gweaver-stream-io

pkg:maven/org.geneweaver/gweaver-stream-io@2.8.5

Used in: 4 components

Overview
Overview

Versions
Versions

Dependents
Dependents

Dependencies
Dependencies

Overview

Description

The IO bundle for Geneweaver.

Snippets

<dependency>
    <groupId>org.geneweaver</groupId>
    <artifactId>gweaver-stream-io</artifactId>
    <version>2.8.5</version>
</dependency>

Maven POM File


<!-- We can deploy to gene weaver jfrog artifcatory: https://geneweaver.jfrog.io/ui/login/ 
	Also to deploy to maven central: https://dzone.com/articles/publish-your-artifacts-to-maven-central -->
<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>org.geneweaver</groupId>
	<artifactId>gweaver-stream-io</artifactId>
	<packaging>jar</packaging>
	<version>2.8.5</version>
	<name>Geneweaver Stream IO</name>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<maven.compiler.target>17</maven.compiler.target>
		<maven.compiler.source>17</maven.compiler.source>
		<neo4j-ogm.version>3.2.37</neo4j-ogm.version>
		<deploy.repo.name>maven</deploy.repo.name>
		
		<deployJax>true</deployJax>
		<performRelease>false</performRelease>
	</properties>

	<description>The IO bundle for Geneweaver.</description>
	
	<inceptionYear>2020</inceptionYear>
	<url>http://www.geneweaver.org</url>
	<organization>
		<name>Jackson Laboratory</name>
		<url>http://www.jax.org</url>
	</organization>
	<licenses>
		<license>
			<name>Apache 2</name>
			<url>https://www.apache.org/licenses/LICENSE-2.0</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<developers>
		<developer>
			<id>gerrim</id>
			<name>Matthew Gerring</name>
			<url>https://www.jax.org/people/matthew-gerring</url>
		</developer>
	</developers>

	<contributors>
		<contributor>
			<name>None</name>
		</contributor>
	</contributors>

	<scm>
		<connection>scm:git:https://bitbucket.org/geneweaver/gweaver-stream-io/src/master/</connection>
		<developerConnection>scm:git:ssh://git@bitbucket.org:geneweaver/gweaver-stream-io.git</developerConnection>
		<tag>gweaver-stream-io-2.8.5</tag>
		<url>https://www.geneweaver.org</url>
	</scm>
	<ciManagement>
		<system>None</system>
	</ciManagement>

	<dependencies>

		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.7</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/commons-beanutils/commons-beanutils -->
		<dependency>
			<groupId>commons-beanutils</groupId>
			<artifactId>commons-beanutils</artifactId>
			<version>1.9.4</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.google.guava/guava -->
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<version>31.1-jre</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/junit/junit -->
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.13</version>
			<scope>test</scope>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>1.7.21</version>
		</dependency>

		<!-- NEEDED FOR DOMAIN -->
		<!-- https://mvnrepository.com/artifact/org.neo4j/neo4j-ogm-core -->
		<dependency>
			<groupId>org.neo4j</groupId>
			<artifactId>neo4j-ogm-core</artifactId>
			<version>${neo4j-ogm.version}</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
		<dependency>
		    <groupId>commons-cli</groupId>
		    <artifactId>commons-cli</artifactId>
		    <version>1.4</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-csv</artifactId>
			<version>1.10.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-compress</artifactId>
			<version>1.20</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
		<dependency>
			<groupId>org.apache.poi</groupId>
			<artifactId>poi</artifactId>
			<version>5.2.3</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
		<dependency>
		    <groupId>com.h2database</groupId>
		    <artifactId>h2</artifactId>
		    <version>2.1.214</version>
		</dependency>	
			
		<!-- https://mvnrepository.com/artifact/org.jetbrains.bio/big -->
		<dependency>
		    <groupId>org.jetbrains.bio</groupId>
		    <artifactId>big</artifactId>
		    <version>0.9.1</version>
		</dependency>
	
		<!-- https://mvnrepository.com/artifact/com.github.samtools/htsjdk -->
		<!-- Contains readers which work with streams
		<dependency>
		    <groupId>com.github.samtools</groupId>
		    <artifactId>htsjdk</artifactId>
		    <version>2.24.1</version>
		</dependency>
		 -->

		<!-- https://mvnrepository.com/artifact/uk.co.jemos.podam/podam -->
		<dependency>
			<groupId>uk.co.jemos.podam</groupId>
			<artifactId>podam</artifactId>
			<version>7.2.10.RELEASE</version>
			<scope>test</scope>
		</dependency>

