The EDI data repository has a “staging” environment to test the upload and rendering of new data packages before publishing to “production”. These environments are functionally equivalent but the contained values are independent. For example, a data package identifier reserved by a user in “staging” will not work in “production” and vise versa.
Evaluation and upload to the repository requires data entities are described with EML metadata. There are many tools for creating EML, EDI supports two: the EMLassemblyline R package for programmatic workflows, and the ezEML web form wizard. Research groups managing large volumes of metadata may want to consider the LTER core-metabase.
Authentication is required by functions involving data evaluation and upload, audit report access, event notifications, and other account based features. Request an account from email@example.com. There are three options for authenticating:
# Interactively at the console login() #> User name: "my_name" #> User password: "my_secret" # Programmatically with function arguments login(userId = "my_name", userPass = "my_secret") # Programmatically with a file containing userId and userPass arguments login(config = paste0(tempdir(), "/config.txt"))
login() function exchanges credentials for a temporary (~10 hour) authentication token, which is written to the
EDI_TOKEN environment variable referenced by EDIutils functions requiring authentication.
Data package reservations prevent conflicting use of the same identifier.
Evaluation checks for metadata accuracy and completeness.
The evaluation report summary provides a quick look at the data package evaluation results. Specifically, the total number of checks run and how many of these checks resulted in statuses of “valid”, “info”, “warn”, or “error”.
# Summarize report read_evaluate_report_summary(transaction, env = "staging") #> =================================================== #> EVALUATION REPORT #> =================================================== #> #> PackageId: edi.595.1 #> Report Date/Time: 2021-12-16T22:49:25 #> Total Quality Checks: 29 #> Valid: 21 #> Info: 8 #> Warn: 0 #> Error: 0
The meaning of these status messages:
Any evaluation check that results in a warning or error status should be resolved before moving ahead (note that errors must be corrected). Resolve problems with the data and metadata and repeat the evaluation process until all errors (and preferably all warnings) are resolved.
The full evaluation report provides detailed information on each check and some diagnostics to help resolve issues. The full report can be printed to the console or written to file as plain text or as html to be viewed in a web browser (recommended). See
?read_evaluate_report for details.
# Read the evaluation report report <- read_evaluate_report(transaction, as = "char", env = "staging") message(report) #> =================================================== #> EVALUATION REPORT #> =================================================== #> #> PackageId: edi.595.1 #> Report Date/Time: 2021-12-16T08:17:40 #> Total Quality Checks: 29 #> Valid: 21 #> Info: 8 #> Warn: 0 #> Error: 0 #> #> --------------------------------------------------- #> DATASET REPORT #> --------------------------------------------------- #> #> IDENTIFIER: packageIdPattern #> NAME: packageId pattern matches "scope.identifier.revision" #> DESCRIPTION: Check against LTER requirements for scope.identifier.revision #> EXPECTED: 'scope.n.m', where 'n' and 'm' are integers and 'scope' is one ... #> FOUND: edi.595.1 #> STATUS: valid #> EXPLANATION: #> SUGGESTION: #> REFERENCE: #> #> IDENTIFIER: emlVersion #> NAME: EML version 2.1.0 or beyond #> DESCRIPTION: Check the EML document declaration for version 2.1.0 or higher #> EXPECTED: eml://ecoinformatics.org/eml-2.1.0 or higher #> FOUND: https://eml.ecoinformatics.org/eml-2.2.0 #> STATUS: valid #> EXPLANATION: Validity of this quality report is dependent on this check ... #> SUGGESTION: #> REFERENCE: #> ...
The Evaluation Report is broken into multiple parts, always starting with the Dataset Report, and followed by an Entity Report for each entity (data object/file) included in the data package. These are differentiated by header lines with the Entity Name and Identifier.
The Dataset and Entity Reports share the same layout:
Parse through the document and address any errors or warnings (denoted by the Error and Warn labels). To understand why a quality check failed, first read the Name and Description of the quality check to determine what was being tested and how the test was being conducted. Then, compare the Expected result to what was Found. If it is still not clear what caused the failure, try to gain additional insight from the Explanation, Suggestion, and Reference fields, or contact the EDI Data Curation Team for clarification (firstname.lastname@example.org).
Upload after errors and warnings are fixed.
Update is the same as upload, but with an incremented data package version number (e.g. “edi.595.2” supersedes “edi.595.1”). NOTE: The new identifier must be added to the “packageId” element in the EML and as the new EML file name.
#' # Update data package #' transaction <- update_data_package( #' eml = paste0(tempdir(), "/edi.595.2.xml"), #' env = "staging") #' transaction #' #>  "update_edi.595_163966788658131920__edi.595.2" #' #' # Check status #' status <- check_status_update( #' transaction = transaction, #' env = "staging") #' status #' #>  TRUE
Once everything looks good in the “staging” environment, then repeat the above reservation and upload steps in the “production” environment where the data package will be assigned a DOI and made discoverable with other published data.