The toolkit described herein is currently not user-friendly (though it works well – we use it routinely to bulk-upload data for the Consortium members). If you encounter issues, please do not hesitate to contact us. |
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 Load). The figure below is a high level depiction of the ETL process. Currently the toolkit supports only Excel spreadsheets as input files.
This guide provides an overview of tasks pertaining to ETL and the usage of the SWIFT toolkit. The ETL workflow requires a person with domain knowledge and understanding of the eagle-i resource ontology to prepare the input files for optimal upload, and a person with basic knowledge of Unix to run the commands and troubleshoot potential errors. A detailed description is provided in: Data preparation and ETL Workflow
The SWIFT toolkit is comprised of:
The SWIFT Toolkit requires:
The SWIFT toolkit is packaged as a zip file, and can be downloaded from our software repository.
Download the SWIFT toolkit distribution that matches the version of your eagle-i repository, named eagle-i-datatools-swift-[version]-dist.zip
, Unzip it into a dedicated directory, and navigate to it. For example
mkdir ~/eagle-i unzip -d ~/eagle-i eagle-i-datatools-swift-2.0MS3.01-dist.zip cd ~/eagle-i/swift-2.0MS3.01 |
To generate etl templates and maps, navigate to the dedicated directory (above) and run the script:
./generate-inputs.sh -t typeURI |
*You may obtain the type URI from the eagle-i ontology browser . Use the left bar to find the most specific type you need, select it and grab its URI, e.g. http://purl.obolibrary.org/obo/ERO_0000229 for Monoclonal Antibodies.
Innocuous warnings are produced when generating the templates; these may safely be ignored. If you encounter errors or issues, please do not hesitate to contact us. |
This script will create/use two directories with obvious meanings: ./maps
and ./templates.
The ETLer expects data to be entered into one of the generated templates, and a few conventions to be respected (see Data preparation and ETL Workflow) . 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. |
dataDirectory
. All files contained in this directory will be processed by the ETLer.To run an ETL, execute one of the two following commands.
For creating new resources:
./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL |
Note that all resources will be uploaded in the requested workflow state - we recommend to choose CURATION, verify the resources were ETLd correctly, and then publish using the bulk workflow command (see below). If you've already ran a test ETL in a staging environment, choose PUBLISH directly.
For replacing existing resources:
./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL -eid property-uri |
If you are practicing the ETL process, you may wish to upload your data to the common eagle-i training node. In this case, if your directory is named dataDirectory, the script would be executed as follows (default workflow state is DRAFT):
Note that the data that is uploaded to the training node CAN be viewed and modified by others even in a draft state (even if you subsequently lock the records). Note also that the information in the training node is not persistent as the node is refreshed periodically. |
./logs
directory; please inspect it to verify that all rows were correctly uploaded. The RDF version of generated resources is also logged in this directory.Resources that are uploaded to an eagle-i repository via ETL are tagged with the name of the file from which they were extracted. It is therefore relatively simple to de-ETL an entire file. To do so, execute the following command:
./deETLer -f filename -c username:password -r repositoryURL |
Execute the following command to perform workflow actions (e.g. send to curation, publish, unpublish) on all resources ETLd from a particular file (i.e. resources that are tagged with the filename in the eagle-i repository):
./bulk-workflow -f filename -p DRAFT|CURATION|PUBLISH -c username:password -r repositoryURL |
Note the following limitations of bulk workflow: