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#38 enable ISO 19110 production/publication
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| geometa_create_iso_19110 <- function(entity, config, options){ | ||
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| ISOMetadataNamespace$GML$uri <- "http://www.opengis.net/gml/3.2" | ||
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| if(!require("geometa")){ | ||
| stop("This action requires the 'geometa' package") | ||
| } | ||
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| #features if any | ||
| features = entity$data$features | ||
| if(is.null(features)){ | ||
| warnMsg <- sprintf("No data features associated to entity '%s'. Skip feature catalogue creation", entity$identifiers[["id"]]) | ||
| config$logger.warn(warnMsg) | ||
| return(FALSE) | ||
| } | ||
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| #options | ||
| doi <- if(!is.null(options$doi)) options$doi else FALSE | ||
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| #feature catalogue creation | ||
| #----------------------------------------------------------------------------------------------------- | ||
| fcIdentifier <- paste0(entity$identifiers[["id"]],"_dsd") | ||
| #produce feature catalogue | ||
| fc <- ISOFeatureCatalogue$new(uuid = fcIdentifier) | ||
| fc$setName(paste0(entity$title, " - Feature Catalogue")) | ||
| fc$addFieldOfApplication("Open Science") | ||
| fc$addFieldOfApplication("FAIR") | ||
| versionDate <- as.POSIXct(Sys.time()) | ||
| versionNumber <- format(versionDate, "%Y%m%dT%H%M%S") | ||
| fc$setVersionNumber(versionNumber) | ||
| fc$setVersionDate(versionDate) | ||
| fc$setFunctionalLanguage(entity$language) | ||
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| #add scopes | ||
| #-------------------------------------------------------------------------- | ||
| #-> geoflow scope | ||
| fc$addScope(paste0("geoflow:", entity$data$uploadType)) | ||
| #-> ofv (openfairviewer) scope | ||
| ofv_scope <- "ogc_filters" | ||
| if(entity$data$uploadType == "dbquery" & length(entity$data$parameters)>0){ | ||
| ofv_scope <- "ogc_viewparams" | ||
| } | ||
| if(length(entity$data$dimensions)>0){ | ||
| ofv_scope <- "ogc_dimensions" | ||
| } | ||
| fc$addScope(paste0("openfairviewer:", ofv_scope)) | ||
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| #producer | ||
| #-------------------------------------------------------------------------- | ||
| main_entity <- NULL | ||
| owners <- entity$contacts[sapply(entity$contacts, function(x){x$role == "owner"})] | ||
| if(length(owners)==0) main_entity <- entity$contacts[[1]] else main_entity <- owners[[1]] | ||
| producer <- ISOResponsibleParty$new() | ||
| producer$setIndividualName(paste(main_entity$firstName, main_entity$lastName)) | ||
| producer$setOrganisationName(main_entity$organizationName) | ||
| producer$setPositionName(main_entity$positionName) | ||
| producer$setRole(main_entity$role) | ||
| contact <- ISOContact$new() | ||
| phone <- ISOTelephone$new() | ||
| phone$setVoice(main_entity$voice) | ||
| phone$setFacsimile(main_entity$facsimile) | ||
| contact$setPhone(phone) | ||
| address <- ISOAddress$new() | ||
| address$setDeliveryPoint(main_entity$postalAddress) | ||
| address$setCity(main_entity$city) | ||
| address$setPostalCode(main_entity$postalCode) | ||
| address$setCountry(main_entity$country) | ||
| address$setEmail(main_entity$email) | ||
| contact$setAddress(address) | ||
| res <- ISOOnlineResource$new() | ||
| res$setLinkage(main_entity$websiteUrl) | ||
| res$setName(main_entity$websiteName) | ||
| contact$setOnlineResource(res) | ||
| producer$setContactInfo(contact) | ||
| fc$setProducer(producer) | ||
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| #citation | ||
| #-------------------------------------------------------------------------- | ||
| ct <- ISOCitation$new() | ||
| ct$setTitle(entity$title) | ||
| d <- ISODate$new() | ||
| d$setDate(Sys.Date()) | ||
| d$setDateType("publication") | ||
| ct$addDate(d) | ||
| ct$setEdition(versionNumber) | ||
| editionDate <- if(!is.null(entity$date)) entity$date else Sys.Date() | ||
| ct$setEditionDate(editionDate) | ||
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| #set metadata identifier | ||
| ct$addIdentifier(ISOMetaIdentifier$new(code = entity$identifiers[["id"]])) | ||
| #methodology to set DOI inspired by NOAA wiki | ||
| #https://geo-ide.noaa.gov/wiki/index.php?title=DOI_Minting_Procedure#Third.2C_Include_the_DOI_and_citation_text_in_the_ISO_Metadata_Record | ||
| the_doi <- entity$identifiers[["doi"]] | ||
