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@ebremer
ebremer authored Sep 17, 2024
2 parents 6209f15 + 444da84 commit eedc89f
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302 changes: 151 additions & 151 deletions dependency-reduced-pom.xml
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Original file line number Diff line number Diff line change
@@ -1,151 +1,151 @@
<?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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.stonybrook.bmi</groupId>
<artifactId>hatch</artifactId>
<version>4.0.0</version>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**</include>
</includes>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
</build>
<profiles>
<profile>
<id>hatchjar</id>
<build>
<finalName>hatch-${project.version}</finalName>
<plugins>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.4.1</version>
<executions>
<execution>
<id>enforce</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<banDuplicatePomDependencyVersions />
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.5.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<shadedArtifactAttached>false</shadedArtifactAttached>
<transformers>
<transformer>
<mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
<manifestEntries>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
<transformer />
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>hatch</id>
<build>
<plugins>
<plugin>
<groupId>org.graalvm.buildtools</groupId>
<artifactId>native-maven-plugin</artifactId>
<version>0.10.1</version>
<extensions>true</extensions>
<executions>
<execution>
<id>build-native</id>
<phase>package</phase>
<goals>
<goal>compile-no-fork</goal>
</goals>
</execution>
</executions>
<configuration>
<imageName>hatch</imageName>
<mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
<debug>true</debug>
<skipNativeTests>true</skipNativeTests>
<verbose>true</verbose>
<buildArgs>
<buildArg>--no-fallback</buildArg>
<buildArg>-H:ConfigurationFileDirectories=config</buildArg>
<buildArg>--enable-url-protocols=https</buildArg>
<buildArg>-H:+AddAllCharsets</buildArg>
</buildArgs>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<repositories>
<repository>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
</repository>
<repository>
<id>ome</id>
<name>OME Artifactory</name>
<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
</repository>
<repository>
<id>halcyon</id>
<url>https://cursus.bmi.stonybrookmedicine.edu/releases</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>5.0.0</version>
<type>pom</type>
<scope>compile</scope>
</dependency>
</dependencies>
<properties>
<maven.compiler.target>21</maven.compiler.target>
<twelvemonkeys.version>3.10.1</twelvemonkeys.version>
<maven.compiler.source>21</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<ver.bioformats>7.3.0</ver.bioformats>
</properties>
</project>
<?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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.stonybrook.bmi</groupId>
<artifactId>hatch</artifactId>
<version>4.0.1</version>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**</include>
</includes>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
</build>
<profiles>
<profile>
<id>hatchjar</id>
<build>
<finalName>hatch-${project.version}</finalName>
<plugins>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.4.1</version>
<executions>
<execution>
<id>enforce</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<banDuplicatePomDependencyVersions />
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.5.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<shadedArtifactAttached>false</shadedArtifactAttached>
<transformers>
<transformer>
<mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
<manifestEntries>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
<transformer />
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>hatch</id>
<build>
<plugins>
<plugin>
<groupId>org.graalvm.buildtools</groupId>
<artifactId>native-maven-plugin</artifactId>
<version>0.10.1</version>
<extensions>true</extensions>
<executions>
<execution>
<id>build-native</id>
<phase>package</phase>
<goals>
<goal>compile-no-fork</goal>
</goals>
</execution>
</executions>
<configuration>
<imageName>hatch</imageName>
<mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
<debug>true</debug>
<skipNativeTests>true</skipNativeTests>
<verbose>true</verbose>
<buildArgs>
<buildArg>--no-fallback</buildArg>
<buildArg>-H:ConfigurationFileDirectories=config</buildArg>
<buildArg>--enable-url-protocols=https</buildArg>
<buildArg>-H:+AddAllCharsets</buildArg>
</buildArgs>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<repositories>
<repository>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
</repository>
<repository>
<id>ome</id>
<name>OME Artifactory</name>
<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
</repository>
<repository>
<id>halcyon</id>
<url>https://cursus.bmi.stonybrookmedicine.edu/releases</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>5.1.0</version>
<type>pom</type>
<scope>compile</scope>
</dependency>
</dependencies>
<properties>
<maven.compiler.target>21</maven.compiler.target>
<twelvemonkeys.version>3.10.1</twelvemonkeys.version>
<maven.compiler.source>21</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<ver.bioformats>7.3.1</ver.bioformats>
</properties>
</project>
2 changes: 0 additions & 2 deletions error.log
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Original file line number Diff line number Diff line change
@@ -1,2 +0,0 @@
2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\Image_01_M200_40X_A36.tif ==> index >= numImages (0 >= 0)
2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\ugh.tif ==> Invalid TIFF byte order mark 'sd', expected: 'II' or 'MM'
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