diff --git a/.gitignore b/.gitignore index cfcc4605..0b5a49d0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,30 +1,2 @@ -.classpath -.project -.settings .DS_Store -BioFormats Unit Tests -IO_Tests -Missing JAI ImageIO Service Tests -Missing LuraWave Service Tests -Missing MDB Service Tests -Missing NetCDF Service Tests -Missing OME ReaderWriter Service Tests -Missing OME-XML Service Tests -Missing POI Service Tests -OME ReaderWriter Service Tests -OMEXMLTests -artifacts -build -components/*/utils/*.class -emailable-report.html -index.html target -test-output -testng-results.xml -testng.css -tools/*.jar -*.log -*.xpr - -# For Fiji # -loci_tools.jar diff --git a/.travis.yml b/.travis.yml index 3ba4cda0..88930e8e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,8 +1,5 @@ language: java -# This (sudo: false) is needed to "run on container-based infrastructure" on -# which cache: is available -# http://docs.travis-ci.com/user/workers/container-based-infrastructure/ sudo: false # http://docs.travis-ci.com/user/caching/#Arbitrary-directories @@ -10,41 +7,15 @@ cache: directories: - $HOME/.m2 -addons: - apt_packages: - - git - - cmake - - build-essential - - libboost-all-dev - jdk: - oraclejdk8 - openjdk7 env: - - BUILD=maven_findbugs - - BUILD=maven - - BUILD=sphinx_html - - BUILD=ant + - BUILD=build matrix: fast_finish: true -before_install: - - if [[ $BUILD == 'sphinx_html' ]]; then pip install --user flake8 Sphinx==1.2.3; fi - install: - - if [[ $BUILD != 'ant' ]] && [[ $BUILD != 'sphinx_html' ]]; then git fetch --tags; fi - - if [[ $BUILD == 'maven_findbugs' ]]; then mvn install -DskipTests=true; fi - -script: - - ./tools/test-build $BUILD - -matrix: - exclude: - - jdk: openjdk7 - env: BUILD=sphinx_html - - jdk: openjdk7 - env: BUILD=maven_findbugs - - jdk: oraclejdk8 - env: BUILD=maven + - if [[ $BUILD == 'build' ]]; then mvn install; fi diff --git a/LICENSE.txt b/LICENSE.txt index d511905c..d52561a3 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,339 +1,27 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change free -software--to make sure the software is free for all its users. This -General Public License applies to most of the Free Software -Foundation's software and to any other program whose authors commit to -using it. (Some other Free Software Foundation software is covered by -the GNU Lesser General Public License instead.) You can apply it to -your programs, too. - - When we speak of free software, we are referring to freedom, not -price. Our General Public Licenses are designed to make sure that you -have the freedom to distribute copies of free software (and charge for -this service if you wish), that you receive source code or can get it -if you want it, that you can change the software or use pieces of it -in new free programs; and that you know you can do these things. - - To protect your rights, we need to make restrictions that forbid -anyone to deny you these rights or to ask you to surrender the rights. -These restrictions translate to certain responsibilities for you if you -distribute copies of the software, or if you modify it. - - For example, if you distribute copies of such a program, whether -gratis or for a fee, you must give the recipients all the rights that -you have. You must make sure that they, too, receive or can get the -source code. And you must show them these terms so they know their -rights. - - We protect your rights with two steps: (1) copyright the software, and -(2) offer you this license which gives you legal permission to copy, -distribute and/or modify the software. - - Also, for each author's protection and ours, we want to make certain -that everyone understands that there is no warranty for this free -software. If the software is modified by someone else and passed on, we -want its recipients to know that what they have is not the original, so -that any problems introduced by others will not reflect on the original -authors' reputations. - - Finally, any free program is threatened constantly by software -patents. We wish to avoid the danger that redistributors of a free -program will individually obtain patent licenses, in effect making the -program proprietary. To prevent this, we have made it clear that any -patent must be licensed for everyone's free use or not licensed at all. - - The precise terms and conditions for copying, distribution and -modification follow. - - GNU GENERAL PUBLIC LICENSE - TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION - - 0. This License applies to any program or other work which contains -a notice placed by the copyright holder saying it may be distributed -under the terms of this General Public License. The "Program", below, -refers to any such program or work, and a "work based on the Program" -means either the Program or any derivative work under copyright law: -that is to say, a work containing the Program or a portion of it, -either verbatim or with modifications and/or translated into another -language. (Hereinafter, translation is included without limitation in -the term "modification".) Each licensee is addressed as "you". - -Activities other than copying, distribution and modification are not -covered by this License; they are outside its scope. The act of -running the Program is not restricted, and the output from the Program -is covered only if its contents constitute a work based on the -Program (independent of having been made by running the Program). -Whether that is true depends on what the Program does. - - 1. You may copy and distribute verbatim copies of the Program's -source code as you receive it, in any medium, provided that you -conspicuously and appropriately publish on each copy an appropriate -copyright notice and disclaimer of warranty; keep intact all the -notices that refer to this License and to the absence of any warranty; -and give any other recipients of the Program a copy of this License -along with the Program. - -You may charge a fee for the physical act of transferring a copy, and -you may at your option offer warranty protection in exchange for a fee. - - 2. You may modify your copy or copies of the Program or any portion -of it, thus forming a work based on the Program, and copy and -distribute such modifications or work under the terms of Section 1 -above, provided that you also meet all of these conditions: - - a) You must cause the modified files to carry prominent notices - stating that you changed the files and the date of any change. - - b) You must cause any work that you distribute or publish, that in - whole or in part contains or is derived from the Program or any - part thereof, to be licensed as a whole at no charge to all third - parties under the terms of this License. - - c) If the modified program normally reads commands interactively - when run, you must cause it, when started running for such - interactive use in the most ordinary way, to print or display an - announcement including an appropriate copyright notice and a - notice that there is no warranty (or else, saying that you provide - a warranty) and that users may redistribute the program under - these conditions, and telling the user how to view a copy of this - License. (Exception: if the Program itself is interactive but - does not normally print such an