From 881746cf9da0b724e57e79b54bef70dfd9d51841 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Mon, 13 Jul 2020 07:21:33 -0700 Subject: [PATCH] Item 7490: upgrade log4j --- .../atlas/pepdb/PepDBBaseController.java | 28 +++++---- .../atlas/pepdb/PepDBContainerListener.java | 7 ++- .../scharp/atlas/pepdb/PepDBController.java | 57 ++++++++++++++----- src/org/scharp/atlas/pepdb/PepDBManager.java | 5 +- src/org/scharp/atlas/pepdb/PepDBModule.java | 5 +- .../scharp/atlas/pepdb/PeptideImporter.java | 17 ++++-- src/org/scharp/atlas/pepdb/PoolImporter.java | 20 ++++--- .../scharp/atlas/pepdb/model/PeptidePool.java | 5 +- .../atlas/pepdb/query/PepDBQuerySchema.java | 4 -- .../scharp/atlas/pepdb/view/PepDBWebPart.java | 9 +-- .../scharp/atlas/pepdb/view/pepDBWebPart.jsp | 2 +- .../atlas/pepdb/view/peptideDetails.jsp | 6 +- .../atlas/pepdb/view/peptideGroupSelect.jsp | 7 +-- 13 files changed, 109 insertions(+), 63 deletions(-) diff --git a/src/org/scharp/atlas/pepdb/PepDBBaseController.java b/src/org/scharp/atlas/pepdb/PepDBBaseController.java index 90fab2d..c43f2a3 100644 --- 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 index 553fb08..8802713 100644 --- 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 index 90ce2e0..10d2e24 100644 --- 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 index 7076668..251e17a 100644 --- 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 index 729db7a..6296370 100644 --- 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 index 07ae3f9..6e38e84 100644 --- 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 index f9a68b5..21ec2fa 100644 --- 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 index 9fe8fa1..6d8fe14 100644 --- 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 index 06e03b2..44bf18d 100644 --- 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 index 6196b09..ec1dfce 100644 --- 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 { - 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 index c62ebdb..6751e91 100644 --- 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 index ddda419..f1dc3f8 100644 --- 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 me = (JspView) HttpView.currentView(); diff --git a/src/org/scharp/atlas/pepdb/view/peptideGroupSelect.jsp b/src/org/scharp/atlas/pepdb/view/peptideGroupSelect.jsp index b003473..bb9849a 100644 --- 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" %>