molgenis-downloader

Standalone tool to download data in EMX or RDF format from molgenis servers. Download latest releases here.

Example usages

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

Available options:

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_entity in 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