improve zen4R action integration tests

r-geoflow · Sep 21, 2023 · cb00ae2 · cb00ae2
1 parent 394c0ed
commit cb00ae2
Show file tree

Hide file tree

Showing 2 changed files with 64 additions and 64 deletions.
diff --git a/inst/extdata/workflows/config_metadata_gsheets_zenodo_full.json b/inst/extdata/workflows/config_metadata_gsheets_zenodo_full.json
@@ -35,7 +35,7 @@
 		  },
 		  "properties": {
 		    "clean": {
-		      "run": true
+		      "run": false
 		    }
 		  }
 		}

diff --git a/tests/testthat/test_config_metadata_gsheets_zenodo_full.R b/tests/testthat/test_config_metadata_gsheets_zenodo_full.R
@@ -7,66 +7,66 @@ require(geoflow, quietly = TRUE)
 require(testthat)
 
 #execute - with publication & versioning
-# test_that("execute - with publication & versioning",{
-#   testthat::skip_on_cran()
-#   cfg_file_full = system.file("extdata/workflows/config_metadata_gsheets_zenodo_full.json", package = "geoflow")
-#   
-#   #deposit
-#   EXEC <- geoflow::executeWorkflow(cfg_file_full, 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")))
-#   expect_true(file.exists(file.path(EXEC, "config_copyof_contacts_1.csv")))
-#   expect_true(file.exists(file.path(EXEC, "config_copyof_entities_1.csv")))
-#   expect_true(dir.exists(file.path(EXEC, "entities")))
-#   expect_true(dir.exists(file.path(EXEC, "zenodo")))
-#   zenodo_files <- list.files(file.path(EXEC, "zenodo"))
-#   expect_equal(zenodo_files, c("zenodo_entities_1_with_pids_for_publication.csv",
-#                                "zenodo_geoflow_config_for_publication.json",
-#                                "zenodo_pids.csv"))
-#   
-#   config <- geoflow::initWorkflow(cfg_file_full, dir = ".")
-#   zenodo = config$software$output$zenodo
-#   
-#   zenodo_records <- as.data.frame(readr::read_csv(file.path(EXEC, "zenodo", "zenodo_pids.csv")))
-#   expect_equal(zenodo_records$Identifier, c("my-geoflow-zenodo-record1", "my-geoflow-zenodo-record2"))
-#   expect_equal(zenodo_records$Status, c("draft", "draft"))
-#   for(id in zenodo_records$Identifier){
-#     conceptdoi <- zenodo_records[zenodo_records$Identifier == id, "DOI_for_allversions"]
-#     rec <- zenodo$getDepositionByConceptDOI(conceptdoi)
-#     expect_is(rec, "ZenodoRecord")
-#   }
-#   
-#   #publication
-#   wd <- getwd()
-#   setwd(file.path(EXEC, "zenodo"))
-#   
-#   #modify files attached (publication of a new version requires new files each time)
-#   entities_filename <- "zenodo_entities_1_with_pids_for_publication.csv"
-#   src_entities <- as.data.frame(readr::read_csv(entities_filename))
-#   src_entities$Data <- sapply(1:nrow(src_entities), function(i){
-#     src_entity <- src_entities[i,]
-#     filename <- paste0(unlist(strsplit(geoflow::extract_cell_components(src_entity$Identifier)[1],"id:"))[2], "_", 
-#                        format(Sys.time(), "%Y%m%d%H%M%S"), ".csv")
-#     write.csv(src_entity, filename)
-#     outdata <- paste0("source:", filename, "@", tools::file_path_as_absolute(filename))
-#     return(outdata)
-#   })
-#   readr::write_csv(src_entities, entities_filename)
-#   
-#   #publication
-#   cfg_file_publish <- "zenodo_geoflow_config_for_publication.json"
-#   EXEC2 <- geoflow::executeWorkflow(cfg_file_publish, dir = ".")
-#   expect_true(dir.exists(EXEC2))
-#   setwd(wd)
-#   
-#   zenodo_published_records <- as.data.frame(readr::read_csv(file.path(EXEC2, "zenodo", "zenodo_pids.csv")))
-#   expect_equal(zenodo_published_records$Identifier, c("my-geoflow-zenodo-record1", "my-geoflow-zenodo-record2"))