announcement, your work based on - the Program is not required to print an announcement.) - -These requirements apply to the modified work as a whole. If -identifiable sections of that work are not derived from the Program, -and can be reasonably considered independent and separate works in -themselves, then this License, and its terms, do not apply to those -sections when you distribute them as separate works. But when you -distribute the same sections as part of a whole which is a work based -on the Program, the distribution of the whole must be on the terms of -this License, whose permissions for other licensees extend to the -entire whole, and thus to each and every part regardless of who wrote it. - -Thus, it is not the intent of this section to claim rights or contest -your rights to work written entirely by you; rather, the intent is to -exercise the right to control the distribution of derivative or -collective works based on the Program. - -In addition, mere aggregation of another work not based on the Program -with the Program (or with a work based on the Program) on a volume of -a storage or distribution medium does not bring the other work under -the scope of this License. - - 3. You may copy and distribute the Program (or a work based on it, -under Section 2) in object code or executable form under the terms of -Sections 1 and 2 above provided that you also do one of the following: - - a) Accompany it with the complete corresponding machine-readable - source code, which must be distributed under the terms of Sections - 1 and 2 above on a medium customarily used for software interchange; or, - - b) Accompany it with a written offer, valid for at least three - years, to give any third party, for a charge no more than your - cost of physically performing source distribution, a complete - machine-readable copy of the corresponding source code, to be - distributed under the terms of Sections 1 and 2 above on a medium - customarily used for software interchange; or, - - c) Accompany it with the information you received as to the offer - to distribute corresponding source code. (This alternative is - allowed only for noncommercial distribution and only if you - received the program in object code or executable form with such - an offer, in accord with Subsection b above.) - -The source code for a work means the preferred form of the work for -making modifications to it. For an executable work, complete source -code means all the source code for all modules it contains, plus any -associated interface definition files, plus the scripts used to -control compilation and installation of the executable. However, as a -special exception, the source code distributed need not include -anything that is normally distributed (in either source or binary -form) with the major components (compiler, kernel, and so on) of the -operating system on which the executable runs, unless that component -itself accompanies the executable. - -If distribution of executable or object code is made by offering -access to copy from a designated place, then offering equivalent -access to copy the source code from the same place counts as -distribution of the source code, even though third parties are not -compelled to copy the source along with the object code. - - 4. You may not copy, modify, sublicense, or distribute the Program -except as expressly provided under this License. Any attempt -otherwise to copy, modify, sublicense or distribute the Program is -void, and will automatically terminate your rights under this License. -However, parties who have received copies, or rights, from you under -this License will not have their licenses terminated so long as such -parties remain in full compliance. - - 5. You are not required to accept this License, since you have not -signed it. However, nothing else grants you permission to modify or -distribute the Program or its derivative works. These actions are -prohibited by law if you do not accept this License. Therefore, by -modifying or distributing the Program (or any work based on the -Program), you indicate your acceptance of this License to do so, and -all its terms and conditions for copying, distributing or modifying -the Program or works based on it. - - 6. Each time you redistribute the Program (or any work based on the -Program), the recipient automatically receives a license from the -original licensor to copy, distribute or modify the Program subject to -these terms and conditions. You may not impose any further -restrictions on the recipients' exercise of the rights granted herein. -You are not responsible for enforcing compliance by third parties to -this License. - - 7. If, as a consequence of a court judgment or allegation of patent -infringement or for any other reason (not limited to patent issues), -conditions are imposed on you (whether by court order, agreement or -otherwise) that contradict the conditions of this License, they do not -excuse you from the conditions of this License. If you cannot -distribute so as to satisfy simultaneously your obligations under this -License and any other pertinent obligations, then as a consequence you -may not distribute the Program at all. For example, if a patent -license would not permit royalty-free redistribution of the Program by -all those who receive copies directly or indirectly through you, then -the only way you could satisfy both it and this License would be to -refrain entirely from distribution of the Program. - -If any portion of this section is held invalid or unenforceable under -any particular circumstance, the balance of the section is intended to -apply and the section as a whole is intended to apply in other -circumstances. - -It is not the purpose of this section to induce you to infringe any -patents or other property right claims or to contest validity of any -such claims; this section has the sole purpose of protecting the -integrity of the free software distribution system, which is -implemented by public license practices. Many people have made -generous contributions to the wide range of software distributed -through that system in reliance on consistent application of that -system; it is up to the author/donor to decide if he or she is willing -to distribute software through any other system and a licensee cannot -impose that choice. - -This section is intended to make thoroughly clear what is believed to -be a consequence of the rest of this License. - - 8. If the distribution and/or use of the Program is restricted in -certain countries either by patents or by copyrighted interfaces, the -original copyright holder who places the Program under this License -may add an explicit geographical distribution limitation excluding -those countries, so that distribution is permitted only in or among -countries not thus excluded. In such case, this License incorporates -the limitation as if written in the body of this License. - - 9. The Free Software Foundation may publish revised and/or new versions -of the General Public License from time to time. Such new versions will -be similar in spirit to the present version, but may differ in detail to -address new problems or concerns. - -Each version is given a distinguishing version number. If the Program -specifies a version number