bchemxtract

pkg:maven/org.beilstein/bchemxtract@1.4.1

Used in:

components

Overview
Overview

Versions
Versions

Dependents
Dependents

Dependencies
Dependencies

Overview

Description

A pure-Java extractor of ChemDraw structures.

<dependency>
    <groupId>org.beilstein</groupId>
    <artifactId>bchemxtract</artifactId>
    <version>1.4.1</version>
</dependency>

<?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/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<groupId>org.beilstein</groupId>
	<artifactId>bchemxtract</artifactId>
	<packaging>jar</packaging>
	<name>BChemXtract</name>
	<version>1.4.1</version>
	<url>https://github.com/Beilstein-Institut/BChemXtract</url>
	<description>A pure-Java extractor of ChemDraw structures.</description>

	<licenses>
		<license>
			<name>MIT License</name>
			<url>https://mit-license.org/</url>
		</license>
	</licenses>

	<developers>
		<developer>
			<name>Felix Bänsch</name>
			<email>open-source@beilstein-institut.de</email>
			<organization>Beilstein Institut</organization>
			<organizationUrl>https://github.com/Beilstein-Institut</organizationUrl>
		</developer>
		<developer>
			<name>Markus Nietfeld</name>
			<email>open-source@beilstein-institut.de</email>
			<organization>Beilstein Institut</organization>
			<organizationUrl>https://github.com/Beilstein-Institut</organizationUrl>
		</developer>
		<developer>
			<name>Udo Reschel</name>
			<email>open-source@beilstein-institut.de</email>
			<organization>Beilstein Institut</organization>
			<organizationUrl>https://github.com/Beilstein-Institut</organizationUrl>
		</developer>
	</developers>

	<scm>
		<connection>scm:git:git://github.com/Beilstein-Institut/BChemXtract</connection>
		<developerConnection>
			scm:git:ssh://github.com/Beilstein-Institut/BChemXtract</developerConnection>
		<url>https://github.com/Beilstein-Institut/BChemXtract</url>
	</scm>


	<properties>
		<cdk.version>2.12</cdk.version>
		<maven.compiler.source>17</maven.compiler.source>
		<maven.compiler.target>17</maven.compiler.target>
		<java.version>17</java.version>
		<source.encoding>UTF-8</source.encoding>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<bchemlookup.abbreviations.url>https://raw.githubusercontent.com/Beilstein-Institut/BChemLookup/main/abbreviations.smi</bchemlookup.abbreviations.url>
	</properties>


	<build>

		<resources>
			<resource>
				<directory>src/main/java</directory>
				<excludes>
					<exclude>**/*.java</exclude>
					<exclude>**/package.html</exclude>
				</excludes>
			</resource>
			<resource>
				<directory>src/main/resources</directory>
			</resource>
		</resources>

		<testResources>
			<testResource>
				<directory>src/test/java</directory>
				<excludes>
					<exclude>**/*.java</exclude>
					<exclude>**/package.html</exclude>
				</excludes>
			</testResource>
			<testResource>
				<directory>src/test/resources</directory>
			</testResource>
		</testResources>

		<plugins>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-source-plugin</artifactId>
				<version>3.4.0</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>3.12.0</version>
				<executions>
					<execution>
						<id>attach-javadocs</id>
						<goals>
							<goal>jar</goal>
						</goals>
					</execution>
				</executions>
			</plugin>


			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.15.0</version>
				<configuration>
					<release>${java.version}</release>
					<encoding>${source.encoding}</encoding>
				</configuration>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-resources-plugin</artifactId>
				<version>3.5.0</version>
				<configuration>
					<encoding>${source.encoding}</encoding>
				</configuration>
			</plugin>

