diff --git a/R/Kelly Wang/kelly-code-review.R b/R/Kelly Wang/kelly-code-review.R new file mode 100644 index 0000000..0497c1e --- /dev/null +++ b/R/Kelly Wang/kelly-code-review.R @@ -0,0 +1,79 @@ +#ticket 20632 + +library(arcticdatautils) +library(dataone) +library(EML) +library(dplyr) +library(datapack) +library(ncdf4) + +rm <- "resource_map_urn:uuid:610b0253-5fa1-492b-a6af-abdd012ed325" +pkg <- get_package(adc, rm) +doc <- read_eml(getObject(adc, pkg$metadata)) + +# abstract: a number of the borehole +doc$dataset$abstract <- gsub("\\(C43-MS1\\)", "borehole with number C43-MS1", doc$dataset$abstract) +doc$dataset$abstract <- gsub("45 km", "45 kilometers (km)", doc$dataset$abstract) +doc$dataset$abstract <- gsub("5.2 m", "5.2 meters (m)", doc$dataset$abstract) + +# add decription of images +for (i in 2:length(doc$dataset$otherEntity)) { + doc$dataset$otherEntity[[i]]$entityDescription <- paste("Photographs of frozen cores for", substr(doc$dataset$otherEntity[[i]]$entityName, start = 30, stop = 40)) +} + +# remove attribute for otherEntity +for (i in 1:length(doc$dataset$otherEntity)) { + doc$dataset$otherEntity[[i]]$attributeList <- NULL +} + +# add physical +for (i in 1:length(doc$dataset$otherEntity)) { + id <- gsub("urn-uuid-", "urn:uuid:", doc$dataset$otherEntity[[i]]$id) + doc$dataset$otherEntity[[i]]$physical <- pid_to_eml_physical(adc, id) +} + +# add creator info +doc$dataset$creator[[2]]$electronicMailAddress <- "ecoscience@alaska.net" +doc$dataset$creator[[2]]$userId$directory <- "https://orcid.org" +doc$dataset$creator[[2]]$userId$userId <- "https://orcid.org/0000-0002-9834-8851" + +doc$dataset$creator[[3]]$electronicMailAddress <- "akliljedahl@alaska.edu" +doc$dataset$creator[[3]]$userId$directory <- "https://orcid.org" +doc$dataset$creator[[3]]$userId$userId <- "https://orcid.org/0000-0001-7114-6443" + +doc$dataset$creator[[4]]$electronicMailAddress <- "ronald.daanen@alaska.gov" +doc$dataset$creator[[4]]$userId$directory <- "https://orcid.org" +doc$dataset$creator[[4]]$userId$userId <- "https://orcid.org/0000-0001-7511-1491" +doc$dataset$creator[[4]]$individualName$givenName <- "Ronald P." + +# set contact = creator for MK +doc$dataset$contact <- doc$dataset$creator[[1]] +doc$dataset$contact$id <- NULL + +# set nsf +awards <- c("1722572", "1820883") %>% unlist() +doc$dataset$project <- eml_nsf_to_project(awards) + +# add FAIR +doc <- eml_add_publisher(doc) +doc <- eml_add_entity_system(doc) + +# methods: expand acronym +doc$dataset$methods$methodStep$description$para <- gsub("cu. in.", "cubic inches", doc$dataset$methods$methodStep$description$para) +doc$dataset$methods$methodStep$description$para <- gsub("h.p.", "horsepower", doc$dataset$methods$methodStep$description$para) +doc$dataset$methods$methodStep$description$para <- gsub("72 h", "72 hours", doc$dataset$methods$methodStep$description$para) + +# valid EML +eml_validate(doc) + +# write EML +eml_path <- "/home/kwang/MikhailK_JagoRiver/metadata.xml" +write_eml(doc, eml_path) + +# update EML +#update <- publish_update(adc, +# metadata_pid = pkg$metadata, +# resource_map_pid = pkg$resource_map, +# data_pids = pkg$data, +# metadata_path = eml_path, +# public = FALSE)