Standalone tool to download data in EMX or RDF format from molgenis servers. Download latest releases here.
java -jar downloader-1.2.jar -f filename.xlsx -u https://molgenis##.gcc.rug.nl/ -a account -p password my_test_entity
java -jar downloader-1.2.jar -f filename.zip -u https://molgenis##.gcc.rug.nl/ -a account -p password -o -s 1000 my_test_entity
java -jar downloader-1.2.jar -f filename.ttl --rdf --defaultNamespace ex:http://example.org/ -u https://molgenis##.gcc.rug.nl/ -a account -p password -o -s 1000 my_test_entity
| Option (* = required) | Description |
|---|---|
| -D, --dataOnly | Write only the data for the entities to the output file. |
| -a, --account | MOLGENIS username to login with to download the data. |
| -d, --debug | print debug logging to console |
| --defaultNamespace | The default namespace for newly created IRIs in RDF download. Format is prefix:namespace. Default value is mlg:http://molgenis.org/ |
| * -f, --outputFile | Name of the file to write the data to. |
| -i, --insecureSSL | Ignore SSL certicate chain errors and hostname mismatches. |
| --namespaces | A properties file containing namespace prefixes to add to the defaults. |
| -o, --overwrite | Overwrite the file if it exists. |
| -p, --password | Password for the MOLGENIS user to login |
| --rdf | Specifies that the output should be in RDF format instead of EMX. Implies that only data gets exported. |
| -s, --pageSize | The pagesize for the REST responses, increase in case of large datasets, maximum value=10000 |
| -t, --timeout | The socket timeout in seconds, default value is 60 |
| * -u, --url | URL of the MOLGENIS instance |
| -v, --version | Overrides the result from /api/v2/version |
- Entities to be downloaded should be added at the end of the command (see
my_test_entityin examples above). - Multiple entities can be specified separated by a whitespace.
- Entities linked to the specified entities (for example by XREF or MREF) are downloaded automatically in the case of an EMX export