User Manual

Running the Metadata-Manager can be performed by command line by invoking the following line:

java –jar Metadata-Manager-1.0-SNAPSHOT-jar-with-dependencies.jar configuration_xml_path gmql_conf_folder

(assuming the compiled Scala code is in Metadata-Manager.jar)

where:

• configuration_xml_path is the location for the configuration file
• gmql_conf_folder contains the path to the folder with corresponding variables to start GMQLRepository service.

Optional following arguments can be:

• log: shows the number of executions already performed and stored in the database);
• log –n (where n is the n-th last execution): the statistical summary for that run is shown. Multiple runs can be requested at the same time by separating them with comma. For example log -1, 2, 3 will show the last execution’s statistics, plus the statistics for the 2 executions done before (if they exist). When input numbers are not valid user is notified.
• –retry Metadata-Manager tries to download the failed files on the local datasets (when download is enabled).

Inside the project, we also provide two other small tools, which can be run in the following ways:

• Rule Base Generator: java -cp Metadata-Manager-1.0-SNAPSHOT-jar-with-dependencies.jar it.polimi.genomics.metadata.cleaner.RuleBaseGenerator transformed_files_directory rules_file key_files_directory

  where:

  • transformed_files_directory is the folder of the transformed files.
  • rules_file is the file that contains the Rule Base
  • key_files_directory contains the seen keys, all keys and unseen keys files.

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