Nothing
R/attr_builder.R
In BeeBDC: Occurrence Data Cleaning
Defines functions
attr_builder
##### 2.2 attr_builder ####
#' @importFrom lubridate as_date
#' @importFrom stringr str_to_sentence
#' @importFrom dplyr %>%
attr_builder <- function(path_i = path_i, occ_input = data_i){
# locally bind variables to the function
lubridate <- stringr <- family <- data_i <- NULL
requireNamespace("lubridate")
requireNamespace("dplyr")
requireNamespace("xml2")
# This function behaves differently depending on the data source, but returns common outputs.
#### ALA START ####
if(grepl("/data.csv", path_i) == "TRUE"){
# Find and take the citations file
citations_i <- gsub("/data.csv", "/citation.csv", path_i) %>%
readr::read_csv(col_types = readr::cols(.default = readr::col_character()))
# Find and take the download information file
galahDL_i <- gsub("/data.csv", "/galah_DL_info.csv", path_i) %>%
readr::read_csv(n_max = 1, col_types = readr::cols(.default = readr::col_character()))
# Read in the closest thing ALA has to an abstract
galahAbstract_i <- gsub("/data.csv", "/README.html", path_i) %>%
rvest::read_html() %>%
rvest::html_text2()
# Combine all of these attributes into a tibble
Attributes_i <- dplyr::tibble(dataSource = paste("ALA_",
galahDL_i$taxon,
sep = ""),
alternateIdentifier = if("search_url" %in% colnames(galahDL_i)){
galahDL_i$search_url}else(NA_character_),
title = "ALA Occurrence Download. ",
pubDate = galahDL_i$download_date %>%
lubridate::as_date(),
dateStamp = galahDL_i$download_date,
doi = galahDL_i$doi,
downloadLink = galahDL_i$download_link,
abstract = dplyr::lst(galahAbstract_i),
citations = dplyr::lst(citations_i),
downloadCitation = paste("ALA.org.au. (",
lubridate::as_date(galahDL_i$download_date) %>%
format("%d %B %Y"),
"). ALA Occurrence Download. ",
galahDL_i$doi,
sep = ""),
rights = dplyr::lst("See occurrence records"),
taxon = galahDL_i$taxon)
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list("No_eml_from_ALA", Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # ALA END
#### GBIF START ####
if(grepl("occurrence.txt", path_i) == "TRUE"){
# Find and take the metadata file
sourceEML_i <- emld::as_emld(gsub("/occurrence.txt", "/metadata.xml", path_i), from = "xml" )
# Find and take the citations file - convert into a list
citations_i <- gsub("/occurrence.txt", "/citations.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Find and take the rights file - convert into a list
rights_i <- gsub("/occurrence.txt", "/rights.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Find the download name
fam_name <- tidyr::drop_na(
occ_input, tidyselect::any_of("family")) %>%
dplyr::pull(family) %>%
unique()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("GBIF_",
fam_name,
sep = ""),
alternateIdentifier = sourceEML_i$dataset$alternateIdentifier,
title = sourceEML_i$dataset$title,
pubDate = sourceEML_i$dataset$pubDate %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = sourceEML_i$additionalMetadata$metadata$gbif$dateStamp,
doi = paste("https://doi.org/",
sourceEML_i$additionalMetadata$metadata$gbif$citation$identifier, sep = ""),
downloadLink = sourceEML_i$additionalMetadata$metadata$gbif$physical$distribution$online$url$url,
abstract = dplyr::lst(sourceEML_i$dataset$abstract),
citations = dplyr::lst(citations_i),
downloadCitation = paste("GBIF.org. (",
lubridate::as_date(sourceEML_i$dataset$pubDate) %>%
format("%d %B %Y"),
"). GBIF Occurrence Download. ",
paste("https://doi.org/",
sourceEML_i$additionalMetadata$metadata$gbif$citation$identifier,
sep = ""),
sep = ""),
rights = dplyr::lst(rights_i),
taxon = fam_name)
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list(sourceEML_i, Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # GBIF END
#### iDigBio START ####
if(grepl("occurrence_raw.csv", path_i) == "TRUE"){
# Find and take the citations file - convert into a list
citations_i <- gsub("/occurrence_raw.csv", "/records.citation.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("iDigBio_", citations_i$.[2] %>%
stringr::str_match_all("[A-Za-z]+") %>%
unlist() %>%
dplyr::last(), sep = ""),
# Check for alt identifier and include if there
alternateIdentifier =
if(length(path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+") %>%
unlist()) > 0){
# TRUE
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+") %>%
unlist()
}else{
# FALSE
NA_character_},
title = citations_i$.[1],
pubDate = citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}") %>%
as.character(),
doi = "Use downloadLink for iDigBio",
downloadLink = paste("http://s.idigbio.org/idigbio-downloads/",
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+"),
".zip", sep = ""),
abstract = dplyr::lst(citations_i$.[1:4]),
citations = dplyr::lst(citations_i$.[4:length(citations_i$.)]),
downloadCitation = paste("iDigBio.org. (",
citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date() %>%
format("%d %B %Y"),
"). iDigBio Occurrence Download. ",
paste("http://s.idigbio.org/idigbio-downloads/",
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+"),
".zip", sep = ""),
sep = ""),
rights = dplyr::lst("See occurrence records"),
taxon = (citations_i$.[2] %>%
stringr::str_match_all("[A-Za-z]+") %>%
unlist() %>%
dplyr::last())
) # END tibble()
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list("No_eml_from_iDigBio", Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # iDigBio END
#### SCAN START ####
if(grepl("occurrences.csv", path_i) == "TRUE"){
# Find and take the metadata file
sourceEML_i <- xml2::read_xml(gsub("/occurrences.csv", "/eml.xml", path_i), from = "xml" ) %>%
emld::as_emld()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("SCAN_",
unique(stringr::str_to_sentence(occ_input$family)),
sep = ""),
alternateIdentifier = sourceEML_i$additionalMetadata$metadata$symbiota$citation$identifier,
title = sourceEML_i$dataset$title$title,
pubDate = sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp,
doi = "SCAN does not provide a doi. See download link.",
downloadLink = "SCAN does not provide a download link.",
abstract = dplyr::lst("SCAN does not provide a single abstract"),
citations = dplyr::lst(paste("SCAN. ",
(sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}")),
". http//:scan-bugs.org/portal/index.php. ",
"accessed on ",
(sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}")),
". ", sourceEML_i$additionalMetadata$metadata$symbiota$citation$citation,
sep = "" ) ),
downloadCitation = paste("SCAN. (",
sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date() %>%
format("%d %B %Y"),
"). SCAN-Bugs Occurrence Download ",
"http//:scan-bugs.org/portal/index.php. uuid - ",
sourceEML_i$additionalMetadata$metadata$symbiota$citation$identifier,
sep = ""),
rights = dplyr::lst("See .xml for rights"),
taxon = unique(stringr::str_to_sentence(occ_input$family)))
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list(sourceEML_i, Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # SCAN END
} # END attr_builder
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BeeBDC documentation built on Nov. 4, 2024, 9:06 a.m.
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Defines functions attr_builder
##### 2.2 attr_builder ####
#' @importFrom lubridate as_date
#' @importFrom stringr str_to_sentence
#' @importFrom dplyr %>%
attr_builder <- function(path_i = path_i, occ_input = data_i){
# locally bind variables to the function
lubridate <- stringr <- family <- data_i <- NULL
requireNamespace("lubridate")
requireNamespace("dplyr")
requireNamespace("xml2")
# This function behaves differently depending on the data source, but returns common outputs.
#### ALA START ####
if(grepl("/data.csv", path_i) == "TRUE"){
# Find and take the citations file
citations_i <- gsub("/data.csv", "/citation.csv", path_i) %>%
readr::read_csv(col_types = readr::cols(.default = readr::col_character()))
# Find and take the download information file
galahDL_i <- gsub("/data.csv", "/galah_DL_info.csv", path_i) %>%
readr::read_csv(n_max = 1, col_types = readr::cols(.default = readr::col_character()))
# Read in the closest thing ALA has to an abstract
galahAbstract_i <- gsub("/data.csv", "/README.html", path_i) %>%
rvest::read_html() %>%
rvest::html_text2()
# Combine all of these attributes into a tibble
Attributes_i <- dplyr::tibble(dataSource = paste("ALA_",
galahDL_i$taxon,
sep = ""),
alternateIdentifier = if("search_url" %in% colnames(galahDL_i)){
galahDL_i$search_url}else(NA_character_),
title = "ALA Occurrence Download. ",
pubDate = galahDL_i$download_date %>%
lubridate::as_date(),
dateStamp = galahDL_i$download_date,
doi = galahDL_i$doi,
downloadLink = galahDL_i$download_link,
abstract = dplyr::lst(galahAbstract_i),
citations = dplyr::lst(citations_i),
downloadCitation = paste("ALA.org.au. (",
lubridate::as_date(galahDL_i$download_date) %>%
format("%d %B %Y"),
"). ALA Occurrence Download. ",
galahDL_i$doi,
sep = ""),
rights = dplyr::lst("See occurrence records"),
taxon = galahDL_i$taxon)
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list("No_eml_from_ALA", Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # ALA END
#### GBIF START ####
if(grepl("occurrence.txt", path_i) == "TRUE"){
# Find and take the metadata file
sourceEML_i <- emld::as_emld(gsub("/occurrence.txt", "/metadata.xml", path_i), from = "xml" )
# Find and take the citations file - convert into a list
citations_i <- gsub("/occurrence.txt", "/citations.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Find and take the rights file - convert into a list
rights_i <- gsub("/occurrence.txt", "/rights.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Find the download name
fam_name <- tidyr::drop_na(
