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HBASE-18683 Upgrade hbase to commons-math 3

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Upgrade commons-math:2.2 to commons-math3:3.6.1
Remove commons-math 2 specific content from LICENSE.vm
Add missing jersey-client dependency to hbase-it module

Signed-off-by: Michael Stack <stack@apache.org>
This commit is contained in:
Peter Somogyi 2017-08-25 13:34:03 +02:00 committed by Michael Stack
parent 42f140d9fb
commit d7824f739d
7 changed files with 96 additions and 241 deletions
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7
hbase-it/pom.xml
View File

@ -258,7 +258,7 @@
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
@ -273,6 +273,11 @@
<artifactId>javax.ws.rs-api</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>${jersey.version}</version>
</dependency>
<!-- Hadoop needs Netty 3.x at test scope for the minicluster -->
<dependency>
<groupId>io.netty</groupId>

2
hbase-it/src/test/java/org/apache/hadoop/hbase/mttr/IntegrationTestMTTR.java
View File

@ -32,7 +32,7 @@ import java.util.concurrent.TimeUnit;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.apache.hadoop.hbase.ClusterStatus;
import org.apache.hadoop.hbase.HColumnDescriptor;
import org.apache.hadoop.hbase.HTableDescriptor;

310
hbase-resource-bundle/src/main/resources/META-INF/LICENSE.vm
View File

@ -896,8 +896,7 @@ facade for Java, which can be obtained at:
* http://www.slf4j.org/
#end
## Supplemental from commons-math
## parameter two-and-three true = updated to also cover commons-math 2, just 3 otherwise
#macro(commons_math_license $two-and-three)
#macro(commons_math_license)
----
APACHE COMMONS MATH DERIVATIVE WORKS:
@ -910,10 +909,6 @@ are reproduced below.
For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in
the LevenbergMarquardtOptimizer class in package
org.apache.commons.math3.optimization.general
#if(${two-and-three})
and package
org.apache.commons.math.optimization.general
#end
Original source copyright and license statement:
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
@ -972,9 +967,7 @@ POSSIBILITY OF SUCH LOSS OR DAMAGES.
Copyright and license statement for the odex Fortran routine developed by
E. Hairer and G. Wanner and translated in GraggBulirschStoerIntegrator class
in package org.apache.commons.math3.ode.nonstiff:
#if(${two-and-three})
and in package org.apache.commons.math.ode.nonstiff:
#end
Copyright (c) 2004, Ernst Hairer
@ -1002,58 +995,9 @@ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
Copyright and license statement for the original lapack fortran routines
translated in EigenDecompositionImpl class in package
org.apache.commons.math3.linear:
#if(${two-and-three})
and package
org.apache.commons.math.linear:
#end
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer listed
in this license in the documentation and/or other materials
provided with the distribution.
- Neither the name of the copyright holders nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
Copyright and license statement for the original Mersenne twister C
routines translated in MersenneTwister class in package
org.apache.commons.math3.random:
#if(${two-and-three})
and package
org.apache.commons.math.random:
#end
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved.
@ -1087,191 +1031,103 @@ org.apache.commons.math.random:
===============================================================================
The class "org.apache.commons.math3.exception.util.LocalizedFormatsTest" is
an adapted version of "OrekitMessagesTest" test class for the Orekit library
The "org.apache.commons.math3.analysis.interpolation.HermiteInterpolator"
has been imported from the Orekit space flight dynamics library.
Th Orekit library is described at:
https://www.orekit.org/forge/projects/orekit
The original files are distributed under the terms of the Apache 2 license
which is: Copyright 2010 CS Communication & Systèmes
#end
## Supplemental from commons-math if just commons-math 2 is present
#macro(commons_math_two_license)
----
APACHE COMMONS MATH DERIVATIVE WORKS:
The Apache commons-math library includes a number of subcomponents
whose implementation is derived from original sources written
in C or Fortran. License terms of the original sources
are reproduced below.
The initial code for shuffling an array (originally in class
"org.apache.commons.math3.random.RandomDataGenerator", now replaced by
a method in class "org.apache.commons.math3.util.MathArrays") was
inspired from the algorithm description provided in
"Algorithms", by Ian Craw and John Pulham (University of Aberdeen 1999).
The textbook (containing a proof that the shuffle is uniformly random) is
available here:
http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf
===============================================================================
For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in
the LevenbergMarquardtOptimizer class in package
org.apache.commons.math.optimization.general
Original source copyright and license statement:
License statement for the direction numbers in the resource files for Sobol sequences.
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
-----------------------------------------------------------------------------
Licence pertaining to sobol.cc and the accompanying sets of direction numbers
Redistribution and use in source and binary forms, with or
without modification, are permitted provided that the
following conditions are met:
1. Redistributions of source code must retain the above
copyright notice, this list of conditions and the following
disclaimer.
2. Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials
provided with the distribution.
3. The end-user documentation included with the
redistribution, if any, must include the following
acknowledgment:
"This product includes software developed by the
University of Chicago, as Operator of Argonne National
Laboratory.
Alternately, this acknowledgment may appear in the software
itself, if and wherever such third-party acknowledgments
normally appear.
4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS"
WITHOUT WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE
UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND
THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE
OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY
OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF
THE SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4)
DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL
BE CORRECTED.
5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
HOLDER, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF
ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,
INCIDENTAL, CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF
ANY KIND OR NATURE, INCLUDING BUT NOT LIMITED TO LOSS OF
PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, WHETHER
SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,
EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
POSSIBILITY OF SUCH LOSS OR DAMAGES.
===============================================================================
Copyright and license statement for the odex Fortran routine developed by
E. Hairer and G. Wanner and translated in GraggBulirschStoerIntegrator class
in package org.apache.commons.math.ode.nonstiff:
Copyright (c) 2004, Ernst Hairer
-----------------------------------------------------------------------------
Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
modification, are permitted provided that the following conditions are met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* Neither the names of the copyright holders nor the names of the
University of New South Wales and the University of Waikato
and its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
Copyright and license statement for the original lapack fortran routines
translated in EigenDecompositionImpl class in package
org.apache.commons.math.linear:
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer listed
in this license in the documentation and/or other materials
provided with the distribution.
- Neither the name of the copyright holders nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
The initial commit of package "org.apache.commons.math3.ml.neuralnet" is
an adapted version of code developed in the context of the Data Processing
and Analysis Consortium (DPAC) of the "Gaia" project of the European Space
Agency (ESA).
===============================================================================
Copyright and license statement for the original Mersenne twister C
routines translated in MersenneTwister class in package
org.apache.commons.math.random:
The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
an adapted version of code translated from the netlib Fortran program, rjbesl
http://www.netlib.org/specfun/rjbesl by R.J. Cody at Argonne National
Laboratory (USA). There is no license or copyright statement included with the
original Fortran sources.
===============================================================================
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
The BracketFinder (package org.apache.commons.math3.optimization.univariate)
and PowellOptimizer (package org.apache.commons.math3.optimization.general)
classes are based on the Python code in module "optimize.py" (version 0.5)
developed by Travis E. Oliphant for the SciPy library (http://www.scipy.org/)
Copyright © 2003-2009 SciPy Developers.
1. Redistributions of source code must retain the above copyright
SciPy license
Copyright © 2001, 2002 Enthought, Inc.
All rights reserved.
Copyright © 2003-2013 SciPy Developers.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. The names of its contributors may not be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
* Neither the name of Enthought nor the names of the SciPy Developers may
be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
#end
## Hadoop supplemental
@ -1472,8 +1328,7 @@ You can redistribute it and/or modify it under either the terms of the
## gather up EPL 1.0 works
#set($epl = [])
## track commons-math
#set($commons-math-two = false)
#set($commons-math-three = false)
#set($commons-math = false)
## track if we need jruby additionals.
#set($jruby = false)
## track hadoops
@ -1518,11 +1373,8 @@ ${dep.scm.url}
#end
#set($aggregated=false)
## Check for our set of known dependencies that require manual LICENSE additions.
#if($dep.artifactId.equals("commons-math"))
#set($commons-math-two=true)
#end
#if($dep.artifactId.equals("commons-math3"))
#set($commons-math-three=true)
#set($commons-math=true)
#end
#if($dep.artifactId.equals("jruby-complete"))
#set($jruby=true)
@ -1625,10 +1477,8 @@ ${dep.scm.url}
#if($hadoop)
#hadoop_license()
#end
#if($commons-math-three)
#commons_math_license($commons-math-two)
#elseif($commons-math-two)
#commons_math_two_license()
#if($commons-math)
#commons_math_license()
#end
#if(!(${mit.isEmpty()}))
====

