Move study design features into a new module

api/src/org/labkey/api/study/Study.java

@@ -19,7 +19,6 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.attachments.Attachment;
 import org.labkey.api.attachments.AttachmentFile;
-import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 import org.labkey.api.util.HtmlString;
 
@@ -58,18 +57,6 @@ public interface Study extends StudyEntity
 
     Collection<? extends Cohort> getCohorts(User user);
 
-    Collection<? extends AssaySpecimenConfig> getAssaySpecimenConfigs();
-
-    List<? extends Visit> getVisitsForAssaySchedule();
-
-    List<? extends Product> getStudyProducts(User user, String role);
-
-    List<? extends Treatment> getStudyTreatments(User user);
-
-    List<? extends TreatmentVisitMap> getStudyTreatmentVisitMap(Container container, @Nullable Integer cohortId);
-
-    List<? extends Visit> getVisitsForTreatmentSchedule();
-
     List<? extends ParticipantCategory> getParticipantCategories(User user);
 
     @Nullable String getParticipantCohortProperty();

api/src/org/labkey/api/study/StudyService.java

@@ -28,6 +28,7 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.query.UserSchema;
+import org.labkey.api.query.ValidationException;
 import org.labkey.api.reports.model.ViewCategory;
 import org.labkey.api.reports.report.view.ReportUtil;
 import org.labkey.api.security.User;
@@ -233,4 +234,7 @@ interface StudyTabProvider
     ReportUtil.ReportFilter getStudyReportFilter(boolean editOnly);
 
     Map<String, BigDecimal> getVisitImportMap(Study study, boolean includeStandardMapping);
+
+    // Methods created to support Vaccine study designs
+    ValidationException updateAssayPlan(User user, Study study, String assayPlan);
 }

api/src/org/labkey/api/study/StudyUrls.java

@@ -40,8 +40,6 @@ public interface StudyUrls extends UrlProvider
     ActionURL getDatasetsURL(Container container);
     ActionURL getManageDatasetsURL(Container container);
     ActionURL getManageReportPermissions(Container container);
-    ActionURL getManageAssayScheduleURL(Container container, boolean useAlternateLookupFields);
-    ActionURL getManageTreatmentsURL(Container container, boolean useSingleTableEditor);
     ActionURL getManageFileWatchersURL(Container container);
     ActionURL getLinkToStudyURL(Container container, ExpSampleType sampleType);
     ActionURL getLinkToStudyURL(Container container, ExpProtocol protocol);
@@ -50,4 +48,9 @@ public interface StudyUrls extends UrlProvider
     ActionURL getTypeNotFoundURL(Container container, int datasetId);
 
     void addManageStudyNavTrail(NavTree root, Container container, User user);
+
+    ActionURL getManageLocationsURL(Container container);
+    ActionURL getManageVisitsURL(Container container);
+    ActionURL getManageCohortsURL(Container container);
+    ActionURL getVisitOrderURL(Container container);
 }

study/api-src/org/labkey/api/study/StudyUtils.java

@@ -28,8 +28,6 @@ public class StudyUtils
     public static final String SUBMISSION_WARNING = "Once a request is submitted, its specimen list may no longer be modified. Continue?";
     public static final String CANCELLATION_WARNING = "Canceling will permanently delete this pending request. Continue?";
 
-    public static final String STUDY_DESIGN_FEATURE_FLAG = "studyDesignFlag";
-
     //Create a fixed point number encoding the date.
     public static double sequenceNumFromDate(Date d)
     {

study/api-src/org/labkey/api/study/model/CohortService.java

@@ -2,10 +2,12 @@
 
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.study.Cohort;
 import org.labkey.api.study.CohortFilter;
+import org.labkey.api.study.Study;
 import org.labkey.api.view.ActionURL;
 
 import java.util.Collection;
@@ -37,4 +39,15 @@ static void setInstance(CohortService impl)
     Collection<CohortFilter> getCohortFilters(CohortFilter.Type type, Container c, User user);
 
     Collection<? extends Cohort> getCohorts(Container container, User user);
+
+    // Methods created to support Vaccine study designs
+    Cohort getCohortByLabel(Container container, User user, String label);
+
+    Cohort getCohortForRowId(Container container, User user, int rowId);
+
+    void deleteCohort(Cohort cohort);
+
+    Cohort updateCohort(Container container, User user, int rowId, String label, Integer subjectCount);
+
+    Cohort createCohort(Study study, User user, String newLabel, boolean enrolled, Integer subjectCount, String description) throws ValidationException;
 }

study/api-src/org/labkey/api/study/model/VisitService.java

@@ -1,13 +1,15 @@
 package org.labkey.api.study.model;
 