			<!-- abbreviations.smi is curated upstream in Beilstein-Institut/BChemLookup.
			     On every build we fetch the current list and prepend it to the
			     checked-in copy, which therefore serves two purposes: offline/CI
			     fallback when the download fails (ignoreerrors), and home for
			     entries not (yet) upstream. SMILESLookupReader uses putIfAbsent on
			     the lowercased key, so on a duplicate key upstream wins. -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-antrun-plugin</artifactId>
				<version>3.1.0</version>
				<executions>
					<execution>
						<id>fetch-upstream-abbreviations</id>
						<phase>process-resources</phase>
						<goals>
							<goal>run</goal>
						</goals>
						<configuration>
							<target>
								<mkdir dir="${project.build.directory}/bchemlookup"/>
								<get src="${bchemlookup.abbreviations.url}" dest="${project.build.directory}/bchemlookup/abbreviations.smi" usetimestamp="true" ignoreerrors="true" verbose="false"/>
								<concat destfile="${project.build.outputDirectory}/org/beilstein/chemxtract/lookups/abbreviations.smi" encoding="UTF-8" outputencoding="UTF-8" fixlastline="true">
									<fileset file="${project.build.directory}/bchemlookup/abbreviations.smi"/>
									<fileset file="${project.basedir}/src/main/resources/org/beilstein/chemxtract/lookups/abbreviations.smi"/>
								</concat>
							</target>
						</configuration>
					</execution>
				</executions>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>3.5.6</version>
				<dependencies>
					<!-- P-9 fix: pin the full junit-platform triplet (launcher + engine +
					     commons) to the JUnit-6-aligned (6.0.3) version, overriding
					     Surefire 3.5.5's transitive 1.12.x bundle pulled via
					     surefire-junit-platform; see apache/maven-surefire#3216.
					     Pinning launcher alone is insufficient because Surefire's fork
					     classpath construction loaded both 6.0.3 and 1.12.2 jars,
					     producing OutputDirectoryCreator-not-available at discovery.
					     Maven plugin <dependencies> do NOT honor the project's
					     <dependencyManagement> (BOM imports), so versions are explicit
					     literals here — keep them in lock-step with the junit-bom version
					     above. -->
					<dependency>
						<groupId>org.junit.platform</groupId>
						<artifactId>junit-platform-launcher</artifactId>
						<version>6.1.3</version>
					</dependency>
					<dependency>
						<groupId>org.junit.platform</groupId>
						<artifactId>junit-platform-engine</artifactId>
						<version>6.1.3</version>
					</dependency>
					<dependency>
						<groupId>org.junit.platform</groupId>
						<artifactId>junit-platform-commons</artifactId>
						<version>6.1.3</version>
					</dependency>
					<!-- Run Jupiter tests via the JUnit Platform provider -->
					<dependency>
						<groupId>org.apache.maven.surefire</groupId>
						<artifactId>surefire-junit-platform</artifactId>
						<version>3.5.6</version>
					</dependency>
				</dependencies>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-site-plugin</artifactId>
				<version>3.22.0</version>
				<configuration>
					<siteDirectory>doc</siteDirectory>
					<inputEncoding>${source.encoding}</inputEncoding>
				</configuration>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-assembly-plugin</artifactId>
				<version>3.8.0</version>
				<configuration>
					<archive>
						<manifest>
							<mainClass>
								org.beilstein.chemxtract.samples.BCXTractSubstances</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
				</configuration>
				<executions>
					<execution>
						<id>make-assembly</id>
						<!-- bind to the packaging phase -->
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

			<plugin>
				<groupId>com.diffplug.spotless</groupId>
				<artifactId>spotless-maven-plugin</artifactId>
				<version>3.9.0</version>
				<configuration>
					<java>
						<googleJavaFormat/>
						<licenseHeader>
							<file>${project.basedir}/doc/license-header/License-header.txt</file>
						</licenseHeader>
						<removeUnusedImports/>
						<trimTrailingWhitespace/>
						<endWithNewline/>
						<formatAnnotations/>
						<encoding>UTF-8</encoding>
					</java>
				</configuration>
				<executions>
					<execution>
						<goals>
							<goal>check</goal>
						</goals>
						<phase>package</phase>
					</execution>
				</executions>
			</plugin>

