public int generateDerivedSamples(ExpSampleType sampleType, Collection<String> p
         {
             parentInput = "DataInputs";
             parentQueryNames.forEach(parentQueryName -> {
-                ExpObject parentObject = ExperimentService.get().getDataClass(_container, _user, parentQueryName);
+                ExpObject parentObject = ExperimentService.get().getDataClass(_container, parentQueryName, true);
                 if (parentObject != null)
                     parentObjects.add(parentObject);
             });
@@ -711,7 +711,7 @@ public int generateDerivedSamples(ExpSampleType sampleType, Collection<String> p
         {
             parentInput = "MaterialInputs";
             parentQueryNames.forEach(parentQueryName -> {
-                ExpObject parentObject = SampleTypeService.get().getSampleType(_container, _user, parentQueryName);
+                ExpObject parentObject = SampleTypeService.get().getSampleType(_container, parentQueryName, true);
                 if (parentObject != null)
                     parentObjects.add(parentObject);
             });

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

@@ -505,7 +505,7 @@ else if (materialObject.has(ExperimentJSONConverter.LSID))
                 else if (sampleTypeJson.has(ExperimentJSONConverter.NAME))
                 {
                     String sampleTypeName = sampleTypeJson.getString(ExperimentJSONConverter.NAME);
-                    sampleType = SampleTypeService.get().getSampleType(context.getContainer(), context.getUser(), sampleTypeName);
+                    sampleType = SampleTypeService.get().getSampleType(context.getContainer(), sampleTypeName, true);
                     if (sampleType == null)
                         throw new NotFoundException("A sample type named '" + sampleTypeName + "' doesn't exist.");
                 }

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

@@ -251,7 +251,7 @@ ExpRun createRunForProvenanceRecording(Container container, User user,
     ExpData getEffectiveData(@NotNull ExpDataClass dataClass, String name, @NotNull Date effectiveDate, @NotNull Container container, @Nullable ContainerFilter cf);
 
     /**
-     * Create a data object.  The object will be unsaved, and will have a name which is a GUID.
+     * Create a data object. The object will be unsaved, and will have a name which is a GUID.
      */
     ExpData createData(Container container, @NotNull DataType type);
 
@@ -293,66 +293,52 @@ ValidationException updateDataClass(
     void validateDataClassName(@NotNull Container c, @NotNull User u, String name, boolean skipExisting);
 
     /**
-     * Get all DataClass definitions in the container.  If <code>includeOtherContainers</code> is true,
-     * a user must be provided to check for read permission of the containers in scope.
+     * Get all DataClass definitions in the container
      */
-    // TODO: Remove user parameter (not used)
-    List<? extends ExpDataClass> getDataClasses(@NotNull Container container, @Nullable User user, boolean includeOtherContainers);
+    List<? extends ExpDataClass> getDataClasses(@NotNull Container container, boolean includeOtherContainers);
 
     /**
-     * Get a DataClass by name within the definition container.
+     * Get a DataClass by name within the definition container
      */
     ExpDataClass getDataClass(@NotNull Container definitionContainer, @NotNull String dataClassName);
 
     /**
-     * Get a DataClass by name within scope -- current, project, and shared.
-     * Requires a user to check for container read permission.
+     * Get a DataClass by name within scope -- current plus, if <code>includeOtherContainers</code> is true, project and shared
      */
-    // TODO: Remove user parameter (not used)
-    ExpDataClass getDataClass(@NotNull Container scope, @NotNull User user, @NotNull String dataClassName);
+    ExpDataClass getDataClass(@NotNull Container scope, @NotNull String dataClassName, boolean includeProjectAndShared);
 
     /**
-     * Get a DataClass by rowId within the definition container.
+     * Get a DataClass by rowId within the definition container
      */
     ExpDataClass getDataClass(@NotNull Container definitionContainer, long rowId);
 
     /**
-     * Get a DataClass by rowId within scope -- current, project, and shared.
-     * Requires a user to check for container read permission.
+     * Get a DataClass by rowId within scope -- current plus, if <code>includeOtherContainers</code> is true, project and shared
      */
-    // TODO: Remove user parameter (not used)
-    ExpDataClass getDataClass(@NotNull Container scope, @NotNull User user, long rowId);
+    ExpDataClass getDataClass(@NotNull Container scope, long rowId, boolean includeProjectAndShared);
 
     /**
      * Get a DataClass by LSID.
-     * NOTE: Prefer using one of the getDataClass methods that accept a Container and User for permission checking.
+     * NOTE: Prefer using one of the getDataClass methods that accept a Container
      */
     @Nullable ExpDataClass getDataClass(@NotNull String lsid);
 