| if(is.null(the_doi)) the_doi <- entity$identifiers[["conceptdoi_to_save"]] | ||
| if(is.null(the_doi)) the_doi <- entity$identifiers[["doi_to_save"]] | ||
| if(!is.null(the_doi) & doi){ | ||
| mdIdentifier <- ISOAnchor$new( | ||
| name = paste0("doi:", the_doi), | ||
| href = paste0("http://dx.doi.org/", the_doi) | ||
| ) | ||
| mdIdentifier$setAttr("xlink:title", "DOI") | ||
| mdIdentifier$setAttr("xlink:actuate", "onRequest") | ||
| ct$addIdentifier(ISOMetaIdentifier$new(code = mdIdentifier)) | ||
| } | ||
| ct$addPresentationForm("mapDigital") | ||
| fc$addDefinitionSource(ct) | ||
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| #add feature type / attributes | ||
| #-------------------------------------------------------------------------- | ||
| layername <- if(!is.null(entity$data$layername)) entity$data$layername else entity$identifiers$id | ||
| #create featureType | ||
| ft <- ISOFeatureType$new() | ||
| ft$setTypeName(layername) | ||
| ft$setDefinition(entity$title) | ||
| ft$setCode(layername) | ||
| ft$setIsAbstract(FALSE) | ||
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| add_all_attrs <- TRUE | ||
| if(length(entity$data$attributes)>0 | length(entity$data$variables)>0) add_all_attrs <- FALSE | ||
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| for(featureAttrName in colnames(features)){ | ||
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| #create attribute | ||
| fat <- ISOFeatureAttribute$new() | ||
| #name | ||
| memberName <- featureAttrName | ||
| fat_attrs <- entity$data$attributes[unlist(entity$data$attributes) == featureAttrName] | ||
| if(length(fat_attrs)>0){ | ||
| fat_attr_desc <- attr(fat_attrs[[1]], "description") | ||
| if(!is.null(fat_attr_desc)) memberName <- fat_attr_desc | ||
| } | ||
| fat_vars <- entity$data$variables[unlist(entity$data$variables) == featureAttrName] | ||
| if(length(fat_vars)>0){ | ||
| fat_var_desc <- attr(fat_vars[[1]], "description") | ||
| if(!is.null(fat_var_desc)) memberName <- fat_var_desc | ||
| } | ||
| fat$setMemberName(memberName) | ||
| #type (definition) -> attribute or variable | ||
| fat_def <- "attribute" #default definition | ||
| if(featureAttrName %in% entity$data$variables) fat_def <- "variable" | ||
| fat$setDefinition(fat_def) | ||
| fat$setCardinality(lower=1,upper=1) | ||
| #code | ||
| fat$setCode(featureAttrName) | ||
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| #add listed values | ||
| featureAttrValues <- features[,featureAttrName][[1]] | ||
| addValues <- TRUE | ||
| if(is(featureAttrValues, "sfc")){ | ||
| addValues <- FALSE | ||
| }else{ | ||
| if(!add_all_attrs & !(featureAttrName %in% entity$data$attributes)) addValues <- FALSE | ||
| if(featureAttrName %in% entity$data$variables) addValues <- FALSE | ||
| } | ||
| if(addValues){ | ||
| featureAttrValues <- unique(featureAttrValues) | ||
| for(featureAttrValue in featureAttrValues){ | ||
| val <- ISOListedValue$new() | ||
| if(!is(featureAttrValue, "character")) featureAttrValue <- as(featureAttrValue, "character") | ||
| val$setCode(featureAttrValue) | ||
| val$setLabel(featureAttrValue) | ||
| val$setDefinition(featureAttrValue) | ||
| fat$listedValue <- c(fat$listedValue, val) | ||
| } | ||
| } | ||
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| #add type | ||
| fat_type <- switch(class(featureAttrValues)[1], | ||
| "integer" = "xsd:int", | ||
| "numeric" = "xsd:decimal", | ||
| "character" = "xsd:string", | ||
| "logical" = "xsd:boolean", | ||
| "Date" = "xsd:date", | ||
| "POSIXct" = "xsd:datetime", | ||
| "sfc_POINT" = "gml:PointPropertyType", | ||
| "sfc_MULTIPOINT" = "gml:MultiPointPropertyType", | ||
| "sfc_LINESTRING" = "gml:LineStringPropertyType", | ||
| "sfc_MULTILINESTRING" = "gml:MultiLineStringPropertyType", | ||
| "sfc_POLYGON" = "gml:PolygonPropertyType", | ||
| "sfc_MULTIPOLYGON" = "gml:MultiPolygonPropertyType" | ||
| ) | ||
| fat$setValueType(fat_type) | ||
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| #add feature attribute as carrierOfCharacteristic | ||
| ft$carrierOfCharacteristics <- c(ft$carrierOfCharacteristics, fat) | ||
| } | ||
| #add featureType to catalogue | ||
| fc$addFeatureType(ft) | ||
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| #we save the metadata | ||
| saveRDS(fc, file.path(getwd(), "metadata", paste0(fcIdentifier, ".rds"))) | ||
| fc$save(file.path(getwd(), "metadata", paste0(entity$identifiers[["id"]], "_ISO-19110.xml"))) | ||
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| return(fc) | ||
| } |
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