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lint ebv_metadata
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@LuiseQuoss
LuiseQuoss committed Jul 11, 2024
1 parent b60e58f commit 5f0798f
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Showing 3 changed files with 59 additions and 58 deletions.
1 change: 1 addition & 0 deletions .lintr
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ linters: linters_with_defaults(
line_length_linter = NULL,
quotes_linter = NULL,
commented_code_linter = NULL,
object_length_linter = NULL,
cyclocomp_linter = NULL,
paren_body_linter = NULL,
infix_spaces_linter = NULL,
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110 changes: 55 additions & 55 deletions R/ebv_metadata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -170,10 +170,10 @@ ebv_metadata <- function(outputpath, title, summary,
}

#check logical arguments
if(checkmate::checkLogical(overwrite, len=1, any.missing=F) != TRUE){
if(checkmate::checkLogical(overwrite, len=1, any.missing=FALSE) != TRUE){
stop('overwrite must be of type logical.')
}
if(checkmate::checkLogical(verbose, len=1, any.missing=F) != TRUE){
if(checkmate::checkLogical(verbose, len=1, any.missing=FALSE) != TRUE){
stop('verbose must be of type logical.')
}

Expand Down Expand Up @@ -213,13 +213,13 @@ ebv_metadata <- function(outputpath, title, summary,
}
}

if(scenario_no>0 & is.null(ebv_scenario_classification_name)){
if(scenario_no>0 && is.null(ebv_scenario_classification_name)){
warning('You defined at least one scenario but did not define the ebv_scenario_classification_name. Are you sure you do not want to give that information?')
}
if(scenario_no>0 & is.null(ebv_scenario_classification_version)){
if(scenario_no>0 && is.null(ebv_scenario_classification_version)){
warning('You defined at least one scenario but did not define the ebv_scenario_classification_version. Are you sure you do not want to give that information?')
}
if(scenario_no>0 & is.null(ebv_scenario_classification_url)){
if(scenario_no>0 && is.null(ebv_scenario_classification_url)){
warning('You defined at least one scenario but did not define the ebv_scenario_classification_url. Are you sure you do not want to give that information?')
}

Expand Down Expand Up @@ -287,10 +287,10 @@ ebv_metadata <- function(outputpath, title, summary,
if(! ebv_spatial_scope %in% c('Continental/Regional', 'National', 'Sub-national/Local', 'Global')){
stop('The ebv_spatial_scope needs to be one of the following: ‘Continental/Regional’, ‘National’, ‘Sub-national/Local’ or ‘Global’.')
}
if(ebv_spatial_scope != 'Global' & is.null(ebv_spatial_description)){
if(ebv_spatial_scope != 'Global' && is.null(ebv_spatial_description)){
stop('You chose an ebv_spatial_scope that requires an ebv_spatial_description. Please add.')
}
if(ebv_spatial_scope == 'Global' & !is.null(ebv_spatial_description)){
if(ebv_spatial_scope == 'Global' && !is.null(ebv_spatial_description)){
if(verbose){
warning('You set the ebv_spatial_scope to Global and added some spatial description. The latter is set to NA as this is the rule in the EBV Data Portal.')
}
Expand All @@ -307,7 +307,7 @@ ebv_metadata <- function(outputpath, title, summary,
}

#check content coverage type----
if(! ebv_i_contained(coverage_content_type, c('image','thematicClassification',
if(! ebv_i_contained(coverage_content_type, c('image', 'thematicClassification',
'physicalMeasurement', 'auxiliaryInformation',
'qualityInformation', 'referenceInformation',
'modelResult', 'coordinate'))){
Expand Down Expand Up @@ -362,38 +362,38 @@ ebv_metadata <- function(outputpath, title, summary,
stop('You need to define at least one metric.')
}else if(metric_no>1){
ebv_metric <- paste0('"ebv_metric_1": {
":standard_name": "',metric[[1]]$standard_name,'",
":long_name": "',metric[[1]]$long_name,'",
":units": "',metric[[1]]$units,'"\n\t\t\t\t}')
":standard_name": "', metric[[1]]$standard_name, '",
":long_name": "', metric[[1]]$long_name, '",
":units": "', metric[[1]]$units, '"\n\t\t\t\t}')
if(metric_no>1){
ebv_metric <- paste0(ebv_metric, ',')
for(i in 2:metric_no){
ebv_metric <- paste0(ebv_metric, '\n\t\t\t\t"ebv_metric_',i,'": {
":standard_name": "',metric[[i]]$standard_name,'",
":long_name": "',metric[[i]]$standard_name,'",
":units": "',metric[[i]]$standard_name,'"\n\t\t\t\t}')
ebv_metric <- paste0(ebv_metric, '\n\t\t\t\t"ebv_metric_', i, '": {
":standard_name": "', metric[[i]]$standard_name, '",
":long_name": "', metric[[i]]$standard_name, '",
":units": "', metric[[i]]$standard_name, '"\n\t\t\t\t}')
if(i != metric_no){
ebv_metric <- paste0(ebv_metric, ',')
}
}
}
}else{
ebv_metric <- paste0('"ebv_metric_1": {
":standard_name": "',metric$standard_name,'",
":long_name": "',metric$long_name,'",
":units": "',metric$units,'"\n\t\t\t\t}')
":standard_name": "', metric$standard_name, '",
":long_name": "', metric$long_name, '",
":units": "', metric$units, '"\n\t\t\t\t}')
}