			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>0.8.15</version>
				<executions>
					<execution>
						<id>prepare-agent</id>
						<goals>
							<goal>prepare-agent</goal>
						</goals>
					</execution>
					<execution>
						<id>report</id>
						<phase>verify</phase>
						<goals>
							<goal>report</goal>
						</goals>
					</execution>
				</executions>
			</plugin>
		</plugins>

	</build>

	<profiles>
		<!--
			Quality profile: runs Checkstyle, PMD and SpotBugs. Activate with
			`mvn -Pquality verify`. All gates FAIL the build on violations. Kept
			off the default lifecycle so day-to-day developer builds stay fast.
			Dependency CVE scanning is handled in CI by Trivy (security.yml).
		-->
		<profile>
			<id>quality</id>
			<build>
				<plugins>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-checkstyle-plugin</artifactId>
						<version>3.6.0</version>
						<dependencies>
							<dependency>
								<groupId>com.puppycrawl.tools</groupId>
								<artifactId>checkstyle</artifactId>
								<version>13.10.0</version>
							</dependency>
						</dependencies>
						<configuration>
							<configLocation>${project.basedir}/checkstyle.xml</configLocation>
							<suppressionsLocation>${project.basedir}/checkstyle-suppressions.xml</suppressionsLocation>
							<consoleOutput>true</consoleOutput>
							<failsOnError>true</failsOnError>
							<failOnViolation>true</failOnViolation>
							<!-- checkstyle.xml sets severity=warning globally; without this
							     the check goal only counts 'error' and never fails. -->
							<violationSeverity>warning</violationSeverity>
							<includeTestSourceDirectory>false</includeTestSourceDirectory>
						</configuration>
						<executions>
							<execution>
								<id>checkstyle-check</id>
								<phase>verify</phase>
								<goals>
									<goal>check</goal>
								</goals>
							</execution>
						</executions>
					</plugin>

					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-pmd-plugin</artifactId>
						<version>3.28.0</version>
						<configuration>
							<targetJdk>${java.version}</targetJdk>
							<failOnViolation>true</failOnViolation>
							<printFailingErrors>true</printFailingErrors>
							<includeTests>false</includeTests>
						</configuration>
						<executions>
							<execution>
								<id>pmd-check</id>
								<phase>verify</phase>
								<goals>
									<goal>check</goal>
								</goals>
							</execution>
						</executions>
					</plugin>

					<plugin>
						<groupId>com.github.spotbugs</groupId>
						<artifactId>spotbugs-maven-plugin</artifactId>
						<version>4.10.3.0</version>
						<configuration>
							<effort>Max</effort>
							<threshold>Default</threshold>
							<failOnError>true</failOnError>
							<excludeFilterFile>${project.basedir}/spotbugs-exclude.xml</excludeFilterFile>
							<includeTests>false</includeTests>
						</configuration>
						<executions>
							<execution>
								<id>spotbugs-check</id>
								<phase>verify</phase>
								<goals>
									<goal>check</goal>
								</goals>
							</execution>
						</executions>
					</plugin>
				</plugins>
			</build>
		</profile>

		<!--
			Release profile: signs artifacts with GPG and publishes to Maven Central
			via the new Central Portal (central.sonatype.com).

