diff --git a/ebv_metadata_app.R b/ebv_metadata_app.R
deleted file mode 100644
index 381ec0e8c8946678a4bb458eddc78909d10a8317..0000000000000000000000000000000000000000
--- a/ebv_metadata_app.R
+++ /dev/null
@@ -1,1106 +0,0 @@
-#install all packages if not yet installed
-t <- tryCatch(
- {find.package("shiny")},
- error = function(e){
- install.packages('shiny')
- }
-)
-t <- tryCatch(
- {find.package("stringr")},
- error = function(e){
- install.packages('stringr')
- }
-)
-t <- tryCatch(
- {find.package("checkmate")},
- error = function(e){
- install.packages('checkmate')
- }
-)
-t <- tryCatch(
- {find.package("withr")},
- error = function(e){
- install.packages('withr')
- }
-)
-
-#load libraries
-library(shiny)
-library(stringr)
-library(checkmate)
-library(withr)
-
-
-ui <- fluidPage(
- #set style
- #tags$style(type='text/css', '.selectize-label { font-size: 60px;}'),
- #".selectize-input { font-size: 32px; line-height: 32px;} .selectize-dropdown { font-size: 28px; line-height: 28px; }"),
- #tags$span(style="color:red", 'Summary*')
-
- #set theme
- theme = bslib::bs_theme(bootswatch = "flatly"),
-
- #title
- titlePanel("EBV netCDF Metadata - Terranova Atlas"),
-
- #create several tabs
- tabsetPanel(
- #1. tab: general information----
- tabPanel('General Information',
- #2 cols
- fluidRow(
- #title
- column(6,
- textInput('title', tags$span(style="font-size: 18px; font-weight: bold", 'Title*'), width='80%',
- placeholder='The title of the dataset.'),
- #span(textOutput("title_desc"), style="font-size:14px")
- ),
- #date of creation
- column(6,
- dateInput('date_created', tags$span(style="font-size: 18px; font-weight: bold", 'Date of creation*'), width='80%', max = Sys.Date())
- )
- ),
-
- #Summary
- textAreaInput('summary', tags$span(style="font-size: 18px; font-weight: bold", 'Summary*'), width='90.5%',
- placeholder = 'A paragraph describing the dataset. Allowed: 1500 characters'),
- span(textOutput("summary_error"), style="color:red"),
- #actionButton("summary_example", "Look at an example for a summary."),
-
- #references
- textAreaInput('references', tags$span(style="font-size: 18px; font-weight: bold", 'References'), width='90.5%',
- placeholder = 'Provide the DOI URL of the dataset and/or associated publications. You can add several DOIs by seperating them by comma.'),
-
- #Methods
- textAreaInput('methods', tags$span(style="font-size: 18px; font-weight: bold", 'Methods*'), width='90.5%',
- placeholder = 'The method of production of the original data. If it was model-generated, source should name the model and its version. If it is observational, source should characterize it.'),
-
- #2 cols
- #coverage content type
-
- selectInput('coverage_content_type', tags$span(style="font-size: 18px; font-weight: bold", 'Coverage Content Type*'), width='90.5%',
- c("Image" = "image",
- "Thematic Classification" = "thematicClassification",
- "Physical Measurement" = "physicalMeasurement",
- "Auxiliary Information" = "auxiliaryInformation",
- "Quality Information" = "qualityInformation",
- "Reference Information" = "referenceInformation",
- "Model Result" = "modelResult",
- "Coordinate" = "coordinate"),
- multiple = T
- ),
- span(textOutput("cct_desc"), style="font-size:14px"),
-
-
- #2 cols
- fluidRow(
- #project name
- column(6,
- textInput('project_name', tags$span(style="font-size: 18px; font-weight: bold", 'Project Name'), width='80%',
- value = 'TERRANOVA - The European Landscape Learning Initiative',
- placeholder='The name(s) of the Project principally responsible for originating this data. Several values should be separated by comma.'),
- #span(textOutput("title_desc"), style="font-size:14px")
- ),
- #project url
- column(6,
- textInput('project_url', tags$span(style="font-size: 18px; font-weight: bold", 'Project URL'), width='80%',
- value = "https://www.terranova-itn.eu",
- placeholder='The URL from the project(s) website. Several values should be separated by comma.')
- )
- ),
-
- #2 cols
- fluidRow(
- #Creator Name
- column(6,
- textInput('creator_name', tags$span(style="font-size: 18px; font-weight: bold", 'Creator Name*'), width='80%',
- placeholder='The name of the person or other creator type principally responsible for creating this data.'),
-
- ),
- #Creator Email
- column(6,
- textInput('creator_email', tags$span(style="font-size: 18px; font-weight: bold", 'Creator Email'), width='80%',
- placeholder='The email of the person or other creator type principally responsible for creating this data.')
