Immutable TableInfo

TODO_ContainerFilter.md

@@ -0,0 +1,48 @@
+remove interface ContainerFilterable (migrate method to protected methods e.g. on FilteredTable)
+
+remove class DelegatingContainerFilter
+
+test ContainerFilter for ExperimentService.get().createQCFlagsTable
+
+SpecimenForeignKey calls to getSpecimenTableInfo(null)
+
+Find classes that override:
+- UserSchema.createTable(String name)
+- AssayProtocolSchema.createProviderTable(String name)
+- AssayProtocolSchema.createDataTable(boolean includeCopiedToStudyColumns)
+- AssayProtocolSchema.createRunsTable()
+- AssayResultTable.AssayResultTable(AssayProtocolSchema schema, boolean includeCopiedToStudyColumns)
+
+convert schemas: ms2, study, annoucements, flow
+
+Find classes that use constructor
+- SimpleTable(SchemaType schema, TableInfo table)
+
+Who is still depending on AbstractExpSchema.setupTable(T table) to set containerFilter???
+
+LineageTableInfo
+
+More clean up of QueryForeignKey (Builder?)
+More clean up of PdLookupForeignKey (.create()?)
+
+QueryDefinitionImpl.getTable() remove usage of deprecated method w/o ContainerFilter
+
+Issues.AllIssuesTable
+IsuesTable.RelatedIssues lookup uses setFk() on locked table
+
+search for "TODO ContainerFilter"
+
+Check subclasses of LookupForeignKey.  getLookupTableInfo() should use getLookupContainerFilter()
+
+update MultiValuedForeignKey to take CF, check usages of passed in FK to make sure they are configured with CF
+
+Check that subclasses of QueryView initialize ContainerFilter when they construct TableInfo
+
+How does setting effectiveContainer (when != source container) on QFK affect the ContainerFilter?  If effectiveContainer != sourceContainer
+maybe it should have the same effect as setting lookupContainer?  see for instance, ExperimentsTable in oconnorexperiments
+
+
+
+OTHER BIGGER IDEAS
+* separate ContainerFilter factory e.g. CurrentContainer(?) from  ContainerFilter bound instance e.g. "CurrentContainer("/home")
+* Make ColumnInfo and ColumnRenderProperties read-only interfaces and AbstactColumnInfo the constrctable implementation 

elisa/src/org/labkey/elisa/ElisaProtocolSchema.java

@@ -18,6 +18,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.security.User;
@@ -36,8 +37,8 @@ public ElisaProtocolSchema(User user, Container container, @NotNull ElisaAssayPr
     }
 
     @Override
-    public FilteredTable createDataTable(boolean includeCopiedToStudyColumns)
+    public FilteredTable createDataTable(ContainerFilter cf, boolean includeCopiedToStudyColumns)
     {
-        return new ElisaResultsTable(this, includeCopiedToStudyColumns);
+        return new ElisaResultsTable(this, cf, includeCopiedToStudyColumns);
     }
 }

elisa/src/org/labkey/elisa/query/ElisaResultsTable.java

@@ -15,7 +15,9 @@
  */
 package org.labkey.elisa.query;
 
+import org.labkey.api.data.BaseColumnInfo;
 import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpSampleSet;
 import org.labkey.api.exp.api.ExperimentService;
@@ -41,9 +43,9 @@
  */
 public class ElisaResultsTable extends AssayResultTable
 {
-    public ElisaResultsTable(final AssayProtocolSchema schema, boolean includeCopiedToStudyColumns)
+    public ElisaResultsTable(final AssayProtocolSchema schema, ContainerFilter cf, boolean includeCopiedToStudyColumns)
     {
-        super(schema, includeCopiedToStudyColumns);
+        super(schema, cf, includeCopiedToStudyColumns);
 
         List<FieldKey> visibleColumns = new ArrayList<>();
 
@@ -60,19 +62,19 @@ public ElisaResultsTable(final AssayProtocolSchema schema, boolean includeCopied
         }
 
