I am trying to use visual studio code on my linux ubuntu machine to debug a repo BigStitcher-Spark, specifically for one of its dependencies titled multiview-reconstruction.
I can see the dependency inside my BigStitcher-Spark pom.xml file below, it is pointing to version 5.2.2, which it downloads from online and places into my .m2 folder:
<project xmlns=".0.0"
xmlns:xsi=";
xsi:schemaLocation=".0.0 .0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>39.0.0</version>
<relativePath/>
</parent>
<groupId>net.preibisch</groupId>
<artifactId>BigStitcher-Spark</artifactId>
<version>0.1.0-SNAPSHOT</version>
<name>BigStitcher Spark</name>
<description>Spark-based parallel BigStitcher project.</description>
<url>;/url>
<inceptionYear>2021</inceptionYear>
<anization>
<name>Fiji</name>
<url>/</url>
</anization>
<licenses>
<license>
<name>GNU General Public License v2+</name>
<url>.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>StephanPreibisch</id>
<name>Stephan Preibisch</name>
<url>:StephanP</url>
<roles>
<role>founder</role>
<role>lead</role>
<role>developer</role>
<role>debugger</role>
<role>reviewer</role>
<role>support</role>
<role>maintainer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>Marwan Zouinkhi</name>
</contributor>
<contributor>
<name>Tobias Pietzsch</name>
<url>;/url>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>ImageJ Forum</name>
<archive>/</archive>
</mailingList>
</mailingLists>
<scm>
<connection>scm:git:;/connection>
<developerConnection>scm:git:[email protected]:JaneliaSciComp/BigStitcher-Spark</developerConnection>
<tag>HEAD</tag>
<url>;/url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>;/url>
</issueManagement>
<ciManagement>
<system>GitHub Actions</system>
<url>;/url>
</ciManagement>
<properties>
<package-name>net.preibisch.bigstitcher.spark</package-name>
<!-- <scijava.jvm.version>1.8</scijava.jvm.version> -->
<license.licenseName>bsd</license.licenseName>
<license.copyrightOwners>Developers.</license.copyrightOwners>
<!--
<imglib2.version>7.1.2</imglib2.version>
<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
<imglib2-cache.version>1.0.0-beta-19</imglib2-cache.version>
<imglib2-algorithm.version>0.16.0</imglib2-algorithm.version>
<imglib2-roi.version>0.15.1</imglib2-roi.version>
<n5-imglib2.version>7.0.2</n5-imglib2.version>
<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
-->
<!-- <n5-zarr.version>1.3.5</n5-zarr.version> -->
<imglib2.version>7.1.4</imglib2.version>
<imglib2-algorithm.version>0.17.2</imglib2-algorithm.version>
<bigdataviewer-core.version>10.6.3</bigdataviewer-core.version>
<spim_data.version>2.3.5</spim_data.version>
<multiview-reconstruction.version>5.2.2</multiview-reconstruction.version>
<BigStitcher.version>2.3.4</BigStitcher.version>
<!--for the old bioformats to work properly (compared with old main branch to find out)-->
<ome-codecs.version>0.3.0</ome-codecs.version>
</properties>
<repositories>
<!-- NB: for project parent -->
<repository>
<id>imagej.public</id>
<url>;/url>
</repository>
<repository>
<id>jitpack.io</id>
<url>;/url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
<!-- <version>10.4.6</version> -->
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-vistools</artifactId>
<!-- <version>1.0.0-beta-32</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-cache</artifactId>
<!-- <version>1.0.0-beta-17</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
<!-- <version>6.3.0</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-algorithm</artifactId>
<!-- <version>0.15.0</version> -->
</dependency>
<dependency>
<groupId>.bigdataviewer</groupId>
<artifactId>bigdataviewer-n5</artifactId>
<version>1.0.1</version>
<exclusions>
<exclusion>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>spim_data</artifactId>
</dependency>
<!-- <dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-s3</artifactId>
<version>${aws-java-sdk-s3.version}</version>
</dependency> -->
<!-- <dependency>
<groupId>.bigdataviewer</groupId>
<artifactId>bigdataviewer-omezarr</artifactId>
<version>0.2.3</version>
</dependency> -->
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-zarr</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-aws-s3</artifactId>
<!-- <version>4.0.0</version> -->
</dependency>
<!-- Scala is sensitive to fasterxml version -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.4</version>
</dependency>
<dependency>
<groupId>.apache.spark</groupId>
<!-- Spark 3.3.2 release comes with scala 2.12.15 -->
<artifactId>spark-core_2.12</artifactId>
<version>3.3.2</version>
<exclusions>
<exclusion>
<artifactId>netty-all</artifactId>
<groupId>ioty</groupId>
</exclusion>
<exclusion>
<artifactId>netty</artifactId>
<groupId>ioty</groupId>
</exclusion>
<exclusion>
<artifactId>jcl-over-slf4j</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>jul-to-slf4j</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>aopalliance-repackaged</artifactId>