     /**
      * Get a DataClass by RowId
-     * NOTE: Prefer using one of the getDataClass methods that accept a Container and User for permission checking.
+     * NOTE: Prefer using one of the getDataClass methods that accept a Container
      */
     ExpDataClass getDataClass(long rowId);
 
     /**
      * Get a DataClass with name at a specific time.
      */
-    // TODO: Remove user parameter (not used)
     @Nullable ExpDataClass getEffectiveDataClass(
         @NotNull Container definitionContainer,
-        @NotNull User user,
         @NotNull String dataClassName,
         @NotNull Date effectiveDate,
         @Nullable ContainerFilter cf
     );
 
-    /**
-     * Get a ExpProtocol with name at a specific time.
-     */
-    // TODO: Delete?
-    ExpProtocol getEffectiveProtocol(Container container, User user, String schemaName, Date effectiveDate, ContainerFilter dataTypeCF);
-
     /**
      * Get materials by rowId in this, project, or shared container and within the provided sample type.
      *
@@ -622,9 +608,10 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
      * ignoring any sample children derived from ExpData children.
      */
     Set<ExpMaterial> getRelatedChildSamples(Container c, User user, ExpData start);
+
     /**
-     * Get the lineage for the seed Identifiable object.  Typically, the seed object is a ExpMaterial,
-     * a ExpData (in a DataClass), or an ExpRun.
+     * Get the lineage for the seed Identifiable object. Typically, the seed object is an ExpMaterial,
+     * an ExpData (in a DataClass), or an ExpRun.
      */
     @NotNull
     ExpLineage getLineage(Container c, User user, @NotNull Identifiable start, @NotNull ExpLineageOptions options);

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

@@ -172,23 +172,15 @@ ExpSampleType createSampleType(Container c, User u, String name, String descript
      */
     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.
+     * Get a SampleType by name within scope -- current plus, if <code>includeOtherContainers</code> is true, project and shared
      */
-    // TODO: Remove user parameter (not used)
-    ExpSampleType getSampleType(@NotNull Container scope, @NotNull User user, @NotNull String sampleTypeName);
+    ExpSampleType getSampleType(@NotNull Container scope, @NotNull String sampleTypeName, boolean includeOtherContainers);
 
     /** Get the sample type with name at a specific time */
     @Nullable
@@ -205,11 +197,9 @@ default List<? extends ExpSampleType> getSampleTypes(@NotNull Container containe
     ExpSampleType getSampleType(@NotNull Container definitionContainer, long rowId);
 
     /**
-     * Get a SampleType by rowId within scope -- current, project, and shared.
-     * Requires a user to check for container read permission.
+     * Get a SampleType by rowId within scope -- current plus, if <code>includeOtherContainers</code> is true, project and shared
      */
-    // TODO: Remove user parameter (not used)
-    ExpSampleType getSampleType(@NotNull Container scope, @NotNull User user, long rowId);
+    ExpSampleType getSampleType(@NotNull Container scope, long rowId, boolean includeOtherContainers);
 
     Lsid getSampleTypeLsid(String name, Container container);
 

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

@@ -48,11 +48,11 @@ public class DataClassUserSchema extends AbstractExpSchema
 
     private Map<String, ExpDataClass> _map;
 
-    static private Map<String, ExpDataClass> getDataClassMap(Container container, User user)
+    static private Map<String, ExpDataClass> getDataClassMap(Container container)
     {
         Map<String, ExpDataClass> map = new CaseInsensitiveTreeMap<>();
         // User can be null if we're running in a background thread, such as doing a study export.
-        for (ExpDataClass dataClass : ExperimentService.get().getDataClasses(container, user, true))
+        for (ExpDataClass dataClass : ExperimentService.get().getDataClasses(container, true))
         {
             map.put(dataClass.getName(), dataClass);
         }
@@ -73,7 +73,7 @@ private DataClassUserSchema(Container container, User user, Map<String, ExpDataC
     private Map<String, ExpDataClass> getDataClasses()
     {
         if (_map == null)
-            _map = getDataClassMap(getContainer(), getUser());
+            _map = getDataClassMap(getContainer());
         return _map;
     }
 

assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java

@@ -259,7 +259,7 @@ private static List<? extends ExpMaterial> createExpMaterials(Container c, User
     // If none exist, a new SampleType named "Samples" is created.
     private static @NotNull ExpSampleType ensureSampleType(Container c, User user) throws ExperimentException
     {
-        List<? extends ExpSampleType> sampleTypes = SampleTypeService.get().getSampleTypes(c, user, true);
+        List<? extends ExpSampleType> sampleTypes = SampleTypeService.get().getSampleTypes(c, true);
         if (sampleTypes.isEmpty())
         {
             return createSampleType(c, user);