Move study design features into a new module

Original PR: LabKey/platform#6686

Author: labkey-klum

…y/controllers/StudyDesignController.java …y/studydesign/StudyDesignController.javastudy/src/org/labkey/study/controllers/StudyDesignController.java renamed to studydesign/src/org/labkey/studydesign/StudyDesignController.java study/src/org/labkey/study/controllers/StudyDesignController.java renamed to studydesign/src/org/labkey/studydesign/StudyDesignController.java

@@ -0,0 +1,83 @@
+package org.labkey.studydesign;
+
+import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.module.ModuleContext;
+import org.labkey.api.module.SpringModule;
+import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.studydesign.StudyDesignService;
+import org.labkey.api.util.logging.LogHelper;
+import org.labkey.api.view.WebPartFactory;
+import org.labkey.studydesign.model.TreatmentManager;
+import org.labkey.studydesign.view.AssayScheduleWebpartFactory;
+import org.labkey.studydesign.view.ImmunizationScheduleWebpartFactory;
+import org.labkey.studydesign.view.VaccineDesignWebpartFactory;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+
+public class StudyDesignModule extends SpringModule
+{
+    private static final Logger LOG = LogHelper.getLogger(StudyDesignModule.class, "Study Design");
+    public static final String NAME = "StudyDesign";
+
+    @Override
+    public String getName()
+    {
+        return NAME;
+    }
+
+    @Override
+    @NotNull
+    protected Collection<WebPartFactory> createWebPartFactories()
+    {
+        return List.of(
+                new AssayScheduleWebpartFactory(),
+                new ImmunizationScheduleWebpartFactory(),
+                new VaccineDesignWebpartFactory()
+        );
+    }
+
+    @Override
+    public @Nullable Double getSchemaVersion()
+    {
+        return null;
+    }
+
+    @Override
+    public boolean hasScripts()
+    {
+        return false;
+    }
+
+    @Override
+    protected void init()
+    {
+        addController("study-design", StudyDesignController.class);
+
+        ServiceRegistry.get().registerService(StudyDesignService.class, new StudyDesignServiceImpl());
+    }
+
+    @Override
+    protected void startupAfterSpringConfig(ModuleContext moduleContext)
+    {
+    }
+
+    @Override
+    public @NotNull Collection<String> getSchemaNames()
+    {
+        return Set.of();
+    }
+
+    @Override
+    @NotNull
+    public Set<Class> getIntegrationTests()
+    {
+        return Set.of(
+                TreatmentManager.TreatmentDataTestCase.class,
+                TreatmentManager.AssayScheduleTestCase.class
+        );
+    }
+}

studydesign/src/org/labkey/studydesign/StudyDesignModule.java

@@ -0,0 +1,68 @@
+package org.labkey.studydesign;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.User;
+import org.labkey.api.study.AssaySpecimenConfig;
+import org.labkey.api.study.Product;
+import org.labkey.api.study.Treatment;
+import org.labkey.api.study.Visit;
+import org.labkey.api.studydesign.StudyDesignService;
+import org.labkey.api.studydesign.query.StudyDesignSchema;
+import org.labkey.studydesign.model.AssaySpecimenConfigImpl;
+import org.labkey.studydesign.model.TreatmentManager;
+
+import java.util.Collection;
+import java.util.List;
+
+public class StudyDesignServiceImpl implements StudyDesignService
+{
+    @Override
+    public List<? extends Product> getStudyProducts(Container c, User user, String role)
+    {
+        return TreatmentManager.getInstance().getStudyProducts(c, user, role, null);
+    }
+
+    @Override
+    public List<? extends Treatment> getStudyTreatments(Container c, User user)
+    {
+        return TreatmentManager.getInstance().getStudyTreatments(c, user);
+    }
+
+    @Override
+    public List<? extends Visit> getVisitsForTreatmentSchedule(Container c)
+    {
+        return TreatmentManager.getInstance().getVisitsForTreatmentSchedule(c);
+    }
+
+    @Override
+    public Collection<? extends AssaySpecimenConfig> getAssaySpecimenConfigs(Container c)
+    {
+        return new TableSelector(
+                StudyDesignSchema.getInstance().getTableInfoAssaySpecimen(),
+                SimpleFilter.createContainerFilter(c), null).getCollection(AssaySpecimenConfigImpl.class);
+    }
+
+    @Override
+    public void deleteTreatmentVisitMapForCohort(Container container, Integer cohortId)
+    {
+        TreatmentManager.getInstance().deleteTreatmentVisitMapForCohort(container, cohortId);
+    }
+
+    @Override
+    public void deleteTreatmentVisitMapForVisit(Container container, Integer visitId)
+    {
+        TreatmentManager.getInstance().deleteTreatmentVisitMapForVisit(container, visitId);
+    }
+
+    @Override
+    public void deleteAssaySpecimenVisits(Container container, int visitId)
+    {
+        SimpleFilter filter = SimpleFilter.createContainerFilter(container);
+        filter.addCondition(FieldKey.fromParts("VisitId"), visitId);
+        Table.delete(StudyDesignSchema.getInstance().getTableInfoAssaySpecimenVisit(), filter);
+    }
+}