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.appveyor.yml 0 → 100644
View file @ bd200a1f
environment:
AV_PROJECTS: 'c:\projects'
AV_BF_M2: 'c:\projects\m2'
AV_BF_SOURCE: 'c:\projects\bioformats'
# Note that only Oracle JDK is provided.
matrix:
- java: 11
build: maven
- java: 1.8
build: maven
- java: 1.8
build: ant
ant_version: 1.10.1
cache:
- '%AV_BF_M2% -> appveyor.yml'
os: 'Visual Studio 2015'
clone_folder: '%AV_BF_SOURCE%'
clone_depth: 5
platform: x64
init:
- git config --global core.autocrlf input
- if [%build%] == [ant] appveyor-retry cinst -y ant --version %ant_version%
- refreshenv
- 'if [%java%] == [1.8] set "JAVA_HOME=C:\Program Files\Java\jdk1.8.0"'
- 'if [%java%] == [11] set "JAVA_HOME=C:\Program Files\Java\jdk11"'
- PATH=%JAVA_HOME%\bin;%PATH%
- 'if [%build%] == [maven] set "MAVEN_OPTS=-Dmaven.repo.local=%AV_BF_M2%"'
- 'if [%build%] == [ant] set "ANT_OPTS=-Dmaven.repo.local=%AV_BF_M2%"'
build_script:
- tools\test-build %build%
.classpath-template
View file @ bd200a1f
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="components/autogen/src"/>
<classpathentry kind="src" path="components/formats-api/build/src"/>
<classpathentry kind="src" path="components/formats-api/src"/>
<classpathentry kind="src" path="components/formats-bsd/build/src"/>
......
.gitignore
View file @ bd200a1f
.classpath
.idea
.project
.settings
.DS_Store
.idea
artifacts
build
components/*/utils/*.class
......@@ -14,3 +16,6 @@ testng.css
tools/*.jar
*.log
*.xpr
*.class
*.iml
.*.swp
.travis.yml
View file @ bd200a1f
......@@ -9,14 +9,17 @@ sudo: false
cache:
directories:
- $HOME/.m2
- downloads
addons:
apt_packages:
- git
jdk:
- openjdk11
- oraclejdk11
- openjdk8
- oraclejdk8
- openjdk7
env:
- BUILD=maven
......@@ -24,9 +27,15 @@ env:
matrix:
fast_finish: true
before_install:
- if [[ $BUILD == 'ant' ]]; then pip install --user flake8 Sphinx; fi
exclude:
- jdk: oraclejdk11
env: BUILD=ant
- jdk: openjdk11
env: BUILD=ant
- jdk: oraclejdk8
env: BUILD=ant
- jdk: openjdk8
env: BUILD=maven
script:
- ./tools/test-build $BUILD
CONTRIBUTING.md
View file @ bd200a1f
......@@ -51,13 +51,6 @@ please ensure you read these.
The documentation hosted at
https://docs.openmicroscopy.org/bio-formats/ is built from the
`/docs/sphinx/` directory. Contributions are welcome but please follow the
style guidance from the
[Bio-Formats Documentation Repository](https://github.com/ome/bio-formats-documentation).
Contributions are welcome but please follow the style guidance from the
[OME Documentation Repository README](https://github.com/openmicroscopy/ome-documentation/blob/develop/README.rst#conventions-used).
Documentation for new supported formats is auto-generated - see
[Adding format/reader documentation pages](https://docs.openmicroscopy.org/latest/bio-formats/developers/format-documentation.html). If you need any assistance please
contact the [mailing list](https://www.openmicroscopy.org/support)
before embarking on such a change, or submit your new reader code and let one
of the main OME team deal with the documentation for you.
Dockerfile 0 → 100644
View file @ bd200a1f
FROM openjdk:8
MAINTAINER ome-devel@lists.openmicroscopy.org.uk
# Installs Ant
ENV ANT_VERSION 1.9.4
RUN wget -q http://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.zip && \
unzip apache-ant-${ANT_VERSION}-bin.zip && \
mv apache-ant-${ANT_VERSION} /opt/ant && \
rm apache-ant-${ANT_VERSION}-bin.zip
RUN useradd -m bf
COPY . /opt/bioformats/
RUN chown -R bf /opt/bioformats
USER bf
WORKDIR /opt/bioformats
RUN /opt/ant/bin/ant clean jars tools
ENV TZ "Europe/London"
WORKDIR /opt/bioformats/components/test-suite
ENTRYPOINT ["/opt/ant/bin/ant", "test-automated", "-Dtestng.directory=/opt/data", "-Dtestng.configDirectory=/opt/config"]
README.md
View file @ bd200a1f
......@@ -6,6 +6,8 @@ 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.
