inst/doc/evaluate_and_upload.R

In EDIutils: An API Client for the Environmental Data Initiative Repository

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(EDIutils)

## ----eval=FALSE---------------------------------------------------------------
#  # 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"))

## ----eval=FALSE---------------------------------------------------------------
#  # Create reservation
#  identifier <- create_reservation(scope = "edi", env = "staging")
#  identifier
#  #> [1] 595

## ----eval=FALSE---------------------------------------------------------------
#  
#  # Evaluate data package
#  transaction <- evaluate_data_package(
#   eml = paste0(tempdir(), "/edi.595.1.xml"),
#   env = "staging")
#  transaction
#  #> [1] "evaluate_163966785813042760"
#  
#  # Check status
#  status <- check_status_evaluate(transaction, env = "staging")
#  status
#  #> [1] TRUE

## ----eval=FALSE---------------------------------------------------------------
#  # 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

## ----eval=FALSE---------------------------------------------------------------
#  # 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:
#  #> ...

## ----eval=FALSE---------------------------------------------------------------
#  # Create a new data package
#  transaction <- create_data_package(
#   eml = paste0(tempdir(), "/edi.595.1.xml"),
#   env = "staging")
#  transaction
#  #> [1] "create_163966765080210573__edi.595.1"
#  
#  # Check status
#  status <- check_status_create(
#   transaction = transaction,
#   env = "staging")
#  status
#  #> [1] TRUE

## ----eval=FALSE---------------------------------------------------------------
#  #' # Update data package
#  #' transaction <- update_data_package(
#  #'   eml = paste0(tempdir(), "/edi.595.2.xml"),
#  #'   env = "staging")
#  #' transaction
#  #' #> [1] "update_edi.595_163966788658131920__edi.595.2"
#  #'
#  #' # Check status
#  #' status <- check_status_update(
#  #'   transaction = transaction,
#  #'   env = "staging")
#  #' status
#  #' #> [1] TRUE