	</dependencies>

	<build>
		<plugins>
			
			<plugin>
		    <groupId>cz.habarta.typescript-generator</groupId>
		    <artifactId>typescript-generator-maven-plugin</artifactId>
		    <version>3.2.1263</version>
		    <executions>
		        <execution>
		            <id>generate</id>
		            <goals>
		                <goal>generate</goal>
		            </goals>
		            <phase>process-classes</phase>
		        </execution>
		    </executions>
		    <configuration>
		        <jsonLibrary>jackson2</jsonLibrary>
		        <classes>
                               <class>org.geneweaver.domain.Located</class>
                                <class>org.geneweaver.domain.Entity</class>
                                <class>org.geneweaver.domain.AbstractEntity</class>
                                <class>org.geneweaver.domain.GeneticEntity</class>
                                <class>org.geneweaver.domain.Gene</class>
                                <class>org.geneweaver.domain.Peak</class>
                                <class>org.geneweaver.domain.NamedEntity</class>
                                <class>org.geneweaver.domain.Variant</class>
		        </classes>
		        <outputKind>module</outputKind>
		    </configuration>
		</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.6.0</version>
				<configuration>
					<fork>true</fork>
					<compilerArgs>
						<arg>-Xlint:unchecked</arg>
					</compilerArgs>
					<source>${maven.compiler.source}</source>
					<target>${maven.compiler.target}</target>
					<encoding>UTF-8</encoding>
					<forceJavacCompilerUse>true</forceJavacCompilerUse>
				</configuration>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.22.1</version>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-checkstyle-plugin</artifactId>
				<version>3.1.1</version>
				<configuration>
					<encoding>UTF-8</encoding>
					<configLocation>src/main/resources/checkstyle/checkstyle-rules.xml</configLocation>
					<headerLocation>src/main/resources/checkstyle/header.txt</headerLocation>
					<consoleOutput>true</consoleOutput>
					<failsOnError>true</failsOnError>
				</configuration>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-source-plugin</artifactId>
				<version>3.1.0</version>
				<executions>
					<execution>
						<id>attach-sources</id>
						<goals>
							<goal>jar</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>3.0.1</version>
				<configuration>
					<additionalparam>-Xdoclint:none</additionalparam>
					<doclint>none</doclint>
					<failOnError>false</failOnError>
				</configuration>
				<executions>
					<execution>
						<id>attach-javadocs</id>
						<goals>
							<goal>jar</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-assembly-plugin</artifactId>
				<version>3.1.1</version>

				<configuration>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
					<archive>
						<manifest>
							<mainClass>org.geneweaver.io.CLI</mainClass>
						</manifest>
					</archive>
				</configuration>

				<executions>
					<execution>
						<id>assemble-all</id>
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
					</execution>
				</executions>

			</plugin>

			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>0.8.12</version>
				<executions>
					<execution>
						<goals>
							<goal>prepare-agent</goal>
						</goals>
					</execution>
					<execution>
						<id>report</id>
						<phase>prepare-package</phase>
						<goals>
							<goal>report</goal>
						</goals>
					</execution>
					<!-- Threshold -->

					<execution>
						<id>jacoco-check</id>
						<goals>
							<goal>check</goal>
						</goals>
						<configuration>
							<rules>
								<rule>
									<element>PACKAGE</element>
									<excludes>
										<!-- Exceptions do not need tests usually. -->
										<exclude>*Exception</exclude>

										<!-- This is tested throughly in geweaver-bulk-import -->
										<exclude>org.geneweaver.io.connector</exclude>

									</excludes>

									<limits>
										<limit>
											<counter>LINE</counter>
											<value>COVEREDRATIO</value>
											<minimum>80%</minimum>
										</limit>
									</limits>
								</rule>
							</rules>
						</configuration>
					</execution>

				</executions>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-release-plugin</artifactId>
				<version>2.5.3</version>
				<configuration>
					<localCheckout>true</localCheckout>
					<pushChanges>false</pushChanges>
					<mavenExecutorId>forked-path</mavenExecutorId>
        			<arguments>-DskipTests</arguments>
				</configuration>
			</plugin>
		</plugins>
		
		<extensions>
	      <extension>
	        <groupId>com.google.cloud.artifactregistry</groupId>
	        <artifactId>artifactregistry-maven-wagon</artifactId>
	        <version>2.2.2</version>
	      </extension>
	    </extensions>