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.Visit;
 
+import java.math.BigDecimal;
 import java.util.Collection;
 
 /**
@@ -34,4 +36,9 @@ static void setInstance(VisitService impl)
      * Updates this study's participant, visit, and participant visit tables. Also updates automatic cohort assignments.
      */
     ValidationException updateParticipantVisits(Study study, User user);
+
+    // Methods created to support Vaccine study designs
+    Visit createVisit(Study study, User user, @NotNull BigDecimal seqMin, String label, Visit.Type type);
+
+    void deleteVisit(Study study, User user, Visit visit);
 }

study/api-src/org/labkey/api/studydesign/StudyDesignManager.java

@@ -22,6 +22,8 @@
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.property.PropertyService;
+import org.labkey.api.module.Module;
+import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.studydesign.query.AbstractStudyDesignDomainKind;
 import org.labkey.api.studydesign.query.StudyDesignQuerySchema;
@@ -43,12 +45,22 @@
 public class StudyDesignManager
 {
     private static final StudyDesignManager _instance = new StudyDesignManager();
+    public static final String MODULE_NAME = "StudyDesign";
 
     public static StudyDesignManager get()
     {
         return _instance;
     }
 
+    public boolean isModuleActive(Container c)
+    {
+        if (c == null)
+            return false;
+
+        Module studyDesignModule = ModuleLoader.getInstance().getModule(MODULE_NAME);
+        return null != studyDesignModule && c.getActiveModules().contains(studyDesignModule);
+    }
+
     public void deleteStudyDesignData(Container c, Set<TableInfo> deletedTables)
     {
         Filter filter = SimpleFilter.createContainerFilter(c);
@@ -77,6 +89,11 @@ public void deleteStudyDesignData(Container c, Set<TableInfo> deletedTables)
         deletedTables.add(StudyDesignSchema.getInstance().getTableInfoTreatmentVisitMap());
         Table.delete(StudyDesignSchema.getInstance().getTableInfoObjective(), filter);
         deletedTables.add(StudyDesignSchema.getInstance().getTableInfoObjective());
+
+        Table.delete(StudyDesignSchema.getInstance().getTableInfoAssaySpecimenVisit(), filter);
+        deletedTables.add(StudyDesignSchema.getInstance().getTableInfoAssaySpecimenVisit());
+        Table.delete(StudyDesignSchema.getInstance().getTableInfoAssaySpecimen(), filter);
+        deletedTables.add(StudyDesignSchema.getInstance().getTableInfoAssaySpecimen());
     }
 
     // Proactively create the domains at study creation time to avoid problems with lazy creation, #42641

study/api-src/org/labkey/api/studydesign/StudyDesignService.java

@@ -0,0 +1,31 @@
+package org.labkey.api.studydesign;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
+import org.labkey.api.services.ServiceRegistry;
+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 java.util.Collection;
+import java.util.List;
+
+public interface StudyDesignService
+{
+    @Nullable
+    static StudyDesignService get()
+    {
+        return ServiceRegistry.get().getService(StudyDesignService.class);
+    }
+
+    List<? extends Product> getStudyProducts(Container c, User user, String role);
+    List<? extends Treatment> getStudyTreatments(Container c, User user);
+    List<? extends Visit> getVisitsForTreatmentSchedule(Container c);
+    Collection<? extends AssaySpecimenConfig> getAssaySpecimenConfigs(Container c);
+    void deleteTreatmentVisitMapForCohort(Container container, Integer cohortId);
+    void deleteTreatmentVisitMapForVisit(Container container, Integer visitId);
+    void deleteAssaySpecimenVisits(Container container, int visitId);
+
+}

study/api-src/org/labkey/api/studydesign/StudyDesignUrls.java

@@ -0,0 +1,12 @@
+package org.labkey.api.studydesign;
+
+import org.labkey.api.action.UrlProvider;
+import org.labkey.api.data.Container;
+import org.labkey.api.view.ActionURL;
+
+public interface StudyDesignUrls extends UrlProvider
+{
+    ActionURL getManageAssayScheduleURL(Container container, boolean useAlternateLookupFields);
+    ActionURL getManageStudyProductsURL(Container container);
+    ActionURL getManageTreatmentsURL(Container container, boolean useSingleTableEditor);
+}