debian/artemis.install

@@ -3,4 +3,3 @@ jar_build/act.jar     		usr/share/java/
 jar_build/bamview.jar 		usr/share/java/
 jar_build/dnaplotter.jar	usr/share/java/
 debian/desktop/*.desktop	usr/share/applications/
-images/helix.png		usr/share/icons/hicolor/96x96/apps/

debian/artemis.poms

+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]*
+# where option can be:
+#   --ignore: ignore this POM and its artifact if any
+#   --ignore-pom: don't install the POM. To use on POM files that are created
+#     temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
+#   --no-parent: remove the <parent> tag from the POM
+#   --package=<package>: an alternative package to use when installing this POM
+#      and its artifact
+#   --has-package-version: to indicate that the original version of the POM is the same as the upstream part
+#      of the version for the package.
+#   --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
+#      during a clean operation with mh_cleanpom or mh_installpom
+#   --artifact=<path>: path to the build artifact associated with this POM,
+#      it will be installed when using the command mh_install. [mh_install]
+#   --java-lib: install the jar into /usr/share/java to comply with Debian
+#      packaging guidelines
+#   --usj-name=<name>: name to use when installing the library in /usr/share/java
+#   --usj-version=<version>: version to use when installing the library in /usr/share/java
+#   --no-usj-versionless: don't install the versionless link in /usr/share/java
+#   --dest-jar=<path>: the destination for the real jar.
+#     It will be installed with mh_install. [mh_install]
+#   --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
+#   --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
+#     Empty by default. [mh_install]
+#
+pom.xml --has-package-version

debian/control

@@ -4,13 +4,20 @@ Uploaders: Afif Elghraoui <afif@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
-               default-jdk-headless,
-               javahelper,
-               maven-debian-helper,
+               default-jdk,
+               maven-debian-helper (>= 2.1)
+Build-Depends-Indep: junit4 (>= 4.12),
+                     libbatik-java (>= 1.10),
+                     libcommons-lang3-java,
+                     libcommons-logging-java (>= 1.2),
+                     libcommons-net-java (>= 3.6),
+                     liblog4j1.2-java (>= 1.2.17),
+                     libmaven-antrun-plugin-java (>= 1.8),
+                     libmaven-install-plugin-java (>= 2.5.2),
+                     libmaven-shade-plugin-java (>= 3.1.1),
+                     libpostgresql-jdbc-java (>= 42.2.5),
+                     libslf4j-java (>= 1.7.25),
                      libmaven-enforcer-plugin-java,
-               libmaven-install-plugin-java,
-               libproperties-maven-plugin-java,
-               libmaven-antrun-plugin-java,
                      libmaven-resources-plugin-java,
                      libbuild-helper-maven-plugin-java,
                      libmaven-jar-plugin-java,
@@ -19,21 +26,9 @@ Build-Depends: debhelper (>= 12~),
                      libbiojava-java,
                      libj2ssh-java,
                      libibatis-java,
-               liblog4j1.2-java,
-               libpostgresql-jdbc-java,
                      picard-tools,
                      libhtsjdk-java,
-               libcommons-net-java,
-               libcommons-lang3-java,
-               libbatik-java,
                      jemboss,
-# For tests
-               ant,
-               ant-optional,
-               junit4,
-               libhamcrest-java,
-               libjs-jquery,
-# To convert gifs to png because gif is not a supported icon format
                      imagemagick
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/artemis

debian/maven.cleanIgnoreRules

+

debian/maven.ignoreRules

 # see https://lists.debian.org/debian-java/2019/01/msg00063.html
-org.jacoco jacoco-maven-plugin
-org.apache.maven.plugins maven-enforcer-plugin
+cglib cglib-nodep * * * *
+org.apache.maven.plugins maven-jarsigner-plugin * * * *
+org.apache.maven.plugins maven-javadoc-plugin * * * *
+org.codehaus.mojo properties-maven-plugin * * * *
+org.evosuite evosuite-standalone-runtime * * * *
+org.jacoco jacoco-maven-plugin * * * *
+org.mockito mockito-core * * * *