         // add a lookup to the material table
-        ColumnInfo specimenColumn = _columnMap.get(ElisaDataHandler.ELISA_INPUT_MATERIAL_DATA_PROPERTY);
+        BaseColumnInfo specimenColumn = (BaseColumnInfo)_columnMap.get(ElisaDataHandler.ELISA_INPUT_MATERIAL_DATA_PROPERTY);
         specimenColumn.setFk(new LookupForeignKey("LSID")
         {
             public TableInfo getLookupTableInfo()
             {
-                ExpMaterialTable materials = ExperimentService.get().createMaterialTable(ExpSchema.TableType.Materials.toString(), schema);
+                ExpMaterialTable materials = ExperimentService.get().createMaterialTable(ExpSchema.TableType.Materials.toString(), schema, cf);
                 // Make sure we are filtering to the same set of containers
                 materials.setContainerFilter(getContainerFilter());
                 if (sampleSet != null)
                 {
                     materials.setSampleSet(sampleSet, true);
                 }
-                ColumnInfo propertyCol = materials.addColumn(ExpMaterialTable.Column.Property);
+                var propertyCol = materials.addColumn(ExpMaterialTable.Column.Property);
                 if (propertyCol.getFk() instanceof PropertyForeignKey)
                 {
                     ((PropertyForeignKey)propertyCol.getFk()).addDecorator(new SpecimenPropertyColumnDecorator(_provider, _protocol, schema));

elispotassay/src/org/labkey/elispot/ElispotProtocolSchema.java

@@ -21,6 +21,7 @@
 import org.labkey.api.data.ActionButton;
 import org.labkey.api.data.ButtonBar;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.CrosstabMember;
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.data.TableInfo;
@@ -67,6 +68,7 @@ public ElispotAssayProvider getProvider()
         return (ElispotAssayProvider)super.getProvider();
     }
 
+    @Override
     public Set<String> getTableNames()
     {
         Set<String> names = super.getTableNames();
@@ -75,26 +77,27 @@ public Set<String> getTableNames()
         return names;
     }
 
-    public TableInfo createProviderTable(String name)
+    @Override
+    public TableInfo createProviderTable(String name, ContainerFilter cf)
     {
         if (name.equalsIgnoreCase(ANTIGEN_TABLE_NAME))
         {
             Domain domain = AbstractAssayProvider.getDomainByPrefix(getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
             if (null != domain)
-                return new ElispotRunAntigenTable(this, domain, getProtocol());
+                return new ElispotRunAntigenTable(this, cf, domain, getProtocol());
         }
         else if (name.equalsIgnoreCase(ANTIGEN_STATS_TABLE_NAME))
         {
-            return ElispotAntigenCrosstabTable.create((ElispotRunAntigenTable) createProviderTable(ANTIGEN_TABLE_NAME), getProtocol(), this);
+            return ElispotAntigenCrosstabTable.create((ElispotRunAntigenTable) createProviderTable(ANTIGEN_TABLE_NAME, cf), getProtocol(), this);
         }
 
-        return super.createProviderTable(name);
+        return super.createProviderTable(name, cf);
     }
 
     @Override
-    public ElispotRunDataTable createDataTable(boolean includeCopiedToStudyColumns)
+    public ElispotRunDataTable createDataTable(ContainerFilter cf, boolean includeCopiedToStudyColumns)
     {
-        ElispotRunDataTable table = new ElispotRunDataTable(this, getProtocol());
+        ElispotRunDataTable table = new ElispotRunDataTable(this, cf, getProtocol());
         if (includeCopiedToStudyColumns)
         {
             addCopiedToStudyColumns(table, true);
@@ -116,6 +119,7 @@ public ElispotResultsQueryView(ExpProtocol protocol, ViewContext context, QueryS
             super(protocol, context, settings);
         }
 
+        @Override
         public DataView createDataView()
         {
             DataView view = super.createDataView();

elispotassay/src/org/labkey/elispot/ElispotProviderSchema.java

@@ -18,6 +18,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.EnumTableInfo;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.security.User;
@@ -53,7 +54,7 @@ public Set<String> getTableNames()
     }
 
     @Override
-    public TableInfo createTable(String name)
+    public TableInfo createTable(String name, ContainerFilter cf)
     {
         if (name.equalsIgnoreCase(ELISPOT_PLATE_READER_TABLE))
         {
@@ -69,6 +70,6 @@ public String getValue(ElispotAssayProvider.PlateReaderType e)
 
             return result;
         }
-        return super.createTable(name);
+        return super.createTable(name, cf);
     }
 }

