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

specimen/api-src/org/labkey/api/specimen/SpecimensPage.java

@@ -0,0 +1,69 @@
+/*
+ * 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.api.specimen;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
+import org.labkey.api.study.Study;
+import org.labkey.api.study.StudyService;
+import org.labkey.api.view.FolderTab;
+import org.labkey.api.view.Portal;
+import org.labkey.api.view.ViewContext;
+import org.labkey.api.view.WebPartFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class SpecimensPage extends FolderTab.PortalPage
+{
+    public static final String PAGE_ID = "study.SPECIMENS";
+    public static final String SPECIMEN_TOOLS_WEBPART_NAME = "Specimen Tools";  // TODO: Move back to SpecimenToolsWebPartFactory
+
+    public SpecimensPage(String caption)
+    {
+        super(PAGE_ID, caption);
+    }
+
+    @Override
+    public boolean isSelectedPage(ViewContext viewContext)
+    {
+        return super.isSelectedPage(viewContext) ||
+                "specimen".equals(viewContext.getActionURL().getController());
+    }
+
+    @Override
+    public boolean isVisible(Container c, User user)
+    {
+        Study study = StudyService.get().getStudy(c);
+        if (study != null)
+        {
+            return SpecimenManager.get().isSpecimenModuleActive(c);
+        }
+        return false;
+    }
+
+    @Override
+    public List<Portal.WebPart> createWebParts()
+    {
+        List<Portal.WebPart> parts = new ArrayList<>();
+        parts.add(Portal.getPortalPart(StudyService.SPECIMEN_SEARCH_WEBPART).createWebPart());
+        parts.add(Portal.getPortalPart(StudyService.SPECIMEN_BROWSE_WEBPART).createWebPart());
+        Portal.WebPart toolsWebPart = Portal.getPortalPart(SPECIMEN_TOOLS_WEBPART_NAME).createWebPart();
+        toolsWebPart.setLocation(WebPartFactory.LOCATION_RIGHT);
+        parts.add(toolsWebPart);
+        return parts;
+    }
+}

specimen/build.gradle

@@ -20,6 +20,7 @@ plugins {
 }
 
 dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "jspImplementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "apiJarFile")
 

specimen/src/org/labkey/specimen/SpecimenManager.java

@@ -38,7 +38,6 @@
 import org.labkey.api.security.User;
 import org.labkey.api.specimen.SpecimenEvent;
 import org.labkey.api.specimen.SpecimenEventManager;
-import org.labkey.api.specimen.SpecimenQuerySchema;
 import org.labkey.api.specimen.SpecimenSchema;
 import org.labkey.api.specimen.Vial;
 import org.labkey.api.specimen.location.LocationImpl;

specimen/src/org/labkey/specimen/SpecimenModule.java

@@ -47,7 +47,6 @@
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.roles.RoleManager;
 import org.labkey.api.specimen.SpecimenMigrationService;
-import org.labkey.api.specimen.SpecimenQuerySchema;
 import org.labkey.api.specimen.SpecimenSchema;
 import org.labkey.api.specimen.SpecimensPage;
 import org.labkey.api.specimen.model.SpecimenTablesProvider;

specimen/src/org/labkey/specimen/SpecimenQuerySchema.java

@@ -0,0 +1,64 @@
+/*
+ * 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.specimen;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.query.UserSchema;
+import org.labkey.api.security.User;
+import org.labkey.api.study.Study;
+import org.labkey.api.study.StudyService;
+
+import java.util.Set;
+
+public class SpecimenQuerySchema extends UserSchema
+{
+    public static final String SCHEMA_NAME = "Study";
+    public static final String LOCATION_TABLE_NAME = "Location";
+
+    private final UserSchema _studySchema;
+    private final Study _study;
+
+    public SpecimenQuerySchema(Study study, UserSchema studySchema)
+    {
+        super(studySchema.getName(), studySchema.getDescription(), studySchema.getUser(), studySchema.getContainer(), studySchema.getDbSchema());
+        _study = study;
+        _studySchema = studySchema;
+    }
+
+    public static SpecimenQuerySchema get(Study study, User user)
+    {
+        return new SpecimenQuerySchema(study, StudyService.get().getStudyQuerySchema(study, user));
+    }
+
+    public Study getStudy()
+    {
+        return _study;
+    }
+
+    @Override
+    public @Nullable TableInfo createTable(String name, ContainerFilter cf)
+    {
+        return _studySchema.createTable(name, cf);
+    }
+
+    @Override
+    public Set<String> getTableNames()
+    {
+        return _studySchema.getTableNames();
+    }
+}