- )
- ),
-
-
- #Creator Institution
- textAreaInput('creator_institution', tags$span(style="font-size: 18px; font-weight: bold", 'Creator Institution*'), width='90.5%',
- placeholder = 'Name of the institution of the creator.'),
-
- #2 cols
- fluidRow(
- #publisher Name
- column(6,
- textInput('publisher_name', tags$span(style="font-size: 18px; font-weight: bold", 'Publisher Name* (responsible PI)'), width='80%',
- placeholder='The name of the person publishing the data. The publisher is also the contact person.'),
-
- ),
- #publisher Email
- column(6,
- textInput('publisher_email', tags$span(style="font-size: 18px; font-weight: bold", 'Publisher Email*'), width='80%',
- placeholder='The email of the person publishing the data. The publisher is also the contact person.')
- )
- ),
-
-
- #Publisher Institution
- textAreaInput('publisher_institution', tags$span(style="font-size: 18px; font-weight: bold", 'Publisher Institution*'), width='90.5%',
- placeholder = 'Name of the institution of the publisher.'),
-
- #Co-creators
- textAreaInput('contributor_names', tags$span(style="font-size: 18px; font-weight: bold", 'Co-creators '), width='90.5%',
- placeholder = 'The names of the co-creators responsible for creating this data. Seperate several by comma.'),
-
- #license
- textAreaInput('license', tags$span(style="font-size: 18px; font-weight: bold", 'License*'), width='90.5%',
- value = "https://creativecommons.org/licenses/by/4.0",
- placeholder = 'Give the URL of a licence. Prefereble CC-License, e.g. https://creativecommons.org/licenses/by/4.0/'),
- #add a text: link to CC licenses
- tags$a(href="https://creativecommons.org/licenses/", "Link to CC licenses."),
-
- #comment
- textAreaInput('comment', tags$span(style="font-size: 18px; font-weight: bold", 'Comment'), width='90.5%',
- placeholder = 'Miscellaneous information about the data, not captured elsewhere.'),
-
-
- #end tabPanel 1
- ),
-
- #2. tab: ebv attributes----
- tabPanel('EBV Attributes',
-
-
- #2 cols
- fluidRow(
- #EBV Class and EBV Name
- column(6,
- #EBV Class
- selectInput("ebv_class", tags$span(style="font-size: 18px; font-weight: bold", "EBV Class"),
- c("Genetic composition" = "Genetic composition",
- "Species populations" = "Species populations",
- "Species traits" = "Species traits",
- "Community composition"="Community composition",
- "Ecosystem functioning"="Ecosystem functioning",
- "Ecosystem structure"="Ecosystem structure",
- "None"="N/A"),
- width='80%'),
-
- #EBV Name - in server: create selectInput based on EBV Class
- uiOutput('ebv_name'),
-
- #environmental domain
- selectInput('ebv_domain', tags$span(style="font-size: 18px; font-weight: bold", 'Environmental Domain*'), width='80%',
- c("Terrestrial" = "Terrestrial",
- "Marine" = "Marine",
- "Freshwater" = "Freshwater",
- "Other" = "Other",
- "None" = "N/A"),
- #selected = 'N/A',
- multiple = T
- ),
- #define other for environmental domain
- uiOutput('ebv_domain_other'),
-
- #terranova type (keywords)
- selectInput('terranova_type', tags$span(style="font-size: 18px; font-weight: bold", 'Type of Data*'), width='80%',
- c("Climate " = "climate",
- "Biodiversity" = "biodiversity ",
- 'Anthropogenic activity'='anthropogenic activity ')
- ),
-
-
- ),
- #Biological entity
- column(6,
- selectInput("biological_entity", tags$span(style="font-size: 18px; font-weight: bold", "Entity type"),
- c( "None"="N/A",
- "Species" = "Species",
- "Communities" = "Communities",
- "Ecosystems" = "Ecosystems",
- "Other"="Other"
- ),
- width='80%'),
- uiOutput('entity_other'),
- uiOutput('entity_scope'),
- uiOutput('entity_classification_name'),
- uiOutput('entity_classification_ref')
- )
- ),
-
- #2 cols
- fluidRow(
- #metric
- column(6,
- span(textOutput("metric_header"), style="font-size:21px; font-weight: bold"),
- numericInput('metric_no', 'Please inicate the amount of Metrics. Minimum 1.', value = 1,
- width = '80%',min = 1, max = 10),
- span(textOutput("metric_desc"), style="font-size:14px"),
- uiOutput('metric_container')
- ),
- #scenario
- column(6,
- span(textOutput("scenario_header"), style="font-size:21px; font-weight: bold"),
- numericInput('scenario_no', 'Please inicate the amount of Scenarios. None needed.', value = 0,
- width = '80%', min = 0, max = 10),
- span(textOutput("scenario_desc"), style="font-size:14px"),
- uiOutput('scenario_container'),
-
- )
- )
-
- #end 2. tab
- ),
- #3. tab: spat. temp. attributes----
- tabPanel('Spatial and temporal domain',
- #2 cols
- fluidRow(
- #spatial domain
- column(6,
- #tags$b('Spatial Domain'),
-
- #spatial scope
- selectInput("spatial_scope", tags$span(style="font-size: 18px; font-weight: bold", "Spatial Scope*"),
- c("Global" = "Global",
- "Continental/Regional" = "Continental/Regional",
- "National" = "National",
- "Sub-national/Local"="Sub-national/Local"),
- width='80%'),
-
- #spatial description
- uiOutput('spatial_desc'),
