LabKey · labkey-ankurj · Aug 5, 2020 · Jul 13, 2020
diff --git a/src/org/scharp/atlas/pepdb/PepDBBaseController.java b/src/org/scharp/atlas/pepdb/PepDBBaseController.java
@@ -1,23 +1,31 @@
 package org.scharp.atlas.pepdb;
 
+import org.apache.commons.beanutils.ConversionException;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.action.SpringActionController;
-import org.labkey.api.data.*;
-import org.labkey.api.util.DateUtil;
 import org.labkey.api.attachments.AttachmentFile;
-import org.apache.log4j.Logger;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.beanutils.ConversionException;
-import org.springframework.validation.Errors;
+import org.labkey.api.data.BeanViewForm;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.DataColumn;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.util.DateUtil;
 import org.scharp.atlas.pepdb.model.PeptideGroup;
+import org.scharp.atlas.pepdb.model.PeptidePool;
 import org.scharp.atlas.pepdb.model.Peptides;
 import org.scharp.atlas.pepdb.model.ProteinCategory;
-import org.scharp.atlas.pepdb.model.PeptidePool;
+import org.springframework.validation.Errors;
 
-import java.util.*;
-import java.io.Writer;
 import java.io.IOException;
+import java.io.Writer;
 import java.sql.SQLException;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
@@ -28,7 +36,7 @@
  */
 public class PepDBBaseController extends SpringActionController
 {
-    private final static Logger _log = Logger.getLogger(PepDBBaseController.class);
+    private final static Logger _log = LogManager.getLogger(PepDBBaseController.class);
 
     private static final String VIEW_DISPLAY_PEPTIDE = "displayPeptide.view";
     protected static final String QRY_STRING_PEPTIDE_ID = "peptideId";

diff --git a/src/org/scharp/atlas/pepdb/PepDBContainerListener.java b/src/org/scharp/atlas/pepdb/PepDBContainerListener.java
@@ -1,10 +1,11 @@
 package org.scharp.atlas.pepdb;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.ContainerManager.ContainerListener;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager.ContainerListener;
 import org.labkey.api.security.User;
-import org.apache.log4j.Logger;
 
 import java.beans.PropertyChangeEvent;
 import java.util.Collection;
@@ -20,7 +21,7 @@
 public class PepDBContainerListener implements ContainerListener
 {
 
-    private static final Logger _log = Logger.getLogger(PepDBContainerListener.class);
+    private static final Logger _log = LogManager.getLogger(PepDBContainerListener.class);
 
     @Override
     public void containerCreated(Container c, User user)

diff --git a/src/org/scharp/atlas/pepdb/PepDBController.java b/src/org/scharp/atlas/pepdb/PepDBController.java
@@ -1,29 +1,58 @@
 package org.scharp.atlas.pepdb;
 
-import org.labkey.api.action.*;
-import org.labkey.api.security.RequiresPermission;
-import org.labkey.api.view.*;
-import org.labkey.api.data.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.labkey.api.action.ExportAction;
+import org.labkey.api.action.FormViewAction;
+import org.labkey.api.action.SimpleViewAction;
+import org.labkey.api.attachments.AttachmentFile;
+import org.labkey.api.data.ActionButton;
+import org.labkey.api.data.Aggregate;
+import org.labkey.api.data.ButtonBar;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.DataRegion;
+import org.labkey.api.data.DisplayColumn;
+import org.labkey.api.data.ExcelWriter;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TSVGridWriter;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QuerySettings;
+import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.attachments.AttachmentFile;
-import org.labkey.api.query.QuerySettings;
-import org.apache.log4j.Logger;
-import org.springframework.web.servlet.ModelAndView;
+import org.labkey.api.view.ActionURL;
+import org.labkey.api.view.DetailsView;
+import org.labkey.api.view.GridView;
+import org.labkey.api.view.HttpView;
+import org.labkey.api.view.InsertView;
+import org.labkey.api.view.JspView;
+import org.labkey.api.view.NavTree;
+import org.labkey.api.view.UpdateView;
+import org.labkey.api.view.VBox;
+import org.labkey.api.view.ViewContext;
+import org.scharp.atlas.pepdb.model.PeptideGroup;
+import org.scharp.atlas.pepdb.model.PeptidePool;
+import org.scharp.atlas.pepdb.model.Peptides;
+import org.scharp.atlas.pepdb.model.ProteinCategory;
+import org.springframework.beans.PropertyValues;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
-import org.springframework.beans.PropertyValues;
-import org.scharp.atlas.pepdb.model.*;
+import org.springframework.web.servlet.ModelAndView;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
-import java.util.List;
+import java.io.IOException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.LinkedList;
-import java.sql.SQLException;
-import java.io.IOException;
+import java.util.List;
 
