adding processing scripts for ticket #19667 Russell #12
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| #ticket #20492 Norman | ||
| #Human dataset: | ||
| #https://arcticdata.io/catalog/#view/urn:uuid:c715fe12-6c05-4c27-8d00-b9c0c536c54b | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:2a957ad3-1c0f-44e9-b79d-5ea2a2ed76bf', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| id_new <- publish_object( | ||
| adc, | ||
| path = "~/ticket #20492 Norman/CEBP_HumanGeneticData_Summary.csv", | ||
| format_id = "text/csv", | ||
| public = FALSE | ||
| ) | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$metadata, | ||
| resource_map_pid = pkg$resource_map, | ||
| data_pids = id_new, | ||
| public = FALSE) | ||
| #https://arcticdata.io/catalog/view/urn%3Auuid%3Ab7b1a184-4f25-4c7f-b66d-240e2dfcd348 | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:b7b1a184-4f25-4c7f-b66d-240e2dfcd348', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| doc <- eml_add_publisher(doc) | ||
| doc <- eml_add_entity_system(doc) | ||
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| CEBP_HumanGeneticData_Summary <- read_csv("~/ticket #20492 Norman/CEBP_HumanGeneticData_Summary.csv") | ||
| out <- shiny_attributes(CEBP_HumanGeneticData_Summary, NULL) | ||
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There was a problem hiding this comment. I'm curious what this step was used for, could you explain?
Author
There was a problem hiding this comment. @eeerika |
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| doc$dataset$otherEntity <- NULL | ||
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| physical <- pid_to_eml_physical(adc, "urn:uuid:c17ef00e-7202-49b5-aa8e-a51afc999f41") | ||
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| Attributes_Table <- read_csv("~/ticket #20492 Norman/Attributes_Table.csv") | ||
| attributeList <- set_attributes(attributes=Attributes_Table) | ||
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| dataTable <- eml$dataTable(entityName = "CEBP_HumanGeneticData_Summary.csv", | ||
| entityDescription = "Summary of the genetic data collected from individuals", | ||
| physical = physical, | ||
| attributeList = attributeList | ||
| ) | ||
| doc$dataset$dataTable[[1]] <- dataTable | ||
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| doc$dataset$contact[[3]] <- NULL | ||
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| doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$westBoundingCoordinate <- "156.51550" | ||
| doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$eastBoundingCoordinate <- "156.64143" | ||
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| doc$dataset$project <- eml_nsf_to_project("1523059") | ||
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| eml_validate(doc) | ||
| doc_path <- file.path(tempdir(), 'science_metadata.xml') | ||
| write_eml(doc, doc_path) | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$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 | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:fff9acca-9e4c-481a-8186-678892ca5a6e', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$westBoundingCoordinate <- "-156.51550" | ||
| doc$dataset$coverage$geographicCoverage[[2]]$boundingCoordinates$eastBoundingCoordinate <- "-156.64143" | ||
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| eml_validate(doc) | ||
| doc_path <- file.path(tempdir(), 'science_metadata.xml') | ||
| write_eml(doc, doc_path) | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$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 | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:8b86d811-2b0e-48ae-9f48-7a57d67eccfe', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| doc$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$eastBoundingCoordinate <- "-152.862827" | ||
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| eml_validate(doc) | ||
| doc_path <- file.path(tempdir(), 'science_metadata.xml') | ||
| write_eml(doc, doc_path) | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$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 | ||
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| #https://arcticdata.io/catalog/view/urn%3Auuid%3Adda6d1ed-b817-42ad-9c23-a33b01c59a88 | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:160fbcbf-92af-4d3b-8ebf-6092a4435a27', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| set_rights_and_access(adc, pids = unlist(pkg), subject = 'http://orcid.org/0000-0002-5718-6032') | ||
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There was a problem hiding this comment. does just writing the subject with http:// instead of https:// replace the need for this step: There was a problem hiding this comment. yes it is convenient for if you have lots of orcids |
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| doc$dataset$title <- "Cape Espenberg Birnirk Project (CEBP) human mitogenome summary analysis (2016-2019)" | ||
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| eml_validate(doc) | ||
| doc_path <- file.path(tempdir(), 'science_metadata.xml') | ||
| write_eml(doc, doc_path) | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$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 | ||
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| pkg <- get_package(adc, 'resource_map_urn:uuid:ec4f2c29-bdb2-4927-b364-20f2d6ead811', file_names = TRUE) | ||
| doc <- read_eml(getObject(adc, pkg$metadata)) | ||
| emld::eml_version("eml-2.1.1") | ||
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| update <- publish_update(adc, | ||
| metadata_pid = pkg$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 | ||
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| datamgmt::categorize_dataset("doi:10.18739/A2CZ32589", c("archaeology","anthropology"), "Angel") | ||
| datamgmt::categorize_dataset("doi:10.18739/A2NC5SD2M", c("archaeology","anthropology"), "Angel") | ||
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There was a problem hiding this comment. nice! seems like you've been able to simplify some steps down through your experience which is cool! |
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I usually do this near the end but it's smart to do it at the beginning. I just don't usually think about it until the end
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hopefully this will be something we won't need to think about as much moving forward with everything in 2.2.0 but yeah we need to keep this in mind when working with older datasets