If you are having an issue with Bio-Formats and need support, please see the
[support page](./SUPPORT.md).
Purpose
-------
......@@ -15,7 +17,6 @@ an open standard called the OME data model, particularly into the OME-TIFF
file format. See [About Bio-Formats](https://docs.openmicroscopy.org/latest/bio-formats/about/index.html)
for further information.
Supported formats
-----------------
......@@ -42,7 +43,6 @@ More information
For more information, see the [Bio-Formats web
site](https://www.openmicroscopy.org/bio-formats).
Pull request testing
--------------------
......@@ -57,7 +57,7 @@ following before submitting a pull request:
* test at least one file in each affected format, using the ```showinf```
command
* internal developers only: [run the data
tests](docs/sphinx/developers/commit-testing.rst)
tests](https://github.com/ome/bio-formats-documentation/blob/master/sphinx/developers/commit-testing.rst)
against directories corresponding to the affected format(s)
* make sure that your commits contain the correct authorship information and,
if necessary, a signed-off-by line
......
SUPPORT.md 0 → 100644
View file @ bd200a1f
# Support for Bio-Formats
Full documentation is hosted at
https://docs.openmicroscopy.org/latest/bio-formats/
If you need to contact us for further assistance, please see the
[support page](https://www.openmicroscopy.org/support/) - our preferred
channels for support are our mailing lists and forums.
Before filing a bug report, please read and follow the
[guidance for bug reporting](https://docs.openmicroscopy.org/latest/bio-formats/about/bug-reporting.html).
You can submit files to our [QA system](http://qa.openmicroscopy.org.uk/qa/upload/)
or for large files (>2 GB), please write to the
[OME Users mailing list](http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users)
and we will contact you privately with an FTP server address. If possible,
please submit a file we can make public for testing purposes. However, we will
keep files private on request.
\ No newline at end of file
ant/global.xml
View file @ bd200a1f
......@@ -14,17 +14,8 @@ Type "ant -p" for a list of targets.
<!-- Convenient JDK version properties -->
<available property="jdk1.7+" classname="java.util.Objects"/>
<available property="jdk1.8+" classname="java.util.stream.IntStream"/>
<target name="javadoc-properties">
<if>
<isset property="jdk1.8+"/>
<then>
<property name="javadoc.doclint" value="-Xdoclint:none"/>
</then>
</if>
<property name="javadoc.doclint" value=""/>
</target>
<!-- Convenient platform properties -->
......
ant/java.xml
View file @ bd200a1f
......@@ -112,6 +112,7 @@ Type "ant -p" for a list of targets.
<pathelement location="${test-classes.dir}"/>
<pathelement location="${test.dir}"/>
</classpath>
<sysproperty key="bioformats_can_do_upgrade_check" value="false"/>
<xmlfileset file="${testng.xml}"/>
<jvmarg value="-mx${testng.memory}"/>
</testng>
......@@ -127,7 +128,7 @@ Type "ant -p" for a list of targets.
<then>
<findbugs home="${findbugs.home}" jvmargs="-Xmx512m"
output="xml:withMessages" outputFile="${build.dir}/findbugs.xml"
excludeFilter="${root.dir}/excludebugs.xml" reportLevel="high"
excludeFilter="${root.dir}/excludebugs.xml" reportLevel="medium"
errorProperty="findbugsErrors"
warningsProperty="findbugsWarnings">
<auxClasspath refid="runtime.classpath"/>
......@@ -228,7 +229,7 @@ your FindBugs installation's lib directory. E.g.:
<fileset dir="${utils.dir}" includes="**/*.class"/>
</delete>
<javac debug="true" includeantruntime="false" fork="true"
deprecation="true" source="1.7" target="1.7"
deprecation="true" source="1.8" target="1.8"
encoding="UTF-8"
srcdir="${utils.dir}" includes="**/*.java"
classpath="${artifact.dir}/${component.jar}">
......@@ -249,11 +250,9 @@ your FindBugs installation's lib directory. E.g.:
<classpath refid="runtime.classpath"/>
<doctitle><![CDATA[<h1>Bio-Formats</h1>]]></doctitle>
<bottom><![CDATA[${copyright.begin} ${YEAR} ${copyright.end}]]></bottom>
<link href="http://docs.oracle.com/javase/7/docs/api/"/>
<link href="http://rsbweb.nih.gov/ij/developer/api/"/>
<link href="http://www.ssec.wisc.edu/visad-docs/javadoc/"/>
<!--<link href="http://www.jdocs.com/formlayout/1.0.4/api/"/>-->
<!--<link href="http://www.jdocs.com/looks/1.2.2/api/"/>-->
<link href="http://docs.oracle.com/javase/8/docs/api/"/>
<link href="https://imagej.net/developer/api/"
offline="true" packagelistLoc="${root.dir}/ant/package-list"/>
</javadoc>
</target>
......
ant/package-list 0 → 100644
View file @ bd200a1f
ij
ij.gui
ij.io
ij.macro
ij.measure
ij.plugin
ij.plugin.filter
ij.plugin.frame
ij.plugin.tool
ij.process
ij.text
ij.util
ant/toplevel.xml
View file @ bd200a1f
......@@ -13,8 +13,7 @@ Type "ant -p" for a list of targets.
