diff --git a/R/Angel Chen/ticket #20492 Norman.R b/R/Angel Chen/ticket #20492 Norman.R new file mode 100644 index 0000000..9039c29 --- /dev/null +++ b/R/Angel Chen/ticket #20492 Norman.R @@ -0,0 +1,144 @@ +#ticket #20492 Norman +#Human dataset: +#https://arcticdata.io/catalog/#view/urn:uuid:c715fe12-6c05-4c27-8d00-b9c0c536c54b + +pkg <- get_package(adc, 'resource_map_urn:uuid:2a957ad3-1c0f-44e9-b79d-5ea2a2ed76bf', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + +id_new <- publish_object( + adc, + path = "~/ticket #20492 Norman/CEBP_HumanGeneticData_Summary.csv", + format_id = "text/csv", + public = FALSE +) + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = id_new, + public = FALSE) +#https://arcticdata.io/catalog/view/urn%3Auuid%3Ab7b1a184-4f25-4c7f-b66d-240e2dfcd348 + +pkg <- get_package(adc, 'resource_map_urn:uuid:b7b1a184-4f25-4c7f-b66d-240e2dfcd348', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + +doc <- eml_add_publisher(doc) +doc <- eml_add_entity_system(doc) + +CEBP_HumanGeneticData_Summary <- read_csv("~/ticket #20492 Norman/CEBP_HumanGeneticData_Summary.csv") +out <- shiny_attributes(CEBP_HumanGeneticData_Summary, NULL) + +doc$dataset$otherEntity <- NULL + +physical <- pid_to_eml_physical(adc, "urn:uuid:c17ef00e-7202-49b5-aa8e-a51afc999f41") + +Attributes_Table <- read_csv("~/ticket #20492 Norman/Attributes_Table.csv") +attributeList <- set_attributes(attributes=Attributes_Table) + +dataTable <- eml$dataTable(entityName = "CEBP_HumanGeneticData_Summary.csv", + entityDescription = "Summary of the genetic data collected from individuals", + physical = physical, + attributeList = attributeList +) +doc$dataset$dataTable[[1]] <- dataTable + + +doc$dataset$contact[[3]] <- NULL + +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$westBoundingCoordinate <- "156.51550" +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$eastBoundingCoordinate <- "156.64143" + +doc$dataset$project <- eml_nsf_to_project("1523059") + +eml_validate(doc) +doc_path <- file.path(tempdir(), 'science_metadata.xml') +write_eml(doc, doc_path) + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = pkg$data, + metadata_path = doc_path, + public = FALSE) +#https://arcticdata.io/catalog/view/urn%3Auuid%3Afff9acca-9e4c-481a-8186-678892ca5a6e + +pkg <- get_package(adc, 'resource_map_urn:uuid:fff9acca-9e4c-481a-8186-678892ca5a6e', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + + +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$westBoundingCoordinate <- "-156.51550" +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$eastBoundingCoordinate <- "-156.64143" + +eml_validate(doc) +doc_path <- file.path(tempdir(), 'science_metadata.xml') +write_eml(doc, doc_path) + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = pkg$data, + metadata_path = doc_path, + public = FALSE) +#https://arcticdata.io/catalog/view/urn%3Auuid%3A8b86d811-2b0e-48ae-9f48-7a57d67eccfe + +pkg <- get_package(adc, 'resource_map_urn:uuid:8b86d811-2b0e-48ae-9f48-7a57d67eccfe', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$northBoundingCoordinate <- "69.057876" +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$southBoundingCoordinate <- "69.057876" +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$westBoundingCoordinate <- "-152.862827" +doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$eastBoundingCoordinate <- "-152.862827" + +eml_validate(doc) +doc_path <- file.path(tempdir(), 'science_metadata.xml') +write_eml(doc, doc_path) + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = pkg$data, + metadata_path = doc_path, + public = FALSE) +#https://arcticdata.io/catalog/view/urn:uuid:5b6546c3-b8a6-420f-b1ba-1422c4479f6b + +#https://arcticdata.io/catalog/view/urn%3Auuid%3Adda6d1ed-b817-42ad-9c23-a33b01c59a88 + +pkg <- get_package(adc, 'resource_map_urn:uuid:160fbcbf-92af-4d3b-8ebf-6092a4435a27', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + +set_rights_and_access(adc, pids = unlist(pkg), subject = 'http://orcid.org/0000-0002-5718-6032') + +doc$dataset$title <- "Cape Espenberg Birnirk Project (CEBP) human mitogenome summary analysis (2016-2019)" + +eml_validate(doc) +doc_path <- file.path(tempdir(), 'science_metadata.xml') +write_eml(doc, doc_path) + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = pkg$data, + metadata_path = doc_path, + public = FALSE) +#https://arcticdata.io/catalog/view/urn:uuid:ec4f2c29-bdb2-4927-b364-20f2d6ead811 + +pkg <- get_package(adc, 'resource_map_urn:uuid:ec4f2c29-bdb2-4927-b364-20f2d6ead811', file_names = TRUE) +doc <- read_eml(getObject(adc, pkg$metadata)) +emld::eml_version("eml-2.1.1") + +update <- publish_update(adc, + metadata_pid = pkg$metadata, + resource_map_pid = pkg$resource_map, + data_pids = pkg$data, + use_doi=TRUE, + public = TRUE) +#https://arcticdata.io/catalog/view/doi%3A10.18739%2FA2NC5SD2M + +datamgmt::categorize_dataset("doi:10.18739/A2CZ32589", c("archaeology","anthropology"), "Angel") +datamgmt::categorize_dataset("doi:10.18739/A2NC5SD2M", c("archaeology","anthropology"), "Angel") +