specimen/src/org/labkey/specimen/SpecimenRequestManager.java

@@ -49,7 +49,6 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.settings.AppProps;
-import org.labkey.api.specimen.SpecimenQuerySchema;
 import org.labkey.api.specimen.SpecimenSchema;
 import org.labkey.api.specimen.Vial;
 import org.labkey.api.specimen.importer.RollupHelper;

specimen/src/org/labkey/specimen/actions/ReportConfigurationBean.java

@@ -20,7 +20,7 @@
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.SchemaKey;
 import org.labkey.api.query.UserSchema;
-import org.labkey.api.specimen.SpecimenQuerySchema;
+import org.labkey.specimen.SpecimenQuerySchema;
 import org.labkey.specimen.report.SpecimenVisitReportParameters;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyService;

specimen/src/org/labkey/specimen/actions/SpecimenController.java

@@ -107,7 +107,6 @@
 import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.specimen.SpecimenQuerySchema;
 import org.labkey.api.specimen.SpecimenSchema;
 import org.labkey.api.specimen.Vial;
 import org.labkey.api.specimen.location.LocationImpl;
@@ -116,7 +115,6 @@
 import org.labkey.api.specimen.model.SpecimenTablesProvider;
 import org.labkey.api.study.CohortFilter;
 import org.labkey.api.study.Dataset;
-import org.labkey.api.study.MapArrayExcelWriter;
 import org.labkey.api.study.SpecimenService;
 import org.labkey.api.study.SpecimenTransform;
 import org.labkey.api.study.SpecimenUrls;
@@ -168,6 +166,7 @@
 import org.labkey.specimen.RequestedSpecimens;
 import org.labkey.specimen.SpecimenManager;
 import org.labkey.specimen.SpecimenModule;
+import org.labkey.specimen.SpecimenQuerySchema;
 import org.labkey.specimen.SpecimenRequestException;
 import org.labkey.specimen.SpecimenRequestManager;
 import org.labkey.specimen.SpecimenRequestStatus;
@@ -206,6 +205,7 @@
 import org.labkey.specimen.settings.RequestNotificationSettings;
 import org.labkey.specimen.settings.SettingsManager;
 import org.labkey.specimen.settings.StatusSettings;
+import org.labkey.specimen.study.MapArrayExcelWriter;
 import org.labkey.specimen.view.NotificationBean;
 import org.labkey.specimen.view.SpecimenRequestNotificationEmailTemplate;
 import org.labkey.specimen.view.SpecimenSearchWebPart;

specimen/src/org/labkey/specimen/actions/SpecimenHeaderBean.java

@@ -19,12 +19,12 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
-import org.labkey.api.specimen.SpecimenQuerySchema;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyService;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewContext;
+import org.labkey.specimen.SpecimenQuerySchema;
 import org.labkey.specimen.actions.SpecimenController.PtidVisit;
 import org.labkey.specimen.query.SpecimenQueryView;
 

specimen/src/org/labkey/specimen/importer/QueryBasedTransformTask.java

@@ -18,12 +18,12 @@
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
-import org.labkey.api.pipeline.AbstractSpecimenTransformTask;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.reader.DataLoader;
 import org.labkey.api.reader.DataLoaderFactory;
 import org.labkey.api.writer.PrintWriters;
+import org.labkey.specimen.pipeline.AbstractSpecimenTransformTask;
 import org.labkey.vfs.FileLike;
 
 import java.io.IOException;