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dataset.R
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dataset.R
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datasetfun<-function(datasetid,dataTable=NULL,otherentity=NULL)
{
#dataset table
project1 <- dataset[dataset$datasetid==datasetid,]
#creator
creator_s <- creator[creator$datasetid==datasetid & creator$authorshiprole=="creator",]
for (i in 1: nrow(creator_s)) {
if (i == 1) {
p <- new("creator", organizationName = creator_s$organization[i],
address = new("address", deliveryPoint = paste0(creator_s$address1[i],',',creator_s$address2[i]),
city = creator_s$city[i],
administrativeArea = creator_s$state[i],
postalCode = creator_s$zipcode[i],
country = creator_s$country[i]),
electronicMailAddress = creator_s$email[i])
pall=list(p)
}
else {
givenname <- ifelse(!is.na(creator_s$givenname2[i]),paste0(creator_s$givenname[i]," ",creator_s$givenname2[i]),creator_s$givenname[i])
p <- new("creator", individualName = new("individualName",
givenName=givenname,
surName=creator_s$surname[i]),
electronicMailAddress = if (is.na(creator_s$email[i])) (NULL) else (creator_s$email[i]),
userId = if (!is.na(creator_s$orcid[i])) {new("userId",paste0("https://orcid.org/",creator_s$orcid[i]),directory = "http://orcid.org/")} else {NULL})
pall=c(pall,list(p))
}
}
#---------------------------------------------
#methods
method1 <- method[method$datasetid==datasetid,]
for (k in 1: nrow(method1)) {
software <- if (is.na(method1$softwareDescription[k])) {NULL} else {
new("software",
title = if (is.na(method1$softwareTitle[k])) {NULL} else {method1$softwareTitle[k]},
distribution= new("distribution",
online = new("online",url = new("url",
method1$softwareDescription[k],
"function" = new("xml_attribute", "download")))))}
protocol<-if (is.na(method1$protocolDescription[k])) {NULL} else {
new("protocol",
title=if (is.na(method1$protocolTitle[k])) {NULL} else {method1$protocolTitle[k]},
creator = if (is.na(method1$protocolOwner[k])) {NULL} else {new("creator",individualName = new("individualName",
surName = method1$protocolOwner[k]))},
distribution= new("distribution",
online = new("online",url = new("url",
method1$protocolDescription[k],
"function" = new("xml_attribute", "download")))))}
instrument<-if (is.na(method1$instrumentDescription[k])) {NULL} else {
new("instrument",
title=if (is.na(method1$instrumentTitle[k])) {NULL} else {method1$instrumentTitle[k]},
creator = if (is.na(method1$instrumentOwner[k])) {NULL} else {new("creator",individualName = new("individualName",
surName = method1$instrumentOwner[k]))},
distribution= new("distribution",
online = new("online",url = new("url",
method1$instrumentDescription[k],
"function" = new("xml_attribute", "download")))))}
methodstep = new(
"methodStep",
description = as(set_TextType(method1$methodDocument[k]), "description"),
instrumentation = instrument,
software = software,
protocol =protocol)
if (k == 1) {
methodall=list(methodstep)
}
else {
methodall=c(methodall,list(methodstep))
}
}
method_xml <- new(
"methods",
methodStep=methodall)
#abstract
abstract <- as(set_TextType(project1$abstract), "abstract")
#date info
tempcover<-new(
"temporalCoverage",
rangeOfDates =
new(
"rangeOfDates",
beginDate =
new("beginDate",
calendarDate = tempo[tempo$datasetid==datasetid,"begindate"]),
endDate =
new("endDate",
calendarDate = tempo[tempo$datasetid==datasetid,"enddate"])))
#-------------
#spatial extend
geo_s <-geo[geo$datasetid==datasetid,]
for (i in 1: nrow(geo_s)) {
geocover <-new(
"geographicCoverage",
geographicDescription = geo_s$"geographicdescription"[i],
boundingCoordinates = new(
"boundingCoordinates",
westBoundingCoordinate = as.character(geo_s$"westboundingcoordinate"[i]),
eastBoundingCoordinate = as.character(geo_s$"eastboundingcoordinate"[i]),
northBoundingCoordinate = as.character(geo_s$"northboundingcoordinate"[i]),
southBoundingCoordinate = as.character(geo_s$"southboundingcoordinate"[i])))
if (i == 1) {
geoall=list(geocover)
}
else {
geoall=c(geoall,list(geocover))
}
}
coverage1<-new("Coverage",geographicCoverage = geoall,
temporalCoverage = tempcover)
#keyword
keyword1 <- droplevels(keyword[keyword$datasetid==datasetid,])
nkey<-unique(keyword1$keyword_thesaurus)
for (i in 1: length(nkey)) {
if ( nkey[i]=="none") {
k<-new("keywordSet", keyword = as.vector(keyword1[keyword1$keyword_thesaurus==nkey[i],"keyword"]))
}else {
k <- new("keywordSet", keyword = as.vector(keyword1[keyword1$keyword_thesaurus==nkey[i],"keyword"]),keywordThesaurus = nkey[i])
}
if (i == 1) {
kall=list(k)
}else {
kall=c(kall,list(k))
}
}
#the boilerplate information
sharefile = "PATH-TO-SHARE-FILE"
xml_in <- read_eml(paste0(sharefile,"boilerplate.xml"),sep = "")
access1 <- eml_get(xml_in@access)
contact1 <- eml_get(xml_in@dataset, element = "contact")
distribution1<-eml_get(xml_in@dataset, element = "distribution")
publisher1<-eml_get(xml_in@dataset, element = "publisher")
#intellectualrights1<-eml_get(xml_in@dataset, element = "intellectualRights")
project_xml <-eml_get(xml_in@dataset, element = "project")
intellectualrights1 <- as(set_TextType(paste0(sharefile,"IntellectualRights.docx")), "intellectualRights")
#put the dataset together
dataset1 <- new("dataset",
title = project1$title,
alternateIdentifier = project1$alternatedid,
shortName = project1$shortname,
creator = pall,
pubDate = as.character(as.Date(project1$pubdate)),
intellectualRights = intellectualrights1,
abstract = abstract,
keywordSet = kall,
coverage = coverage1,
contact = contact1,
publisher = publisher1,
distribution = distribution1,
project = project_xml,
methods = method_xml,
language = "English",
dataTable = dataTable,
otherEntity = otherentity)
#-------------------------------------------------------------------
# unit list
unit1 <- unit[unit$datasetid==datasetid,]
# EML
if (dim(unit1)[1] > 0){
eml <- new("eml",
packageId = project1$edinum,
system = "knb",
schemaLocation="eml://ecoinformatics.org/eml-2.1.1 http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd",
access=access1,
dataset = dataset1,
additionalMetadata=as(set_unitList(unit1), "additionalMetadata"))
} else {
eml <- new("eml",
packageId = project1$edinum,
system = "knb",
schemaLocation="eml://ecoinformatics.org/eml-2.1.1 http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd",
access=access1,
dataset = dataset1)
}
return(eml)
}