Well table contextual role support

api/src/org/labkey/api/assay/plate/AssayPlateMetadataService.java

@@ -19,13 +19,17 @@
 import org.labkey.api.gwt.client.model.GWTDomain;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
 import org.labkey.api.qc.DataLoaderSettings;
+import org.labkey.api.query.QuerySchema;
+import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
+import org.labkey.api.security.roles.Role;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.vfs.FileLike;
 
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public interface AssayPlateMetadataService
 {
@@ -178,4 +182,13 @@ void applyHitSelectionCriteria(
         TableInfo resultsTable,
         List<Integer> runIds
     ) throws ValidationException;
+
+    /**
+     * Should only be used to get a local instance of a plate schema where a contextual role might be involved. Schemas created this way are not cached,
+     * and all other usages should retrieve schemas from the QueryService.
+     * <p>
+     * This method would be better placed in the PlateService interface, but it would have required moving that (and other) classes into API.
+     */
+    @NotNull
+    UserSchema getPlateSchema(QuerySchema schema, Set<Role> contextualRoles);
 }

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

@@ -38,6 +38,7 @@
 import org.labkey.api.query.QuerySettings;
 import org.labkey.api.query.QueryView;
 import org.labkey.api.query.SchemaKey;
+import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.roles.ReaderRole;
@@ -56,7 +57,7 @@
 import java.util.Map;
 import java.util.Set;
 
-public class SamplesSchema extends AbstractExpSchema
+public class SamplesSchema extends AbstractExpSchema implements UserSchema.HasContextualRoles
 {
     public static final String SCHEMA_NAME = "samples";
     public static final String STUDY_LINKED_SCHEMA_NAME = "~~STUDY.LINKED.SAMPLE~~";
@@ -107,7 +108,7 @@ public SamplesSchema(QuerySchema schema)
         setDefaultSchema(schema.getDefaultSchema());
     }
 
-    public SamplesSchema(QuerySchema schema, boolean studyLinkedSamples)
+    private SamplesSchema(QuerySchema schema, boolean studyLinkedSamples)
     {
         this(schema.getUser(), schema.getContainer());
         setDefaultSchema(schema.getDefaultSchema());
@@ -126,6 +127,12 @@ public SamplesSchema(User user, Container container)
         this(SchemaKey.fromParts(SCHEMA_NAME), user, container);
     }
 
+    @Override
+    public @NotNull Set<Role> getContextualRoles()
+    {
+        return contextualRoles;
+    }
+
     @Override
     public boolean canReadSchema()
     {

assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java

@@ -78,12 +78,15 @@
 import org.labkey.api.qc.DataState;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QuerySchema;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.RuntimeValidationException;
+import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.DataLoader;
 import org.labkey.api.security.User;
+import org.labkey.api.security.roles.Role;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.Pair;
@@ -93,6 +96,7 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.assay.TSVProtocolSchema;
 import org.labkey.assay.plate.model.WellBean;
+import org.labkey.assay.plate.query.PlateSchema;
 import org.labkey.assay.plate.query.PlateTable;
 import org.labkey.assay.plate.query.WellTable;
 import org.labkey.assay.query.AssayDbSchema;
@@ -1485,6 +1489,12 @@ public String format(FieldKey fieldKey)
         return StringUtils.join(parts, " and ");
     }
 
+    @Override
+    public UserSchema getPlateSchema(QuerySchema querySchema, Set<Role> contextualRoles)
+    {
+        return new PlateSchema(querySchema, contextualRoles);
+    }
+
     private static class PlateMetadataImportHelper extends SimpleAssayDataImportHelper
     {
         private final Map<Integer, Map<Position, Lsid>> _wellPositionMap;       // map of plate position to well table

assay/src/org/labkey/assay/plate/query/PlateSchema.java

@@ -16,6 +16,7 @@
 
 package org.labkey.assay.plate.query;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveTreeSet;
 import org.labkey.api.data.Container;
@@ -25,13 +26,16 @@
 import org.labkey.api.query.DefaultSchema;
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.query.SimpleUserSchema;
+import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.security.roles.Role;
 import org.labkey.assay.query.AssayDbSchema;
 
 import java.util.List;
 import java.util.Set;
 
-public class PlateSchema extends SimpleUserSchema
+public class PlateSchema extends SimpleUserSchema implements UserSchema.HasContextualRoles
 {
     public static final String SCHEMA_NAME = "plate";
     private static final String DESCRIPTION = "Contains data about defined plates";
@@ -48,12 +52,21 @@ public class PlateSchema extends SimpleUserSchema
         AmountUnitsTable.NAME
     ));
 
+    Set<Role> contextualRoles = Set.of();
+
     public PlateSchema(User user, Container container)
     {
         super(SCHEMA_NAME, DESCRIPTION, user, container, AssayDbSchema.getInstance().getSchema(),
                 null, AVAILABLE_TABLES, null);
     }
 
+    public PlateSchema(QuerySchema schema, Set<Role> contextualRoles)
+    {
+        this(schema.getUser(), schema.getContainer());
+        setDefaultSchema(schema.getDefaultSchema());
+        this.contextualRoles = contextualRoles;
+    }
+
     @Override
     public Set<String> getTableNames()
     {
@@ -85,6 +98,18 @@ public TableInfo createTable(String name, ContainerFilter cf)
         return null;
     }
 