-
- #spatial units
- selectInput("spatial_units", tags$span(style="font-size: 18px; font-weight: bold", "Spatial Units*"),
- c("degrees" = "degrees",
- "meters" = "meters"),
- width='80%'),
-
-
- ),
- #temporal domain
- column(6,
- #tags$b('Temporal Domain'),
-
- #temporal resoultion
- selectInput("temporal_resolution", tags$span(style="font-size: 18px; font-weight: bold", "Temporal Resolution*"),
- c("decadal" = "P0010-00-00",
- "annually" = "P0001-00-00",
- "monthly" = "P0000-01-00",
- "weekly" = "P0000-00-07",
- "daily" = "P0000-00-01",
- 'one timestep' = "P0000-00-00",
- "irregular" = "Irregular",
- "paleo" = "Paleo",
- "other" = "other"),
- width='80%'),
-
- #other temporal resolution
- uiOutput('temporal_resoultion_other'),
-
- #irregular temporal resolution
- uiOutput('temporal_resoultion_irregular'),
-
- #temporal extent
- uiOutput('temporal_extent'),
-
- #tags$b('Temporal Extent'),
- # dateInput('temp_start', tags$span(style="font-size: 18px; font-weight: bold",
- # 'Start date of the dataset*'), width='80%',
- # startview ='year'),
- # dateInput('temp_end', tags$span(style="font-size: 18px; font-weight: bold",
- # 'End date of the dataset*'), width='80%',
- # startview ='year')
-
-
-
- )
- )
-
- #end 3. tab
- ),
- #4. tab: check and output generation----
- tabPanel('Save metadata to file',
-
- textInput('outputpath', tags$span(style="font-size: 18px; font-weight: bold", 'Outputpath*')), #value='C:\\Users\\lq39quba\\Desktop\\ebv_terranova\\bla.json'
-
- actionButton('create_json', label = "Create JSON file.", class = "btn-lg btn-success"),
-
- verbatimTextOutput("value")
- )
- )
-)
-
-server <- function(input, output) {
-
- nodata <- 'N/A'
- # #show summary example
- # observeEvent(input$summary_example, {
- # output$summary_error <- renderText({'jey'})
- # showModal(modalDialog(
- # title= "Summary Example",
- # text = "Add a summary Example",
- # type = 'info',
- # closeOnClickOutside = T,
- # easyClose = T
- # ))
- # })
-
- #check summary length
- summary_text <- reactive({input$summary})
- output$summary_error <- renderText({
- if(nchar(summary_text())>1500){
- "Your summary is too long! Max. 1500 characters."
- }
- })
-
- #add info to cct
- output$cct_desc <- renderText({'The coverage content type indicates the source of the data. Several options may be selected.'})
-
- #Get EBV Class to define EBV Names
- output$ebv_name <- renderUI({
- if(input$ebv_class=='Genetic composition'){
- selectInput("ebv_name", tags$span(style="font-size: 18px; font-weight: bold", "EBV Name"),
- c("Genetic diversity (richness and heterozygosity)" = "Genetic diversity",
- "Genetic differentiation (number of genetic units and genetic distance)"="Genetic differentiation",
- "Effective population size"="Effective population size",
- "Inbreeding"="Inbreeding",
- "None"="N/A"),
- width='80%')
- }else if(input$ebv_class=='Species populations'){
- selectInput("ebv_name", "EBV Name",
- c('Species distributions'='Species distributions',
- 'Species abundances'='Species abundances',
- 'None'='N/A'),
- width='80%')
- }else if(input$ebv_class=='Species traits'){
- selectInput("ebv_name", "EBV Name",
- c('Morphology'='Morphology',
- 'Physiology'='Physiology',
- 'Phenology'='Phenology',
- 'Movement'='Movement',
- 'None'='N/A'),
- width='80%')
- }else if(input$ebv_class=='Community composition'){
- selectInput("ebv_name", "EBV Name",
- c('Community abundance'='Community abundance',
- 'Taxonomic/phylogenetic diversity'='Taxonomic/phylogenetic diversity',
- 'Trait diversity'='Trait diversity',
- 'Interaction diversity'='Interaction diversity',
- 'None'='N/A'),
- width='80%')
- }else if(input$ebv_class=='Ecosystem functioning'){
- selectInput("ebv_name", "EBV Name",
- c('Primary productivity'='Primary productivity',
- 'Ecosystem phenology'='Ecosystem phenology',
- 'Ecosystem disturbances'='Ecosystem disturbances',
- 'None'='N/A'),
- width='80%')
- }else if(input$ebv_class=='Ecosystem structure'){
- selectInput("ebv_name", "EBV Name",
- c('Live cover fraction'='Live cover fraction',
- 'Ecosystem distribution'='Ecosystem distribution',
- 'Ecosystem Vertical Profile'='Ecosystem Vertical Profile',
- 'None'='N/A'),
- width='80%')
- }else if(input$ebv_class=='N/A'){
- selectInput("ebv_name", "EBV Name",
- c('None'='N/A'),
- width='80%')
- }
-
- })
-
- #add UI for ebv_domain
- output$ebv_domain_other <- renderUI({
- e <- tryCatch(
- {
- if('Other' %in% input$ebv_domain){
- textInput('ebv_domain_other_txt', tags$span(style="font-weight: bold", 'Other environmental domain*'), width='80%',
- placeholder = 'Name of other environmental domain here.')}
- },
- error = function(e){}
- )
- })
-
- #add UI for biological entity
- output$entity_other <- renderUI({
- if(input$biological_entity=='Other'){
- textAreaInput('entity_other_txt', 'Other', width='90.5%',
- placeholder = 'Name of the other entity type.')