<groupId>.glassfish.hk2.external</groupId>
</exclusion>
<exclusion>
<artifactId>javax.inject</artifactId>
<groupId>.glassfish.hk2.external</groupId>
</exclusion>
<exclusion>
<artifactId>jersey-client</artifactId>
<groupId>.glassfish.jersey.core</groupId>
</exclusion>
<exclusion>
<artifactId>jersey-core</artifactId>
<groupId>com.sun.jersey</groupId>
</exclusion>
<exclusion>
<artifactId>lz4</artifactId>
<groupId>net.jpountz.lz4</groupId>
</exclusion>
<exclusion>
<artifactId>jets3t</artifactId>
<groupId>net.java.dev.jets3t</groupId>
</exclusion>
<!--<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>kryo-shaded</artifactId>
</exclusion>-->
<exclusion>
<groupId>javax.xml.stream</groupId>
<artifactId>stax-api</artifactId>
</exclusion>
</exclusions>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.12.15</version>
</dependency>
<dependency>
<groupId>net.preibisch</groupId>
<artifactId>multiview-reconstruction</artifactId>
<exclusions>
<exclusion>
<groupId>ch.epfl.biop</groupId>
<artifactId>ijp-kheops</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>reflectasm</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ioty</groupId>
<artifactId>netty-all</artifactId>
<version>4.1.68.Final</version>
</dependency>
<dependency>
<groupId>ioty</groupId>
<artifactId>netty</artifactId>
<version>3.9.9.Final</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-hdf5</artifactId>
<!-- <version>2.0.0</version> -->
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-imglib2</artifactId>
</dependency>
<!-- .java.dev.jna/jna needed for M1 native library loading -->
<dependency>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna</artifactId>
<version>5.7.0</version>
</dependency>
<dependency>
<groupId>net.preibisch</groupId>
<artifactId>BigStitcher</artifactId>
<exclusions>
<exclusion>
<groupId>ch.epfl.biop</groupId>
<artifactId>ijp-kheops</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>reflectasm</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- old bioformats -->
<dependency>
<groupId>.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
<version>6.0.4</version>
<exclusions>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
<version>6.5.1</version>
<exclusions>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
<version>6.5.1</version>
<exclusions>
<exclusion>
<groupId>ch.systems.cisd</groupId>
<artifactId>jhdf5</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<profiles>
<profile>
<id>fatjar</id>
<build>
<plugins>
<!-- Maven shade for Uber Jar -->
<!-- .html -->
<!-- .html -->
<plugin>
<groupId>.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<!-- Do not minimize for now to speed up packaging. -->
<transformers combine.children="append">
<transformer
implementation=".apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/json/mpicbg.spim.data.generic.sequence.ImgLoaderIo</resource>
</transformer>
<transformer
implementation=".apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/json/.janelia.saalfeldlab.n5.Compression$CompressionType</resource>
</transformer>
</transformers>
<!--<minimizeJar>true</minimizeJar> -->
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>Angle0.tif</exclude>
<exclude>LICENSE</exclude>
<exclude>LICENSE.txt</exclude>
<exclude>META-INF/DEPENDENCIES</exclude>
<exclude>META-INF/LICENSE</exclude>
<exclude>META-INF/NOTICE</exclude>
<exclude>META-INF/BSDL</exclude>
<exclude>META-INF/COPYING</exclude>
<exclude>META-INF/LEGAL</exclude>
<exclude>META-INF/LICENSE.RUBY</exclude>
<exclude>META-INF/json/.scijava.plugin.Plugin</exclude>
<exclude>META-INF/*.MF</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/*.txt</exclude>
<exclude>module-info.class</exclude>
<exclude>plugins.config</exclude>
<exclude>META-INF/versions/9/module-info.class</exclude>
<exclude>META-INF/okio.kotlin_module</exclude>
<exclude>META-INF/services/com.fasterxml.jackson.core.JsonFactory</exclude>
</excludes>
</filter>
</filters>
<!-- Additional configuration. -->
<artifactSet>
<excludes>
<exclude>xpp3:xpp3</exclude>
</excludes>
</artifactSet>
<relocations>
<relocation>
<pattern>.apachemonspress</pattern>
<shadedPattern>.janelia.saalfeldlab.apachemonspress</shadedPattern>
</relocation>
<!-- Protect newer gson version from the old one preloaded by spark -->
<relocation>
<pattern>com.google.gson</pattern>
<shadedPattern>.janelia.saalfeldlab.google.gson</shadedPattern>
</relocation>
</relocations>
</configuration>
<!-- binds by default to package phase -->
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Maven shade end -->
</plugins>
</build>
</profile>
</profiles>
</project>
If i run my debugger in visual studio code, I can step through the dependency, but I cannot add print statements. I want to be able to edit the code in my dependency.