of this License which applies to it and "any -later version", you have the option of following the terms and conditions -either of that version or of any later version published by the Free -Software Foundation. If the Program does not specify a version number of -this License, you may choose any version ever published by the Free Software -Foundation. - - 10. If you wish to incorporate parts of the Program into other free -programs whose distribution conditions are different, write to the author -to ask for permission. For software which is copyrighted by the Free -Software Foundation, write to the Free Software Foundation; we sometimes -make exceptions for this. Our decision will be guided by the two goals -of preserving the free status of all derivatives of our free software and -of promoting the sharing and reuse of software generally. - - NO WARRANTY - - 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY -FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN -OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES -PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED -OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS -TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE -PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, -REPAIR OR CORRECTION. - - 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING -WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR -REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, -INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING -OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED -TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY -YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER -PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE -POSSIBILITY OF SUCH DAMAGES. - - END OF TERMS AND CONDITIONS - - How to Apply These Terms to Your New Programs - - If you develop a new program, and you want it to be of the greatest -possible use to the public, the best way to achieve this is to make it -free software which everyone can redistribute and change under these terms. - - To do so, attach the following notices to the program. It is safest -to attach them to the start of each source file to most effectively -convey the exclusion of warranty; and each file should have at least -the "copyright" line and a pointer to where the full notice is found. - - - Copyright (C) - - 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. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License along - with this program; if not, write to the Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. - -Also add information on how to contact you by electronic and paper mail. - -If the program is interactive, make it output a short notice like this -when it starts in an interactive mode: - - Gnomovision version 69, Copyright (C) year name of author - Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, the commands you use may -be called something other than `show w' and `show c'; they could even be -mouse-clicks or menu items--whatever suits your program. - -You should also get your employer (if you work as a programmer) or your -school, if any, to sign a "copyright disclaimer" for the program, if -necessary. Here is a sample; alter the names: - - Yoyodyne, Inc., hereby disclaims all copyright interest in the program - `Gnomovision' (which makes passes at compilers) written by James Hacker. - - , 1 April 1989 - Ty Coon, President of Vice - -This General Public License does not permit incorporating your program into -proprietary programs. If your program is a subroutine library, you may -consider it more useful to permit linking proprietary applications with the -library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. +Copyright (C) 2005 - 2016 Open Microscopy Environment: + - Board of Regents of the University of Wisconsin-Madison + - Glencoe Software, Inc. + - University of Dundee +All rights reserved. + +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. + +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 HOLDER 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. diff --git a/README.md b/README.md index b7303b8f..e76d8bdc 100644 --- a/README.md +++ b/README.md @@ -1,41 +1,8 @@ -# Bio-Formats +# OME Common Java -[![Build Status](https://travis-ci.org/openmicroscopy/bioformats.png)](http://travis-ci.org/openmicroscopy/bioformats) +[![Build Status](https://travis-ci.org/ome/ome-common-java.png)](http://travis-ci.org/ome/ome-common-java) -Bio-Formats is a standalone Java library for reading and writing life sciences -image file formats. It is capable of parsing both pixels and metadata for a -large number of formats, as well as writing to several formats. - - -Purpose -------- - -Bio-Formats' primary purpose is to convert proprietary microscopy data into -an open standard called the OME data model, particularly into the OME-TIFF -file format. See the [statement of purpose](http://www.openmicroscopy.org/site/support/bio-formats/about/index.html) -for a thorough explanation and rationale. - - -Supported formats ------------------ - -Bio-Formats supports [more than a hundred file -formats](http://www.openmicroscopy.org/site/support/bio-formats/supported-formats.html). - - -For users ---------- - -[Many software -packages](http://www.openmicroscopy.org/site/support/bio-formats/users/index.html) -use Bio-Formats to read and write microscopy formats. - - -For developers --------------- - -You can use Bio-Formats to easily [support these formats in your -software](http://www.openmicroscopy.org/site/support/bio-formats/developers/java-library.html). +Common I/O, date parsing, and XML processing classes for OME Java components. More information diff --git a/components/formats-common/LICENSE.txt b/components/formats-common/LICENSE.txt deleted file mode 100644 index d52561a3..00000000 --- a/components/formats-common/LICENSE.txt +++ /dev/null @@ -1,27 +0,0 @@ -Copyright (C) 2005 - 2016 Open Microscopy Environment: - - Board of Regents of the University of Wisconsin-Madison - - Glencoe Software, Inc. - - University of Dundee -All rights reserved. - -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. - -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 HOLDER 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. diff --git a/components/formats-common/README.txt b/components/formats-common/README.txt deleted file mode 100644 index c18a943f..00000000 --- a/components/formats-common/README.txt +++ /dev/null @@ -1 +0,0 @@ - Contains common I/O, date parsing, and XML processing classes. diff --git a/components/formats-common/build.properties b/components/formats-common/build.properties deleted file mode 100644 index 66997d27..00000000 --- a/components/formats-common/build.properties +++ /dev/null @@ -1,35 +0,0 @@ -# -# build.properties -# - -# Ant properties file for Bio-Formats. -# Download Apache Ant from http://ant.apache.org/. -# Type "ant -p" for a list of targets. - -component.name = formats-common -component.jar = formats-common.jar -component.version = ${release.version} -component.classpath = ${lib.dir}/jgoodies-forms-1.7.2.jar:\ - ${lib.dir}/joda-time-2.2.jar:\ - ${lib.dir}/kryo-${kryo.version}.jar:\ - ${lib.dir}/logback-classic-${logback.version}.jar:\ - ${lib.dir}/logback-core-${logback.version}.jar:\ - ${lib.dir}/slf4j-api-${slf4j.version}.jar:\ - ${lib.dir}/guava-${guava.version}.jar:\ - ${lib.dir}/testng-${testng.version}.jar -component.java-version = 1.7 -component.deprecation = true - -component.resources-bin = loci/formats/bio-formats-logo.png \ - loci/formats/meta/*.xsl \ - loci/formats/utests/2008-09.ome -component.resources-text = loci/formats/*.txt \ - loci/common/services/services.properties - -component.main-class = loci.formats.gui.ImageViewer -component.runtime-cp = ${component.classpath}:\ - ${lib.dir}/logback-classic-${logback.version}.jar:\ - ${lib.dir}/logback-core-${logback.version}.jar:\ - ${lib.dir}/slf4j-api-${slf4j.version}.jar - -testng.xml.template = ${test.dir}/loci/common/utests/testng-template.xml diff --git a/components/formats-common/build.xml b/components/formats-common/build.xml deleted file mode 100644 index 3ad38986..00000000 --- a/components/formats-common/build.