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nameparser

An experimental parser for scientific names using javacc.

Obtain

Available from maven central as:

 <dependency>
     <groupId>org.filteredpush</groupId>
     <artifactId>nameparser</artifactId>
     <version>0.0.2</version>
 </dependency>

Development snapshots available from:

 https://oss.sonatype.org/content/repositories/snapshots/org/filteredpush/nameparser/

Using as a Java Library

Include the jar (build instructions below) on your classpath, or add as a maven dependency then:

import org.filteredpush.nameparser.generated.NameParse
import org.filteredpush.nameparser.sciname.ScientificName

From the NameParse class you will want either the NameParse.parseToName(String scientificNameString) method which returns a ScientificName object for ease of handling, or NameParse.parseToMap(String scientificNameString) which returns a map of key value pairs, the keys of which may be unstable.

Example invocation:

ScientificName parsedName = NameParse.parseToName(String scientificNameString);
System.out.println(parsedName.getGenericEpithet());

Build

Generate sources using javacc (using the ph-javacc-maven-plugin, requires maven 3):

mvn process-resources

Build a jar file:

mvn clean process-resorces install

For debugging changes to the javacc file, it may be desirable to invoke javacc directly (and possibly also invoke javac directly):

 javacc -OUTPUT_DIRECTORY=target/generated-sources/javacc/org/filteredpush/nameparser/generated/ src/main/javacc/nameparse.jj
 javac -cp target/nameparser-0.0.2-SNAPSHOT.jar -d target/classes/org/filteredpush/nameparser/generated/ target/generated-sources/javacc/org/filteredpush/nameparser/generated/*.java

Run

java -jar target/nameparser-0.0.1-SNAPSHOT.jar < testnameset.txt

Developer deployment:

To deploy a snapshot to the snapshotRepository:

mvn clean deploy

To deploy a new release to maven central, set the version in pom.xml to a non-snapshot version, then deploy with the release profile (which adds package signing and deployment to release staging:

mvn clean deploy -P release

After this, you will need to login to the sonatype oss repository hosting nexus instance (https://oss.sonatype.org/index.html#welcome), find the staged release in the staging repositories, and perform the release.