<!-- Global build targets -->
<target name="compile"
depends="compile-autogen,
compile-formats-gpl,
depends="compile-formats-gpl,
compile-bio-formats-plugins,
compile-formats-api,
compile-formats-bsd,
......@@ -25,7 +24,6 @@ Type "ant -p" for a list of targets.
<target name="jars"
depends="copy-jars,
jar-autogen,
jar-formats-gpl,
jar-bio-formats-plugins,
jar-formats-api,
......@@ -36,8 +34,7 @@ Type "ant -p" for a list of targets.
description="generate JAR files for software packages"/>
<target name="findbugs"
depends="findbugs-autogen,
findbugs-formats-gpl,
depends="findbugs-formats-gpl,
findbugs-bio-formats-plugins,
findbugs-formats-api,
findbugs-formats-bsd,
......@@ -47,7 +44,6 @@ Type "ant -p" for a list of targets.
<target name="clean"
depends="
clean-autogen,
clean-formats-gpl,
clean-bio-formats-plugins,
clean-formats-api,
......@@ -55,7 +51,6 @@ Type "ant -p" for a list of targets.
clean-bio-formats-tools,
clean-tests,
clean-turbojpeg,
clean-docs-sphinx,
clean-bundles"
description="remove build files for all components">
<delete dir="${artifact.dir}"/>
......@@ -63,8 +58,7 @@ Type "ant -p" for a list of targets.
</target>
<target name="test"
depends="test-autogen,
test-formats-gpl,
depends="test-formats-gpl,
test-bio-formats-plugins,
test-formats-api,
test-formats-bsd,
......@@ -89,19 +83,6 @@ Type "ant -p" for a list of targets.
<target name="docs-zip" depends="docs"/>
<target name="docs-sphinx"
description="generate the Sphinx HTML documentation">
<echo>----------=========== Sphinx HTML ===========----------</echo>
<ant dir="docs/sphinx" target="html"/>
<echo>----------=========== Sphinx MAN ===========----------</echo>
<ant dir="docs/sphinx" target="man"/>
</target>
<target name="clean-docs-sphinx"
description="remove build files for the Sphinx HTML documentation">
<ant dir="docs/sphinx" target="clean"/>
</target>
<target name="copy-jars" description="copy JARS (deprecated)"/>
<target name="testing-deps" depends="copy-jars"/>
......@@ -131,11 +112,6 @@ Type "ant -p" for a list of targets.
<ant dir="components/formats-api" target="formats-api.clean"/>
</target>
<target name="utils-formats-api" depends="jar-formats-api"
description="compile extra utilities for reader and writer APIs">
<ant dir="components/formats-api" target="formats-api.utils"/>
</target>
<target name="test-formats-api" depends="jar-formats-api, testing-deps"
description="compile and run tests for reader and writer APIs">
<ant dir="components/formats-api" target="test"/>
......@@ -253,37 +229,6 @@ Type "ant -p" for a list of targets.
<ant dir="components/formats-gpl" target="test"/>
</target>
<!-- Bio-Formats autogen -->
<target name="deps-autogen"
depends="copy-jars, jar-formats-api,jar-formats-bsd,jar-formats-gpl"/>
<target name="compile-autogen" depends="deps-autogen"
description="compile classes for Bio-Formats autogen">
<ant dir="components/autogen" target="autogen.compile"/>
</target>
<target name="jar-autogen" depends="deps-autogen"
description="generate JAR file for Bio-Formats autogen">
<ant dir="components/autogen" target="autogen.jar"/>
</target>
<target name="findbugs-autogen" depends="jar-autogen"
description="run findbugs on Bio-Formats autogen">
<ant dir="components/autogen" target="autogen.findbugs"/>
</target>
<target name="clean-autogen"
depends="clean-formats-api,clean-formats-bsd"
description="remove build files for Bio-Formats autogen">
<ant dir="components/autogen" target="autogen.clean"/>
</target>
<target name="test-autogen" depends="jar-autogen, testing-deps"
description="compile and run tests for Bio-Formats autogen">
<ant dir="components/autogen" target="test"/>
</target>
<!-- Bio-Formats Plugins for ImageJ -->
<target name="deps-bio-formats-plugins"
......@@ -445,8 +390,6 @@ Type "ant -p" for a list of targets.
