niu/bioformats-imageinfo
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revised package development environment.

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This commit is contained in:
Yoshihiro OKUMURA 2022-07-12 17:46:31 +09:00
parent 12c38db496
commit ccb264871f
2 changed files with 67 additions and 29 deletions
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28
README.md
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@ -1,27 +1,27 @@
# BioFormatsImageInfo # BioFormatsImageInfo
Metadata extraction tool based on Bio-Formats Metadata extraction tool based on Bio-Formats
### Compile ### make package
```shell
mvn compile
```
### run
```shell
mvn exec:java -Dexec.mainClass=jp.riken.neurodata.tools.BioFormatsImageInfo -Dexec.args="'[path to image file]'"
```
### make jar package
```shell ```shell
mvn package mvn package
``` ```
### run by jar ### run
```shell ```shell
java -jar target/bioformats-imageinfo-1.0.0.jar "[path to image file]" ./target/dist/bin/bioformats-imageinfo "[path to image file]"
``` ```
### run by class ### run by jar
```shell
java -jar ./target/dist/lib/bioformats-imageinfo-1.0.0.jar "[path to image file]"
```
### run by fat jar
```shell
java -jar ./target/bioformats-imageinfo-1.0.0-jar-with-dependencies.jar "[path to image file]"
```
### library usage
```java ```java
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.Map; import java.util.Map;

68
pom.xml
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@ -11,17 +11,21 @@
<url>https://neurodata.riken.jp</url> <url>https://neurodata.riken.jp</url>
<properties> <properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <bio-formats.version>6.10.0</bio-formats.version>
<bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
<maven.compiler.source>1.8</maven.compiler.source> <maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target> <maven.compiler.target>1.8</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties> </properties>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>ome</groupId> <groupId>ome</groupId>
<artifactId>bioformats_package</artifactId> <artifactId>bio-formats-tools</artifactId>
<version>6.10.0</version> <version>${bio-formats.version}</version>
<type>pom</type>
</dependency> </dependency>
</dependencies> </dependencies>
@ -39,8 +43,8 @@
<goal>copy-dependencies</goal> <goal>copy-dependencies</goal>
</goals> </goals>
<configuration> <configuration>
<outputDirectory>${project.build.directory}/libs</outputDirectory> <overWriteIfNewer>true</overWriteIfNewer>
</configuration> </configuration>
</execution> </execution>
</executions> </executions>
</plugin> </plugin>
@ -52,8 +56,7 @@
<archive> <archive>
<manifest> <manifest>
<addClasspath>true</addClasspath> <addClasspath>true</addClasspath>
<classpathPrefix>libs/</classpathPrefix> <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
<mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass>
</manifest> </manifest>
</archive> </archive>
</configuration> </configuration>
@ -61,14 +64,14 @@
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId> <artifactId>maven-assembly-plugin</artifactId>
<version>3.4.1</version> <version>3.4.1</version>
<configuration> <configuration>
<descriptorRefs> <descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef> <descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs> </descriptorRefs>
<archive> <archive>
<manifest> <manifest>
<mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass> <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
</manifest> </manifest>
</archive> </archive>
</configuration> </configuration>
@ -82,6 +85,42 @@
</execution> </execution>
</executions> </executions>
</plugin> </plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
<version>1.10</version>
<configuration>
<assembleDirectory>${project.build.directory}/dist</assembleDirectory>
<repositoryLayout>flat</repositoryLayout>
<repositoryName>lib</repositoryName>
<programs>
<program>
<mainClass>${bioformats-imageinfo.mainClass}</mainClass>
<id>${project.name}</id>
</program>
</programs>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>assemble</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.owasp</groupId>
<artifactId>dependency-check-maven</artifactId>
<version>7.1.1</version>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins> </plugins>
</build> </build>
@ -98,17 +137,16 @@
<id>central</id> <id>central</id>
<name>Central Repository</name> <name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url> <url>https://repo.maven.apache.org/maven2</url>
</repository>
<repository>
<id>unidata.releases</id>
<url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
<snapshots><enabled>false</enabled></snapshots>
</repository> </repository>
<repository> <repository>
<id>ome</id> <id>ome</id>
<name>OME Artifactory</name> <name>OME Artifactory</name>
<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url> <url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
</repository> </repository>
<repository>
<id>unidata.releases</id>
<url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
</repository>
</repositories> </repositories>
</project> </project>