Pubmed Parser

This project is an attempt to create a Java parser for the Pubmed XML as defined by the Pubmed DTD

The Pubmed Parser gives Java developers an efficient and standard way of mapping between Pubmed XML and Java code. Java developers using the Pubmed Parser are more productive because they can write less code themselves and do not have to be experts in parsing Pubmed XML.

The Pubmed Parser enables developers to perform the following operations:

Unmarshal Pubmed XML content into a Java representation
Access and update the Java representation
Marshal the Java representation of the Pubmed XML content back into XML content

Requirements

JDK 11
Apache Ant
Ensure JAVA_HOME and ANT_HOME variables are set in the environment and are also in the PATH

Build Instructions

This project has the JAXB libraries it needs included since they do not come bundled with the JDK anymore The sample pubmed.xml and pubmed.dtd are located in the schema/ folder The distribution jar is a unified/shaded/fat jar called pubmed-parser.jar created in the 'dist' folder

Run the following command to kick off a build, test, docs and assembly of the Pubmed Parser.

./build.sh

Java Docs

Javadocs for the PubmedParser and all the generated pubmed xml classes will be found under the docs folder

Java Class Usage

//Get XML File Content as a String
Path filePath = Path.of("pubmed.xml");
String fileContent = Files.readString(filePath);
    
//Create Pubmed Parser
//The PubmedParser is built to be thread-safe and should not need to be created more than once per Application
PubmedParser parser = new PubmedParser();

//Parse XML String Content into Java Object
PubmedArticleSet articleSet = parser.parse(fileContent, PubmedArticleSet.class);
    

//Stringify Java object back into a XML String
String xmlContent = parser.stringify(articleSet);

Shaded Jar Usage

Running the following command should validate the shaded jar against the sample pubmed.xml included

java -jar dist/pubmed-parser.jar schema/pubmed.xml

Current Limitations of the parser

Currently the DTD that is used to generate JAXB bindings and classes does not include the MathML related parts of the original Pubmed DTD
DTD Validation will be turned off by default in the Parser. You can turn it back on if needed by calling the right parameter in the parser method. However we have not tested it with being on.

License

Pubmed XML Parser is is licensed under a license - BSD 3.

Contributing

We use contribution policy, so please read it first before contributing

wisecubeai/pubmed-parser