prefix="bioformats/" excludes="DESCRIPTION.in"/>
<tarfileset file="${temp.file}" fullpath="bioformats/DESCRIPTION"/>
<tarfileset file="${root.dir}/LICENSE.txt" fullpath="bioformats/COPYING"/>
<tarfileset file="${root.dir}/docs/sphinx/about/whats-new.rst"
fullpath="bioformats/NEWS"/>
<tarfileset dir="${root.dir}/components/formats-gpl/matlab"
prefix="bioformats/inst/"/>
</tar>
......
build.xml
View file @ bd200a1f
......@@ -10,17 +10,6 @@ This build file handles the following components.
For more information on a component, see the
build.properties file in that component's subtree.
Formats code generator
Package for generating other code, including the Bio-Formats metadata API,
related documentation, Ice bindings, and Bio-Formats C++ bindings headers
-=-
JAR file: bf-autogen.jar
Path: components/autogen
Project deps: Bio-Formats, Formats Common
Library deps: Apache Velocity
Optional: (none)
License: GPL
Bio-Formats
A library for reading and writing popular microscopy file formats
-=-
......
components/autogen/LICENSE.txt deleted 100644 → 0
View file @ e05f283f
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
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When we speak of free software, we are referring to freedom, not
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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.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
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.
<signature of Ty Coon>, 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.
components/autogen/build.properties deleted 100644 → 0
View file @ e05f283f
#
# build.properties
#
# Ant properties file for Bio-Formats code generators.
# Download Apache Ant from http://ant.apache.org/.
# Type "ant -p" for a list of targets.
component.name = bf-autogen
component.jar = bf-autogen.jar
component.version = 1.0.0
component.java-version = 1.7
component.deprecation = true
component.resources-bin =
component.resources-text = *.txt \
**/*.vm \
*.sh
component.main-class = MetaSupportAutogen
component.meta-support-dir = ${root.dir}/components/formats-gpl
omexml.version=2016-06
filelist=src/format-pages.txt
components/autogen/build.xml deleted 100644 → 0
View file @ e05f283f
<!--
build.xml
Ant build file for Bio-Formats code generators.
Download Apache Ant from http://ant.apache.org/.
Type "ant -p" for a list of targets.
-->
<project name="autogen" default="jar" basedir=".">
<description>Build file for Bio-Formats code generators</description>
<property name="root.dir" location="../.."/>
<import file="${root.dir}/ant/java.xml"/>
<property file="build.properties"/>
<target name="gen-metadata-ratings" depends="compile"
description="update format metadata ratings">
<java classname="MetadataRatings"
classpath="${classes.dir}" fork="true" failonerror="true">
<classpath refid="runtime.classpath"/>
<arg value="${src.dir}/format-pages.txt"/>
</java>
</target>
<target name="gen-format-pages" depends="compile"
description="generate Sphinx pages for each supported format">
<java classname="FormatPageAutogen"
classpath="${classes.dir}" fork="true" failonerror="true">
<classpath location="${root.dir}/ant/"/><!-- logback.xml -->
<classpath refid="runtime.classpath"/>
<arg value="${filelist}"/>
</java>
</target>
<target name="gen-structure-table" depends="compile"
description="generate dataset structure table">
<java classname="MakeDatasetStructureTable"
classpath="${classes.dir}" fork="true" failonerror="true">
<classpath location="${root.dir}/ant/"/><!-- logback.xml -->
<classpath refid="runtime.classpath"/>
<arg value="../../docs/sphinx/formats/dataset-table.rst"/>
</java>
</target>
<target name="gen-original-meta-support" depends="compile"
description="generate docs for Bio-Formats original metadata support">
<java classname="OriginalMetadataAutogen"
classpath="${classes.dir}" fork="true" failonerror="true">
<classpath location="${root.dir}/ant/"/><!-- logback.xml -->
<classpath refid="runtime.classpath"/>
<arg value="${filelist}"/>
</java>
</target>
<target name="gen-meta-support" depends="compile"
description="generate docs for Bio-Formats metadata support">
<exec executable="python">
<arg value="${src.dir}/gen-meta-support.py"/>
<arg value="${ome-model.version}"/>
</exec>
<if>
<isset property="omexml.version"/>
<then>
<java classname="${component.main-class}"
classpath="${classes.dir}"
fork="true" dir="${component.meta-support-dir}" failonerror="true">
<classpath location="${root.dir}/ant/"/><!-- logback.xml -->
<classpath refid="runtime.classpath"/>
<arg value="${omexml.version}"/>
</java>
</then>
<else>
<echo>
Please set the omexml.version property to match
the latest release of the OME-XML schema. E.g.:
