tests/testthat/test_config_metadata_gsheets_zenodo_full.R

In geoflow: Orchestrate Geospatial (Meta)Data Management Workflows and Manage FAIR Services

# test_config_metadata_gsheets_zenodo_full.R
# Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
#
# Description: Integration tests for config_metadata_gsheets_zenodo_full.json workflow
#=======================
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 = tempdir())
   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 = tempdir())
   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 = tempdir())
   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")
   }
 
 })