elispotassay/src/org/labkey/elispot/query/ElispotAntigenCrosstabTable.java

@@ -18,7 +18,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.AggregateColumnInfo;
-import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.BaseColumnInfo;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.CrosstabDimension;
 import org.labkey.api.data.CrosstabMeasure;
@@ -110,12 +110,13 @@ public ElispotAntigenCrosstabTable(CrosstabSettings crosstabSettings, ArrayList<
     {
         super(crosstabSettings, members);
         _nonBasePropertyNames = nonBasePropertyNames;
-        getColumn("InstanceCount").setHidden(true);
-        getColumn("Run").setHidden(true);
-        getColumn("SpecimenLsid").setHidden(true);
+        getMutableColumn("InstanceCount").setHidden(true);
+        getMutableColumn("Run").setHidden(true);
+        getMutableColumn("SpecimenLsid").setHidden(true);
         setTitle("AntigenStats");
     }
 
+    @NotNull
     @Override
     public ContainerFilter getContainerFilter()
     {
@@ -153,7 +154,7 @@ public Sort getDefaultSort()
     }
 
     @Override
-    protected ColumnInfo createMemberMeasureCol(@Nullable CrosstabMember member, CrosstabMeasure measure)
+    protected BaseColumnInfo createMemberMeasureCol(@Nullable CrosstabMember member, CrosstabMeasure measure)
     {
         AggregateColumnInfo column = (AggregateColumnInfo)super.createMemberMeasureCol(member, measure);
         column.setCrosstabColumnDimension(measure.getSourceColumn().getFieldKey());

elispotassay/src/org/labkey/elispot/query/ElispotRunAntigenTable.java

@@ -16,6 +16,7 @@
 package org.labkey.elispot.query;
 
 import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.TableInfo;
@@ -41,9 +42,9 @@
  */
 public class ElispotRunAntigenTable extends PlateBasedAssayRunDataTable
 {
-    public ElispotRunAntigenTable(final AssaySchema schema, final Domain domain, ExpProtocol protocol)
+    public ElispotRunAntigenTable(final AssaySchema schema, ContainerFilter cf, final Domain domain, ExpProtocol protocol)
     {
-        super(schema, StorageProvisioner.createTableInfo(domain), protocol);
+        super(schema, StorageProvisioner.createTableInfo(domain), cf, protocol);
         setDescription("Contains one row per well for the \"" + protocol.getName() + "\" ELISpot assay design.");
         setTitle("Antigen");
         this.setPublic(false);
@@ -55,7 +56,7 @@ public ElispotRunAntigenTable(final AssaySchema schema, final Domain domain, Exp
         else
             sql.append("CONCAT(AntigenName, ' (', REPLACE(AntigenWellgroupName, 'Antigen ', ''), ')') END");
 
-        ColumnInfo antigenHeading = new ExprColumn(this, "AntigenHeading", sql, JdbcType.VARCHAR, getColumn("AntigenWellgroupName"), getColumn("AntigenName"));
+        ExprColumn antigenHeading = new ExprColumn(this, "AntigenHeading", sql, JdbcType.VARCHAR, getColumn("AntigenWellgroupName"), getColumn("AntigenName"));
         antigenHeading.setHidden(true);
         addColumn(antigenHeading);
     }
@@ -82,19 +83,20 @@ protected ColumnInfo resolveColumn(String name)
         {
             // Hook up a column that joins back to this table so that the columns formerly under the Properties
             // node can still be queried there.
-            result = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
-            result.setIsUnselectable(true);
-            LookupForeignKey fk = new LookupForeignKey("ObjectId")
+            var wrapped = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
+            wrapped.setIsUnselectable(true);
+            LookupForeignKey fk = new LookupForeignKey(getContainerFilter(), "ObjectId", null)
             {
                 @Override
                 public TableInfo getLookupTableInfo()
                 {
                     Domain domain = AbstractAssayProvider.getDomainByPrefix(_protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
-                    return new ElispotRunAntigenTable(_userSchema, domain, _protocol);
+                    return new ElispotRunAntigenTable(_userSchema, getLookupContainerFilter(), domain, _protocol);
                 }
             };
             fk.setPrefixColumnCaption(false);
-            result.setFk(fk);
+            wrapped.setFk(fk);
+            result = wrapped;
         }
 
         return result;
@@ -109,7 +111,7 @@ protected void addPropertyColumns(final AssaySchema schema, final ExpProtocol pr
             {
                 continue;
             }
-            ColumnInfo wrapColumn = addWrapColumn(column);
+            var wrapColumn = addWrapColumn(column);
             if ("AntigenLsid".equalsIgnoreCase(column.getName()) || "SpecimenLsid".equalsIgnoreCase(column.getName()))
                 wrapColumn.setHidden(true);
             else if ("Mean".equalsIgnoreCase(column.getName()) || "Median".equalsIgnoreCase(column.getName()))