ant -Domexml.version=2008-09 gen-meta-support
</echo>
</else>
</if>
</target>
</project>
components/autogen/pom.xml deleted 100644 → 0
View file @ e05f283f
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ome</groupId>
<artifactId>pom-bio-formats</artifactId>
<version>5.7.2</version>
<relativePath>../..</relativePath>
</parent>
<artifactId>bf-autogen</artifactId>
<name>Bio-Formats code generator</name>
<description>Package for generating other code, particularly the Bio-Formats metadata documentation.</description>
<url>https://www.openmicroscopy.org/bio-formats</url>
<inceptionYear>2007</inceptionYear>
<licenses>
<license>
<name>GNU General Public License v2+</name>
<url>http://www.gnu.org/licenses/gpl-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<dependencies>
<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
<version>${ome-common.version}</version>
</dependency>
<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-xml</artifactId>
<version>${ome-model.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>formats-api</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>formats-bsd</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>formats-gpl</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity</artifactId>
<version>1.6.4</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
<scope>runtime</scope>
</dependency>
</dependencies>
<properties>
<project.rootdir>${basedir}/../..</project.rootdir>
</properties>
<build>
<plugins>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>MetaSupportAutogen</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<configuration>
<licenseName>gpl_v2</licenseName>
<projectName>Bio-Formats autogen package for programmatically generating source code.</projectName>
</configuration>
</plugin>
</plugins>
</build>
<developers>
<developer>
<id>curtis</id>
<name>Curtis Rueden</name>
<email>ctrueden@wisc.edu</email>
<url>http://loci.wisc.edu/people/curtis-rueden</url>
<organization>UW-Madison LOCI</organization>
<organizationUrl>http://loci.wisc.edu/</organizationUrl>
<roles>
<role>architect</role>
<role>developer</role>
</roles>
<timezone>-6</timezone>
<properties>
<picUrl>http://loci.wisc.edu/files/loci/images/people/curtis-2010.jpg</picUrl>
</properties>
</developer>
<developer>
<id>melissa</id>
<name>Melissa Linkert</name>
<email>melissa@glencoesoftware.com</email>
<url>https://www.glencoesoftware.com/melissa-linkert.html</url>
<organization>Glencoe Software</organization>
<organizationUrl>http://glencoesoftware.com/</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>-6</timezone>
</developer>
</developers>
</project>
components/autogen/src/Entity.java deleted 100644 → 0
View file @ e05f283f
/*
* #%L
* Bio-Formats autogen package for programmatically generating source code.
* %%
* Copyright (C) 2007 - 2017 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
import java.util.HashMap;
/**
* An entity is an object that contains a bundle of {@link Property} objects.
* It has a list of default attributes (key/value pairs),
* as well as a list of version overrides for those attributes.
*
* @see {EntityList}
*
* @author Curtis Rueden ctrueden at wisc.edu
*/
public class Entity {
// -- Fields --
/** The entity's attributes. */
protected HashMap<String, String> attrs;
/** The entity's properties. */
protected HashMap<String, Property> props =
new HashMap<String, Property>();
/** The entity's version overrides. */
protected HashMap<String, HashMap<String, String>> versions =
new HashMap<String, HashMap<String, String>>();
// -- Constructor --
/** Creates a new entity with the given attributes. */
public Entity(HashMap<String, String> attrs) {
this.attrs = attrs;
}
}
components/autogen/src/EntityList.java deleted 100644 → 0
View file @ e05f283f
/*
* #%L
* Bio-Formats autogen package for programmatically generating source code.
* %%
* Copyright (C) 2007 - 2017 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.StringTokenizer;
import loci.common.IniList;
import loci.common.IniParser;
import loci.common.IniTable;
/**
* An EntityList is a list of entities parsed from an INI-style resource,
* represented as a hierarchical tree structure. Here is a partial example:
* <pre>
* + entity list
* |--+ versions
* | |--+ 2003FC
* | | ...
* | |--+ 200706
* | | \- name = 200706
* | | \- class = OMEXML200706Metadata
* | | \- id = OMEXML200706Metadata.java
* | | \- basePackage = ome.xml.r200706
* | | \- subPackage = ome
* | | \- version = 2007-06
* | |--+ 200802
* | | ...
* | |...
* |--+ entities
* |--+ Image
* | ...
* |--+ Pixels
* | ...
* |--+ Dimensions
* | |--+ properties
* | | \- path = Image+/Pixels+
* | | \- description = A set of pixel dimensions in the metadata store.
