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SWIFT (Semantic Web Ingest from Tables) is a toolkit that allows experienced users to bulk-upload data into an eagle-i repository, via ETL (Extract, Transform and loadLoad). Currently the toolkit supports only spreadsheets as input files.

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The SWIFT toolkit is packaged as an executable jar, and can be downloaded from our software repository. We have also manually packaged a zip file that contains pre-generated templates and maps (currently only for version 1.7MS1.01.zip); the following is a temporary location, while we integrate the generation of this package into our build processes:

https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/dev-resources/eagleieagle-i-etl-dist-1.7MS17MS2.01.zip
Download the this SWIFT toolkit distribution, unzip it into a dedicated directory, and navigate to it, for example

Code Block
mkdir ~/eagle-i
unzip -d ~/eagle-i eagle-i-etl-dist-1.7MS17MS2.01.zip
cd eagle-i/eagle-i-etl-dist-1.7MS17M2.01


Input generation instructions

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At the moment a third input, mapfileinfo.properties, is not generated. The ETLer looks for it under the type and version subdirectory, e.g. ./maps/instrument_ont_v1.1.0/mapfileinfo.properties
The zip file contains pre-generated maps and templates for instruments, service, person and organization and ontology version 1.1.0, and a few types, and includes these property files. If you need to generate inputs for a different ontology version or a different type, please make sure to copy this property file to the appropriate subdirectory and edit it (mostly the version info).. We are working on automatically generating this file, this step will go away soon ;-)


ETL instructions

Warning

The ETLer expects data to be entered into one of the generated templates, and a few conventions to be respected (outside the scope of this guide) . A data curator usually makes sure that the template is correctly filled. In particular, the location of the resources to be ETLd (e.g. Lab or Core facility name) must be provided in every row of data and must correspind correspond to a location already entered in the eagle-i repository via SWEET.

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