Adding first dataset processing script to the repo

R/ErikaEgg/egg_script_1.R

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+library(arcticdatautils)
+library(dataone)
+library(EML)
+library(tidyverse)
+
+#get auth token
+
+cn <- CNode("PROD")
+adc <- getMNode(cn, "urn:node:ARCTIC")
+
+original_rm <- "resource_map_urn:uuid:1d762afa-8ee9-4afa-af60-f38bcee8d543"
+
+#get the most recent resource map
+all_versions <- get_all_versions(adc, original_rm)
+rm <- all_versions[length(all_versions)]
+
+#read in the metadata
+pkg <- get_package(adc, rm)
+doc <- read_eml(getObject(adc, pkg$metadata))
+
+#FAIR
+doc <- eml_add_publisher(doc)
+doc <- eml_add_entity_system(doc)
+
+#going through and uploading all the files in the zip
+gpr_file <- list.files("EAGER_GPR_Dataset", recursive = TRUE, full.names = TRUE)
+
+#update
+eml_validate(doc)
+
+eml_path <- "/home/egg/Tickets/Ticket 6 - Correa Rangel/cr_updated_eml.xml"
+write_eml(doc, eml_path)
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         resource_map_pid = pkg$resource_map,
+                         data_pids = c(pkg$data, unlist(data_pids)),
+                         metadata_path = eml_path,
+                         public = FALSE)
+
+##including metadata_path in last update overrode creating otherentities for the data objects, so loop to fix it
+gpr_entity <- list()
+for(i in 1:length(data_pids)){
+  en <- pid_to_eml_entity(adc, data_pids[[i]], entity_type = "otherEntity")
+  gpr_entity[[i]] <- en
+}
+doc$dataset$otherEntity[[i]] <- gpr_entity
+
+##another update
+eml_validate(doc)
+
+eml_path <- "/home/egg/Tickets/Ticket 6 - Correa Rangel/cr_updated_eml2.xml"
+write_eml(doc, eml_path)
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         resource_map_pid = pkg$resource_map,
+                         data_pids = pkg$data[-198],
+                         metadata_path = eml_path,
+                         public = FALSE)
+
+##remove the zip
+#did this in the above publish update
+
+##remove the zip's other entity
+doc$dataset$otherEntity[[1]] <- NULL
+
+##run project
+doc$dataset$project <- eml_nsf_to_project("1823717")
+
+##update sysmeta to say format of csv on the csv
+sysmeta <- getSystemMetadata(adc, "urn:uuid:ee35812b-4e81-4069-a244-a9ebce238e96")
+sysmeta@formatId <- "text/csv"
+updateSystemMetadata(adc, "urn:uuid:ee35812b-4e81-4069-a244-a9ebce238e96", sysmeta)
+
+##csv - add attributes
+data<-read.csv("EAGER_GPR.csv")
+atts <- EML::shiny_attributes(data = data)
+att_list <- EML::set_attributes(attributes = atts$attributes)
+phys <- arcticdatautils::pid_to_eml_physical(adc, pkg$data[[197]])
+
+dataTable_new <- eml$dataTable(entityName = "EAGER_GPR.csv",
+                               physical = phys,
+                               attributeList = att_list)
+
+doc$dataset$dataTable <- dataTable_new
+doc$dataset$otherEntity[[1]] <- NULL
+
+##another update - kept rerunning this one for subsequent updates, editing the eml path each time
+eml_validate(doc)
+
+eml_path <- "/home/egg/Tickets/Ticket 6 - Correa Rangel/cr_updated_eml9.xml"
+write_eml(doc, eml_path)
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         resource_map_pid = pkg$resource_map,
+                         data_pids = pkg$data,
+                         metadata_path = eml_path,
+                         public = FALSE)
+
+## fix meters (m) in abstract
+#did this in web editor
+
+##spatial
+#working with spatial files
+
+#checking out layers
+sf::st_layers("EAGER_GPR.kml")
+
+#reading the spatial file to find geometry and crs
+layer_38 <- sf::read_sf("EAGER_GPR.kml", layer = "38")
+View(layer_38)
+
+#if you want to find the entire list of accepted crs and how they should be formatted
+coord_list <- arcticdatautils::get_coord_list()
+
+## spatial atts
+"urn:uuid:a34c2206-1baf-4f3d-902d-4322f9892809"
+library(sf)