* | |--+ entity version overrides
* | | |--+ 2003FC
* | | \- path = Image+/CA/Dimensions
* | |--+ properties
* | |--+ PhysicalSizeX
* | | |--+ properties
* | | | \- type = Float
* | | | \- description = Width of each pixel in microns.
* | | |--+ property version overrides
* | | |-+ 2003FC
* | | \- getter = getPixelSizeX
* | | \- setter = setPixelSizeX
* | |--+ PhysicalSizeY
* | | |--+ properties
* | | | \- type = Float
* | | | \- description = Height of each pixel in microns.
* | | |--+ property version overrides
* | | |-+ 2003FC
* | | \- getter = getPixelSizeY
* | | \- setter = setPixelSizeY
* | |--+ PhysicalSizeZ
* | | |--+ properties
* | | | \- type = Float
* | | | \- description = Distance between focal planes in microns.
* | | |--+ property version overrides
* | | |-+ 2003FC
* | | \- getter = getPixelSizeZ
* | | \- setter = setPixelSizeZ
* | |--+ TimeIncrement
* | | |--+ properties
* | | | \- type = Float
* | | | \- description = Distance between time points in seconds.
* | | |--+ property version overrides
* | | |-+ 2003FC
* | | \- getter = getPixelSizeT
* | | \- setter = setPixelSizeT
* | |--+ WaveStart
* | | |--+ properties
* | | | \- type = Integer
* | | | \- description = Starting wavelength in nanometers.
* | | |--+ property version overrides
* | | |-+ 2003FC
* | | \- available = false
* | |--+ WaveIncrement
* | |--+ properties
* | | \- type = Integer
* | | \- description = Distance between wavelengths in nanometers.
* | |--+ property version overrides
* | |-+ 2003FC
* | \- type = Float
* | \- getter = getPixelSizeC
* | \- setter = setPixelSizeC
* |...
* </pre>
*
* @author Curtis Rueden ctrueden at wisc.edu
*/
public class EntityList {
// -- Constants --
private static final boolean DEBUG = false;
// -- Fields --
/** List of versions and their details. */
protected HashMap<String, HashMap<String, String>> versions =
new HashMap<String, HashMap<String, String>>();
/** List of entities. */
protected HashMap<String, Entity> entities =
new HashMap<String, Entity>();
/** The active version. */
protected String ver;
/** The active entity. */
protected String ent;
/** The active property. */
protected String prop;
// -- Constructor --
/** Constructs an entity list. */
public EntityList(String versionPath, String entityPath) throws IOException {
// parse INI data
System.out.println("Parsing configuration data");
IniParser parser = new IniParser();
IniList versionList = parser.parseINI(versionPath, EntityList.class);
IniList entityList = parser.parseINI(entityPath, EntityList.class);
// convert unprocessed INI-style config data into
// hierarchical entity/property/version structure
// process list of versions
for (HashMap<String, String> attrs : versionList) {
String name = attrs.get(IniTable.HEADER_KEY);
versions.put(name, attrs);
}
// process list of entities
entities = new HashMap<String, Entity>();
for (HashMap<String, String> attrs : entityList) {
String name = attrs.get(IniTable.HEADER_KEY);
if (DEBUG) debug("-- Parsing entry '" + name + "' --");
// "entity" list actually contains attribute tables for entities,
// properties and version overrides; determine which kind this one is
StringTokenizer st = new StringTokenizer(name);
int num = st.countTokens();
switch (num) {
case 1:
// entity header
if (DEBUG) debug("Entry is an entity definition");
entities.put(name, new Entity(attrs));
System.out.println("\t" + name);
if (DEBUG) debug("Added entity '" + name + "'");
break;
case 2:
// property header, or entity version header
String t1 = st.nextToken();
String t2 = st.nextToken();
Entity entity = entities.get(t1);
if (entity == null) {
throw new IOException("bad entity name '" + t1 + "'");
}
attrs.put(IniTable.HEADER_KEY, t2);
if (DEBUG) debug("Reset header value to '" + t2 + "'");
HashMap<String, String> version = versions.get(t2);
if (version == null) {
// property header
if (DEBUG) debug("Entry is a property definition");
entity.props.put(t2, new Property(attrs));
if (DEBUG) {
debug("Added property '" + t2 + "' to entity '" + t1 + "'");
}
}
else {
// entity version header
if (DEBUG) debug("Entry is an entity version definition");
entity.versions.put(t2, attrs);
if (DEBUG) {
debug("Added version '" + t2 + "' to entity '" + t1 + "'");