2
hbase-server/pom.xml
View File

@ -545,7 +545,7 @@
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>log4j</groupId>

4
hbase-server/src/test/java/org/apache/hadoop/hbase/HFilePerformanceEvaluation.java
View File

@ -24,8 +24,8 @@ import java.util.Random;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.math.random.RandomData;
import org.apache.commons.math.random.RandomDataImpl;
import org.apache.commons.math3.random.RandomData;
import org.apache.commons.math3.random.RandomDataImpl;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;

4
hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/compactions/GaussianFileListGenerator.java
View File

@ -22,8 +22,8 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.math.random.GaussianRandomGenerator;
import org.apache.commons.math.random.MersenneTwister;
import org.apache.commons.math3.random.GaussianRandomGenerator;
import org.apache.commons.math3.random.MersenneTwister;
import org.apache.hadoop.hbase.regionserver.StoreFile;
class GaussianFileListGenerator extends StoreFileListGenerator {

4
pom.xml
View File

@ -1354,7 +1354,7 @@
<commons-io.version>2.5</commons-io.version>
<commons-lang3.version>3.6</commons-lang3.version>
<commons-logging.version>1.2</commons-logging.version>
<commons-math.version>2.2</commons-math.version>
<commons-math.version>3.6.1</commons-math.version>
<disruptor.version>3.3.6</disruptor.version>
<!-- Do not use versions earlier than 3.2.2 due to a security vulnerability -->
<collections.version>4.1</collections.version>
@ -1768,7 +1768,7 @@
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<artifactId>commons-math3</artifactId>
<version>${commons-math.version}</version>
</dependency>
<dependency>