-#   expect_equal(zenodo_published_records$Status, c("published", "published"))
-#   for(id in zenodo_published_records$Identifier){
-#     conceptdoi <- zenodo_published_records[zenodo_published_records$Identifier == id, "DOI_for_allversions"]
-#     rec <- zenodo$getRecordByConceptDOI(conceptdoi)
-#     expect_is(rec, "ZenodoRecord")
-#   }
-# 
-# })
+ test_that("execute - with publication & versioning",{
+   testthat::skip_on_cran()
+   cfg_file_full = system.file("extdata/workflows/config_metadata_gsheets_zenodo_full.json", package = "geoflow")
+
+   #deposit
+   EXEC <- geoflow::executeWorkflow(cfg_file_full, dir = ".")
+   expect_true(dir.exists(EXEC))
+   expect_true(file.exists(file.path(EXEC, "job.json")))
+   expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
+   expect_true(file.exists(file.path(EXEC, "config_copyof_contacts_1.csv")))
+   expect_true(file.exists(file.path(EXEC, "config_copyof_entities_1.csv")))
+   expect_true(dir.exists(file.path(EXEC, "entities")))
+   expect_true(dir.exists(file.path(EXEC, "zenodo")))
+   zenodo_files <- list.files(file.path(EXEC, "zenodo"))
+   expect_equal(zenodo_files, c("zenodo_entities_1_with_pids_for_publication.csv",
+                                "zenodo_geoflow_config_for_publication.json",
+                                "zenodo_pids.csv"))
+
+   config <- geoflow::initWorkflow(cfg_file_full, dir = ".")
+   zenodo = config$software$output$zenodo
+
+   zenodo_records <- as.data.frame(readr::read_csv(file.path(EXEC, "zenodo", "zenodo_pids.csv")))
+   expect_equal(zenodo_records$Identifier, c("my-geoflow-zenodo-record-test1", "my-geoflow-zenodo-record-test2"))
+   expect_equal(zenodo_records$Status, c("draft", "draft"))
+   for(id in zenodo_records$Identifier){
+     conceptdoi <- zenodo_records[zenodo_records$Identifier == id, "DOI_for_allversions"]
+     rec <- zenodo$getDepositionByConceptDOI(conceptdoi)
+     expect_is(rec, "ZenodoRecord")
+   }
+
+   #publication
+   wd <- getwd()
+   setwd(file.path(EXEC, "zenodo"))
+
+   #modify files attached (publication of a new version requires new files each time)
+   entities_filename <- "zenodo_entities_1_with_pids_for_publication.csv"
+   src_entities <- as.data.frame(readr::read_csv(entities_filename))
+   src_entities$Data <- sapply(1:nrow(src_entities), function(i){
+     src_entity <- src_entities[i,]
+     filename <- paste0(unlist(strsplit(geoflow::extract_cell_components(src_entity$Identifier)[1],"id:"))[2], "_", 
+                        format(Sys.time(), "%Y%m%d%H%M%S"), ".csv")
+     write.csv(src_entity, filename)
+     outdata <- paste0("source:", filename, "@", tools::file_path_as_absolute(filename))
+     return(outdata)
+   })
+   readr::write_csv(src_entities, entities_filename)
+
+   #publication
+   cfg_file_publish <- "zenodo_geoflow_config_for_publication.json"
+   EXEC2 <- geoflow::executeWorkflow(cfg_file_publish, dir = ".")
+   expect_true(dir.exists(EXEC2))
+   setwd(wd)
+
+   zenodo_published_records <- as.data.frame(readr::read_csv(file.path(EXEC2, "zenodo", "zenodo_pids.csv")))
+   expect_equal(zenodo_published_records$Identifier, c("my-geoflow-zenodo-record-test1", "my-geoflow-zenodo-record-test2"))
+   expect_equal(zenodo_published_records$Status, c("published", "published"))
+   for(id in zenodo_published_records$Identifier){
+     conceptdoi <- zenodo_published_records[zenodo_published_records$Identifier == id, "DOI_for_allversions"]
+     rec <- zenodo$getRecordByConceptDOI(conceptdoi)
+     expect_is(rec, "ZenodoRecord")
+   }
+
+ })