- }
- })
-
- output$entity_scope <- renderUI({
- if(input$biological_entity!='N/A'){
- textAreaInput('entity_scope_txt', tags$span(style="font-weight: bold", 'Entity Scope'), width='90.5%',
- placeholder = 'A description of the range of taxa or ecosystem types addressed in the dataset. E.g. "300 species of mammals”, “Forests”, etc..')
- }
- })
-
- output$entity_classification_name <- renderUI({
- if(input$biological_entity!='N/A'){
- textInput('entity_classification_name_txt', tags$span(style="font-weight: bold", 'Classification System Name'), width='90.5%',
- placeholder = 'E.g. Linnaean classification')
- }
- })
-
- output$entity_classification_ref <- renderUI({
- if(input$biological_entity!='N/A'){
- textInput('entity_classification_ref_txt', tags$span(style="font-weight: bold", 'Classification System Reference'), width='90.5%',
- placeholder = 'Reference of the classification system as a URL.')
- }
- })
-
- #metric definition
- output$metric_header <- renderText({'Metric*'})
- output$metric_desc <- renderText({'Provide the name, description and units of the metric(s).'})
-
- #create input fields for all metrics
- output$metric_container <- renderUI({
- out <- lapply(1:input$metric_no, function(i) {
-
- #linebreak + header per metric
- b <- tags$br()
- h <- tags$b(tags$span(style="font-size: 17px", paste0('Metric ', i)))
-
- #standard_name
- sn <- textInput(paste0('metric_standard_name_',i), 'Name*', width='90.5%',
- placeholder = paste0('Name of Metric ', i))
-
-
- #description/long_name
- ln <- textAreaInput(paste0('metric_long_name_',i), 'Description*', width='90.5%',
- placeholder = paste0('Description of Metric ', i))
-
- #units
- u <- textInput(paste0('metric_units_',i), 'Units*', width='90.5%',
- placeholder = paste0('Units of Metric ', i))
-
- return(list(b, h, sn, ln, u))
-
- })
-
- })
-
- #scenario definition
- output$scenario_header <- renderText({'Scenario'})
- output$scenario_desc <- renderText({
- if(input$scenario_no>0){
- "If applicable, name the scenario's classification system, the version and provide a URL to the reference."
- }
- })
-
- #ask for scenario classification
- output$scenario_container <- renderUI({
- if(input$scenario_no>0){
- #create input fields for all scenarios
- out <- lapply(1:input$scenario_no, function(i) {
-
- if(i==1){
- scn <- textInput('scenario_classification_name', 'Classification Name', width='90.5%',
- placeholder = 'Name of scenario classification system, e.g. SSP')
-
- scv <- textInput('scenario_classification_version', 'Classification Version', width='90.5%',
- placeholder = 'Version of scenario classification system, e.g. 1.0')
-
- scu <- textInput('scenario_classification_url', 'Classification URL', width='90.5%',
- placeholder = 'Reference of scenario classification system, e.g. https://www.aza.org/species-survival-plan-programs')
- }
-
- #linebreak + header per scenario
- b <- tags$br()
- h <- tags$b(tags$span(style="font-size: 17px", paste0('Scenario ', i)))
-
- #standard_name
- sn <- textInput(paste0('scenario_standard_name_',i), 'Name*', width='90.5%',
- placeholder = paste0('Name of Scenario ', i))
-
-
- #description/long_name
- ln <- textAreaInput(paste0('scenario_long_name_',i), 'Description', width='90.5%',
- placeholder = paste0('Description of Scenario ', i))
-
- if(i==1){
- return(list(scn, scv, scu, b, h, sn, ln))
- }else{
- return(list(b, h, sn, ln))
- }
-
- })
- }
-
- })
-
- #spatial description
- output$spatial_desc <- renderUI({
- if(input$spatial_scope!='Global'){
- textInput('spatial_desc_txt', tags$span(style="font-size: 18px; font-weight: bold", 'Spatial Description*'), width='80%',
- placeholder='Name(s)/description of the continent/region/country/area')
- }
- })
-
- #other temporal resoultion
- output$temporal_resoultion_other <- renderUI({
- if(input$temporal_resolution=='other'){
- t <- renderText('Provide the definition of your temporal resoultion in the ISO 8601:2004 duration format P(YYYY)-(MM)-(DD).