+    @Override
+    public @NotNull Set<Role> getContextualRoles()
+    {
+        return contextualRoles;
+    }
+
+    @Override
+    public boolean canReadSchema()
+    {
+        return super.canReadSchema() || getContainer().hasPermission(getUser(), ReadPermission.class, contextualRoles) ;
+    }
+
     public static TableInfo getPlateSetTable(Container container, User user, @Nullable ContainerFilter cf)
     {
         PlateSchema plateSchema = new PlateSchema(user, container);

assay/src/org/labkey/assay/plate/query/WellTable.java

@@ -48,6 +48,7 @@
 import org.labkey.api.security.permissions.DeletePermission;
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.security.permissions.Permission;
+import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.util.UnexpectedException;
 import org.labkey.assay.plate.PlateManager;
 import org.labkey.assay.plate.TsvPlateLayoutHandler;
@@ -374,6 +375,10 @@ public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class<? exten
     {
         if (!_allowInsertDelete && (InsertPermission.class.equals(perm) || DeletePermission.class.equals(perm)))
             return false;
+
+        if (perm.equals(ReadPermission.class))
+            return _userSchema.getContainer().hasPermission(user, perm, _userSchema.getContextualRoles());
+
         return super.hasPermission(user, perm);
     }
 

experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java

@@ -20,14 +20,36 @@
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.plate.AssayPlateMetadataService;
 import org.labkey.api.audit.AuditHandler;
 import org.labkey.api.cache.BlockingCache;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
 import org.labkey.api.compliance.TableRules;
 import org.labkey.api.compliance.TableRulesManager;
-import org.labkey.api.data.*;
+import org.labkey.api.data.ColumnHeaderType;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.CoreSchema;
+import org.labkey.api.data.DataColumn;
+import org.labkey.api.data.DataRegion;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.DisplayColumn;
+import org.labkey.api.data.DisplayColumnFactory;
+import org.labkey.api.data.ImportAliasable;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MaterializedQueryHelper;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.PHI;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.UnionContainerFilter;
 import org.labkey.api.dataiterator.DataIteratorBuilder;
 import org.labkey.api.dataiterator.DataIteratorContext;
 import org.labkey.api.dataiterator.LoggingDataIterator;
@@ -120,7 +142,7 @@
 import static org.labkey.api.exp.query.ExpMaterialTable.Column.AvailableAliquotCount;
 import static org.labkey.api.exp.query.ExpMaterialTable.Column.AvailableAliquotVolume;
 import static org.labkey.api.util.StringExpressionFactory.AbstractStringExpression.NullValueBehavior.NullResult;
-import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.*;
+import static org.labkey.experiment.api.SampleTypeServiceImpl.SampleChangeType.schema;
 
 public class ExpMaterialTableImpl extends ExpRunItemTableImpl<ExpMaterialTable.Column> implements ExpMaterialTable
 {
@@ -780,8 +802,14 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
         if (InventoryService.get() != null && (st == null || !st.isMedia()))
             defaultCols.addAll(InventoryService.get().addInventoryStatusColumns(st == null ? null : st.getMetricUnit(), this, getContainer(), _userSchema.getUser()));
 
-        UserSchema plateUserSchema = QueryService.get().getUserSchema(_userSchema.getUser(), getContainer(), "plate");
         SQLFragment sql;
+        UserSchema plateUserSchema;
+        // Issue 53194 : this would be the case for linked to study samples
+        if (_userSchema instanceof UserSchema.HasContextualRoles samplesSchema && !samplesSchema.getContextualRoles().isEmpty())
+            plateUserSchema = AssayPlateMetadataService.get().getPlateSchema(_userSchema, samplesSchema.getContextualRoles());
+        else
+            plateUserSchema = QueryService.get().getUserSchema(_userSchema.getUser(), _userSchema.getContainer(), "plate");
+
         if (plateUserSchema != null && plateUserSchema.getTable("Well") != null)
         {
             String rowIdField = ExprColumn.STR_TABLE_ALIAS + "." + Column.RowId.name();

experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java

@@ -32,7 +32,25 @@
 import org.labkey.api.audit.TransactionAuditProvider;
 import org.labkey.api.cache.Cache;
 import org.labkey.api.cache.CacheManager;
-import org.labkey.api.data.*;
+import org.labkey.api.data.AuditConfigurable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.DbSequence;
+import org.labkey.api.data.DbSequenceManager;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.NameGenerator;
+import org.labkey.api.data.Parameter;
+import org.labkey.api.data.ParameterMapStatement;
+import org.labkey.api.data.RuntimeSQLException;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.SqlExecutor;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.data.measurement.Measurement;
 import org.labkey.api.defaults.DefaultValueService;

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

@@ -113,7 +113,6 @@ private TableInfo getSamplesTable()
             _sampleType = sampleType;
 
             UserSchema userSchema = QueryService.get().getUserSchema(_userSchema.getUser(), sampleType.getContainer(), SamplesSchema.SCHEMA_NAME);
-
             // Hide 'linked' column for Sample Type Datasets
             if (userSchema instanceof SamplesSchema samplesSchema)
             {