occ_input, tidyselect::any_of("family")) %>%
dplyr::pull(family) %>%
unique()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("GBIF_",
fam_name,
sep = ""),
alternateIdentifier = sourceEML_i$dataset$alternateIdentifier,
title = sourceEML_i$dataset$title,
pubDate = sourceEML_i$dataset$pubDate %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = sourceEML_i$additionalMetadata$metadata$gbif$dateStamp,
doi = paste("https://doi.org/",
sourceEML_i$additionalMetadata$metadata$gbif$citation$identifier, sep = ""),
downloadLink = sourceEML_i$additionalMetadata$metadata$gbif$physical$distribution$online$url$url,
abstract = dplyr::lst(sourceEML_i$dataset$abstract),
citations = dplyr::lst(citations_i),
downloadCitation = paste("GBIF.org. (",
lubridate::as_date(sourceEML_i$dataset$pubDate) %>%
format("%d %B %Y"),
"). GBIF Occurrence Download. ",
paste("https://doi.org/",
sourceEML_i$additionalMetadata$metadata$gbif$citation$identifier,
sep = ""),
sep = ""),
rights = dplyr::lst(rights_i),
taxon = fam_name)
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list(sourceEML_i, Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # GBIF END
#### iDigBio START ####
if(grepl("occurrence_raw.csv", path_i) == "TRUE"){
# Find and take the citations file - convert into a list
citations_i <- gsub("/occurrence_raw.csv", "/records.citation.txt", path_i) %>%
readr::read_lines() %>%
dplyr::lst()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("iDigBio_", citations_i$.[2] %>%
stringr::str_match_all("[A-Za-z]+") %>%
unlist() %>%
dplyr::last(), sep = ""),
# Check for alt identifier and include if there
alternateIdentifier =
if(length(path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+") %>%
unlist()) > 0){
# TRUE
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+") %>%
unlist()
}else{
# FALSE
NA_character_},
title = citations_i$.[1],
pubDate = citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}") %>%
as.character(),
doi = "Use downloadLink for iDigBio",
downloadLink = paste("http://s.idigbio.org/idigbio-downloads/",
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+"),
".zip", sep = ""),
abstract = dplyr::lst(citations_i$.[1:4]),
citations = dplyr::lst(citations_i$.[4:length(citations_i$.)]),
downloadCitation = paste("iDigBio.org. (",
citations_i$.[3] %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date() %>%
format("%d %B %Y"),
"). iDigBio Occurrence Download. ",
paste("http://s.idigbio.org/idigbio-downloads/",
path_i %>%
stringr::str_match_all("[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+"),
".zip", sep = ""),
sep = ""),
rights = dplyr::lst("See occurrence records"),
taxon = (citations_i$.[2] %>%
stringr::str_match_all("[A-Za-z]+") %>%
unlist() %>%
dplyr::last())
) # END tibble()
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list("No_eml_from_iDigBio", Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # iDigBio END
#### SCAN START ####
if(grepl("occurrences.csv", path_i) == "TRUE"){
# Find and take the metadata file
sourceEML_i <- xml2::read_xml(gsub("/occurrences.csv", "/eml.xml", path_i), from = "xml" ) %>%
emld::as_emld()
# Combine all of these attributes int o tibble
Attributes_i <- dplyr::tibble(dataSource = paste("SCAN_",
unique(stringr::str_to_sentence(occ_input$family)),
sep = ""),
alternateIdentifier = sourceEML_i$additionalMetadata$metadata$symbiota$citation$identifier,
title = sourceEML_i$dataset$title$title,
pubDate = sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date(),
dateStamp = sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp,
doi = "SCAN does not provide a doi. See download link.",
downloadLink = "SCAN does not provide a download link.",
abstract = dplyr::lst("SCAN does not provide a single abstract"),
citations = dplyr::lst(paste("SCAN. ",
(sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}")),
". http//:scan-bugs.org/portal/index.php. ",
"accessed on ",
(sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}")),
". ", sourceEML_i$additionalMetadata$metadata$symbiota$citation$citation,
sep = "" ) ),
downloadCitation = paste("SCAN. (",
sourceEML_i$additionalMetadata$metadata$symbiota$dateStamp %>%
stringr::str_match("[0-9]{4}-[0-9]{2}-[0-9]{2}") %>%
lubridate::as_date() %>%
format("%d %B %Y"),
"). SCAN-Bugs Occurrence Download ",
"http//:scan-bugs.org/portal/index.php. uuid - ",
sourceEML_i$additionalMetadata$metadata$symbiota$citation$identifier,
sep = ""),
rights = dplyr::lst("See .xml for rights"),
taxon = unique(stringr::str_to_sentence(occ_input$family)))
# combine the input eml and the attributes tibble into a list for output from the function
EML_attributes <- list(sourceEML_i, Attributes_i)
names(EML_attributes) <- c("source_eml","Source_tibble")
# output this list
return(EML_attributes)
} # SCAN END
} # END attr_builder
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