I can clone the github repo for the dependency, and run 'mvn clean package' to generate the .jar files.
Can I change my pom.xml to point towards my locally installed multiview-reconstruction github repo folder, and tell BigStitcher-Spark to use that for all the dependency calls? So that I can step through the multiview-reconstruction code and edit it as I go?
I am trying to use visual studio code on my linux ubuntu machine to debug a repo BigStitcher-Spark, specifically for one of its dependencies titled multiview-reconstruction.
I can see the dependency inside my BigStitcher-Spark pom.xml file below, it is pointing to version 5.2.2, which it downloads from online and places into my .m2 folder:
<project xmlns="http://maven.apache./POM/4.0.0"
xmlns:xsi="http://www.w3./2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache./POM/4.0.0 https://maven.apache./xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>39.0.0</version>
<relativePath/>
</parent>
<groupId>net.preibisch</groupId>
<artifactId>BigStitcher-Spark</artifactId>
<version>0.1.0-SNAPSHOT</version>
<name>BigStitcher Spark</name>
<description>Spark-based parallel BigStitcher project.</description>
<url>https://github/JaneliaSciComp/BigStitcher-Spark</url>
<inceptionYear>2021</inceptionYear>
<anization>
<name>Fiji</name>
<url>https://fiji.sc/</url>
</anization>
<licenses>
<license>
<name>GNU General Public License v2+</name>
<url>https://www.gnu./licenses/gpl.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>StephanPreibisch</id>
<name>Stephan Preibisch</name>
<url>http://imagej/User:StephanP</url>
<roles>
<role>founder</role>
<role>lead</role>
<role>developer</role>
<role>debugger</role>
<role>reviewer</role>
<role>support</role>
<role>maintainer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>Marwan Zouinkhi</name>
</contributor>
<contributor>
<name>Tobias Pietzsch</name>
<url>https://imagej/people/tpietzsch</url>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>ImageJ Forum</name>
<archive>https://forum.image.sc/</archive>
</mailingList>
</mailingLists>
<scm>
<connection>scm:git:https://github/JaneliaSciComp/BigStitcher-Spark</connection>
<developerConnection>scm:git:[email protected]:JaneliaSciComp/BigStitcher-Spark</developerConnection>
<tag>HEAD</tag>
<url>https://github/JaneliaSciComp/BigStitcher-Spark</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github/JaneliaSciComp/BigStitcher-Spark/issues</url>
</issueManagement>
<ciManagement>
<system>GitHub Actions</system>
<url>https://github/JaneliaSciComp/BigStitcher-Spark/actions</url>
</ciManagement>
<properties>
<package-name>net.preibisch.bigstitcher.spark</package-name>
<!-- <scijava.jvm.version>1.8</scijava.jvm.version> -->
<license.licenseName>bsd</license.licenseName>
<license.copyrightOwners>Developers.</license.copyrightOwners>
<!--
<imglib2.version>7.1.2</imglib2.version>
<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
<imglib2-cache.version>1.0.0-beta-19</imglib2-cache.version>
<imglib2-algorithm.version>0.16.0</imglib2-algorithm.version>
<imglib2-roi.version>0.15.1</imglib2-roi.version>
<n5-imglib2.version>7.0.2</n5-imglib2.version>
<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
-->
<!-- <n5-zarr.version>1.3.5</n5-zarr.version> -->
<imglib2.version>7.1.4</imglib2.version>
<imglib2-algorithm.version>0.17.2</imglib2-algorithm.version>
<bigdataviewer-core.version>10.6.3</bigdataviewer-core.version>
<spim_data.version>2.3.5</spim_data.version>
<multiview-reconstruction.version>5.2.2</multiview-reconstruction.version>
<BigStitcher.version>2.3.4</BigStitcher.version>
<!--for the old bioformats to work properly (compared with old main branch to find out)-->
<ome-codecs.version>0.3.0</ome-codecs.version>
</properties>
<repositories>
<!-- NB: for project parent -->
<repository>
<id>imagej.public</id>
<url>https://maven.imagej/content/groups/public</url>
</repository>
<repository>
<id>jitpack.io</id>
<url>https://jitpack.io</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
<!-- <version>10.4.6</version> -->
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-vistools</artifactId>
<!-- <version>1.0.0-beta-32</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-cache</artifactId>