}
}
break;
case 3:
// property version header
if (DEBUG) debug("Entry is a property version definition");
t1 = st.nextToken();
t2 = st.nextToken();
String t3 = st.nextToken();
entity = entities.get(t1);
if (entity == null) {
throw new IOException("bad entity name '" + t1 + "'");
}
Property prop = entity.props.get(t2);
if (prop == null) {
throw new IOException("bad property name '" +
t2 + "' for entity '" + t1 + "'");
}
attrs.put(IniTable.HEADER_KEY, t2);
if (DEBUG) debug("Reset header value to '" + t2 + "'");
prop.versions.put(t3, attrs);
if (DEBUG) {
debug("Added property '" + t2 +
"' to version '" + t3 + "' of entity '" + t1 + "'");
}
break;
default:
throw new IOException("bad token count for header '" + name + "'");
}
}
}
// -- EntityList API methods --
/** Sets the active version. */
public void setVersion(String version) {
ver = version;
}
/** Gets the active version. */
public String getVersion() {
return ver;
}
/** Sets the active entity. */
public void setEntity(String entity) {
ent = entity;
prop = null;
}
/** Gets the active entity. */
public String getEntity() {
return ent;
}
/** Sets the active property. */
public void setProperty(String property) {
prop = property;
}
/** Gets the active property. */
public String getProperty() {
return prop;
}
/** Gets list of versions in sorted order. */
public List<String> versions() {
List<String> list = new ArrayList<String>(versions.keySet());
Collections.sort(list);
return list;
}
/** Gets the list of entities in sorted order. */
public List<String> entities() {
List<String> list = new ArrayList<String>(entities.keySet());
Collections.sort(list);
return list;
}
/** Gets a sorted list of properties for the active entity. */
public List<String> props() {
if (ent == null) return null;
Entity e = entities.get(ent);
List<String> list = new ArrayList<String>(e.props.keySet());
Collections.sort(list);
return list;
}
/** Gets the attribute value for the header key. */
public String name() { return value(IniTable.HEADER_KEY); }
/**
* Queries the attribute value for the given key, for the active version,
* property and entity.
*/
public String value(String key) {
return value(key, ver, ent, prop);
}
/**
* Queries the attribute value for the given key, for a particular version of
* a particular property of a particular entity. The attribute value is
* obtained from an attributes table according to following order of
* precedence:
* <ol>
* <li>version override of the given property of the given entity</li>
* <li>default value of the given property of the given entity</li>
* <li>version override of the given entity</li>
* <li>default value of the given entity itself</li>
* <li>default value in the given version's attribute table</li>
* </ol>
* Returns null if the attribute is not found in any of the above tables.
*/
public String value(String key,
String version, String entity, String property)
{
Entity e = null;
Property p = null;
if (entity != null) e = entities.get(entity);
if (property != null && e != null) p = e.props.get(property);
String value = null;
// version override of the given property of the given entity
if (value == null && version != null && p != null) {
HashMap<String, String> attrs = p.versions.get(version);
if (attrs != null) value = attrs.get(key);
}
// default value of the given property of the given entity
if (value == null && p != null) value = p.attrs.get(key);
// version override of the given entity
if (value == null && version != null && e != null) {
HashMap<String, String> attrs = e.versions.get(version);
if (attrs != null) value = attrs.get(key);
}
// default value of the given entity itself
if (value == null && e != null) value = e.attrs.get(key);
// default value in the given version's attribute table
if (value == null && version != null) {
HashMap<String, String> attrs = versions.get(version);
if (attrs != null) value = attrs.get(key);
}
return value;
}
// -- Helper methods --
private void debug(String s) {
System.out.println("DEBUG: " + s);
}
}
components/autogen/src/FormatPageAutogen.java deleted 100644 → 0
View file @ e05f283f
/*
* #%L
* Bio-Formats autogen package for programmatically generating source code.
