kelly code review

R/Kelly Wang/kelly-code-review.R

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+#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)