Move specimen permissions into specimen module

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

@@ -42,6 +42,7 @@
 import org.labkey.api.query.QueryView;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
+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;
@@ -52,10 +53,16 @@
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyInternalService;
 import org.labkey.api.study.StudyService;
+import org.labkey.api.study.StudyUrls;
 import org.labkey.api.study.importer.SimpleStudyImportContext;
 import org.labkey.api.study.importer.SimpleStudyImporterRegistry;
 import org.labkey.api.study.writer.SimpleStudyWriterRegistry;
 import org.labkey.api.usageMetrics.UsageMetricsService;
+import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.HtmlStringBuilder;
+import org.labkey.api.util.LinkBuilder;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.SafeToRender;
 import org.labkey.api.util.SystemMaintenance;
 import org.labkey.api.util.emailTemplate.EmailTemplateService;
 import org.labkey.api.util.logging.LogHelper;
@@ -74,12 +81,14 @@
 import org.labkey.specimen.importer.SpecimenSettingsImporter;
 import org.labkey.specimen.model.SpecimenRequestEventType;
 import org.labkey.specimen.pipeline.SpecimenPipeline;
-import org.labkey.specimen.requirements.SpecimenRequestRequirementProvider;
 import org.labkey.specimen.query.SpecimenPivotByDerivativeType;
 import org.labkey.specimen.query.SpecimenPivotByPrimaryType;
 import org.labkey.specimen.query.SpecimenPivotByRequestingLocation;
 import org.labkey.specimen.query.SpecimenQueryView;
 import org.labkey.specimen.query.SpecimenUpdateService;
+import org.labkey.specimen.requirements.SpecimenRequestRequirementProvider;
+import org.labkey.specimen.security.permissions.EditSpecimenDataPermission;
+import org.labkey.specimen.security.permissions.ManageRequestSettingsPermission;
 import org.labkey.specimen.security.roles.SpecimenCoordinatorRole;
 import org.labkey.specimen.security.roles.SpecimenRequesterRole;
 import org.labkey.specimen.settings.RepositorySettings;
@@ -234,6 +243,27 @@ public void addSpecimenPivotTableNames(Set<String> names)
                 }
                 return null;
             }
+
+            @Override
+            public @Nullable SafeToRender getSpecimenSettingsLink(Container c, User user)
+            {
+                // Must have ManageRequestSettingsPermission and requests enabled (otherwise non-admin will see a blank Manage Study page)
+                if (c.hasPermission(user, ManageRequestSettingsPermission.class) && isEnableRequests(c))
+                {
+                    return LinkBuilder.labkeyLink(
+                        "Manage Specimen Request Settings",
+                        PageFlowUtil.urlProvider(StudyUrls.class).getManageStudyURL(c)
+                    );
+                }
+
+                return null;
+            }
+
+            @Override
+            public @NotNull Class<? extends Permission> getEditSpecimenDataPermission()
+            {
+                return EditSpecimenDataPermission.class;
+            }
         });
 
         SystemMaintenance.addTask(new QueryBasedSpecimenImportUploadTask());

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

@@ -56,7 +56,6 @@
 import org.labkey.api.specimen.importer.RollupInstance;
 import org.labkey.api.specimen.importer.VialSpecimenRollup;
 import org.labkey.api.specimen.model.SpecimenTablesProvider;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.QueryHelper;
 import org.labkey.api.study.QueryHelper.StudyCacheCollections;
 import org.labkey.api.study.SpecimenUrls;
@@ -74,6 +73,7 @@
 import org.labkey.specimen.requirements.SpecimenRequestRequirement;
 import org.labkey.specimen.requirements.SpecimenRequestRequirementProvider;
 import org.labkey.specimen.security.permissions.ManageRequestsPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.settings.SettingsManager;
 
 import java.io.IOException;

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

@@ -33,8 +33,6 @@
 import org.labkey.api.specimen.Vial;
 import org.labkey.api.specimen.location.LocationImpl;
 import org.labkey.api.specimen.location.LocationManager;
-import org.labkey.specimen.model.SpecimenTypeSummary;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.StudyUtils;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.NotFoundException;
@@ -48,8 +46,10 @@
 import org.labkey.specimen.model.AdditiveType;
 import org.labkey.specimen.model.DerivativeType;
 import org.labkey.specimen.model.PrimaryType;
+import org.labkey.specimen.model.SpecimenTypeSummary;
 import org.labkey.specimen.requirements.SpecimenRequest;
 import org.labkey.specimen.security.permissions.ManageRequestsPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.settings.RepositorySettings;
 import org.labkey.specimen.settings.SettingsManager;
 import org.springframework.validation.BindException;