- Examples: decadal: P0010-00-00 and daily: P0000-00-01')
-
- s <- textInput('temp_res_txt', '', width='80%', placeholder='P0000-00-00')
- return(list(t,s))
- }
- })
- output$temporal_resoultion_irregular <- renderUI({
- if(input$temporal_resolution=='Irregular' | input$temporal_resolution=='Paleo'){
- if(input$temporal_resolution=='Irregular'){
- t <- renderText('Provide the definition of your timesteps as a comma-separated list in the format YYYY-MM-DD or short YYYY.')
- s <- textInput('temp_res_irr', '', width='80%', placeholder='YYYY, YYYY, ...')
- return(list(t,s))
- }else{
- t <- renderText('Provide the definition of your timesteps as a comma-separated list. The values will represent "kyr B.P.".')
- s <- textInput('temp_res_irr', '', width='80%', placeholder='126, 125, ...')
- return(list(t,s))
- }
- }
- })
-
-
- #check variables
- to_do_list <- c()
- create <- TRUE
-
- #temporal extent----
- output$temporal_extent <- renderUI({
- if(input$temporal_resolution!='Irregular' & input$temporal_resolution!='Paleo'){
- if(input$temporal_resolution=='other'){
- #user defined temporal resolution
- if(grepl('^P{1}\\d{4}-00-00', input$temp_res_txt)){
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "yyyy")
- } else if(grepl('^P{1}\\d{4}-\\d{2}-00$', input$temp_res_txt)){
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "mm-yyyy")
- } else if (grepl('^P{1}\\d{4}-\\d{2}-\\d{2}$', input$temp_res_txt)){
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "dd-mm-yyyy")
- }else{
- create <- FALSE
- to_do_list <- c(to_do_list, 'Your temporal resolution does not match the ISO duration format.')
- }
-
- }else if(input$temporal_resolution=='P0000-00-00'){
- #one timestep only
- dateInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Date of the dataset*'), width='80%',
- startview ='year')
-
- }else if(grepl('^P{1}\\d{4}-00-00$', input$temporal_resolution)){
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "yyyy")
- } else if(grepl('^P{1}\\d{4}-\\d{2}-00$', input$temporal_resolution)){
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "mm-yyyy")
- } else {
- dateRangeInput('temporal_extent_input', tags$span(style="font-size: 18px; font-weight: bold",
- 'Start and end date of the dataset*'),
- format = "dd-mm-yyyy")
- }
- }
-
- })
-
-
- #submit button clicked -----
- observeEvent(input$create_json,{
- #start checks----
-
- #check if outputpath is empty
- if(input$outputpath==''){
- output$value <- renderPrint({'You need to give an outputpath.'})
- }else{
- #check filepath
- if (checkmate::checkCharacter(input$outputpath) != TRUE){
- output$value <- renderPrint({'Outputpath must be of type character.'})
- } else if(checkmate::checkDirectoryExists(dirname(input$outputpath)) != TRUE){
- output$value <- renderPrint({paste0('Output directory does not exist.\n', dirname(input$outputpath))})
- } else if(!endsWith(input$outputpath, '.json')){
- output$value <- renderPrint({'Outputpath needs to end with *.json'})
- } else {
-
- #check title
- if(nchar(input$title)==0){
- to_do_list <- c('You must give a title.', to_do_list)
- create <- FALSE
-
- } else if(!is.na(suppressWarnings(as.numeric(input$title)))){
- to_do_list <- c('You title must contain characters.', to_do_list)
- create <- FALSE
- }
-
- #check summary
- if(nchar(input$summary)==0){
- to_do_list <- c('You must provide a summary.', to_do_list)
- create <- FALSE
-
- } else if(!is.na(suppressWarnings(as.numeric(input$summary)))){
- to_do_list <- c('You summary must contain characters.', to_do_list)
- create <- FALSE
- }
- if (nchar(input$summary)!=0 & nchar(input$summary)>1500){
- to_do_list <- c('Your summary is too long. Max. 1500 characters.', to_do_list)
- create <- FALSE
- }
-
- #check references - not mandatory
- if(nchar(input$references)==0){
- references <- nodata
- }else{
- references <- stringr::str_split(input$references, ',')[[1]]
- references <- stringr::str_remove_all(references, ' ')
- }
-
- #check methods
- if(nchar(input$methods)==0){
- to_do_list <- c('You must provide a description of the method.', to_do_list)
- create <- FALSE
-
- } else if(!is.na(suppressWarnings(as.numeric(input$methods)))){
- to_do_list <- c('You method must contain characters.', to_do_list)
- create <- FALSE
- }
-
- #check content coverage type
- if(!is.null(need(input$coverage_content_type != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to choose at least one value for the content coverage type.')
