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

src/org/labkey/targetedms/data/LazyForeignKey.java

@@ -0,0 +1,138 @@
+/*
+ * Copyright (c) 2021-2026 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.targetedms.data;
+
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.collections.NamedObjectList;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ForeignKey;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.SchemaKey;
+import org.labkey.api.util.StringExpression;
+
+import java.util.Map;
+import java.util.Set;
+import java.util.function.Supplier;
+
+/**
+ * A foreign key implementation that waits until it's asked for something and then uses the Supplier to create the
+ * real foreign key. This lets us postpone potentially expensive initialization of the lookup, and in many cases
+ * avoid needing to do it at all if the lookup isn't being actively used in a given codepath.
+ */
+public class LazyForeignKey implements ForeignKey
+{
+    private final Supplier<ForeignKey> _supplier;
+    private final boolean _suggestColumns;
+
+    private boolean _delegateCreationAttempted = false;
+    private ForeignKey _delegate;
+
+    public LazyForeignKey(Supplier<ForeignKey> supplier, boolean suggestColumns)
+    {
+        _supplier = supplier;
+        _suggestColumns = suggestColumns;
+    }
+
+    private ForeignKey getDelegate()
+    {
+        if (!_delegateCreationAttempted)
+        {
+            _delegate = _supplier.get();
+            _delegateCreationAttempted = true;
+        }
+        return _delegate;
+    }
+
+    @Override
+    public @Nullable ColumnInfo createLookupColumn(ColumnInfo parent, String displayField)
+    {
+        return getDelegate() == null ? null : getDelegate().createLookupColumn(parent, displayField);
+    }
+
+    @Override
+    public @Nullable TableInfo getLookupTableInfo()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupTableInfo();
+    }
+
+    @Override
+    public StringExpression getURL(ColumnInfo parent)
+    {
+        return getDelegate() == null ? null : getDelegate().getURL(parent);
+    }
+
+    @Override
+    public @NotNull NamedObjectList getSelectList(RenderContext ctx)
+    {
+        return getDelegate() == null ? new NamedObjectList() : getDelegate().getSelectList(ctx);
+    }
+
+    @Override
+    public Container getLookupContainer()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupContainer();
+    }
+
+    @Override
+    public String getLookupTableName()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupTableName();
+    }
+
+    @Override
+    public String getLookupSchemaName()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupSchemaName();
+    }
+
+    @Override
+    public SchemaKey getLookupSchemaKey()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupSchemaKey();
+    }
+
+    @Override
+    public String getLookupColumnName()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupColumnName();
+    }
+
+    @Override
+    public String getLookupDisplayName()
+    {
+        return getDelegate() == null ? null : getDelegate().getLookupDisplayName();
+    }
+
+    @Override
+    public @Nullable ForeignKey remapFieldKeys(@Nullable FieldKey parent, @Nullable Map<FieldKey, FieldKey> mapping)
+    {
+        return getDelegate() == null ? null : getDelegate().remapFieldKeys(parent, mapping);
+    }
+
+    @Override
+    public @Nullable Set<FieldKey> getSuggestedColumns()
+    {
+        if (!_suggestColumns)
+        {
+            return null;
+        }
+        return getDelegate() == null ? null : getDelegate().getSuggestedColumns();
+    }
+}

src/org/labkey/targetedms/model/GuideSetStats.java

@@ -15,11 +15,12 @@
  */
 package org.labkey.targetedms.model;
 
-import org.labkey.api.visualization.Stats;
+
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
+import org.labkey.targetedms.visualization.Stats;
 
 public class GuideSetStats
 {

src/org/labkey/targetedms/model/RawMetricDataSet.java

@@ -20,8 +20,8 @@
 import org.labkey.api.targetedms.model.OutlierCounts;
 import org.labkey.api.targetedms.model.QCMetricConfiguration;
 import org.labkey.api.targetedms.model.QCMetricStatus;
-import org.labkey.api.visualization.Stats;
 import org.labkey.targetedms.chart.LabelFactory;
+import org.labkey.targetedms.visualization.Stats;
 
 import java.text.DecimalFormat;
 import java.util.Date;

src/org/labkey/targetedms/query/QCAnnotationTypeTable.java

@@ -32,9 +32,9 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserPrincipal;
 import org.labkey.api.security.permissions.Permission;
-import org.labkey.api.view.ColorPickerDisplayColumn;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
+import org.labkey.targetedms.view.ColorPickerDisplayColumn;
 
 import java.sql.SQLException;
 import java.util.Map;

src/org/labkey/targetedms/query/SampleFileTable.java

@@ -25,7 +25,6 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.JdbcType;
-import org.labkey.api.data.LazyForeignKey;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
@@ -64,6 +63,7 @@
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
 import org.labkey.targetedms.TargetedMSSchema;
+import org.labkey.targetedms.data.LazyForeignKey;
 import org.labkey.targetedms.datasource.MsDataSourceUtil;
 import org.labkey.targetedms.parser.DataSettings;
 import org.labkey.targetedms.parser.SampleFile;

src/org/labkey/targetedms/view/ColorPickerDisplayColumn.java

@@ -0,0 +1,82 @@
+/*
+ * 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.targetedms.view;
+
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.DataColumn;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.util.JavaScriptFragment;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.UniqueID;
+import org.labkey.api.writer.HtmlWriter;
+
+import static org.labkey.api.util.DOM.Attribute.style;
+import static org.labkey.api.util.DOM.DIV;
+import static org.labkey.api.util.DOM.SCRIPT;
+import static org.labkey.api.util.DOM.at;
+import static org.labkey.api.util.DOM.id;
+
+/**
+ * {@link org.labkey.api.data.DisplayColumn} that shows an ExtJS-based color picker component for insert/update forms
+ * and a small square of the color in grid views.
+ */
+public class ColorPickerDisplayColumn extends DataColumn
+{
+    public ColorPickerDisplayColumn(ColumnInfo col)
+    {
+        super(col);
+    }
+
+    @Override
+    public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
+    {
+        Object value = getValue(ctx);
+        if (value != null)
+        {
+            DIV(
+                at(style, "height: 20px; width: 20px; background: #" + value)
+            ).appendTo(out);
+        }
+    }
+
+    @Override
+    public void renderInputHtml(RenderContext ctx, HtmlWriter out, Object value)
+    {
+        String name = getFormFieldName(ctx);
+        renderHiddenFormInput(out, name, value);
+
+        String renderId = "color-picker-div-" + UniqueID.getRequestScopedUID(ctx.getRequest());
+
+        SCRIPT(
+            JavaScriptFragment.unsafe(
+                "   LABKEY.requiresExt4Sandbox(function(){\n" +
+                "      Ext4.onReady(function(){\n" +
+                "        Ext4.create('Ext.picker.Color', {\n" +
+                "            renderTo     : " + PageFlowUtil.jsString(renderId) + ",\n" +
+                "            value        : " + PageFlowUtil.jsString(value == null ? null : value.toString()) + ",\n" +
+                "            listeners: { \n" +
+                "                select: function(picker, selColor) {\n" +
+                "                    document.getElementsByName(" + PageFlowUtil.jsString(name) + ")[0].value = selColor;\n" +
+                "                }\n" +
+                "            }\n" +
+                "        });\n" +
+                "      });\n" +
+                "   });\n")
+        ).appendTo(out);
+
+        DIV(id(renderId)).appendTo(out);
+    }
+}