debian/maven.properties

+# Include here properties to pass to Maven during the build.
+# For example:
+# maven.test.skip=true
+# project.build.sourceEncoding=UTF-8
+

debian/maven.publishedRules

+

debian/maven.rules

+junit junit jar s/4\..*/4.x/ * *
+uk.ac.sanger artemis jar s/.*/debian/ * *
+commons-logging s/commons-logging-api/commons-logging/ * s/.*/debian/ * *
+log4j log4j * s/1\.2\..*/1.2.x/ * *
+org.apache.maven.plugins maven-enforcer-plugin * s/.*/debian/ * *
+org.apache.rat apache-rat-plugin * s/.*/debian/ * *
+org.codehaus.plexus plexus-container-default * * * *

debian/patches/maven_depencencies.patch

---- a/pom.xml
-+++ b/pom.xml
-@@ -360,7 +360,6 @@ Artemis is written in Java, and is avail
-                 <inherited>true</inherited>
-                 <groupId>org.apache.maven.plugins</groupId>
-                 <artifactId>maven-enforcer-plugin</artifactId>
--                <version>1.3.1</version>
-                 <executions>
-                     <execution>
-                         <id>enforce-maven-3</id>
-@@ -499,7 +498,6 @@ Artemis is written in Java, and is avail
- 			<plugin>
- 		    		<groupId>org.apache.maven.plugins</groupId>
- 		    		<artifactId>maven-resources-plugin</artifactId>
--		    		<version>3.0.2</version>
- 		    		<executions>
- 		      		<!--  Copy etc on to classpath -->
- 		      		<execution>
-@@ -554,7 +552,6 @@ Artemis is written in Java, and is avail
- 			<plugin>
- 				<groupId>org.apache.maven.plugins</groupId>
- 				<artifactId>maven-jar-plugin</artifactId>
--				<version>3.1.0</version>
- 				<configuration>
- 					<archive>
- 						<manifest>
-@@ -616,55 +613,12 @@ Artemis is written in Java, and is avail
-                 </configuration>
-             </plugin>
-             
--            <!-- ===================================   Run Jacoco coverage report ======================================-->
--            
--            <plugin>
--				<groupId>org.jacoco</groupId>
--				<artifactId>jacoco-maven-plugin</artifactId>
--				<version>0.8.2</version>
--				<configuration>
--                    <skip>${skip.coverage.reporting}</skip>
--                </configuration>
--				<executions>
--					<execution>
--						<id>pre-unit-test</id>
--						<goals>
--							<goal>prepare-agent</goal>
--						</goals>
--						<configuration>
--							<output>file</output>
--							<!-- Sets the path to the file which contains the execution data. -->
--							<destFile>${project.build.directory}/jacoco-ut.exec</destFile>
--							<!-- Sets the name of the property containing the settings for JaCoCo 
--								runtime agent. -->
--							<propertyName>surefireArgLine</propertyName>
--						</configuration>
--					</execution>
--					<!-- Ensures that the code coverage report for unit tests is created after 
--						unit tests have been run. -->
--					<execution>
--						<id>post-unit-test</id>
--						<phase>test</phase>
--						<goals>
--							<goal>report</goal>
--						</goals>
--						<configuration>
--							<dataFile>${project.build.directory}/jacoco-ut.exec</dataFile>
--            					<outputDirectory>${project.build.directory}/coverage-report</outputDirectory>
--            					<excludes>
--        							<exclude>org/**</exclude>
--        						</excludes>
--						</configuration>
--					</execution>
--				</executions>
--			</plugin>
- 			
- 			<!-- ============= Package the code and dependent jars into one executable jar for each applications ========= -->
- 			
- 			<plugin>
- 				<groupId>org.apache.maven.plugins</groupId>
- 				<artifactId>maven-shade-plugin</artifactId>
--				<version>3.1.0</version>
- 				<executions>
- 					<execution>
- 						<id>package-win-artemis-jar</id>
-@@ -1005,66 +959,12 @@ Artemis is written in Java, and is avail
- 			</plugin>
- 			
- 			
--			<!-- ============================= Sign executable jar files ============================ -->
--			
--			<plugin>
--				<groupId>org.apache.maven.plugins</groupId>
--				<artifactId>maven-jarsigner-plugin</artifactId>
--				<version>1.4</version>
--				<executions>
--					<execution>
--						<id>sign-win-jars</id>
--						<phase>package</phase>
--						<goals>
--							<goal>sign</goal>
--						</goals>
--						<configuration>
--							<skip>${jarsigner.skip}</skip>
--							<verbose>false</verbose>
--							<processMainArtifact>false</processMainArtifact>
--							<processAttachedArtifacts>false</processAttachedArtifacts>
--							<archiveDirectory>target/win-jars</archiveDirectory>
--							<keystore>${signer-keystore-path}</keystore>
--							<storetype>${signer-keystore-type}</storetype>
--							<alias>${signer-keystore-alias}</alias>
--							<storepass>${signer-keystore-password}</storepass>
--							<keypass>${signer-keystore-password}</keypass>
--							<removeExistingSignatures>true</removeExistingSignatures>
--							<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
--						</configuration>
--					</execution>
--					<execution>
--						<id>sign-default-jars</id>
--						<phase>package</phase>
--						<goals>
--							<goal>sign</goal>
--						</goals>
--						<configuration>
--							<skip>${jarsigner.skip}</skip>
--							<verbose>false</verbose>
--							<processMainArtifact>false</processMainArtifact>
--							<processAttachedArtifacts>false</processAttachedArtifacts>
--							<archiveDirectory>target/jars</archiveDirectory>
--							<keystore>${signer-keystore-path}</keystore>
--							<storetype>${signer-keystore-type}</storetype>
--							<alias>${signer-keystore-alias}</alias>
--							<storepass>${signer-keystore-password}</storepass>
--							<keypass>${signer-keystore-password}</keypass>
--							<removeExistingSignatures>true</removeExistingSignatures>
--							<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
--						</configuration>
--					</execution>
--				</executions>
--				
--			</plugin>
--
- 
- 			<!-- ==========================   Create release zips ============================ -->
- 			
- 			<plugin>
- 				<groupId>org.apache.maven.plugins</groupId>
- 				<artifactId>maven-assembly-plugin</artifactId>
--				<version>3.1.0</version>
- 				<executions>
- 					<execution>
- 						<id>create-unix-release</id>
-@@ -1350,10 +1250,6 @@ Artemis is written in Java, and is avail
- 	        <properties>
- 	        		<skip.tests>false</skip.tests>
-         			<evosuite.exclude.filter></evosuite.exclude.filter>
--        			<jarsigner.skip>false</jarsigner.skip>
--        			<skip.artifact.creation>false</skip.artifact.creation>
--        			<skip.coverage.reporting>false</skip.coverage.reporting>
--        			<skip.javadoc>false</skip.javadoc>
-         			
- 	            <build.profile.id>release</build.profile.id>
- 	        </properties>  

debian/patches/series

@@ -2,4 +2,3 @@ samreader.patch
 use-lang3.patch
 #build-test.patch
 #disable-tests.patch
-maven_depencencies.patch

debian/rules

@@ -35,13 +35,17 @@ CLASSPATH += /usr/share/EMBOSS/jemboss/lib/jemboss.jar \
 export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))
 
 %:
-	dh $@ --with javahelper --buildsystem=maven
+	dh $@
 
 __override_dh_auto_build:
 	dh_auto_build -- jar
 	sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \
 		debian/artemis.manifest
-	convert images/helix.gif -resize 96x96\! images/helix.png
+
+override_dh_install:
+	dh_install
+	mkdir -p debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/
+	convert src/main/resources/images/helix.gif -resize 96x96\! debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/helix.png
 
 __override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))