checkpoint for immutable TableInfo (set ContainerFilter at construct …

TODO_ContainerFilter.md

@@ -0,0 +1,42 @@
+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

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

@@ -16,6 +16,7 @@
 package org.labkey.elisa.query;
 
 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 +42,9 @@
  */
 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<>();
 
@@ -65,7 +66,7 @@ public ElisaResultsTable(final AssayProtocolSchema schema, boolean includeCopied
         {
             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)

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;
@@ -75,26 +76,26 @@ public Set<String> getTableNames()
         return names;
     }
 
-    public TableInfo createProviderTable(String name)
+    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);

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

@@ -116,6 +116,7 @@ public ElispotAntigenCrosstabTable(CrosstabSettings crosstabSettings, ArrayList<
         setTitle("AntigenStats");
     }
 
+    @NotNull
     @Override
     public ContainerFilter getContainerFilter()
     {

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);
@@ -84,13 +85,13 @@ protected ColumnInfo resolveColumn(String name)
             // node can still be queried there.
             result = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
             result.setIsUnselectable(true);
-            LookupForeignKey fk = new LookupForeignKey("ObjectId")
+            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);

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;
@@ -49,14 +50,14 @@
  */
 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.");
 
@@ -116,11 +117,12 @@ protected void addPropertyColumns(final AssaySchema schema, final ExpProtocol pr
 
         ColumnInfo antigenLsidColumn = getColumn("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);
             }
         });
@@ -138,12 +140,12 @@ protected ColumnInfo resolveColumn(String name)
             // node can still be queried there.
             result = wrapColumn("Properties", getRealTable().getColumn("ObjectId"));
             result.setIsUnselectable(true);
-            LookupForeignKey fk = new LookupForeignKey("ObjectId")
+            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);

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

@@ -17,7 +17,6 @@
 package org.labkey.elispot.query;
 
 import org.labkey.api.data.*;
-import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpSampleSet;
 import org.labkey.api.exp.api.ExperimentService;
@@ -47,9 +46,9 @@ public String getInputMaterialPropertyName()
         return ElispotDataHandler.ELISPOT_INPUT_MATERIAL_DATA_PROPERTY;
     }
 
-    public PlateBasedAssayRunDataTable(final AssaySchema schema, final TableInfo table, final ExpProtocol protocol)
+    public PlateBasedAssayRunDataTable(final AssaySchema schema, final TableInfo table, ContainerFilter cf, final ExpProtocol protocol)
     {
-        super(table, schema);
+        super(table, schema, cf);
         _protocol = protocol;
 
         final AssayProvider provider = AssayService.get().getProvider(protocol);
@@ -63,7 +62,7 @@ public PlateBasedAssayRunDataTable(final AssaySchema schema, final TableInfo tab
         {
             public TableInfo getLookupTableInfo()
             {
-                ExpRunTable expRunTable = AssayService.get().createRunTable(protocol, provider, schema.getUser(), schema.getContainer());
+                ExpRunTable expRunTable = AssayService.get().createRunTable(protocol, provider, schema.getUser(), schema.getContainer(), PlateBasedAssayRunDataTable.this.getContainerFilter());
                 expRunTable.setContainerFilter(getContainerFilter());
                 return expRunTable;
             }
@@ -79,13 +78,11 @@ public TableInfo getLookupTableInfo()
         ColumnInfo materialColumn = getColumn("SpecimenLsid"); //  new PropertyColumn(materialProperty, objectUriColumn, getContainer(), schema.getUser(), false);
         materialColumn.setLabel("Specimen");
         materialColumn.setHidden(true);
-        materialColumn.setFk(new LookupForeignKey("LSID")
+        materialColumn.setFk(new LookupForeignKey(cf,"LSID", null)
         {
             public TableInfo getLookupTableInfo()
             {
-                ExpMaterialTable materials = ExperimentService.get().createMaterialTable(ExpSchema.TableType.Materials.toString(), schema);
-                // Make sure we are filtering to the same set of containers
-                materials.setContainerFilter(getContainerFilter());
+                ExpMaterialTable materials = ExperimentService.get().createMaterialTable(ExpSchema.TableType.Materials.toString(), schema, getLookupContainerFilter());
                 if (sampleSet != null)
                 {
                     materials.setSampleSet(sampleSet, true);

flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java

@@ -25,6 +25,7 @@
 import org.labkey.api.data.ButtonBar;
 import org.labkey.api.data.CachedResultSets;
 import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.InputColumn;
@@ -36,6 +37,7 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.User;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.SimpleNamedObject;
@@ -45,6 +47,7 @@
 import org.labkey.flow.analysis.model.Workspace;
 import org.labkey.flow.data.FlowFCSFile;
 import org.labkey.flow.data.FlowRun;
+import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.util.KeywordUtil;
 import org.springframework.validation.Errors;
 
