Extracts MeSH descriptors and associated data from a given XML file into a SQL file which can be inserted into a MySQL database.
Go to https://github.com/ilios/mesh-parser/releases and download the latest JAR file.
If you want to build the mesh parser yourself then:
Run mvn package in the project's root directory.
This will generate an executable jar file mesh_parser-1.1.0-jar-with-dependencies.jar in the target sub-directory.
Run the jar file whilst providing a path to the MeSH descriptor file and the destination for the output SQL
$ java -jar mesh_parser-1.1.0-jar-with-dependencies.jar <mesh-descriptor-file> <sql-output-file>This will parse the given MeSH descriptor file and create the SQL file.
If you wish to test the SQL file an example database can be found in resources/db/schema/mesh_tables.sql
Input parameters:
- mesh-descriptor-file ... location of the MeSH descriptor XML file
- sql-output-file ... location where the new SQL file should be written
- The DTD file corresponding to the MeSH descriptor file must be located in the same directory as the descriptor file.
- The sql-output-file should not exist before running the script, it will be created.