Move single-module classes out of api into their owning modules

OConnorExperiments/src/org/labkey/oconnorexperiments/data/TableExtension.java

@@ -0,0 +1,134 @@
+/*
+ * Copyright (c) 2014-2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.oconnorexperiments.data;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.AbstractTableInfo;
+import org.labkey.api.data.BaseColumnInfo;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.LookupColumn;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.query.AliasedColumn;
+import org.labkey.api.query.QueryForeignKey;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+
+/**
+ * User: kevink
+ * Date: 4/4/14
+ *
+ * Convenience class to add columns from the extension table to the primary table.
+ */
+public final class TableExtension
+{
+    private final AbstractTableInfo _primaryTable;
+    private final TableInfo _extensionTable;
+    private final ColumnInfo _extensionCol;
+    private final QueryForeignKey _extensionFK;
+
+    private TableExtension(AbstractTableInfo primaryTable, TableInfo extensionTable, ColumnInfo extensionCol, QueryForeignKey extensionFK)
+    {
+        _primaryTable = primaryTable;
+        _extensionTable = extensionTable;
+        _extensionCol = extensionCol;
+        _extensionFK = extensionFK;
+    }
+
+    public static TableExtension create(AbstractTableInfo primaryTable, TableInfo extensionTable)
+    {
+        String pkColumn = extensionTable.getPkColumnNames().getFirst(); // Note this only works for simple primary keys, not compound.
+        String fkColumn = extensionTable.getColumn(pkColumn).getFk().getLookupColumnName();
+
+        return create(primaryTable, extensionTable, fkColumn, pkColumn, LookupColumn.JoinType.leftOuter);
+    }
+
+    public static TableExtension create(AbstractTableInfo primaryTable, TableInfo extensionTable, String foreignKey, String lookupKey, LookupColumn.JoinType joinType)
+    {
+        ColumnInfo extensionCol = primaryTable.getColumn(foreignKey);
+        assert extensionCol != null;
+
+        QueryForeignKey extensionFK = (QueryForeignKey)QueryForeignKey
+                .from(primaryTable.getUserSchema(), primaryTable.getContainerFilter())
+                .table(extensionTable).key(lookupKey)
+                .build();
+        extensionFK.setJoinType(joinType);
+
+        return new TableExtension(primaryTable, extensionTable, extensionCol, extensionFK);
+    }
+
+    public TableInfo getExtensionTable()
+    {
+        return _extensionTable;
+    }
+
+    public Collection<ColumnInfo> addAllColumns()
+    {
+        String lookupKey = getLookupColumnName();
+        List<ColumnInfo> baseColumns = _extensionTable.getColumns();
+        Collection<ColumnInfo> columns = new ArrayList<>(baseColumns.size());
+        for (ColumnInfo col : baseColumns)
+        {
+            // Skip the lookup column itself
+            if (col.getName().equalsIgnoreCase(lookupKey))
+                continue;
+
+            ColumnInfo lookupCol = addExtensionColumn(col, col.getName());
+            columns.add(lookupCol);
+        }
+
+        return columns;
+    }
+
+    public MutableColumnInfo addExtensionColumn(String baseColName, @Nullable String newColName)
+    {
+        ColumnInfo baseCol = _extensionTable.getColumn(baseColName);
+        return addExtensionColumn(baseCol, newColName);
+    }
+
+    public MutableColumnInfo addExtensionColumn(ColumnInfo baseCol, @Nullable String newColName)
+    {
+        var aliased = wrapExtensionColumn(baseCol, newColName);
+        return _primaryTable.addColumn(aliased);
+    }
+
+    public ColumnInfo wrapExtensionColumn(String baseColName, @Nullable String newColName)
+    {
+        ColumnInfo baseCol = _extensionTable.getColumn(baseColName);
+        return wrapExtensionColumn(baseCol, newColName);
+    }
+
+    public BaseColumnInfo wrapExtensionColumn(ColumnInfo baseCol, @Nullable String newColName)
+    {
+        newColName = Objects.toString(newColName, baseCol.getName());
+
+        ColumnInfo lookupCol = _extensionFK.createLookupColumn(_extensionCol, baseCol.getName());
+        AliasedColumn aliased = new AliasedColumn(_primaryTable, newColName, lookupCol);
+        if (lookupCol.isHidden() || baseCol.isHidden())
+            aliased.setHidden(true);
+
+        return aliased;
+    }
+
+    public String getLookupColumnName()
+    {
+        return _extensionFK.getLookupColumnName();
+    }
+
+}

OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java

@@ -35,7 +35,6 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.SqlExecutor;
-import org.labkey.api.data.TableExtension;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.UpdateableTableInfo;
@@ -73,6 +72,7 @@
 import org.labkey.oconnorexperiments.OConnorExperimentFolderType;
 import org.labkey.oconnorexperiments.OConnorExperimentsController;
 import org.labkey.oconnorexperiments.OConnorExperimentsSchema;
+import org.labkey.oconnorexperiments.data.TableExtension;
 
 import java.sql.SQLException;
 import java.util.ArrayList;

genotyping/src/org/labkey/genotyping/GenotypingManager.java

@@ -18,7 +18,6 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.data.AtomicDatabaseInteger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
 import org.labkey.api.data.PropertyManager.WritablePropertyMap;
@@ -35,6 +34,7 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.SafeToRenderEnum;
 import org.labkey.api.view.NotFoundException;
+import org.labkey.genotyping.data.AtomicDatabaseInteger;
 import org.labkey.vfs.FileLike;
 
 import java.io.FileNotFoundException;

genotyping/src/org/labkey/genotyping/GenotypingModule.java

@@ -32,6 +32,7 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.WebPartFactory;
+import org.labkey.genotyping.data.AtomicDatabaseInteger;
 import org.labkey.genotyping.sequences.SequenceManager;
 
 import java.util.Collection;
@@ -155,6 +156,6 @@ public Set<String> getSchemaNames()
     @Override
     public @NotNull Set<Class<?>> getIntegrationTests()
     {
-        return PageFlowUtil.set(IlluminaFastqParser.HeaderTestCase.class, ImportAnalysisJob.TestCase.class);
+        return PageFlowUtil.set(AtomicDatabaseInteger.TestCase.class, IlluminaFastqParser.HeaderTestCase.class, ImportAnalysisJob.TestCase.class);
     }
 }

genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java

@@ -53,6 +53,7 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.genotyping.data.HighlightingDisplayColumn;
 import org.springframework.validation.BindException;
 
 import java.sql.SQLException;