- create <- FALSE
- }
-
- #check project_name
- if(!is.null(need(input$project_name != '', TRUE))){
- project_name <- 'TERRANOVA - The European Landscape Learning Initiative'
- }else{
- project_name <- 'TERRANOVA - The European Landscape Learning Initiative'
- }
-
- #check project_url
- if(!is.null(need(input$project_url != '', TRUE))){
- project_url <- 'https://www.terranova-itn.eu'
- }else{
- project_url <- 'https://www.terranova-itn.eu'
- }
-
- #check creator_name
- if(!is.null(need(input$creator_name != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a creator name.')
- create <- FALSE
- }
-
- #check creator_email
- if(!is.null(need(input$creator_email != '', TRUE))){
- creator_email <- nodata
- }else{
- creator_email <- input$creator_email
- }
-
- #check creator_institution
- if(!is.null(need(input$creator_institution != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a creator institution.')
- create <- FALSE
- }
-
- #check publisher_name
- if(!is.null(need(input$publisher_name != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a publisher name.')
- create <- FALSE
- }
-
- #check publisher_email
- if(!is.null(need(input$publisher_email != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a publisher email.')
- create <- FALSE
- }
-
- #check publisher_instiution
- if(!is.null(need(input$publisher_institution != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a publisher institution.')
- create <- FALSE
- }
-
- #check contributors_names
- if(!is.null(need(input$contributor_names != '', TRUE))){
- contributors_names <- nodata
- }else{
- contributors_names <- input$contributor_names
- }
-
- #check license
- if(!is.null(need(input$license != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a license URL.')
- create <- FALSE
- }
-
- #check comment
- if(!is.null(need(input$comment != '', TRUE))){
- comment <- nodata
- }else{
- comment <- input$comment
- }
-
- #check ebv_class
- if(!is.null(need(input$ebv_class != '', TRUE))){
- ebv_class <- nodata
- }else{
- ebv_class <- input$ebv_class
- }
-
- #check ebv_name
- if(!is.null(need(input$ebv_name != '', TRUE))){
- ebv_name <- nodata
- }else{
- ebv_name <- input$ebv_name
- }
-
- #check ebv_domain
- if(!is.null(need(input$ebv_domain != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide an environmental domain.')
- create <- FALSE
- }else{
- if('Other' %in% input$ebv_domain){
- if(!is.null(need(input$ebv_domain_other_txt != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a description of the other environmental domain.')
- create <- FALSE
- }
- #create ebv_domain value
- ebv_domain_value <- c(input$ebv_domain[! input$ebv_domain %in% c('Other')], input$ebv_domain_other_txt)
-
- }else{
- #create ebv_domain value
- ebv_domain_value <- c(input$ebv_domain)
- }
- }
-
- #check biological_entity
- if(!is.null(need(input$biological_entity != '', TRUE))){
- biological_entity <- nodata
- }else{
- biological_entity <- input$biological_entity
- }
-
- #check entity_scope
- if(biological_entity=='Other'){
- if(!is.null(need(input$entity_other_txt != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a description of the entity type as you chose Other.')
- create <- FALSE
- }
- } else{
- #entity_other_txt
- if(!is.null(need(input$entity_other_txt != '', TRUE))){
- entity_other_txt <- nodata
- }else{
- entity_other_txt <- input$entity_other_txt
- }
- }
-
- #entity_class_name
- if(!is.null(need(input$entity_scope_txt != '', TRUE))){#HERE
- entity_scope_txt <- nodata
- }else{
- entity_scope_txt <- input$entity_scope_txt
- }
-
- #entity_class_name
- if(!is.null(need(input$entity_classification_name_txt != '', TRUE))){
- entity_classification_name_txt <- nodata
- }else{
- entity_classification_name_txt <- input$entity_classification_name_txt
- }
-
- #entity_class_url
- if(!is.null(need(input$entity_classification_ref_txt != '', TRUE))){
- entity_classification_ref_txt <- nodata
- }else{
- entity_classification_ref_txt <- input$entity_classification_ref_txt
- }
-
-
- #check metric attributes
- if(input$metric_no>0){
- for(i in 1:input$metric_no){
- if(!is.null(need(eval(parse(text = paste0('input$metric_standard_name_', i))) != '', TRUE))){
- to_do_list <- c(to_do_list, paste0('The name for metric ',i,' is missing.'))
- create <- FALSE
- }
- if(!is.null(need(eval(parse(text = paste0('input$metric_long_name_', i))) != '', TRUE))){
- to_do_list <- c(to_do_list, paste0('The description for metric ',i,' is missing.'))
- create <- FALSE
- }
- if(!is.null(need(eval(parse(text = paste0('input$metric_units_', i))) != '', TRUE))){
- to_do_list <- c(to_do_list, paste0('The units for metric ',i,' are missing.'))