+data2 <- sf::read_sf("EAGER_GPR.kml")
+atts2 <- EML::shiny_attributes(data = data2)
+att_list2 <- EML::set_attributes(attributes = atts2$attributes)
+phys2 <- arcticdatautils::pid_to_eml_physical(adc, pkg$data[[119]])
+spatialVector <- pid_to_eml_entity(adc,
+                                   pkg$data[122],
+                                   entity_type = "spatialVector",
+                                   entityName = "EAGER_GPR.kml",
+                                   entityDescription = "Spatial vector containing GPR data",
+                                   attributeList = att_list2,
+                                   geometry = "Point",
+                                   spatialReference = list(horizCoordSysName = "GCS_WGS_1984"))
+doc$dataset$spatialVector <- spatialVector
+doc$dataset$otherEntity[[1]] <- NULL
+
+doc$dataset$spatialVector[[1]]$attributeList <- att_list2
+
+##adding 195 entity descriptions
+#make sure to change spatial vector from otherentity to spatialvector before running the below
+library(stringr)
+for(i in 1:length(doc$dataset$otherEntity)){
+  if (str_detect(doc$dataset$otherEntity[[i]]$entityName, ".cor")) {
+    doc$dataset$otherEntity[[i]]$entityDescription <- paste("GPS coordinates file for", str_remove(doc$dataset$otherEntity[[i]]$entityName, "\\.cor"))
+  } else if (str_detect(doc$dataset$otherEntity[[i]]$entityName, ".rad")) {
+    doc$dataset$otherEntity[[i]]$entityDescription <- paste("Acquisition parameter file for", str_remove(doc$dataset$otherEntity[[i]]$entityName, "\\.rad"))
+  } else {
+    doc$dataset$otherEntity[[i]]$entityDescription <- paste("Raw GPR data file for", str_remove(doc$dataset$otherEntity[[i]]$entityName, "\\.rd3"))
+  }
+}
+##define mhz, gps, kml in abstract
+#done on web editor
+
+##delete otherEntity of EAGER_GPR.kml and extra spatial vector
+doc$dataset$spatialVector[[4]] <- NULL
+doc$dataset$spatialVector[[3]] <- NULL
+doc$dataset$spatialVector[[2]] <- NULL
+doc$dataset$otherEntity[[195]] <- NULL
+
+##make sure it is SHA-1
+#loop
+for(i in 1:length(pkg$data)){
+  sysmeta <- getSystemMetadata(adc, pkg$data[i])
+  sysmeta@checksumAlgorithm <- "SHA-1"
+  updateSystemMetadata(adc, pkg$data[i], sysmeta)
+}
+
+##update physicals
+#csv
+"urn-uuid-ee35812b-4e81-4069-a244-a9ebce238e96"
+phys3 <- arcticdatautils::pid_to_eml_physical(adc, pkg$data[[196]])
+doc$dataset$dataTable$physical <- phys3
+
+#kml
+"urn:uuid:48f737a5-7b48-4465-83a0-8e7643b6ab16"
+phys4 <- arcticdatautils::pid_to_eml_physical(adc, pkg$data[[156]])
+doc$dataset$spatialVector$physical <- phys4
+
+#loop for otherEntities
+for (i in seq_along(doc$dataset$otherEntity)) {
+  otherEntity <- doc$dataset$otherEntity[[i]]
+  id <- otherEntity$id
+
+  if (!grepl("urn-uuid-", id)) {
+    warning("otherEntity ", i, " is not a pid")
+
+  } else {
+    id <- gsub("urn-uuid-", "urn:uuid:", id)
+    physical <- arcticdatautils::pid_to_eml_physical(adc, id)
+    doc$dataset$otherEntity[[i]]$physical <- physical
+  }
+}
+
+##fix typo in abstract - doing it this way because web editor causes duplicates of entities to be made
+doc$dataset$abstract$para[[1]] <- str_replace(doc$dataset$abstract$para[[1]], "estimated", "estimate")
+
+##set rights and access
+# Set ORCiD
+subject <- 'https://orcid.org/0000-0003-4934-7016'
+
+# 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$resource_map),
+                      subject = subject,
+                      permissions = c('read','write','changePermission'))
+
+##final publish
+update <- publish_update(adc,
+                         metadata_pid = pkg$metadata,
+                         data_pids = pkg$data,
+                         resource_map_pid = pkg$resource_map,
+                         metadata_path = eml_path,
+                         public = T,
+                         use_doi = T)