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

@@ -107,17 +107,13 @@
 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.security.roles.ReaderRole;
 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;
 import org.labkey.api.specimen.location.LocationManager;
 import org.labkey.api.specimen.model.SpecimenComment;
 import org.labkey.api.specimen.model.SpecimenTablesProvider;
-import org.labkey.api.specimen.security.permissions.EditSpecimenDataPermission;
-import org.labkey.api.specimen.security.permissions.ManageRequestSettingsPermission;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.CohortFilter;
 import org.labkey.api.study.Dataset;
 import org.labkey.api.study.MapArrayExcelWriter;
@@ -171,11 +167,10 @@
 import org.labkey.specimen.RequestEventType;
 import org.labkey.specimen.RequestedSpecimens;
 import org.labkey.specimen.SpecimenManager;
-import org.labkey.specimen.SpecimenRequestException;
 import org.labkey.specimen.SpecimenModule;
+import org.labkey.specimen.SpecimenRequestException;
 import org.labkey.specimen.SpecimenRequestManager;
 import org.labkey.specimen.SpecimenRequestStatus;
-import org.labkey.specimen.security.roles.SpecimenRequesterRole;
 import org.labkey.specimen.importer.QueryBasedSpecimenTransform;
 import org.labkey.specimen.importer.RequestabilityManager;
 import org.labkey.specimen.importer.SimpleSpecimenImporter;
@@ -194,14 +189,18 @@
 import org.labkey.specimen.requirements.SpecimenRequestRequirement;
 import org.labkey.specimen.requirements.SpecimenRequestRequirementProvider;
 import org.labkey.specimen.requirements.SpecimenRequestRequirementType;
+import org.labkey.specimen.security.permissions.EditSpecimenDataPermission;
 import org.labkey.specimen.security.permissions.ManageDisplaySettingsPermission;
 import org.labkey.specimen.security.permissions.ManageNewRequestFormPermission;
 import org.labkey.specimen.security.permissions.ManageNotificationsPermission;
 import org.labkey.specimen.security.permissions.ManageRequestRequirementsPermission;
+import org.labkey.specimen.security.permissions.ManageRequestSettingsPermission;
 import org.labkey.specimen.security.permissions.ManageRequestStatusesPermission;
 import org.labkey.specimen.security.permissions.ManageRequestsPermission;
 import org.labkey.specimen.security.permissions.ManageSpecimenActorsPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.security.permissions.SetSpecimenCommentsPermission;
+import org.labkey.specimen.security.roles.SpecimenRequesterRole;
 import org.labkey.specimen.settings.DisplaySettings;
 import org.labkey.specimen.settings.RepositorySettings;
 import org.labkey.specimen.settings.RequestNotificationSettings;

specimen/src/org/labkey/specimen/query/SpecimenQueryView.java

@@ -50,8 +50,6 @@
 import org.labkey.api.specimen.SpecimenSchema;
 import org.labkey.api.specimen.Vial;
 import org.labkey.api.specimen.model.SpecimenTablesProvider;
-import org.labkey.api.specimen.security.permissions.EditSpecimenDataPermission;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.CohortFilter;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyService;
@@ -66,6 +64,8 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.writer.HtmlWriter;
 import org.labkey.specimen.actions.SpecimenController;
+import org.labkey.specimen.security.permissions.EditSpecimenDataPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.settings.DisplaySettings;
 import org.labkey.specimen.settings.RepositorySettings;
 import org.labkey.specimen.settings.SettingsManager;

specimen/src/org/labkey/specimen/query/SpecimenRequestQueryView.java

@@ -29,7 +29,6 @@
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
 import org.labkey.api.specimen.SpecimenQuerySchema;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyService;
 import org.labkey.api.study.StudyUtils;
@@ -44,6 +43,7 @@
 import org.labkey.specimen.actions.SpecimenController.ManageRequestAction;
 import org.labkey.specimen.actions.SpecimenController.SubmitRequestAction;
 import org.labkey.specimen.security.permissions.ManageRequestsPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.settings.SettingsManager;
 
 import java.util.Set;

study/api-src/org/labkey/api/specimen/security/permissions/EditSpecimenDataPermission.java → specimen/src/org/labkey/specimen/security/permissions/EditSpecimenDataPermission.java