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - Build file for Bio-Formats project - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/components/formats-common/pom.xml b/components/formats-common/pom.xml deleted file mode 100644 index 64fc8478..00000000 --- a/components/formats-common/pom.xml +++ /dev/null @@ -1,184 +0,0 @@ - - - 4.0.0 - - - ome - pom-bio-formats - 5.2.4-SNAPSHOT - ../.. - - - formats-common - - Common - Contains common I/O, date parsing, and XML processing classes. - http://www.openmicroscopy.org/site/products/bio-formats - 2005 - - - - Simplified BSD License - https://opensource.org/licenses/BSD-2-Clause - repo - - - - - - com.esotericsoftware.kryo - kryo - ${kryo.version} - - - joda-time - joda-time - 2.2 - - - com.google.guava - guava - ${guava.version} - - - org.slf4j - slf4j-api - ${slf4j.version} - - - - - - ch.qos.logback - logback-core - ${logback.version} - - - - ch.qos.logback - logback-classic - ${logback.version} - - - - xalan - serializer - 2.7.2 - runtime - - - - xalan - xalan - 2.7.2 - runtime - - - - org.testng - testng - ${testng.version} - test - - - - - ${basedir}/../.. - - - - - - maven-surefire-plugin - - - test/loci/common/utests/testng-template.xml - - - ${basedir}/../../ant/ - - - - - org.codehaus.mojo - license-maven-plugin - - bsd_2 - Common package for I/O and related utilities - - - - - - - - hinerm - Mark Hiner - hinerm@gmail.edu - http://developer.imagej.net/users/hinerm - UW-Madison LOCI - http://loci.wisc.edu/ - - architect - developer - - -6 - - http://developer.imagej.net/files/imagej/profile-pictures/Mark.jpg?1305649677 - - - - melissa - Melissa Linkert - melissa@glencoesoftware.com - http://openmicroscopy.org/site/about/development-teams/glencoe-software - Glencoe Software - http://glencoesoftware.com/ - - architect - developer - - -6 - - http://openmicroscopy.org/site/about/development-teams/glencoe-software/melissalinkert.png - - - - curtis - Curtis Rueden - ctrueden@wisc.edu - http://loci.wisc.edu/people/curtis-rueden - UW-Madison LOCI - http://loci.wisc.edu/ - - architect - developer - - -6 - - http://loci.wisc.edu/files/loci/images/people/curtis-2010.jpg - - - - - - - - central - Central Repository - http://repo.maven.apache.org/maven2 - default - - - ome.releases - http://artifacts.openmicroscopy.org/artifactory/ome.releases - - - ome.snapshots - http://artifacts.openmicroscopy.org/artifactory/ome.snapshots - - - diff --git a/pom.xml b/pom.xml new file mode 100644 index 00000000..a2610533 --- /dev/null +++ b/pom.xml @@ -0,0 +1,488 @@ + + + 4.0.0 + + org.openmicroscopy + ome-common + 5.3.0-SNAPSHOT + + OME Common Java + Contains common I/O, date parsing, and XML processing classes. + http://www.openmicroscopy.org/site/products/bio-formats + 2005 + + + + Simplified BSD License + https://opensource.org/licenses/BSD-2-Clause + repo + + + + + + com.esotericsoftware.kryo + kryo + 2.24.0 + + + joda-time + joda-time + 2.2 + + + com.google.guava + guava + 17.0 + + + org.slf4j + slf4j-api + 1.7.6 + + + + + + ch.qos.logback + logback-core + 1.1.1 + + + + ch.qos.logback + logback-classic + 1.1.1 + + + + xalan + serializer + 2.7.2 + runtime + + + + xalan + xalan + 2.7.2 + runtime + + + + org.testng + testng + 6.8 + test + + + + + + UTF-8 + UTF-8 + + + d MMMMM yyyy + + + + + + + + install + + + + src/main/java + + **/*.properties + + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.5.1 + + + 1.7 + 1.7 + + + + + + + org.codehaus.mojo + license-maven-plugin + 1.9 + + bsd_2 + Open Microscopy Environment: + - Board of Regents of the University of Wisconsin-Madison + - Glencoe Software, Inc. + - University of Dundee + Common package for I/O and related utilities + false + true + + false + + src + + + java + properties + java + + + + + + org.apache.maven.plugins + maven-surefire-plugin + 2.19.1 + + + src/test/java/loci/common/utests/testng-template.xml + + + + + + maven-assembly-plugin + 2.6 + + + + maven-clean-plugin + 3.0.0 + + + + maven-dependency-plugin + 2.10 + + + + maven-deploy-plugin + 2.8.2 + + + + maven-install-plugin + 2.5.2 + + + + maven-jar-plugin + 3.0.2 + + + true + + + true + true + true + + + + ${buildNumber} + + ${maven.build.timestamp} + + + + + + + test-jar + + + + + + + maven-javadoc-plugin + + 2.10.4 + + + false + + + http://docs.oracle.com/javase/7/docs/api/ + + + + + + maven-plugin-plugin + 3.5 + + + + maven-release-plugin + 2.5.3 + + + org.apache.maven.scm + maven-scm-provider-gitexe + 1.9 + + + + + + maven-resources-plugin + 3.0.1 + + + + maven-site-plugin + 3.5.1 + + + + + org.apache.maven.plugins + maven-source-plugin + 3.0.1 + + + + + jar + + + + + + + + org.codehaus.mojo + buildnumber-maven-plugin + 1.4 + + + + validate + + create + + + + + true + UNKNOWN + + + + + + org.codehaus.mojo + versions-maven-plugin + 2.3 + + + + + + + + + + maven-javadoc-plugin + 2.9.1 + + src/main/java + + false + + + http://docs.oracle.com/javase/7/docs/api/ + + + + + + + + 3.0 + + + + Open Microscopy Environment + http://www.openmicroscopy.org/ + + + + Trac + https://trac.openmicroscopy.org/ome + + + + Jenkins + https://ci.openmicroscopy.org/ + + + + + OME-users + http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/ + http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/ + ome-users@lists.openmicroscopy.org.uk + http://lists.openmicroscopy.org.uk/pipermail/ome-users/ + + + OME-devel + http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel/ + http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel/ + ome-devel@lists.openmicroscopy.org.uk + http://lists.openmicroscopy.org.uk/pipermail/ome-devel/ + + + + + scm:git:https://github.com/ome/ome-common-java + scm:git:git@github.com:ome/ome-common-java + HEAD + http://github.com/ome/ome-common-java + + + + + ome.experimental + http://artifacts.openmicroscopy.org/artifactory/ome.experimental + + + ome.external + http://artifacts.openmicroscopy.org/artifactory/ome.external + + + ome.releases + http://artifacts.openmicroscopy.org/artifactory/ome.releases + + + ome.snapshots + http://artifacts.openmicroscopy.org/artifactory/ome.snapshots + + + unidata.releases + http://artifacts.unidata.ucar.edu/content/repositories/unidata-releases + + + + + + central + Central Repository + http://repo.maven.apache.org/maven2 + default + + + ome.releases + http://artifacts.openmicroscopy.org/artifactory/ome.releases + + + ome.snapshots + http://artifacts.openmicroscopy.org/artifactory/ome.snapshots + + true + + + + ome.external + http://artifacts.openmicroscopy.org/artifactory/ome.external + + + ome.experimental + http://artifacts.openmicroscopy.org/artifactory/ome.experimental + + + + + + ome.staging + OME Staging Repository + http://artifacts.openmicroscopy.org/artifactory/ome.staging + + + ome.snapshots + OME Snapshots Repository + http://artifacts.openmicroscopy.org/artifactory/ome.snapshots + + + + + + hinerm + Mark Hiner + hinerm@gmail.edu + http://developer.imagej.net/users/hinerm + UW-Madison LOCI + http://loci.wisc.edu/ + + architect + developer + + -6 + + http://developer.imagej.net/files/imagej/profile-pictures/Mark.jpg?1305649677 + + + + melissa + Melissa Linkert + melissa@glencoesoftware.com + http://openmicroscopy.org/site/about/development-teams/glencoe-software + Glencoe Software + http://glencoesoftware.com/ + + architect + developer + + -6 + + http://openmicroscopy.org/site/about/development-teams/glencoe-software/melissalinkert.png + + + + curtis + Curtis Rueden + ctrueden@wisc.edu + http://loci.wisc.edu/people/curtis-rueden + UW-Madison LOCI + http://loci.wisc.edu/ + + architect + developer + + -6 + + http://loci.wisc.edu/files/loci/images/people/curtis-2010.jpg + + + + + diff --git a/components/formats-common/src/loci/common/AbstractNIOHandle.java b/src/main/java/loci/common/AbstractNIOHandle.java similarity index 100% rename from components/formats-common/src/loci/common/AbstractNIOHandle.java rename to src/main/java/loci/common/AbstractNIOHandle.java diff --git a/components/formats-common/src/loci/common/BZip2Handle.java b/src/main/java/loci/common/BZip2Handle.java similarity index 100% rename from components/formats-common/src/loci/common/BZip2Handle.java rename to src/main/java/loci/common/BZip2Handle.java diff --git a/components/formats-common/src/loci/common/ByteArrayHandle.java b/src/main/java/loci/common/ByteArrayHandle.java similarity index 100% rename from components/formats-common/src/loci/common/ByteArrayHandle.java rename to src/main/java/loci/common/ByteArrayHandle.java diff --git a/components/formats-common/src/loci/common/CBZip2InputStream.java b/src/main/java/loci/common/CBZip2InputStream.java similarity index 100% rename from components/formats-common/src/loci/common/CBZip2InputStream.java rename to src/main/java/loci/common/CBZip2InputStream.java diff --git a/components/formats-common/src/loci/common/CRC.java b/src/main/java/loci/common/CRC.java similarity index 100% rename from components/formats-common/src/loci/common/CRC.java rename to src/main/java/loci/common/CRC.java diff --git a/components/formats-common/src/loci/common/CaseInsensitiveLocation.java b/src/main/java/loci/common/CaseInsensitiveLocation.java similarity index 100% rename from components/formats-common/src/loci/common/CaseInsensitiveLocation.java rename to src/main/java/loci/common/CaseInsensitiveLocation.java diff --git a/components/formats-common/src/loci/common/Constants.java b/src/main/java/loci/common/Constants.java similarity index 100% rename from components/formats-common/src/loci/common/Constants.java rename to src/main/java/loci/common/Constants.java diff --git a/components/formats-common/src/loci/common/DataTools.java b/src/main/java/loci/common/DataTools.java similarity index 100% rename from components/formats-common/src/loci/common/DataTools.java rename to src/main/java/loci/common/DataTools.java diff --git a/components/formats-common/src/loci/common/DateTools.java b/src/main/java/loci/common/DateTools.java similarity index 100% rename from components/formats-common/src/loci/common/DateTools.java rename to src/main/java/loci/common/DateTools.java diff --git a/components/formats-common/src/loci/common/DebugTools.java b/src/main/java/loci/common/DebugTools.java similarity index 100% rename from components/formats-common/src/loci/common/DebugTools.java rename to src/main/java/loci/common/DebugTools.java diff --git a/components/formats-common/src/loci/common/FileHandle.java b/src/main/java/loci/common/FileHandle.java similarity index 100% rename from components/formats-common/src/loci/common/FileHandle.java rename to src/main/java/loci/common/FileHandle.java diff --git a/components/formats-common/src/loci/common/GZipHandle.java b/src/main/java/loci/common/GZipHandle.java similarity index 100% rename from components/formats-common/src/loci/common/GZipHandle.java rename to src/main/java/loci/common/GZipHandle.java diff --git a/components/formats-common/src/loci/common/HandleException.java b/src/main/java/loci/common/HandleException.java similarity index 100% rename from components/formats-common/src/loci/common/HandleException.java rename to src/main/java/loci/common/HandleException.java diff --git a/components/formats-common/src/loci/common/IRandomAccess.java b/src/main/java/loci/common/IRandomAccess.java similarity index 100% rename from components/formats-common/src/loci/common/IRandomAccess.java rename to src/main/java/loci/common/IRandomAccess.java diff --git a/components/formats-common/src/loci/common/IniList.java b/src/main/java/loci/common/IniList.java similarity index 100% rename from components/formats-common/src/loci/common/IniList.java rename to src/main/java/loci/common/IniList.java diff --git a/components/formats-common/src/loci/common/IniParser.java b/src/main/java/loci/common/IniParser.java similarity index 100% rename from components/formats-common/src/loci/common/IniParser.java rename to src/main/java/loci/common/IniParser.java diff --git a/components/formats-common/src/loci/common/IniTable.java b/src/main/java/loci/common/IniTable.java similarity index 100% rename from components/formats-common/src/loci/common/IniTable.java rename to src/main/java/loci/common/IniTable.java diff --git a/components/formats-common/src/loci/common/IniWriter.java b/src/main/java/loci/common/IniWriter.java similarity index 100% rename from components/formats-common/src/loci/common/IniWriter.java rename to src/main/java/loci/common/IniWriter.java diff --git a/components/formats-common/src/loci/common/Location.java b/src/main/java/loci/common/Location.java similarity index 100% rename from components/formats-common/src/loci/common/Location.java rename to src/main/java/loci/common/Location.java diff --git a/components/formats-common/src/loci/common/Log4jTools.java b/src/main/java/loci/common/Log4jTools.java similarity index 100% rename from components/formats-common/src/loci/common/Log4jTools.java rename to src/main/java/loci/common/Log4jTools.java diff --git a/components/formats-common/src/loci/common/LogbackTools.java b/src/main/java/loci/common/LogbackTools.java similarity index 100% rename from components/formats-common/src/loci/common/LogbackTools.java rename to src/main/java/loci/common/LogbackTools.java diff --git a/components/formats-common/src/loci/common/NIOByteBufferProvider.java b/src/main/java/loci/common/NIOByteBufferProvider.java similarity index 100% rename from components/formats-common/src/loci/common/NIOByteBufferProvider.java rename to src/main/java/loci/common/NIOByteBufferProvider.java diff --git a/components/formats-common/src/loci/common/NIOFileHandle.java b/src/main/java/loci/common/NIOFileHandle.java similarity index 100% rename from components/formats-common/src/loci/common/NIOFileHandle.java rename