@@ -80,12 +83,12 @@ public class SamplesConfirmGridView extends GridView
 
     Map<Integer, FlowRun> _runs = new HashMap<>();
 
-    public SamplesConfirmGridView(SelectedSamples data, boolean resolving, Errors errors)
+    public SamplesConfirmGridView(User user, Container container, SelectedSamples data, boolean resolving, Errors errors)
     {
-        this(data.getKeywords(), data.getSamples(), resolving, data.getRows(), errors);
+        this(user, container, data.getKeywords(), data.getSamples(), resolving, data.getRows(), errors);
     }
 
-    public SamplesConfirmGridView(Collection<String> keywords, List<? extends ISampleInfo> samples, boolean resolving, Map<String, SelectedSamples.ResolvedSample> rows, Errors errors)
+    public SamplesConfirmGridView(User user, Container container, Collection<String> keywords, List<? extends ISampleInfo> samples, boolean resolving, Map<String, SelectedSamples.ResolvedSample> rows, Errors errors)
     {
         super(new SamplesConfirmDataRegion(), errors);
 
@@ -225,7 +228,8 @@ public SamplesConfirmGridView(Collection<String> keywords, List<? extends ISampl
             // Add Matched column
             ColumnInfo matchCol = new ColumnInfo(MATCHED_FILE_FIELD_KEY, null, JdbcType.INTEGER);
             matchCol.setLabel("Matched FCS File");
-            matchCol.setFk(new FCSFilesFilesForeignKey(FlowFCSFile.getOriginal(getViewContext().getContainer())));
+            FlowSchema schema = new FlowSchema(user, container);
+            matchCol.setFk(new FCSFilesFilesForeignKey(schema, FlowFCSFile.getOriginal(container)));
             matchCol.setInputType("select");
             dc = new MatchedFileDisplayColumn(matchCol);
             dr.addDisplayColumn(dc);
@@ -380,8 +384,9 @@ private class FCSFilesFilesForeignKey extends AbstractForeignKey
         List<FlowFCSFile> _files;
         NamedObjectList _list;
 
-        FCSFilesFilesForeignKey(List<FlowFCSFile> files)
+        FCSFilesFilesForeignKey(FlowSchema schema, List<FlowFCSFile> files)
         {
+            super(schema, null);
             _files = files;
 
             _list = new NamedObjectList();

flow/src/org/labkey/flow/controllers/executescript/importAnalysisReviewSamples.jsp

@@ -84,7 +84,7 @@
     }
 
     SelectedSamples selectedSamples = form.getSelectedSamples();
-    SamplesConfirmGridView resolveView = new SamplesConfirmGridView(selectedSamples, form.isResolving(), null);
+    SamplesConfirmGridView resolveView = new SamplesConfirmGridView(getUser(), container, selectedSamples, form.isResolving(), null);
 %>
 
 <input type="hidden" name="selectFCSFilesOption" id="selectFCSFilesOption" value="<%=h(form.getSelectFCSFilesOption())%>">

flow/src/org/labkey/flow/data/FlowProtocol.java

@@ -572,7 +572,7 @@ public void updateFCSAnalysisName(User user) throws Exception
         }
         fs.insertParent(FieldKey.fromParts("FCSFile"));
         FlowSchema schema = new FlowSchema(user, getContainer());
-        ExpDataTable table = schema.createFCSAnalysisTable("FCSAnalysis", FlowDataType.FCSAnalysis, false);
+        ExpDataTable table = schema.createFCSAnalysisTable(null,"FCSAnalysis", FlowDataType.FCSAnalysis, false);
         Map<FieldKey, ColumnInfo> columns = new HashMap<>();
         ColumnInfo colRowId = table.getColumn(ExpDataTable.Column.RowId);
         columns.put(new FieldKey(null, "RowId"), colRowId);