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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:
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noformat |
mkdir ~/eagle-i
unzip -d ~/eagle-i eagle-i-datatools-swift-2.0MS3.01-dist.zip
cd ~/eagle-i/swift-2.0MS3.01 |
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To generate etl templates and maps, navigate to the dedicated directory (above) and run the script:
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noformat |
./generate-inputs.sh -t typeURI
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- 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.
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ETL command for creating new resources:
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noformat |
./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL
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- This command will not attempt to determine if matching resources exist already in the eagle-i repository; it is therefore not idempotent - if it is applied two times with the same input file, duplicate resources will be created.
- The value of the
-p parameter indicates the desired workflow state for all resources - 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.
ETL command for replacing existing resources or creating new resources:
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noformat |
./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL -eid property-uri |
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| Info |
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If you are practicing the ETL process, you may wish to upload your data to the common eagle-i training node. For example, if your directory is named dataDirectory and you wish to practice creating new resources, the script would be executed as follows (default workflow state is DRAFT): | Code Block |
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| noformat | ./ETLer.sh -d dataDirectory -c L4:Level4 -r https://training.eagle-i.net
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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. |
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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:
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noformat |
./deETLer -f filename -c username:password -r repositoryURL
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Bulk Workflow
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):
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noformat |
./bulk-workflow -f filename -p DRAFT|CURATION|PUBLISH -c username:password -r repositoryURL
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Note the following limitations of bulk workflow:
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