to src/main/java/loci/common/NIOFileHandle.java diff --git a/components/formats-common/src/loci/common/NIOInputStream.java b/src/main/java/loci/common/NIOInputStream.java similarity index 100% rename from components/formats-common/src/loci/common/NIOInputStream.java rename to src/main/java/loci/common/NIOInputStream.java diff --git a/components/formats-common/src/loci/common/RandomAccessInputStream.java b/src/main/java/loci/common/RandomAccessInputStream.java similarity index 100% rename from components/formats-common/src/loci/common/RandomAccessInputStream.java rename to src/main/java/loci/common/RandomAccessInputStream.java diff --git a/components/formats-common/src/loci/common/RandomAccessOutputStream.java b/src/main/java/loci/common/RandomAccessOutputStream.java similarity index 100% rename from components/formats-common/src/loci/common/RandomAccessOutputStream.java rename to src/main/java/loci/common/RandomAccessOutputStream.java diff --git a/components/formats-common/src/loci/common/ReflectException.java b/src/main/java/loci/common/ReflectException.java similarity index 100% rename from components/formats-common/src/loci/common/ReflectException.java rename to src/main/java/loci/common/ReflectException.java diff --git a/components/formats-common/src/loci/common/ReflectedUniverse.java b/src/main/java/loci/common/ReflectedUniverse.java similarity index 100% rename from components/formats-common/src/loci/common/ReflectedUniverse.java rename to src/main/java/loci/common/ReflectedUniverse.java diff --git a/components/formats-common/src/loci/common/Region.java b/src/main/java/loci/common/Region.java similarity index 100% rename from components/formats-common/src/loci/common/Region.java rename to src/main/java/loci/common/Region.java diff --git a/components/formats-common/src/loci/common/StatusEvent.java b/src/main/java/loci/common/StatusEvent.java similarity index 100% rename from components/formats-common/src/loci/common/StatusEvent.java rename to src/main/java/loci/common/StatusEvent.java diff --git a/components/formats-common/src/loci/common/StatusListener.java b/src/main/java/loci/common/StatusListener.java similarity index 100% rename from components/formats-common/src/loci/common/StatusListener.java rename to src/main/java/loci/common/StatusListener.java diff --git a/components/formats-common/src/loci/common/StatusReporter.java b/src/main/java/loci/common/StatusReporter.java similarity index 100% rename from components/formats-common/src/loci/common/StatusReporter.java rename to src/main/java/loci/common/StatusReporter.java diff --git a/components/formats-common/src/loci/common/StreamHandle.java b/src/main/java/loci/common/StreamHandle.java similarity index 100% rename from components/formats-common/src/loci/common/StreamHandle.java rename to src/main/java/loci/common/StreamHandle.java diff --git a/components/formats-common/src/loci/common/URLHandle.java b/src/main/java/loci/common/URLHandle.java similarity index 100% rename from components/formats-common/src/loci/common/URLHandle.java rename to src/main/java/loci/common/URLHandle.java diff --git a/components/formats-common/src/loci/common/ZipHandle.java b/src/main/java/loci/common/ZipHandle.java similarity index 100% rename from components/formats-common/src/loci/common/ZipHandle.java rename to src/main/java/loci/common/ZipHandle.java diff --git a/components/formats-common/src/loci/common/enumeration/CodedEnum.java b/src/main/java/loci/common/enumeration/CodedEnum.java similarity index 100% rename from components/formats-common/src/loci/common/enumeration/CodedEnum.java rename to src/main/java/loci/common/enumeration/CodedEnum.java diff --git a/components/formats-common/src/loci/common/enumeration/EnumException.java b/src/main/java/loci/common/enumeration/EnumException.java similarity index 100% rename from components/formats-common/src/loci/common/enumeration/EnumException.java rename to src/main/java/loci/common/enumeration/EnumException.java diff --git a/components/formats-common/src/loci/common/services/AbstractService.java b/src/main/java/loci/common/services/AbstractService.java similarity index 100% rename from components/formats-common/src/loci/common/services/AbstractService.java rename to src/main/java/loci/common/services/AbstractService.java diff --git a/components/formats-common/src/loci/common/services/DependencyException.java b/src/main/java/loci/common/services/DependencyException.java similarity index 100% rename from components/formats-common/src/loci/common/services/DependencyException.java rename to src/main/java/loci/common/services/DependencyException.java diff --git a/components/formats-common/src/loci/common/services/Service.java b/src/main/java/loci/common/services/Service.java similarity index 100% rename from components/formats-common/src/loci/common/services/Service.java rename to src/main/java/loci/common/services/Service.java diff --git a/components/formats-common/src/loci/common/services/ServiceException.java b/src/main/java/loci/common/services/ServiceException.java similarity index 100% rename from components/formats-common/src/loci/common/services/ServiceException.java rename to src/main/java/loci/common/services/ServiceException.java diff --git a/components/formats-common/src/loci/common/services/ServiceFactory.java b/src/main/java/loci/common/services/ServiceFactory.java similarity index 100% rename from components/formats-common/src/loci/common/services/ServiceFactory.java rename to src/main/java/loci/common/services/ServiceFactory.java diff --git a/components/formats-common/src/loci/common/services/services.properties b/src/main/java/loci/common/services/services.properties similarity index 100% rename from components/formats-common/src/loci/common/services/services.properties rename to src/main/java/loci/common/services/services.properties diff --git a/components/formats-common/src/loci/common/xml/BaseHandler.java b/src/main/java/loci/common/xml/BaseHandler.java similarity index 100% rename from components/formats-common/src/loci/common/xml/BaseHandler.java rename to src/main/java/loci/common/xml/BaseHandler.java diff --git a/components/formats-common/src/loci/common/xml/LSInputI.java b/src/main/java/loci/common/xml/LSInputI.java similarity index 100% rename from components/formats-common/src/loci/common/xml/LSInputI.java rename to src/main/java/loci/common/xml/LSInputI.java diff --git a/components/formats-common/src/loci/common/xml/MetadataHandler.java b/src/main/java/loci/common/xml/MetadataHandler.java similarity index 100% rename from components/formats-common/src/loci/common/xml/MetadataHandler.java rename to src/main/java/loci/common/xml/MetadataHandler.java diff --git a/components/formats-common/src/loci/common/xml/ParserErrorHandler.java b/src/main/java/loci/common/xml/ParserErrorHandler.java similarity index 100% rename from components/formats-common/src/loci/common/xml/ParserErrorHandler.java rename to src/main/java/loci/common/xml/ParserErrorHandler.java diff --git a/components/formats-common/src/loci/common/xml/ValidationErrorHandler.java b/src/main/java/loci/common/xml/ValidationErrorHandler.java similarity index 100% rename from components/formats-common/src/loci/common/xml/ValidationErrorHandler.java rename to src/main/java/loci/common/xml/ValidationErrorHandler.java