zenodo workflows integration tests

Author: eblondel

inst/extdata/workflows/config_metadata_zenodo.json

@@ -26,7 +26,7 @@
   	  "parameters": {
     		"url": "https://sandbox.zenodo.org/api",
     		"token": "{{ ZENODO_SANDBOX_TOKEN }}",
-    		"logger": "DEBUG"
+    		"logger": "INFO"
   	   }
   	 }
     ],

inst/extdata/workflows/config_metadata_zenodo_with_options.json

@@ -13,7 +13,7 @@
     "entities": [
       {
         "handler": "zenodo",
-        "source": ["10.5281/zenodo.2547036"],
+        "source": ["10.5281/zenodo.7552287"],
         "options": {
           "resource_type": "record",
           "source_type": "doi"

inst/metadata/entity/entity_handler_zenodo.R

@@ -2,7 +2,7 @@
 handle_entities_zenodo <- function(handler, source, config, handle = TRUE){
 
   if(!requireNamespace("zen4R", quietly = TRUE)){
-    stop("The Dataverse handler requires the 'zen4R' package")
+    stop("The ZENODo handler requires the 'zen4R' package")
   }
 
   ZENODO <- config$software$input$zenodo
@@ -65,20 +65,21 @@ handle_entities_zenodo <- function(handler, source, config, handle = TRUE){
 
   entities <- lapply(1:length(results), function(i){
     result <- results[[i]]
-    result_doi = result$pids$doi$identifier
+    print(result)
+    result_doi = result$getDOI()
     config$logger.info(sprintf("Creating entity (%s out of %s) from Zenodo deposit/record with DOI '%s'", i, length(results), result_doi))
 
     #create entity
     entity <- geoflow::geoflow_entity$new()
     #entity Identifier
     entity$setIdentifier("doi", result_doi)
     #semantic identifier
-    identifiers = result$metadata$related_identifiers[sapply(result$metadata$related_identifiers, function(x){x$scheme == "urn" && x$relation == "isIdenticalTo"})]
+    identifiers = result$metadata$related_identifiers[sapply(result$metadata$related_identifiers, function(x){x$scheme == "other" && x$relation_type$id == "isidenticalto"})]
     if(length(identifiers)>0){
       identifier = identifiers[[1]]$identifier
       entity$setIdentifier("id", substr(identifier, 5,nchar(identifier)))
     }else{
-      entity$setIdentifier("id", gsub("/", "_", result_doi))
+      entity$setIdentifier("id", gsub("/", "_", result$getDOI()))
     }
 
     #entity Date

tests/testthat/test_config_metadata_zenodo.R

@@ -6,10 +6,11 @@
 require(geoflow, quietly = TRUE)
 require(testthat)
 
+cfg_file = system.file("extdata/workflows/config_metadata_zenodo.json", package = "geoflow")
+
 #init
 test_that("init",{
   testthat::skip_on_cran()
-  cfg_file = system.file("extdata/workflows/config_metadata_zenodo.json", package = "geoflow")
   CFG <- geoflow::initWorkflow(cfg_file)
   expect_is(CFG$metadata$content, "list")
   expect_equal(length(CFG$metadata$content), 1L)
@@ -27,7 +28,6 @@ test_that("init",{
 #debug
 test_that("debug",{
   testthat::skip_on_cran()
-  cfg_file = system.file("extdata/workflows/config_metadata_zenodo.json", package = "geoflow")
   DEBUG <- geoflow::debugWorkflow(cfg_file, entityIndex = 1, dir = ".")
   expect_equal(names(DEBUG), c("config", "entity"))
   expect_is(DEBUG$config, "list")
@@ -36,11 +36,10 @@ test_that("debug",{
 
 #execute
 test_that("execute",{
-  #testthat::skip_on_cran()
-  #cfg_file = system.file("extdata/workflows/config_metadata_zenodo.json", package = "geoflow")
+  testthat::skip_on_cran()
   #execution
-  #EXEC <- geoflow::executeWorkflow(cfg_file, dir = ".")
-  #expect_true(dir.exists(EXEC))
-  #expect_true(file.exists(file.path(EXEC, "job.json")))
-  #expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
+  EXEC <- geoflow::executeWorkflow(cfg_file, dir = ".")
+  expect_true(dir.exists(EXEC))
+  expect_true(file.exists(file.path(EXEC, "job.json")))
+  expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
 })

tests/testthat/test_config_metadata_zenodo_with_options.R

@@ -6,10 +6,11 @@
 require(geoflow, quietly = TRUE)
 require(testthat)
 
+cfg_file = system.file("extdata/workflows/config_metadata_zenodo_with_options.json", package = "geoflow")
+
 #init
 test_that("init",{
   testthat::skip_on_cran()
-  cfg_file = system.file("extdata/workflows/config_metadata_zenodo_with_options.json", package = "geoflow")
   CFG <- geoflow::initWorkflow(cfg_file)
   expect_is(CFG$metadata$content, "list")
   expect_equal(length(CFG$metadata$content), 1L)
@@ -27,21 +28,19 @@ test_that("init",{
 #debug
 test_that("debug",{
   testthat::skip_on_cran()
-  cfg_file = system.file("extdata/workflows/config_metadata_zenodo_with_options.json", package = "geoflow")
   DEBUG <- geoflow::debugWorkflow(cfg_file, entityIndex = 1, dir = ".")
   expect_equal(names(DEBUG), c("config", "entity"))
   expect_is(DEBUG$config, "list")
   expect_is(DEBUG$entity, "geoflow_entity")
-  expect_equal(DEBUG$entity$identifiers$doi, "10.5281/zenodo.3378733")
+  expect_equal(DEBUG$entity$identifiers$doi, "10.5281/zenodo.7552287")
 })
 
 #execute
 test_that("execute",{
-  #testthat::skip_on_cran()
-  #cfg_file = system.file("extdata/workflows/config_metadata_zenodo_with_options.json", package = "geoflow")
+  testthat::skip_on_cran()
   #execution
-  #EXEC <- geoflow::executeWorkflow(cfg_file, dir = ".")
-  #expect_true(dir.exists(EXEC))
-  #expect_true(file.exists(file.path(EXEC, "job.json")))
-  #expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
+  EXEC <- geoflow::executeWorkflow(cfg_file, dir = ".")
+  expect_true(dir.exists(EXEC))
+  expect_true(file.exists(file.path(EXEC, "job.json")))
+  expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
 })