* %%
* Copyright (C) 2007 - 2017 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Hashtable;
import loci.common.DataTools;
import loci.common.IniList;
import loci.common.IniParser;
import loci.common.IniTable;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.formats.UnknownFormatException;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
/**
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class FormatPageAutogen {
// -- Constants --
private static final String TEMPLATE = "doc/FormatPage.vm";
private static final String TABLE_TEMPLATE = "doc/FormatTable.vm";
// -- Fields --
private IniList data;
// -- Constructor --
public FormatPageAutogen(String dataFile) throws FormatException, IOException
{
String file = DataTools.readFile(dataFile);
IniParser parser = new IniParser();
parser.setCommentDelimiter(null);
data = parser.parseINI(new BufferedReader(new StringReader(file)));
}
// -- API Methods --
public void writeFormatPages() throws Exception {
File doc = new File("../../docs/sphinx/formats/");
if (!doc.exists()) {
boolean success = doc.mkdir();
if (!success) {
throw new IOException("Could not create " + doc.getAbsolutePath());
}
}
VelocityEngine engine = VelocityTools.createEngine();
for (IniTable table : data) {
VelocityContext context = VelocityTools.createContext();
String format = table.get(IniTable.HEADER_KEY);
context.put("format", format);
if (table.containsKey("extensions")) {
context.put("extensions", table.get("extensions"));
}
if (table.containsKey("indexExtensions")) {
context.put("indexExtensions", table.get("indexExtensions"));
}
else if (table.containsKey("extensions")){
context.put("indexExtensions", table.get("extensions"));
}
context.put("owner", table.get("owner"));
context.put("developer", table.get("developer"));
context.put("bsd", table.get("bsd"));
context.put("export", table.get("export"));
context.put("pyramid", table.get("pyramid"));
if (table.containsKey("versions")) {
context.put("versions", table.get("versions"));
}
else {
context.put("versions", "");
}
context.put("pixelsRating", table.get("pixelsRating"));
context.put("metadataRating", table.get("metadataRating"));
context.put("opennessRating", table.get("opennessRating"));
context.put("presenceRating", table.get("presenceRating"));
context.put("utilityRating", table.get("utilityRating"));
context.put("reader", table.get("reader"));
context.put("writer", table.get("writer"));
context.put("mif", table.get("mif"));
context.put("notes", table.get("notes"));
context.put("privateSpecification", table.get("privateSpecification"));
context.put("options", table.get("options"));
context.put("readerextlink",
table.get("bsd").equals("no") ? "bfreader" : "bsd-reader");
context.put("writerextlink",
table.get("bsd").equals("no") ? "bfwriter" : "bsd-writer");
if (table.containsKey("software")) {
String[] software = table.get("software").split("\n");
context.put("software", software);
}
if (table.containsKey("weHave")) {
String[] weHave = table.get("weHave").split("\n");
context.put("weHave", weHave);
}
if (table.containsKey("weWant")) {
String[] weWant = table.get("weWant").split("\n");
context.put("weWant", weWant);
}
if (table.containsKey("samples")) {
String[] samples = table.get("samples").split("\n");
context.put("samples", samples);
}
if (table.containsKey("notes")) {
String[] notes = table.get("notes").split("\n");
context.put("notes", notes);
}
if (table.containsKey("reader")) {
String[] reader = table.get("reader").split(", ");
context.put("reader", reader);
}
String filename = getPageName(format, table.get("pagename"));
if (table.containsKey("metadataPage")) {
String page = table.get("metadataPage");
if (page.length() > 0) {
context.put("metadataPage", page.split(", "));
}
} else {
String[] page = {filename.substring(filename.indexOf(File.separator) + 1) + "-metadata"};
context.put("metadataPage", page);
}
VelocityTools.processTemplate(engine, context, TEMPLATE,
"../../docs/sphinx/" + filename + ".rst");
}
}
public void writeFormatTable() throws Exception {
File doc = new File("../../docs/sphinx/");
if (!doc.exists()) {
boolean success = doc.mkdir();
if (!success) {
throw new IOException("Could not create " + doc.getAbsolutePath());
}
}
VelocityEngine engine = VelocityTools.createEngine();
VelocityContext context = VelocityTools.createContext();
IniTable[] sortedTable = new IniTable[data.size()];
for (int i=0; i<data.size(); i++) {
IniTable table = data.get(i);
table.put("pagename",
getPageName(table.get(IniTable.HEADER_KEY), table.get("pagename")));
sortedTable[i] = table;
}
Arrays.sort(sortedTable, new Comparator<IniTable>() {
@Override
public int compare(IniTable t1, IniTable t2) {
String page1 = t1.get("pagename");
String page2 = t2.get("pagename");
return page1.compareTo(page2);
}
});
context.put("formats", sortedTable);
context.put("count", sortedTable.length);
VelocityTools.processTemplate(engine, context, TABLE_TEMPLATE,
"../../docs/sphinx/supported-formats.rst");
}
// -- Helper methods --
protected static String getPageName(String format, String pagename) {
String realPageName = pagename;
if (realPageName == null) {
realPageName = format.replaceAll("/", "");
realPageName = realPageName.replaceAll("\\(", "");
realPageName = realPageName.replaceAll("\\)", "");
realPageName = realPageName.replaceAll("\\.", "");
realPageName = realPageName.replaceAll("& ", "");
realPageName = realPageName.replaceAll(" ", "-");
realPageName = realPageName.toLowerCase();
}
realPageName = "formats/" + realPageName;
return realPageName;
}
// -- Main method --
public static void main(String[] args) throws Exception {
FormatPageAutogen autogen = new FormatPageAutogen(args[0]);
autogen.writeFormatPages();
autogen.writeFormatTable();
}
}