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Stand alone tool to download data in EMX format from molgenis servers

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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

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Stand alone tool to download data in EMX format from molgenis servers

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