SWIFT ETL commands require that all data be entered into SWIFT templates. One SWIFT template must be used for each resource type to be ETLd. Typically, the primary resource type you are ETLing i (e.g. Plasmid) will require several secondary resource types (e.g. Person, Journal Article, ...) to be fully described in eagle-i -- the secondary resources will be linked from the primary resources.

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• You must always enter the Organization to which the resource is associated, either by name or by URI
  • It is best to use the Sweet to add the Organization (e.g. lab) to which these resources are associated, and then reference this name or URI in the files.
• If there is more than one value for a given column, enter values separated by ; (semicolon). Conversely, check your input file for the presence of ; in values that are not meant to be split and substitute for a different character.
• The first two columns (hidden) of a template are reserved for metadata. Please do not modify them.
• Every resource (primary or secondary) needs to have a name and a type as a minimum. For simplification, the type column is omitted if there are no possible subclasses (e.g. Person, Human Subject). If the template has a type column, you must enter a value.

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• Run the ETL process using dedicated credentials (e.g. create an "automated curator" user in your eagle-i repository), such that it is later possible to easily isolate resources that were bulk loaded.
• ETL needs a Level 4 role
• ETL first the secondary resource type files (i.e. linked resources), then the primary resource type file.

Special rules for embedded instances

Embedded resources are instances of Embedded Classes (see the eagle-i ontology browser). Embedded resources only make sense as part of a "containing" resource and as such they can only be created or updated as part of a creation or update operation for that resource. Examples of embedded classes are Construct Inserts (embedded in Constructs) or Diagnosis (embedded in Human Subjects).

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• In the template for the containing resource, enter a list of semicolon-separated labels for the embedded resources, and fill the type column . This will result in the creation of empty embedded resources
• ETL this file
• In order to ETL the rest of the properties for the embedded resource:
  • Generate a template/map for the embedded resource class
    • Templates generated for embedded classes will have two additional columns: Main Resource Name and Main Resource Type. 
  • Fill the template with the information for the embedded resource (one row per embedded resource), making sure the entries for Main Resource Name and Main Resource Type match the label  and type previously used when ETLing  the main resource.
  • Run the ETL command with the embedded resource file as input. Note that the -p and -eid parameters will be ignored if they are present.

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Examples

This Google Drive folder contains a few annotated examples of SWIFT templates with data.

Running the actual ETL

• Run the ETL process using dedicated credentials (e.g. create an "automated curator" user in your eagle-i repository), such that it is later possible to easily isolate resources that were bulk loaded.
• ETL needs a Level 4 role
• ETL first the secondary resource type files (i.e. linked resources), then the primary resource type file.

Post ETL tasks