diff --git a/components/formats-common/src/loci/common/xml/ValidationSAXHandler.java b/src/main/java/loci/common/xml/ValidationSAXHandler.java similarity index 100% rename from components/formats-common/src/loci/common/xml/ValidationSAXHandler.java rename to src/main/java/loci/common/xml/ValidationSAXHandler.java diff --git a/components/formats-common/src/loci/common/xml/XMLTools.java b/src/main/java/loci/common/xml/XMLTools.java similarity index 100% rename from components/formats-common/src/loci/common/xml/XMLTools.java rename to src/main/java/loci/common/xml/XMLTools.java diff --git a/components/formats-common/test/loci/common/utests/BufferAlignmentReadTest.java b/src/test/java/loci/common/utests/BufferAlignmentReadTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/BufferAlignmentReadTest.java rename to src/test/java/loci/common/utests/BufferAlignmentReadTest.java diff --git a/components/formats-common/test/loci/common/utests/BufferAlignmentWriteTest.java b/src/test/java/loci/common/utests/BufferAlignmentWriteTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/BufferAlignmentWriteTest.java rename to src/test/java/loci/common/utests/BufferAlignmentWriteTest.java diff --git a/components/formats-common/test/loci/common/utests/DataToolsTest.java b/src/test/java/loci/common/utests/DataToolsTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/DataToolsTest.java rename to src/test/java/loci/common/utests/DataToolsTest.java diff --git a/components/formats-common/test/loci/common/utests/DateToolsTest.java b/src/test/java/loci/common/utests/DateToolsTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/DateToolsTest.java rename to src/test/java/loci/common/utests/DateToolsTest.java diff --git a/components/formats-common/test/loci/common/utests/DebugToolsTest.java b/src/test/java/loci/common/utests/DebugToolsTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/DebugToolsTest.java rename to src/test/java/loci/common/utests/DebugToolsTest.java diff --git a/components/formats-common/test/loci/common/utests/EncodingTest.java b/src/test/java/loci/common/utests/EncodingTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/EncodingTest.java rename to src/test/java/loci/common/utests/EncodingTest.java diff --git a/components/formats-common/test/loci/common/utests/EndiannessTest.java b/src/test/java/loci/common/utests/EndiannessTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/EndiannessTest.java rename to src/test/java/loci/common/utests/EndiannessTest.java diff --git a/components/formats-common/test/loci/common/utests/IniParserTest.java b/src/test/java/loci/common/utests/IniParserTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/IniParserTest.java rename to src/test/java/loci/common/utests/IniParserTest.java diff --git a/components/formats-common/test/loci/common/utests/LocationTest.java b/src/test/java/loci/common/utests/LocationTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/LocationTest.java rename to src/test/java/loci/common/utests/LocationTest.java diff --git a/components/formats-common/test/loci/common/utests/RandomAccessInputStreamTest.java b/src/test/java/loci/common/utests/RandomAccessInputStreamTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/RandomAccessInputStreamTest.java rename to src/test/java/loci/common/utests/RandomAccessInputStreamTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadByteArrayTest.java b/src/test/java/loci/common/utests/ReadByteArrayTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadByteArrayTest.java rename to src/test/java/loci/common/utests/ReadByteArrayTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadByteBufferTest.java b/src/test/java/loci/common/utests/ReadByteBufferTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadByteBufferTest.java rename to src/test/java/loci/common/utests/ReadByteBufferTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadByteSubArrayTest.java b/src/test/java/loci/common/utests/ReadByteSubArrayTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadByteSubArrayTest.java rename to src/test/java/loci/common/utests/ReadByteSubArrayTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadByteTest.java b/src/test/java/loci/common/utests/ReadByteTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadByteTest.java rename to src/test/java/loci/common/utests/ReadByteTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadCharTest.java b/src/test/java/loci/common/utests/ReadCharTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadCharTest.java rename to src/test/java/loci/common/utests/ReadCharTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadDoubleTest.java b/src/test/java/loci/common/utests/ReadDoubleTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadDoubleTest.java rename to src/test/java/loci/common/utests/ReadDoubleTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadFloatTest.java b/src/test/java/loci/common/utests/ReadFloatTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadFloatTest.java rename to src/test/java/loci/common/utests/ReadFloatTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadIntTest.java b/src/test/java/loci/common/utests/ReadIntTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadIntTest.java rename to src/test/java/loci/common/utests/ReadIntTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadLineTest.java b/src/test/java/loci/common/utests/ReadLineTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadLineTest.java rename to src/test/java/loci/common/utests/ReadLineTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadLongTest.java b/src/test/java/loci/common/utests/ReadLongTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadLongTest.java rename to src/test/java/loci/common/utests/ReadLongTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadOnlyTest.java b/src/test/java/loci/common/utests/ReadOnlyTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadOnlyTest.java rename to src/test/java/loci/common/utests/ReadOnlyTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadShortTest.java b/src/test/java/loci/common/utests/ReadShortTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadShortTest.java rename to src/test/java/loci/common/utests/ReadShortTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadUnsignedByteTest.java b/src/test/java/loci/common/utests/ReadUnsignedByteTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadUnsignedByteTest.java rename to src/test/java/loci/common/utests/ReadUnsignedByteTest.java diff --git a/components/formats-common/test/loci/common/utests/ReadUnsignedShortTest.java b/src/test/java/loci/common/utests/ReadUnsignedShortTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/ReadUnsignedShortTest.java rename to src/test/java/loci/common/utests/ReadUnsignedShortTest.java diff --git a/components/formats-common/test/loci/common/utests/SkipBytesTest.java b/src/test/java/loci/common/utests/SkipBytesTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/SkipBytesTest.java rename to src/test/java/loci/common/utests/SkipBytesTest.java diff --git a/components/formats-common/test/loci/common/utests/TypeDetectionTest.java b/src/test/java/loci/common/utests/TypeDetectionTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/TypeDetectionTest.java rename to