 /**
  * User: sravani
@@ -32,7 +61,7 @@
  */
 public class PepDBController extends PepDBBaseController
 {
-    private static final Logger _log = Logger.getLogger(PepDBController.class);
+    private static final Logger _log = LogManager.getLogger(PepDBController.class);
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(PepDBController.class);
 
     private static final String PAGE_INDEX = "/org/scharp/atlas/pepdb/view/index.jsp";

diff --git a/src/org/scharp/atlas/pepdb/PepDBManager.java b/src/org/scharp/atlas/pepdb/PepDBManager.java
@@ -1,6 +1,7 @@
 package org.scharp.atlas.pepdb;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
@@ -33,7 +34,7 @@
 public class PepDBManager
 {
 
-    private static Logger log = Logger.getLogger(PepDBManager.class);
+    private static Logger log = LogManager.getLogger(PepDBManager.class);
     private static PepDBSchema schema = PepDBSchema.getInstance();
     /**
      * Static class

diff --git a/src/org/scharp/atlas/pepdb/PepDBModule.java b/src/org/scharp/atlas/pepdb/PepDBModule.java
@@ -1,6 +1,7 @@
 package org.scharp.atlas.pepdb;
 
-import org.apache.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.labkey.api.data.Container;
@@ -24,7 +25,7 @@
 
 public class PepDBModule extends DefaultModule
 {
-    private static final Logger _log = Logger.getLogger(DefaultModule.class);
+    private static final Logger _log = LogManager.getLogger(DefaultModule.class);
     public static final String NAME = "PepDB";
 
     @Override

diff --git a/src/org/scharp/atlas/pepdb/PeptideImporter.java b/src/org/scharp/atlas/pepdb/PeptideImporter.java
@@ -1,16 +1,21 @@
 package org.scharp.atlas.pepdb;
 
-import org.scharp.atlas.pepdb.model.*;
-import org.labkey.api.security.User;
 import org.labkey.api.attachments.AttachmentFile;
+import org.labkey.api.security.User;
+import org.scharp.atlas.pepdb.model.OptimalEpitopeList;
+import org.scharp.atlas.pepdb.model.Parent;
+import org.scharp.atlas.pepdb.model.PeptideGroup;
+import org.scharp.atlas.pepdb.model.Peptides;
+import org.scharp.atlas.pepdb.model.ProteinCategory;
+import org.scharp.atlas.pepdb.model.Source;
 import org.springframework.validation.Errors;
 
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.sql.SQLException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
-import java.util.ArrayList;
-import java.sql.SQLException;
-import java.io.InputStreamReader;
-import java.io.BufferedReader;
 
 /**
  * Created by IntelliJ IDEA.

diff --git a/src/org/scharp/atlas/pepdb/PoolImporter.java b/src/org/scharp/atlas/pepdb/PoolImporter.java
@@ -1,18 +1,22 @@
 package org.scharp.atlas.pepdb;
 
-import org.labkey.api.security.User;
 import org.labkey.api.attachments.AttachmentFile;
-import org.scharp.atlas.pepdb.PepDBBaseController.*;
-import org.scharp.atlas.pepdb.model.*;
+import org.labkey.api.security.User;
+import org.scharp.atlas.pepdb.PepDBBaseController.FileForm;
+import org.scharp.atlas.pepdb.model.PeptideGroup;
+import org.scharp.atlas.pepdb.model.PeptidePool;
+import org.scharp.atlas.pepdb.model.PeptidePoolAssignment;
+import org.scharp.atlas.pepdb.model.Peptides;
+import org.scharp.atlas.pepdb.model.PoolType;
+import org.scharp.atlas.pepdb.model.Source;
 import org.springframework.validation.Errors;
 
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.Arrays;
-import java.sql.SQLException;
-import java.sql.Array;
-import java.io.InputStreamReader;
-import java.io.BufferedReader;
+import java.util.HashMap;
 
 /**
  * Created by IntelliJ IDEA.

diff --git a/src/org/scharp/atlas/pepdb/model/PeptidePool.java b/src/org/scharp/atlas/pepdb/model/PeptidePool.java
@@ -1,7 +1,8 @@
 package org.scharp.atlas.pepdb.model;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Entity;
-import org.apache.log4j.Logger;
 