elispotassay/src/org/labkey/elispot/query/ElispotRunDataTable.java

@@ -18,6 +18,7 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
@@ -49,19 +50,19 @@
  */
 public class ElispotRunDataTable extends PlateBasedAssayRunDataTable
 {
-    public ElispotRunDataTable(final AssaySchema schema, final ExpProtocol protocol)
+    public ElispotRunDataTable(final AssaySchema schema, ContainerFilter cf, final ExpProtocol protocol)
     {
-        this(schema, ElispotManager.getTableInfoElispotRunData(), protocol);
+        this(schema, ElispotManager.getTableInfoElispotRunData(), cf, protocol);
     }
 
-    public ElispotRunDataTable(final AssaySchema schema, TableInfo table, final ExpProtocol protocol)
+    public ElispotRunDataTable(final AssaySchema schema, TableInfo table, ContainerFilter cf, final ExpProtocol protocol)
     {
-        super(schema, table, protocol);
+        super(schema, table, cf, protocol);
 
         setDescription("Contains one row per sample for the \"" + protocol.getName() + "\" ELISpot assay design.");
 
         // display column for spot counts
-        ColumnInfo col = getColumn(FieldKey.fromParts(ElispotDataHandler.SFU_PROPERTY_NAME));
+        var col = getMutableColumn(FieldKey.fromParts(ElispotDataHandler.SFU_PROPERTY_NAME));
         if (col != null)
         {
             col.setDisplayColumnFactory(new DisplayColumnFactory()
@@ -75,7 +76,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
         }
 
         // display column for spot size
-        ColumnInfo spotSizeCol = getColumn(FieldKey.fromParts(ElispotDataHandler.SPOT_SIZE_PROPERTY_NAME));
+        var spotSizeCol = getMutableColumn(FieldKey.fromParts(ElispotDataHandler.SPOT_SIZE_PROPERTY_NAME));
         if (spotSizeCol != null)
         {
             spotSizeCol.setDisplayColumnFactory(new DisplayColumnFactory()
@@ -98,7 +99,7 @@ protected void addPropertyColumns(final AssaySchema schema, final ExpProtocol pr
             {
                 continue;   // already added or added below
             }
-            ColumnInfo wrapColumn = addWrapColumn(column);
+            var wrapColumn = addWrapColumn(column);
             if ("ObjectUri".equalsIgnoreCase(column.getName()) || "RowId".equalsIgnoreCase(column.getName()))
                 wrapColumn.setHidden(true);
         }
@@ -114,13 +115,14 @@ protected void addPropertyColumns(final AssaySchema schema, final ExpProtocol pr
             }
         }
 
-        ColumnInfo antigenLsidColumn = getColumn("AntigenLsid");
+        var antigenLsidColumn = getMutableColumn("AntigenLsid");
         antigenLsidColumn.setLabel("Antigen");
-        antigenLsidColumn.setFk(new LookupForeignKey(null, "AntigenName")
+        antigenLsidColumn.setFk(new LookupForeignKey( (String)null, "AntigenName")
         {
             @Override
             public TableInfo getLookupTableInfo()
             {
+                // TODO ContainerFilter
                 return ElispotManager.getTableInfoElispotAntigen(_protocol);
             }
         });
@@ -136,18 +138,19 @@ protected ColumnInfo resolveColumn(String name)
         {
             // Hook up a column that joins back to this table so that the columns formerly under the Properties
             // node can still be queried there.
-            result = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
-            result.setIsUnselectable(true);
-            LookupForeignKey fk = new LookupForeignKey("ObjectId")
+            var wrapped = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
+            wrapped.setIsUnselectable(true);
+            LookupForeignKey fk = new LookupForeignKey(getContainerFilter(), "ObjectId", null)
             {
                 @Override
                 public TableInfo getLookupTableInfo()
                 {
-                    return new ElispotRunDataTable(_userSchema, _protocol);
+                    return new ElispotRunDataTable(_userSchema, getLookupContainerFilter(), _protocol);
                 }
             };
             fk.setPrefixColumnCaption(false);
-            result.setFk(fk);
+            wrapped.setFk(fk);
+            result = wrapped;
         }
 
         return result;