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Release 2023-05-17-1317
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@TDCasasent
TDCasasent committed May 22, 2023
1 parent 0d51b0d commit 80f7e1b
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -34,11 +34,11 @@ Permissions or ownership of the directories may need to be changed or matched to

In the directory with the docker-compose.yml file run:

docker-compose -p beihub -f docker-compose.yml up --no-build -d
docker compose -p beihub -f docker-compose.yml up --no-build -d

You can stop it with:

docker-compose -p beihub -f docker-compose.yml down
docker compose -p beihub -f docker-compose.yml down

To connect to the MBatch Omic Browser with:

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231 changes: 126 additions & 105 deletions apps/BatchEffectsInterface/pom.xml
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@@ -1,113 +1,134 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<modelVersion>4.0.0</modelVersion>

<groupId>edu.mda.bcb</groupId>
<artifactId>BatchEffectsInterface</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<groupId>edu.mda.bcb</groupId>
<artifactId>BatchEffectsInterface</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>

<name>BatchEffectsInterface</name>
<name>BatchEffectsInterface</name>

<properties>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<properties>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-catalina</artifactId>
<version>9.0.39</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.9</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>GDCAPI</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>SamplesValidation</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>StdMWUtils</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>7.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>test</scope>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${endorsed.dir}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-endorsed-api</artifactId>
<version>7.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-catalina</artifactId>
<version>9.0.74</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>SamplesValidation</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>StdMWUtils</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>8.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-core</artifactId>
<version>2.7.0</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-parsers</artifactId>
<version>2.7.0</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-parser-text-module</artifactId>
<version>2.7.0</version>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>17</source>
<target>17</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.2</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${endorsed.dir}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-endorsed-api</artifactId>
<version>7.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.15.0</version>
<configuration>
<excludes>
<exclude>org.apache.tomcat:tomcat-catalina</exclude>
</excludes>
</configuration>
</plugin>
</plugins>
</build>
</project>
12 changes: 6 additions & 6 deletions apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/authorization/Authorization.java
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@@ -1,4 +1,4 @@
// Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 University of Texas MD Anderson Cancer Center
// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
//
// This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
//
Expand All @@ -14,6 +14,7 @@
import edu.mda.bcb.bei.servlets.AuthUpdate;
import edu.mda.bcb.bei.utils.BEIUtils;
import edu.mda.bcb.bei.servlets.BEIproperties;
import edu.mda.bcb.bei.utils.PropertiesEsc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
Expand All @@ -22,7 +23,6 @@
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.TreeSet;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
Expand Down Expand Up @@ -124,7 +124,7 @@ synchronized static public void removeAuthorizationData(HttpServlet theServlet,
mJobsToUsers.remove(theJobId+ ".USERS");
mJobsToRoles.remove(theJobId+ ".ROLES");
mJobsToOwner.remove(theJobId+ ".OWNER");
Properties props = new Properties();
PropertiesEsc props = new PropertiesEsc();
for (Entry<String, TreeSet<String>> myData : mJobsToUsers.entrySet())
{
props.setProperty(myData.getKey()+ ".USERS", treeSetToString(myData.getValue()));
Expand Down Expand Up @@ -170,7 +170,7 @@ synchronized static public void updateAuthorizationData(HttpServlet theServlet,
mJobsToRoles.put(theJobId, theRoles);
mJobsToOwner.put(theJobId, theJobOwner);
// add job and users to properties
Properties props = new Properties();
PropertiesEsc props = new PropertiesEsc();
for (Entry<String, TreeSet<String>> myData : mJobsToUsers.entrySet())
{
props.setProperty(myData.getKey()+ ".USERS", treeSetToString(myData.getValue()));
Expand Down Expand Up @@ -222,7 +222,7 @@ synchronized static public void readAuthorizationData(HttpServlet theServlet) th
{
//theServlet.log("readAuthorizationData version = " + edu.mda.bioinfo.bei.servlets.BEIUtils.M_VERSION);
long start = System.currentTimeMillis();
Properties props = new Properties();
PropertiesEsc props = new PropertiesEsc();
//authorization properties
try (FileInputStream is = new FileInputStream(new File(BEIUtils.M_PROPS, "auth.properties")))
{
Expand All @@ -232,7 +232,7 @@ synchronized static public void readAuthorizationData(HttpServlet theServlet) th
mJobsToRoles.clear();
mJobsToOwner.clear();

for (Entry<Object, Object> myData : props.entrySet())
for (Entry<String, String> myData : props.entrySet())
{
processProp(theServlet, (String)myData.getKey(), (String)myData.getValue());
}
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6 changes: 3 additions & 3 deletions apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/authorization/UserAndRoleData.java
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@@ -1,4 +1,4 @@
// Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 University of Texas MD Anderson Cancer Center
// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
//
// This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
//
Expand All @@ -11,8 +11,8 @@

package edu.mda.bcb.bei.authorization;

import edu.mda.bcb.bei.utils.PropertiesEsc;
import java.util.HashMap;
import java.util.Properties;
import java.util.TreeSet;

/**
Expand All @@ -29,7 +29,7 @@ private UserAndRoleData()

}

synchronized static public void updateUserAndRoleData(Properties theUsers)
synchronized static public void updateUserAndRoleData(PropertiesEsc theUsers)
{
mUsersToRoles.clear();
mRolesToUsers.clear();
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2 changes: 1 addition & 1 deletion apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/processes/BatchdataObj.java
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@@ -1,4 +1,4 @@
// Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 University of Texas MD Anderson Cancer Center
// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
//
// This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
//
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4 changes: 3 additions & 1 deletion apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthOut.java
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
// Copyright (c) 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 University of Texas MD Anderson Cancer Center
// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
//
// This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
//
Expand All @@ -11,6 +11,7 @@

package edu.mda.bcb.bei.servlets;

import edu.mda.bcb.bei.utils.ScanCheck;
import java.io.IOException;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
Expand Down Expand Up @@ -42,6 +43,7 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
{
try
{
ScanCheck.checkForSecurity(request);
try
{
// *******************************************************************
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