@@ -13,20 +13,19 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package org.labkey.api.specimen.security.permissions;
-
+package org.labkey.specimen.security.permissions;
 
 import org.labkey.api.security.permissions.AbstractPermission;
+import org.labkey.specimen.SpecimenModule;
 
-/**
- * User: davebradlee
- * Date: 6/10/13
- * Time: 2:53 PM
- */
 public class EditSpecimenDataPermission extends AbstractPermission
 {
     public EditSpecimenDataPermission()
     {
-        super("Edit Specimen Data", "Allows editing of specimen data");
+        super(
+            "Edit Specimen Data",
+            "Allows editing of specimen data",
+            SpecimenModule.class
+        );
     }
 }

study/api-src/org/labkey/api/specimen/security/permissions/ManageRequestSettingsPermission.java → specimen/src/org/labkey/specimen/security/permissions/ManageRequestSettingsPermission.java

@@ -13,22 +13,19 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package org.labkey.api.specimen.security.permissions;
+package org.labkey.specimen.security.permissions;
 
 import org.labkey.api.security.permissions.AbstractPermission;
-import org.labkey.api.study.StudyService;
+import org.labkey.specimen.SpecimenModule;
 
-/*
-* User: Dave
-* Date: May 18, 2009
-* Time: 12:01:15 PM
-*/
 public class ManageRequestSettingsPermission extends AbstractPermission
 {
     public ManageRequestSettingsPermission()
     {
-        super("Manage Specimen Request and Tracking Settings",
-                "Allows management of specimen request and tracking settings",
-                StudyService.get().getStudyModuleClass()); // TODO: Switch to SpecimenModule.class
+        super(
+            "Manage Specimen Request and Tracking Settings",
+            "Allows management of specimen request and tracking settings",
+            SpecimenModule.class
+        );
     }
 }

study/api-src/org/labkey/api/specimen/security/permissions/RequestSpecimensPermission.java → specimen/src/org/labkey/specimen/security/permissions/RequestSpecimensPermission.java

@@ -13,22 +13,19 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package org.labkey.api.specimen.security.permissions;
+package org.labkey.specimen.security.permissions;
 
 import org.labkey.api.security.permissions.AbstractPermission;
-import org.labkey.api.study.StudyService;
+import org.labkey.specimen.SpecimenModule;
 
-/*
-* User: Dave
-* Date: May 18, 2009
-* Time: 11:43:40 AM
-*/
 public class RequestSpecimensPermission extends AbstractPermission
 {
     public RequestSpecimensPermission()
     {
-        super("Request Specimens",
-                "Allows request of specimens",
-                StudyService.get().getStudyModuleClass()); // TODO: Switch to SpecimenModule.class
+        super(
+            "Request Specimens",
+            "Allows request of specimens",
+            SpecimenModule.class
+        );
     }
 }

specimen/src/org/labkey/specimen/security/roles/SpecimenCoordinatorRole.java

@@ -17,18 +17,18 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.security.permissions.EditSharedViewPermission;
-import org.labkey.api.specimen.security.permissions.EditSpecimenDataPermission;
-import org.labkey.api.specimen.security.permissions.ManageRequestSettingsPermission;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.security.permissions.ManageStudyPermission;
+import org.labkey.specimen.security.permissions.EditSpecimenDataPermission;
 import org.labkey.specimen.security.permissions.LockSpecimensPermission;
 import org.labkey.specimen.security.permissions.ManageDisplaySettingsPermission;
 import org.labkey.specimen.security.permissions.ManageNewRequestFormPermission;
 import org.labkey.specimen.security.permissions.ManageNotificationsPermission;
 import org.labkey.specimen.security.permissions.ManageRequestRequirementsPermission;
+import org.labkey.specimen.security.permissions.ManageRequestSettingsPermission;
 import org.labkey.specimen.security.permissions.ManageRequestStatusesPermission;
 import org.labkey.specimen.security.permissions.ManageRequestsPermission;
 import org.labkey.specimen.security.permissions.ManageSpecimenActorsPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.security.permissions.SetSpecimenCommentsPermission;
 
 import java.util.Collection;

specimen/src/org/labkey/specimen/security/roles/SpecimenRequesterRole.java

@@ -16,7 +16,7 @@
 package org.labkey.specimen.security.roles;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 
 import java.util.Collection;
 import java.util.Set;

specimen/src/org/labkey/specimen/view/SpecimenToolsWebPartFactory.java

@@ -15,7 +15,6 @@
  */
 package org.labkey.specimen.view;
 