- create <- FALSE
- }
-
- }
- }
-
- #check scenario attributes
- if(input$scenario_no>0){
- for(i in 1:input$scenario_no){
- if(!is.null(need(eval(parse(text = paste0('input$scenario_standard_name_', i))) != '', TRUE))){
- to_do_list <- c(to_do_list, paste0('The name for scenario ',i,' is missing.'))
- create <- FALSE
- }
- # if(!is.null(need(eval(parse(text = paste0('input$scenario_long_name_', i))) != '', TRUE))){
- # to_do_list <- c(to_do_list, paste0('The description for scenario ',i,' is missing.'))
- # create <- FALSE
- # }
- }
-
- #scenario_classification_name
- if(!is.null(need(input$scenario_classification_name != '', TRUE))){
- scenario_classification_name <- nodata
- }else{
- scenario_classification_name <- input$scenario_classification_name
- }
-
- #scenario_classification_version
- if(!is.null(need(input$scenario_classification_version != '', TRUE))){
- scenario_classification_version <- nodata
- }else{
- scenario_classification_version <- input$scenario_classification_version
- }
-
- #scenario_classification_url
- if(!is.null(need(input$scenario_classification_url != '', TRUE))){
- scenario_classification_url <- nodata
- }else{
- scenario_classification_url <- input$scenario_classification_url
- }
- }
-
- #spatial scope
- if(!is.null(need(input$spatial_scope != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a value for the spatial scope.')
- create <- FALSE
- }
-
- #spatial description
- if(input$spatial_scope != 'Global'){
- if(!is.null(need(input$spatial_desc_txt != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a description of the spatial scope.')
- create <- FALSE
- }else{
- spatial_desc_txt <- input$spatial_desc_txt
- }
- } else{
- spatial_desc_txt <- nodata
- }
-
- #temporal resolution
- if(input$temporal_resolution =='other'){
- t_res <- input$temp_res_txt
- if(!is.null(need(input$temp_res_txt != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to define the temporal resolution.')
- create <- FALSE
- }else{
- if(!grepl('^P\\d{4}-\\d{2}-\\d{2}$', input$temp_res_txt)){
- to_do_list <- c(to_do_list, 'The definition of the temporal resoultion is incorrect. Follow the format: PYYYY-MM-DD. Example: P0010-00-00.')
- create <- FALSE
- }
- }
- }else{
- t_res <- input$temporal_resolution
- }
-
- #check the input of the irregulare timesteps
- if(input$temporal_resolution=='Irregular'){
- timestep_list <- stringr::str_split(input$temp_res_irr, ',')[[1]]
- timestep_list <- gsub(' ', '', timestep_list) #remove whitespaces
- print(timestep_list)
- ts_irr_wrong <- FALSE
- for(ts in timestep_list){
- if(grepl('^\\d{4}-\\d{2}-\\d{2}$', ts) | grepl('^\\d{4}$', ts)){
- #pass
- }else{
- ts_irr_wrong <- TRUE
- }
- }
- if(ts_irr_wrong){
- to_do_list <- c(to_do_list, 'You chose "Irregular" temporal resolution and the input you provided does not match the required form: comma-separated YYYY-MM-DD or comma-separated YYYY. Please check.')
- create <- FALSE
- }
- }
- if(input$temporal_resolution=='Paleo'){
- timestep_list <- stringr::str_split(input$temp_res_irr, ',')[[1]]
- for(ts in timestep_list){
- if(is.na(suppressWarnings(as.numeric(ts)))){
- to_do_list <- c(to_do_list, paste0('You chose "paleo" temporal resolution. The value "', ts, '" does not seem to be a numeric value. Please check.'))
- create <- FALSE
- }
- }
- }
-
- #temporal extent
- if(input$temporal_resolution=='Irregular'){
- timestep_list <- stringr::str_split(input$temp_res_irr, ',')[[1]]
- t_start <- min(timestep_list)
- t_end <- max(timestep_list)
- timesteps_irr <- paste0('"', paste0(timestep_list, collapse = '", "'), '"')
- }else if(input$temporal_resolution=='Paleo'){
- timestep_list <- as.numeric(stringr::str_split(input$temp_res_irr, ',')[[1]])
- t_start <- max(timestep_list)
- t_end <- min(timestep_list)
- timesteps_irr <- paste0('"', paste0(timestep_list, collapse = '", "'), '"')
- }else if(input$temporal_resolution=='P0000-00-00'){
- t_start <-input$temporal_extent_input
- t_end <- input$temporal_extent_input
- }else{
- t_start <- input$temporal_extent_input[1]
- t_end <- input$temporal_extent_input[2]
- }
- if(input$temporal_resolution!='Irregular' & input$temporal_resolution!='Paleo'){
- timesteps_irr <- '"N/A"'
- }
-
-
- #check terranova type
- if(!is.null(need(input$terranova_type != '', TRUE))){
- to_do_list <- c(to_do_list, 'You need to provide a value for the type of the data.')
