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• Place your input files (i.e. the completed templates) in a directory of your choice, e.g. dataDirectory. All files contained in this directory will be processed by the ETLer.

• To run an ETL, execute one of the two following commands below. 
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• A detailed report of the ETL results is generated in the ./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.
• To further verify the data upload, log on to the SWEET application and select the lab to which the ETLd resources belong.
  

ETL command for creating new resources:

./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL

• 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 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

ETL command for replacing existing resources or creating new resources:

./ETLer.sh -d dataDirectory [-p DRAFT|CURATION|PUBLISH] -c username:password -r repositoryURL -eid property-uri

 

• Use this command if  the input file represents resources that have been previously uploaded or created in eagle-i

• The value of the -eid parameter (external identifier) is the URI of a property that uniquely identifies the resource outside eagle-i. This property will be used to match the input to a resource in the eagle-i repository. Grab the property URI from the ontology browser (expand the property name). Example properties are: 

   

   
  • Catalog number, -eid http://purl.obolibrary.org/obo/ERO_0001528
  • Inventory number, -eid http://purl.obolibrary.org/obo/ERO_0000044
  • RDFS label, use the shorthand syntax -eid label
• If the ETL process finds a matching resource, it will replace all its properties with the values from the input file; the URI of the matched resource will be preserved.
• If the ETL process does not find a matching resource, a new resource will be created.
• The value of the -p parameter indicates the desired workflow state for newly created resources. Existing resources will retain their workflow state.

Practicing ETL

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./ETLer.sh -d dataDirectory  -c L4:Level4 -r https://training.eagle-i.net

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De-ETL

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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