	</build>

	<profiles>
	
    <profile>
        <id>jax-repository</id>
        <activation>
            <property>
                <name>deployJax</name>
                <value>true</value>
            </property>
        </activation>
        
        <repositories>
				    <repository>
				      <id>artifact-registry</id>
				      <url>artifactregistry://us-maven.pkg.dev/jax-cs-registry/${deploy.repo.name}</url>
				      <releases>
				        <enabled>true</enabled>
				      </releases>
				      <snapshots>
				        <enabled>true</enabled>
				      </snapshots>
				    </repository>
				</repositories>

				<distributionManagement>
		   	 	<snapshotRepository>
		     	 <id>artifact-registry</id>
		    	  <url>artifactregistry://us-maven.pkg.dev/jax-cs-registry/${deploy.repo.name}</url>
		   	 	</snapshotRepository>
		    	<repository>
		     	 <id>artifact-registry</id>
		     	 <url>artifactregistry://us-maven.pkg.dev/jax-cs-registry/${deploy.repo.name}</url>
		    	</repository>
				</distributionManagement>
		
				<build>
					<plugins>
					</plugins>
				</build>

    </profile>

		<!-- Full Release: https://dzone.com/articles/publish-your-artifacts-to-maven-central 
			http://tutorials.jenkov.com/maven/publish-to-central-maven-repository.html 
			https://central.sonatype.org/pages/releasing-the-deployment.html -->
		<!-- Normal snapshot: mvn deploy -->
		<!-- Might need to do: 
							export GPG_TTY=$(tty) see https://github.com/keybase/keybase-issues/issues/2798 -->
		<!-- Full Release:  mvn clean release:prepare release:perform -DdeployJax=false -DperformRelease=true 
		
		Remember that .m2/settings.xml must have JIRA password for sonatype.
		
		If using 'ZScaler' from JAX you will need to stop it or the certificate for oss.sonatype.org will not be 
		accepted.
		
		-->
		<profile>
			<id>release-sign-artifacts</id>
			<activation>
				<property>
					<name>performRelease</name>
					<value>true</value>
				</property>
			</activation>
			
			<distributionManagement>
				<snapshotRepository>
					<id>ossrh</id>
					<url>https://oss.sonatype.org/content/repositories/snapshots</url>
				</snapshotRepository>
				<repository>
					<id>ossrh</id>
					<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
				</repository>
			</distributionManagement>
			
			<build>
				<plugins>
				
					<plugin>
						<groupId>org.sonatype.plugins</groupId>
						<artifactId>nexus-staging-maven-plugin</artifactId>
						<version>1.7.0</version>
						<extensions>true</extensions>
						<configuration>
							<serverId>ossrh</serverId>
							<nexusUrl>https://oss.sonatype.org/</nexusUrl>
							<autoReleaseAfterClose>true</autoReleaseAfterClose>
						</configuration>
					</plugin>

					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-gpg-plugin</artifactId>
						<version>3.2.4</version>
						<executions>
							<execution>
								<id>sign-artifacts</id>
								<phase>verify</phase>
								<goals>
									<goal>sign</goal>
								</goals>
								
								<!--  Get from (where '-' IS TWO!!):       gpg -list-secret-keys -keyid-format=long 
									  Then name is after slash:
									
									sec   rsa4096/ABE36B913FF6D9EA 2025-01-02 [SC]
									      95D4F054EC94347B7B53877BABE36B913FF6D9EA
									uid                 [ultimate] Matthew Gerring (VoICE and Geneweaver developer) <matthew.gerring@gmail.com>
									ssb   rsa4096/6CF47BE2871A2EDA 2025-01-02 [E]
									
									Remember that .m2/settings.xml must have JIRA password for sonatype.
									
									If you forget the gpg key, can create a new one for signing using:
									1. gpg -full-generate-key  # '-' IS TWO!, use rsa 
									3. provide sec in this xml
									4. gpg -keyserver keyserver.ubuntu.com -send-keys <long key id> # '-' IS TWO!!
									5. provide key password during signing (below)
								-->
								<configuration>
        							<keyname>ABE36B913FF6D9EA</keyname>
        				</configuration>
							</execution>
						</executions>
					</plugin>
				</plugins>
			</build>
		</profile>
	</profiles>
	
</project>

Metadata

Age:3 months ago

Licenses:

Apache 2

Organization

org.geneweaver

External Resources

Project URL

Source Control

Known Contributors

NoneMatthew Gerring

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