- create <- FALSE
- }
-
- #output errors for user ----
- if(create==FALSE){
- to_do_list <- c('Your metadata contains the following errors:', to_do_list)
- output$value <- renderPrint({paste(to_do_list, sep='\n')})
- }
-
- #create json----
- if(create){
- #inform user
- output$value <- renderPrint({'Creating Metadata file'})
-
- #create metric
- if(input$metric_no>0){
- ebv_metric <- ''
- for(i in 1:input$metric_no){
- ebv_metric <- paste0(ebv_metric, '\n\t\t\t\t"ebv_metric_',i,'": {
- ":standard_name": "',eval(parse(text = paste0('input$metric_standard_name_', i))),'",
- ":long_name": "',eval(parse(text = paste0('input$metric_long_name_', i))),'",
- ":units": "',eval(parse(text = paste0('input$metric_units_', i))),'"\n\t\t\t\t}')
- if(i != input$metric_no){
- ebv_metric <- paste0(ebv_metric, ',')
- }
- }
- }
-
- #create scenario
- if (input$scenario_no > 0){
- ebv_scenario <- paste0('"ebv_scenario": {
- "ebv_scenario_classification_name": "',scenario_classification_name,'",
- "ebv_scenario_classification_version": "',scenario_classification_version,'",
- "ebv_scenario_classification_url": "',scenario_classification_url,'",')
- for(i in 1:input$scenario_no){
- if(!is.null(need(eval(parse(text = paste0('input$scenario_long_name_', i))) != '', TRUE))){
- long_name <- nodata
- } else{
- long_name <- eval(parse(text = paste0('input$scenario_long_name_', i)))
- }
- ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t\t"ebv_scenario_',i,'": {
- ":standard_name": "',eval(parse(text = paste0('input$scenario_standard_name_', i))),'",
- ":long_name": "',long_name,'"
- }')
- if(i != input$scenario_no){
- ebv_scenario <- paste0(ebv_scenario, ',')
- }
- }
- ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t},')
- } else {
- ebv_scenario <- '"ebv_scenario": "N/A",'
- }
-
-
-
- #create json
- json <- paste0('{
- "data": [
- {
- "id": "pending",
- "naming_authority": "The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig",
- "title": "', input$title ,'",
- "date_created": "',input$date_created,'",
- "summary": "',input$summary,'",
- "references": [\n\t\t\t\t"',paste0(unlist(references), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
- "source": "',input$methods,'",
- "coverage_content_type": [\n\t\t\t\t"',paste0(input$coverage_content_type, collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
- "project": "',project_name,'",
- "project_url": "',project_url,'",
- "creator": {
- "creator_name": "',input$creator_name,'",
- "creator_email": "', creator_email,'",
- "creator_institution": "',input$creator_institution,'"
- },
- "contributor_name": [\n\t\t\t\t"',paste0(stringr::str_remove_all(stringr::str_split(contributors_names, ',')[[1]], ' '), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
- "license": "',input$license,'",
- "publisher": {
- "publisher_name": "',input$publisher_name,'",
- "publisher_email": "',input$publisher_email,'",
- "publisher_institution": "',input$publisher_institution,'"
- },
- "ebv": {
- "ebv_class": "',ebv_class,'",
- "ebv_name": "',ebv_name,'"
- },
- "ebv_entity": {
- "ebv_entity_type": "',biological_entity,'",
- "ebv_entity_scope": "', entity_scope_txt,'",
- "ebv_entity_classification_name": "',entity_classification_name_txt,'",
- "ebv_entity_classification_url": "',entity_classification_ref_txt,'"
- },
- "ebv_metric": {',
- ebv_metric,
- '\n\t\t\t},\n\t\t\t',
- ebv_scenario,
- '\n\t\t\t"ebv_geospatial": {
- "ebv_geospatial_scope": "',input$spatial_scope,'",
- "ebv_geospatial_description": "',spatial_desc_txt,'"
- },
- "geospatial_lat_units": "',input$spatial_units,'",
- "geospatial_lon_units": "',input$spatial_units,'",
- "time_coverage": {
- "time_coverage_resolution": "',t_res,'",
- "time_coverage_start": "',t_start,'",
- "time_coverage_end": "',t_end,'"
- },
- "ebv_domain": [\n\t\t\t\t"', paste0(ebv_domain_value, collapse = '",\n\t\t\t\t"'),'"\n\t\t\t],
- "comment": "',comment,'",
- "terranova_type": "', input$terranova_type,'",
- "timesteps": [\n\t\t\t\t', timesteps_irr, '\n\t\t\t]
- }
- ]
-}')
-
-
- #write to file and set encoding
- withr::with_options(list(encoding = "UTF-8"), write(json, input$outputpath))
- }
-
-
- }
- }
- })
-
-
-
-}
-
-shinyApp(ui, server)
-
-#To Do
-#pre-filled values for keywords: keywords:
-#Anthropogenic activity / biodiversity / climate /