src/test/java/loci/common/utests/TypeDetectionTest.java diff --git a/components/formats-common/test/loci/common/utests/URLHandleTest.java b/src/test/java/loci/common/utests/URLHandleTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/URLHandleTest.java rename to src/test/java/loci/common/utests/URLHandleTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteByteArrayTest.java b/src/test/java/loci/common/utests/WriteByteArrayTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteByteArrayTest.java rename to src/test/java/loci/common/utests/WriteByteArrayTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteByteBufferTest.java b/src/test/java/loci/common/utests/WriteByteBufferTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteByteBufferTest.java rename to src/test/java/loci/common/utests/WriteByteBufferTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteByteTest.java b/src/test/java/loci/common/utests/WriteByteTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteByteTest.java rename to src/test/java/loci/common/utests/WriteByteTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteBytesTest.java b/src/test/java/loci/common/utests/WriteBytesTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteBytesTest.java rename to src/test/java/loci/common/utests/WriteBytesTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteCharTest.java b/src/test/java/loci/common/utests/WriteCharTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteCharTest.java rename to src/test/java/loci/common/utests/WriteCharTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteCharsTest.java b/src/test/java/loci/common/utests/WriteCharsTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteCharsTest.java rename to src/test/java/loci/common/utests/WriteCharsTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteDoubleTest.java b/src/test/java/loci/common/utests/WriteDoubleTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteDoubleTest.java rename to src/test/java/loci/common/utests/WriteDoubleTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteFloatTest.java b/src/test/java/loci/common/utests/WriteFloatTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteFloatTest.java rename to src/test/java/loci/common/utests/WriteFloatTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteIntTest.java b/src/test/java/loci/common/utests/WriteIntTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteIntTest.java rename to src/test/java/loci/common/utests/WriteIntTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteLongTest.java b/src/test/java/loci/common/utests/WriteLongTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteLongTest.java rename to src/test/java/loci/common/utests/WriteLongTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteShortTest.java b/src/test/java/loci/common/utests/WriteShortTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteShortTest.java rename to src/test/java/loci/common/utests/WriteShortTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteUTFTest.java b/src/test/java/loci/common/utests/WriteUTFTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteUTFTest.java rename to src/test/java/loci/common/utests/WriteUTFTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteUnsignedByteTest.java b/src/test/java/loci/common/utests/WriteUnsignedByteTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteUnsignedByteTest.java rename to src/test/java/loci/common/utests/WriteUnsignedByteTest.java diff --git a/components/formats-common/test/loci/common/utests/WriteUnsignedShortTest.java b/src/test/java/loci/common/utests/WriteUnsignedShortTest.java similarity index 100% rename from components/formats-common/test/loci/common/utests/WriteUnsignedShortTest.java rename to src/test/java/loci/common/utests/WriteUnsignedShortTest.java diff --git a/components/formats-common/test/loci/common/utests/providers/BZip2HandleProvider.java b/src/test/java/loci/common/utests/providers/BZip2HandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/BZip2HandleProvider.java rename to src/test/java/loci/common/utests/providers/BZip2HandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/ByteArrayHandleProvider.java b/src/test/java/loci/common/utests/providers/ByteArrayHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/ByteArrayHandleProvider.java rename to src/test/java/loci/common/utests/providers/ByteArrayHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/ExistingByteArrayHandleProvider.java b/src/test/java/loci/common/utests/providers/ExistingByteArrayHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/ExistingByteArrayHandleProvider.java rename to src/test/java/loci/common/utests/providers/ExistingByteArrayHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/GZipHandleProvider.java b/src/test/java/loci/common/utests/providers/GZipHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/GZipHandleProvider.java rename to src/test/java/loci/common/utests/providers/GZipHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/IRandomAccessProvider.java b/src/test/java/loci/common/utests/providers/IRandomAccessProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/IRandomAccessProvider.java rename to src/test/java/loci/common/utests/providers/IRandomAccessProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/IRandomAccessProviderFactory.java b/src/test/java/loci/common/utests/providers/IRandomAccessProviderFactory.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/IRandomAccessProviderFactory.java rename to src/test/java/loci/common/utests/providers/IRandomAccessProviderFactory.java diff --git a/components/formats-common/test/loci/common/utests/providers/NIOFileHandleProvider.java b/src/test/java/loci/common/utests/providers/NIOFileHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/NIOFileHandleProvider.java rename to src/test/java/loci/common/utests/providers/NIOFileHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/NewByteArrayHandleProvider.java b/src/test/java/loci/common/utests/providers/NewByteArrayHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/NewByteArrayHandleProvider.java rename to src/test/java/loci/common/utests/providers/NewByteArrayHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/URLHandleProvider.java b/src/test/java/loci/common/utests/providers/URLHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/URLHandleProvider.java rename to src/test/java/loci/common/utests/providers/URLHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/providers/ZipHandleProvider.java b/src/test/java/loci/common/utests/providers/ZipHandleProvider.java similarity index 100% rename from components/formats-common/test/loci/common/utests/providers/ZipHandleProvider.java rename to src/test/java/loci/common/utests/providers/ZipHandleProvider.java diff --git a/components/formats-common/test/loci/common/utests/testng-template.xml b/src/test/java/loci/common/utests/testng-template.xml similarity index 100% rename from components/formats-common/test/loci/common/utests/testng-template.xml rename to src/test/java/loci/common/utests/testng-template.xml diff --git a/src/test/resources/logback.xml b/src/test/resources/logback.xml new file mode 100644 index 00000000..16d0f9af --- /dev/null +++ b/src/test/resources/logback.xml @@ -0,0 +1,11 @@ + + + + + %d [%t] %-5p %c - %m%n + + + + + +