code sample from, Julia DiLena

R/JuliaDiLena/first code sample.R

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+library(dataone)
+library(arcticdatautils)
+library(tidyverse)
+library(reprex)
+library(EML)
+library(stringr)
+library(dataone)
+library(datamgmt)
+
+cn <- CNode("PROD")
+adc <- getMNode(cn, "urn:node:ARCTIC")
+
+#get resource map
+rm <- "resource_map_urn:uuid:eb8a029b-4f1c-4244-9ef3-1c181c6c2094"
+pkg <- get_package(adc, rm)
+
+#load in the metadata
+doc <- read_eml(getObject(adc, pkg$metadata))
+
+id_new <- arcticdatautils::update_object(adc, 
+                                         pid = "urn:uuid:d5cf2773-6081-4395-af51-a7c532b30fcf",
+                                         path = "Arctic_Data_Center_2017_2018_Biogeochemistry 3.csv",
+                                         format_id = "text/csv")
+
+physical <- arcticdatautils::pid_to_eml_physical(adc, id_new)
+
+doc <- read_eml(getObject(adc, pkg$metadata))
+doc$dataset$dataTable[[4]]$physical <- physical
+eml_validate(doc)
+
+
+eml_path <- "Pain_2019_Hydrogeochemistry.xml"
+write_eml(doc, eml_path)
+
+# Manually set ORCiD
+subject <- 'http://orcid.org/0000-0002-2873-3180'
+
+# Set ORCiD from EML creator
+
+# if more than 1 creator exists and you want the first one
+subject <- doc$dataset$creator[[1]]$userId$userId
+
+# As a convention we use `http:` instead of `https:` in our system metadata
+subject <- sub("^https://", "http://", subject)
+
+set_rights_and_access(adc, 
+                      pids = c(pkg$metadata, pkg$data, pkg$resource_map),
+                      subject = subject,
+                      permissions = c('read','write','changePermission'))
+
+update <- publish_update(adc, 
+                         metadata_pid = "urn:uuid:394bace0-ee04-4f4a-b21a-6ab99726ecaa",
+                         resource_map_pid = "resource_map_urn:uuid:3ddbe853-a40d-414d-b16b-51d3b6e50779",
+                         data_pids = c(pkg$data, id_new), # add new pid
+                         metadata_path = eml_path, 
+                         public = TRUE)
+
+all_ver <- get_all_versions(adc, 'urn:uuid:394bace0-ee04-4f4a-b21a-6ab99726ecaa')
+most_recent <- all_ver[length(all_ver)]
+most_recent
+
+update$resource_map
+
+all_ver_rm <- get_all_versions(adc, update$resource_map)
+most_recent_rm <- all_ver_rm[length(all_ver_rm)]
+most_recent_rm
+
+
+getSystemMetadata(adc, "urn:uuid:ef271d62-22f9-4866-9b76-1b042cf4bd8b")
+
+
+#keywords
+kw_list_1 <- eml$keywordSet(keyword = list("Greenland", "glacial meltwater", "stream water chemistry", "watersheds", "hydrology", "biogeochemistry", "hydrogeochemistry", "trace metals"))
+doc$dataset$keywordSet <- list(kw_list_1)
+
+rm <- "resource_map_urn:uuid:3ddbe853-a40d-414d-b16b-51d3b6e50779"
+pkg <- get_package(adc, rm)
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         data_pids = pkg$data,
+                         resource_map_pid = pkg$resource_map,
+                         metadata_path ="Pain_2019_Hydrogeochemistry.xml",
+                         public = T)
+
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         data_pids = pkg$data,
+                         resource_map_pid = pkg$resource_map,
+                         metadata_path = eml_path,
+                         public = T,
+                         use_doi = T)
+
+datamgmt::categorize_dataset("doi:10.18739/A2PC2T94T", c("glaciology", "atmosphere"), "Julia DiLena", overwrite = TRUE)