<!-- <version>1.0.0-beta-17</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
<!-- <version>6.3.0</version> -->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-algorithm</artifactId>
<!-- <version>0.15.0</version> -->
</dependency>
<dependency>
<groupId>.bigdataviewer</groupId>
<artifactId>bigdataviewer-n5</artifactId>
<version>1.0.1</version>
<exclusions>
<exclusion>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>spim_data</artifactId>
</dependency>
<!-- <dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-s3</artifactId>
<version>${aws-java-sdk-s3.version}</version>
</dependency> -->
<!-- <dependency>
<groupId>.bigdataviewer</groupId>
<artifactId>bigdataviewer-omezarr</artifactId>
<version>0.2.3</version>
</dependency> -->
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-zarr</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-aws-s3</artifactId>
<!-- <version>4.0.0</version> -->
</dependency>
<!-- Scala is sensitive to fasterxml version -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.4</version>
</dependency>
<dependency>
<groupId>.apache.spark</groupId>
<!-- Spark 3.3.2 release comes with scala 2.12.15 -->
<artifactId>spark-core_2.12</artifactId>
<version>3.3.2</version>
<exclusions>
<exclusion>
<artifactId>netty-all</artifactId>
<groupId>ioty</groupId>
</exclusion>
<exclusion>
<artifactId>netty</artifactId>
<groupId>ioty</groupId>
</exclusion>
<exclusion>
<artifactId>jcl-over-slf4j</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>jul-to-slf4j</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
<groupId>.slf4j</groupId>
</exclusion>
<exclusion>
<artifactId>aopalliance-repackaged</artifactId>
<groupId>.glassfish.hk2.external</groupId>
</exclusion>
<exclusion>
<artifactId>javax.inject</artifactId>
<groupId>.glassfish.hk2.external</groupId>
</exclusion>
<exclusion>
<artifactId>jersey-client</artifactId>
<groupId>.glassfish.jersey.core</groupId>
</exclusion>
<exclusion>
<artifactId>jersey-core</artifactId>
<groupId>com.sun.jersey</groupId>
</exclusion>
<exclusion>
<artifactId>lz4</artifactId>
<groupId>net.jpountz.lz4</groupId>
</exclusion>
<exclusion>
<artifactId>jets3t</artifactId>
<groupId>net.java.dev.jets3t</groupId>
</exclusion>
<!--<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>kryo-shaded</artifactId>
</exclusion>-->
<exclusion>
<groupId>javax.xml.stream</groupId>
<artifactId>stax-api</artifactId>
</exclusion>
</exclusions>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.12.15</version>
</dependency>
<dependency>
<groupId>net.preibisch</groupId>
<artifactId>multiview-reconstruction</artifactId>
<exclusions>
<exclusion>
<groupId>ch.epfl.biop</groupId>
<artifactId>ijp-kheops</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>reflectasm</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ioty</groupId>
<artifactId>netty-all</artifactId>
<version>4.1.68.Final</version>
</dependency>
<dependency>
<groupId>ioty</groupId>
<artifactId>netty</artifactId>
<version>3.9.9.Final</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-hdf5</artifactId>
<!-- <version>2.0.0</version> -->
</dependency>
<dependency>
<groupId>.janelia.saalfeldlab</groupId>
<artifactId>n5-imglib2</artifactId>
</dependency>
<!-- https://mvnrepository/artifact/net.java.dev.jna/jna needed for M1 native library loading -->
<dependency>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna</artifactId>
<version>5.7.0</version>
</dependency>
<dependency>
<groupId>net.preibisch</groupId>
<artifactId>BigStitcher</artifactId>
<exclusions>
<exclusion>
<groupId>ch.epfl.biop</groupId>
<artifactId>ijp-kheops</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware</groupId>
<artifactId>reflectasm</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
</exclusion>
<exclusion>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- old bioformats -->
<dependency>
<groupId>.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
<version>6.0.4</version>
<exclusions>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
<version>6.5.1</version>
<exclusions>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
<version>6.5.1</version>
<exclusions>
<exclusion>
<groupId>ch.systems.cisd</groupId>
<artifactId>jhdf5</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<profiles>