			Required environment / GitHub Actions secrets:
			  MAVEN_GPG_PRIVATE_KEY  - ASCII-armored private key
			  MAVEN_GPG_PASSPHRASE   - passphrase
			  CENTRAL_USERNAME       - Central Portal user-token name
			  CENTRAL_PASSWORD       - Central Portal user-token value

			Activate with `mvn -Prelease deploy`.
		-->
		<profile>
			<id>release</id>
			<build>
				<plugins>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-gpg-plugin</artifactId>
						<version>3.2.8</version>
						<executions>
							<execution>
								<id>sign-artifacts</id>
								<phase>verify</phase>
								<goals>
									<goal>sign</goal>
								</goals>
								<configuration>
									<gpgArguments>
										<arg>--pinentry-mode</arg>
										<arg>loopback</arg>
									</gpgArguments>
								</configuration>
							</execution>
						</executions>
					</plugin>

					<plugin>
						<groupId>org.sonatype.central</groupId>
						<artifactId>central-publishing-maven-plugin</artifactId>
						<version>0.11.0</version>
						<extensions>true</extensions>
						<configuration>
							<publishingServerId>central</publishingServerId>
							<autoPublish>true</autoPublish>
							<waitUntil>published</waitUntil>
						</configuration>
					</plugin>
				</plugins>
			</build>
		</profile>
	</profiles>


	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>org.junit</groupId>
				<artifactId>junit-bom</artifactId>
				<version>6.1.3</version>
				<type>pom</type>
				<scope>import</scope>
			</dependency>
		</dependencies>
	</dependencyManagement>


	<dependencies>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-extra</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-depict</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-inchi</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-jniinchi-support</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-rinchi</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-fingerprint</artifactId>
			<version>${cdk.version}</version>
			<exclusions>
				<exclusion>
					<groupId>xml-apis</groupId>
					<artifactId>xml-apis</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<!--    <dependency>-->
		<!--      <groupId>org.openscience.cdk</groupId>-->
		<!--      <artifactId>cdk-bundle</artifactId>-->
		<!--      <version>${cdk.version}</version>-->
		<!--      <exclusions>-->
		<!--        <exclusion>-->
		<!--          <groupId>xml-apis</groupId>-->
		<!--          <artifactId>xml-apis</artifactId>-->
		<!--        </exclusion>-->
		<!--      </exclusions>-->
		<!--    </dependency>-->

		<!-- ================= Tests =========================== -->
		<!-- JUnit 6 (Jupiter) — version managed by junit-bom -->
		<dependency>
			<groupId>org.junit.jupiter</groupId>
			<artifactId>junit-jupiter</artifactId>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>org.mockito</groupId>
			<artifactId>mockito-core</artifactId>
			<version>5.23.0</version>
			<scope>test</scope>
		</dependency>

		<!-- Mockito Jupiter integration — provides MockitoExtension -->
		<dependency>
			<groupId>org.mockito</groupId>
			<artifactId>mockito-junit-jupiter</artifactId>
			<version>5.23.0</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>org.assertj</groupId>
			<artifactId>assertj-core</artifactId>
			<version>3.27.7</version>
			<scope>test</scope>
		</dependency>

		<!-- SLF4J is the logging facade. This is the ONLY logging artifact
		     consumers of this library inherit; they choose their own backend. -->
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>2.0.18</version>
		</dependency>

		<!-- Log4j2 backend for this project's own tests and the runnable
		     demo (fat) JAR. Marked optional so it is NOT forced onto library
		     consumers; optional deps stay on our own runtime/test classpath
		     and are still bundled by the assembly plugin. -->
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-core</artifactId>
			<version>2.26.1</version>
			<scope>runtime</scope>
			<optional>true</optional>
		</dependency>

		<!-- Log4j 2 provider for the SLF4J 2.x API (ServiceLoader-based). -->
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-slf4j2-impl</artifactId>
			<version>2.26.1</version>
			<scope>runtime</scope>
			<optional>true</optional>
		</dependency>


	</dependencies>


</project>

Metadata

Age:6 days ago

Licenses:

MIT License

Organization

org.beilstein

External Resources

Project URL

Source Control

Known Contributors

Markus NietfeldUdo ReschelFelix Bänsch

Sonatype GuideSee vulnerability infoView

bchemxtract

bchemxtract

Overview

Description

Snippets

Maven POM File

Metadata

Organization

External Resources

Known Contributors