-import org.labkey.api.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.api.study.StudyUrls;
 import org.labkey.api.study.security.permissions.ManageStudyPermission;
 import org.labkey.api.study.view.StudyToolsWebPart;
@@ -27,6 +26,7 @@
 import org.labkey.specimen.actions.ShowSearchAction;
 import org.labkey.specimen.actions.SpecimenController.AutoReportListAction;
 import org.labkey.specimen.actions.SpecimenController.ShowCreateSpecimenRequestAction;
+import org.labkey.specimen.security.permissions.RequestSpecimensPermission;
 import org.labkey.specimen.settings.SettingsManager;
 
 import java.util.ArrayList;

specimen/src/org/labkey/specimen/view/manageSpecimens.jsp

@@ -15,13 +15,12 @@
  * limitations under the License.
  */
 %>
-<%@ page import="com.google.common.collect.Iterables"%>
+<%@ page import="com.google.common.collect.Iterables" %>
 <%@ page import="org.labkey.api.data.Container" %>
 <%@ page import="org.labkey.api.exp.property.Domain" %>
 <%@ page import="org.labkey.api.security.User" %>
 <%@ page import="org.labkey.api.security.permissions.AdminPermission" %>
 <%@ page import="org.labkey.api.specimen.model.SpecimenTablesProvider" %>
-<%@ page import="org.labkey.api.specimen.security.permissions.ManageRequestSettingsPermission" %>
 <%@ page import="org.labkey.api.study.SpecimenService" %>
 <%@ page import="org.labkey.api.study.SpecimenTransform" %>
 <%@ page import="org.labkey.api.study.Study" %>
@@ -41,6 +40,7 @@
 <%@ page import="org.labkey.specimen.actions.SpecimenController.ManageSpecimenWebPartAction" %>
 <%@ page import="org.labkey.specimen.actions.SpecimenController.ManageStatusesAction" %>
 <%@ page import="org.labkey.specimen.requirements.SpecimenRequestRequirementProvider" %>
+<%@ page import="org.labkey.specimen.security.permissions.ManageRequestSettingsPermission" %>
 <%@ page import="org.labkey.specimen.settings.SettingsManager" %>
 <%@ page import="java.util.Collection" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>

specimen/src/org/labkey/specimen/view/webPart.jsp

@@ -15,10 +15,9 @@
  * limitations under the License.
  */
 %>
-<%@ page import="org.labkey.api.data.Container"%>
-<%@ page import="org.labkey.api.security.User"%>
-<%@ page import="org.labkey.api.security.permissions.AdminPermission"%>
-<%@ page import="org.labkey.api.specimen.security.permissions.RequestSpecimensPermission"%>
+<%@ page import="org.labkey.api.data.Container" %>
+<%@ page import="org.labkey.api.security.User" %>
+<%@ page import="org.labkey.api.security.permissions.AdminPermission" %>
 <%@ page import="org.labkey.api.study.StudyUrls" %>
 <%@ page import="org.labkey.api.util.HtmlString" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
@@ -29,6 +28,7 @@
 <%@ page import="org.labkey.specimen.actions.SpecimenController.AutoReportListAction" %>
 <%@ page import="org.labkey.specimen.actions.SpecimenController.ShowCreateSpecimenRequestAction" %>
 <%@ page import="org.labkey.specimen.actions.SpecimenController.ViewRequestsAction" %>
+<%@ page import="org.labkey.specimen.security.permissions.RequestSpecimensPermission" %>
 <%@ page import="org.labkey.specimen.settings.SettingsManager" %>
 <%@ page import="org.labkey.specimen.view.SpecimenWebPart" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>

study/api-src/org/labkey/api/specimen/SpecimenMigrationService.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.api.specimen;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
@@ -26,9 +27,11 @@
 import org.labkey.api.query.QueryView;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.importer.SimpleStudyImportContext;
+import org.labkey.api.util.SafeToRender;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewContext;
 import org.labkey.vfs.FileLike;
@@ -74,4 +77,8 @@ void importSpecimenArchive(@Nullable FileLike inputFile, PipelineJob job, Simple
      * Returns a specimen pivot TableInfo, if that's what was requested
      */
     @Nullable TableInfo getSpecimenPivotTable(UserSchema schema, String name, Study study, ContainerFilter cf);
+
+    @Nullable SafeToRender getSpecimenSettingsLink(Container c, User user);
+
+    @NotNull Class<? extends Permission> getEditSpecimenDataPermission();
 }