<profile>
<id>fatjar</id>
<build>
<plugins>
<!-- Maven shade for Uber Jar -->
<!-- https://maven.apache./plugins/maven-shade-plugin/shade-mojo.html -->
<!-- https://databricks.gitbooks.io/databricks-spark-knowledge-base/content/troubleshooting/missing_dependencies_in_jar_files.html -->
<plugin>
<groupId>.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<!-- Do not minimize for now to speed up packaging. -->
<transformers combine.children="append">
<transformer
implementation=".apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/json/mpicbg.spim.data.generic.sequence.ImgLoaderIo</resource>
</transformer>
<transformer
implementation=".apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/json/.janelia.saalfeldlab.n5.Compression$CompressionType</resource>
</transformer>
</transformers>
<!--<minimizeJar>true</minimizeJar> -->
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>Angle0.tif</exclude>
<exclude>LICENSE</exclude>
<exclude>LICENSE.txt</exclude>
<exclude>META-INF/DEPENDENCIES</exclude>
<exclude>META-INF/LICENSE</exclude>
<exclude>META-INF/NOTICE</exclude>
<exclude>META-INF/BSDL</exclude>
<exclude>META-INF/COPYING</exclude>
<exclude>META-INF/LEGAL</exclude>
<exclude>META-INF/LICENSE.RUBY</exclude>
<exclude>META-INF/json/.scijava.plugin.Plugin</exclude>
<exclude>META-INF/*.MF</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/*.txt</exclude>
<exclude>module-info.class</exclude>
<exclude>plugins.config</exclude>
<exclude>META-INF/versions/9/module-info.class</exclude>
<exclude>META-INF/okio.kotlin_module</exclude>
<exclude>META-INF/services/com.fasterxml.jackson.core.JsonFactory</exclude>
</excludes>
</filter>
</filters>
<!-- Additional configuration. -->
<artifactSet>
<excludes>
<exclude>xpp3:xpp3</exclude>
</excludes>
</artifactSet>
<relocations>
<relocation>
<pattern>.apachemonspress</pattern>
<shadedPattern>.janelia.saalfeldlab..apachemonspress</shadedPattern>
</relocation>
<!-- Protect newer gson version from the old one preloaded by spark -->
<relocation>
<pattern>com.google.gson</pattern>
<shadedPattern>.janelia.saalfeldlab.google.gson</shadedPattern>
</relocation>
</relocations>
</configuration>
<!-- binds by default to package phase -->
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Maven shade end -->
</plugins>
</build>
</profile>
</profiles>
</project>
If i run my debugger in visual studio code, I can step through the dependency, but I cannot add print statements. I want to be able to edit the code in my dependency.
I can clone the github repo for the dependency, and run 'mvn clean package' to generate the .jar files.
Can I change my pom.xml to point towards my locally installed multiview-reconstruction github repo folder, and tell BigStitcher-Spark to use that for all the dependency calls? So that I can step through the multiview-reconstruction code and edit it as I go?
Share Improve this question edited Mar 15 at 17:56 aled 26k4 gold badges34 silver badges48 bronze badges asked Mar 15 at 16:15 MartinMartin 1,5924 gold badges43 silver badges91 bronze badges 4- 1 You seem to be confusing a git repository (which is local and not on GitHub) and a Maven repository. Different things. – aled Commented Mar 15 at 17:58
- The github repo in question (multiview-reconstruction) is the repo used to build and publish the package which maven installs – Martin Commented Mar 15 at 18:01
- Correct. Once you install the package into a Maven repository you can use it from your project. – aled Commented Mar 15 at 18:05
- I want to add System.out.println statements into my the multiview-reconstruction dependency, when I run the project as-is with the pom.xml, the .jar it downloads is read-only and I can't edit it. I'm trying to point my project pom.xml to a locally downloaded folder instead, where I can edit the files – Martin Commented Mar 15 at 18:16
1 Answer
Reset to default 1Eclipse supports "workspace resolution", which allows you to use different checked out projects as if they were dependencies in Maven. I don't think Visual Studio Code has such a feature.
The best idea I have would be to insert the print statements, build the project under a different version number and then use that version number for the dependency in your original project.