 /**
  * Created by IntelliJ IDEA.
@@ -21,7 +22,7 @@ public class PeptidePool extends Entity
     private Integer parent_pool_id;
     private String parent_pool_name;
     private String matrix_peptide_pool_id;
-    private static Logger log = Logger.getLogger(PeptidePool.class);
+    private static Logger log = LogManager.getLogger(PeptidePool.class);
 
     public PeptidePool()
     {

diff --git a/src/org/scharp/atlas/pepdb/query/PepDBQuerySchema.java b/src/org/scharp/atlas/pepdb/query/PepDBQuerySchema.java
@@ -1,17 +1,13 @@
 package org.scharp.atlas.pepdb.query;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.DatabaseTableType;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.module.Module;
 import org.labkey.api.query.DefaultSchema;
 import org.labkey.api.query.QuerySchema;
-import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.SimpleQueryUpdateService;
 import org.labkey.api.query.SimpleUserSchema;
 import org.labkey.api.security.User;
 

diff --git a/src/org/scharp/atlas/pepdb/view/PepDBWebPart.java b/src/org/scharp/atlas/pepdb/view/PepDBWebPart.java
@@ -1,16 +1,17 @@
 package org.scharp.atlas.pepdb.view;
 
-import javax.servlet.ServletException;
-
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.view.JspView;
 
+import javax.servlet.ServletException;
+
 /**
  * @version $Id$ 
  */
 public class PepDBWebPart extends JspView<Object> {
 
-    private static Logger _log = Logger.getLogger(PepDBWebPart.class);
+    private static Logger _log = LogManager.getLogger(PepDBWebPart.class);
 
     /**
      * 

diff --git a/src/org/scharp/atlas/pepdb/view/pepDBWebPart.jsp b/src/org/scharp/atlas/pepdb/view/pepDBWebPart.jsp
@@ -1,6 +1,6 @@
+<%@ page import="org.labkey.api.view.ActionURL"%>
 <%@ page import="org.labkey.api.view.HttpView"%>
 <%@ page import="org.labkey.api.view.ViewContext"%>
-<%@ page import="org.labkey.api.view.ActionURL"%>
 <%@ page import="org.scharp.atlas.pepdb.model.PeptideGroup" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%

diff --git a/src/org/scharp/atlas/pepdb/view/peptideDetails.jsp b/src/org/scharp/atlas/pepdb/view/peptideDetails.jsp
@@ -1,12 +1,12 @@
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page import="org.labkey.api.view.HttpView"%>
-<%@ page import="org.scharp.atlas.pepdb.PepDBManager" %>
-<%@ page import="org.scharp.atlas.pepdb.PepDBBaseController.*" %>
 <%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.scharp.atlas.pepdb.PepDBBaseController.PeptideQueryForm" %>
+<%@ page import="org.scharp.atlas.pepdb.PepDBManager" %>
 <%@ page import="org.scharp.atlas.pepdb.model.PeptidePool" %>
 <%@ page import="org.scharp.atlas.pepdb.model.Source" %>
-<%@ page import="java.util.List" %>
 <%@ page import="java.util.Arrays" %>
+<%@ page import="java.util.List" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     JspView<PeptideQueryForm> me = (JspView<PeptideQueryForm>) HttpView.currentView();

diff --git a/src/org/scharp/atlas/pepdb/view/peptideGroupSelect.jsp b/src/org/scharp/atlas/pepdb/view/peptideGroupSelect.jsp
@@ -1,11 +1,10 @@
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page import="org.labkey.api.view.HttpView"%>
+<%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.scharp.atlas.pepdb.PepDBBaseController.PeptideQueryForm" %>
 <%@ page import="org.scharp.atlas.pepdb.PepDBManager" %>
-<%@ page import="org.scharp.atlas.pepdb.model.PeptideGroup" %>
-<%@ page import="org.scharp.atlas.pepdb.PepDBBaseController.*" %>
-<%@ page import="java.sql.SQLException" %>
 <%@ page import="org.scharp.atlas.pepdb.PepDBSchema" %>
-<%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.scharp.atlas.pepdb.model.PeptideGroup" %>
 <%@ page import="org.scharp.atlas.pepdb.model.PeptidePool" %>
 <%@ page import="org.scharp.atlas.pepdb.model.ProteinCategory" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>