Merge remote-tracking branch 'origin/develop' into fb_jsonutil

Author: labkey-matthewb

LDK/api-src/org/labkey/api/ldk/ExtendedSimpleModule.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.api.ldk;
 
+import jakarta.servlet.http.HttpServletRequest;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.ModuleContext;
@@ -25,8 +26,6 @@
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.web.servlet.mvc.Controller;
 
-import javax.servlet.http.HttpServletRequest;
-
 /**
  * User: bimber
  * Date: 2/6/13

LDK/api-src/org/labkey/api/ldk/notification/Notification.java

@@ -15,15 +15,14 @@
  */
 package org.labkey.api.ldk.notification;
 
+import jakarta.mail.MessagingException;
+import jakarta.mail.internet.MimeMessage;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 import org.labkey.api.util.MailHelper;
 
-import javax.mail.MessagingException;
-import javax.mail.internet.MimeMessage;
-
 /**
  * User: bbimber
  * Date: 7/14/12

LDK/api-src/org/labkey/api/ldk/notification/NotificationService.java

@@ -15,12 +15,12 @@
  */
 package org.labkey.api.ldk.notification;
 
+import jakarta.mail.Address;
 import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserPrincipal;
 import org.labkey.api.security.ValidEmail;
 
-import javax.mail.Address;
 import java.util.Date;
 import java.util.List;
 import java.util.Set;

LDK/src/org/labkey/ldk/LDKController.java

@@ -16,6 +16,7 @@
 
 package org.labkey.ldk;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -86,7 +87,6 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
 import java.net.URISyntaxException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -98,9 +98,6 @@
 import java.util.Set;
 import java.util.function.Predicate;
 
-
-
-
 public class LDKController extends SpringActionController
 {
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(LDKController.class);
@@ -115,7 +112,7 @@ public LDKController()
     public class GetNotificationsAction extends ReadOnlyApiAction<Object>
     {
         @Override
-        public ApiResponse execute(Object form, BindException errors) throws Exception
+        public ApiResponse execute(Object form, BindException errors)
         {
             Map<String, Object> result = new HashMap<>();
             Set<Notification> set = NotificationServiceImpl.get().getNotifications(getContainer(), false);

LDK/src/org/labkey/ldk/notification/NotificationJob.java

@@ -1,36 +1,19 @@
 package org.labkey.ldk.notification;
 
-import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.ldk.notification.Notification;
 import org.labkey.api.ldk.notification.NotificationService;
-import org.labkey.api.security.User;
-import org.labkey.api.security.permissions.AdminPermission;
-import org.labkey.api.util.ExceptionUtil;
-import org.labkey.api.util.MailHelper;
-import org.quartz.CronScheduleBuilder;
 import org.quartz.Job;
-import org.quartz.JobBuilder;
-import org.quartz.JobDetail;
 import org.quartz.JobExecutionContext;
 import org.quartz.JobExecutionException;
-import org.quartz.Scheduler;
-import org.quartz.SchedulerException;
-import org.quartz.Trigger;
-import org.quartz.TriggerBuilder;
-import org.quartz.impl.StdSchedulerFactory;
 
-import javax.mail.Address;
-import javax.mail.Message;
 import java.util.Date;
-import java.util.List;
 import java.util.Set;
 
 
 /**
- * Created with IntelliJ IDEA.
  * User: bimber
  * Date: 12/19/12
  * Time: 7:59 PM

LDK/src/org/labkey/ldk/notification/NotificationServiceImpl.java

@@ -15,10 +15,14 @@
  */
 package org.labkey.ldk.notification;
 
+import jakarta.mail.Address;
+import jakarta.mail.Message;
+import jakarta.mail.MessagingException;
+import jakarta.mail.internet.MimeMessage;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DurationFormatUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
@@ -54,10 +58,6 @@
 import org.quartz.TriggerBuilder;
 import org.quartz.impl.StdSchedulerFactory;
 
-import javax.mail.Address;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.internet.MimeMessage;
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -71,7 +71,6 @@
 import java.util.Set;
 
 /**
- * Created by IntelliJ IDEA.
  * User: bbimber
  * Date: 7/14/12
  * Time: 2:49 PM

laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayImportMethod.java

@@ -15,10 +15,14 @@
  */
 package org.labkey.api.laboratory.assay;
 
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.poi.ss.usermodel.Workbook;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
+import org.labkey.api.assay.AssayProvider;
+import org.labkey.api.assay.AssayService;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.ExcelWriter;
@@ -34,13 +38,9 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.ExcelFactory;
 import org.labkey.api.security.User;
-import org.labkey.api.assay.AssayProvider;
-import org.labkey.api.assay.AssayService;
 import org.labkey.api.util.JsonUtil;
 import org.labkey.api.view.ViewContext;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;

laboratory/src/org/labkey/laboratory/LaboratoryController.java

@@ -16,6 +16,7 @@
 
 package org.labkey.laboratory;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
@@ -56,6 +57,7 @@
 import org.labkey.api.laboratory.assay.AssayDataProvider;
 import org.labkey.api.laboratory.assay.AssayImportMethod;
 import org.labkey.api.laboratory.assay.AssayParser;
+import org.labkey.api.laboratory.query.ContainerIncrementingTable;
 import org.labkey.api.laboratory.security.LaboratoryAdminPermission;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleHtmlView;
@@ -85,13 +87,11 @@
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.laboratory.assay.AssayHelper;
-import org.labkey.api.laboratory.query.ContainerIncrementingTable;
 import org.labkey.laboratory.query.WorkbookModel;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;

laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java

@@ -15,8 +15,12 @@
  */
 package org.labkey.laboratory.assay;
 
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
+import org.labkey.api.assay.AssayProvider;
+import org.labkey.api.assay.AssayRunUploadContext;
+import org.labkey.api.assay.AssayService;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ExperimentException;
@@ -26,24 +30,14 @@
 import org.labkey.api.qc.DefaultTransformResult;
 import org.labkey.api.qc.TransformResult;
 import org.labkey.api.security.User;
-import org.labkey.api.assay.AssayProvider;
-import org.labkey.api.assay.AssayRunUploadContext;
-import org.labkey.api.assay.AssayService;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewContext;
 
-import javax.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
-/**
- * User: bimber
- * Date: 9/24/12
- * Time: 4:35 PM
- */
-
 /**
  * This primariy serves as a shim between the laboratory assay import pathway and the core.
  * @param <ProviderType>
@@ -59,7 +53,7 @@ public class RunUploadContext<ProviderType extends AssayProvider> implements Ass
     private final ViewContext _ctx;
 
     private TransformResult _transformResult;
-    private final Map _uploadedData;
+    private final Map<String, File> _uploadedData;
 
     public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, File> uploadedData)
     {
@@ -81,7 +75,7 @@ public ExpProtocol getProtocol()
     }
 
     @Override
-    public Map<DomainProperty, String> getRunProperties() throws ExperimentException
+    public Map<DomainProperty, String> getRunProperties()
     {
         if (_runProperties != null)
         {
@@ -206,15 +200,13 @@ public Integer getReRunId()
     }
 
     @Override
-    public void uploadComplete(ExpRun run) throws ExperimentException
+    public void uploadComplete(ExpRun run)
     {
-
     }
 
 	@Override
     public Logger getLogger()
 	{
 		return null;
     }
-
 }