#create scenarios ----
if (scenario_no > 1){
ebv_scenario <- paste0('"ebv_scenario": {
"ebv_scenario_classification_name": "',ebv_scenario_classification_name,'",
"ebv_scenario_classification_version": "',ebv_scenario_classification_version,'",
"ebv_scenario_classification_url": "',ebv_scenario_classification_url,'",')
"ebv_scenario_classification_name": "', ebv_scenario_classification_name, '",
"ebv_scenario_classification_version": "', ebv_scenario_classification_version, '",
"ebv_scenario_classification_url": "', ebv_scenario_classification_url, '",')
for(i in 1:scenario_no){
ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t\t"ebv_scenario_',i,'": {
":standard_name": "',scenario[[i]]$standard_name,'",
":long_name": "',scenario[[i]]$long_name,'"
ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t\t"ebv_scenario_', i, '": {
":standard_name": "', scenario[[i]]$standard_name, '",
":long_name": "', scenario[[i]]$long_name, '"
}')
if(i != scenario_no){
ebv_scenario <- paste0(ebv_scenario, ',')
Expand All @@ -402,12 +402,12 @@ ebv_metadata <- function(outputpath, title, summary,
ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t},')
} else if (scenario_no==1){
ebv_scenario <- paste0('"ebv_scenario": {
"ebv_scenario_classification_name": "',ebv_scenario_classification_name,'",
"ebv_scenario_classification_version": "',ebv_scenario_classification_version,'",
"ebv_scenario_classification_url": "',ebv_scenario_classification_url,'",')
"ebv_scenario_classification_name": "', ebv_scenario_classification_name, '",
"ebv_scenario_classification_version": "', ebv_scenario_classification_version, '",
"ebv_scenario_classification_url": "', ebv_scenario_classification_url, '",')
ebv_scenario <- paste0(ebv_scenario, '\n\t\t\t\t"ebv_scenario_1": {
":standard_name": "',scenario$standard_name,'",
":long_name": "',scenario$long_name,'"
":standard_name": "', scenario$standard_name, '",
":long_name": "', scenario$long_name, '"
}')
}else{
ebv_scenario <- '"ebv_scenario": "N/A",'
Expand All @@ -419,53 +419,53 @@ ebv_metadata <- function(outputpath, title, summary,
{
"id": "pending",
"naming_authority": "The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig",
"title": "', title ,'",
"date_created": "',date_created,'",
"summary": "',summary,'",
"references": [\n\t\t\t\t"',paste0(unlist(references), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
"source": "',source,'",
"coverage_content_type": [\n\t\t\t\t"',paste0(unlist(coverage_content_type), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
"project": "',project_name,'",
"project_url": "',project_url,'",
"title": "', title, '",
"date_created": "', date_created, '",
"summary": "', summary, '",
"references": [\n\t\t\t\t"', paste0(unlist(references), collapse='",\n\t\t\t\t"'), '"\n\t\t\t],
"source": "', source, '",
"coverage_content_type": [\n\t\t\t\t"', paste0(unlist(coverage_content_type), collapse='",\n\t\t\t\t"'), '"\n\t\t\t],
"project": "', project_name, '",
"project_url": "', project_url, '",
"creator": {
"creator_name": "',creator_name,'",
"creator_email": "',creator_email,'",
"creator_institution": "',creator_institution,'"
"creator_name": "', creator_name, '",
"creator_email": "', creator_email, '",
"creator_institution": "', creator_institution, '"
},
"contributor_name": [\n\t\t\t\t"',paste0(unlist(contributor_name), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
"license": "',license,'",
"contributor_name": [\n\t\t\t\t"', paste0(unlist(contributor_name), collapse='",\n\t\t\t\t"'), '"\n\t\t\t],
"license": "', license, '",
"publisher": {
"publisher_name": "N/A",
"publisher_email": "N/A",
"publisher_institution": "N/A"
},
"ebv": {
"ebv_class": "',ebv_class,'",
"ebv_name": "',ebv_name,'"
"ebv_class": "', ebv_class, '",
"ebv_name": "', ebv_name, '"
},
"ebv_entity": {
"ebv_entity_type": "',ebv_entity_type,'",
"ebv_entity_scope": "',ebv_entity_scope,'",
"ebv_entity_classification_name": "',ebv_entity_classification_name,'",
"ebv_entity_classification_url": "',ebv_entity_classification_url,'"
"ebv_entity_type": "', ebv_entity_type, '",
"ebv_entity_scope": "', ebv_entity_scope, '",
"ebv_entity_classification_name": "', ebv_entity_classification_name, '",
"ebv_entity_classification_url": "', ebv_entity_classification_url, '"
},
"ebv_metric": {\n\t\t\t\t',
ebv_metric,
'\n\t\t\t},\n\t\t\t',
ebv_scenario,
'\n\t\t\t"ebv_spatial": {
"ebv_spatial_scope": "',ebv_spatial_scope,'",
"ebv_spatial_description": "',ebv_spatial_description,'"
"ebv_spatial_scope": "', ebv_spatial_scope, '",
"ebv_spatial_description": "', ebv_spatial_description, '"
},
"geospatial_lat_units": "N/A",
"geospatial_lon_units": "N/A",
"time_coverage": {
"time_coverage_resolution": "',time_coverage_resolution,'",
"time_coverage_start": "',time_coverage_start,'",
"time_coverage_end": "',time_coverage_end,'"
"time_coverage_resolution": "', time_coverage_resolution, '",
"time_coverage_start": "', time_coverage_start, '",
"time_coverage_end": "', time_coverage_end, '"
},
"ebv_domain": [\n\t\t\t\t"',paste0(unlist(ebv_domain), collapse='",\n\t\t\t\t"'),'"\n\t\t\t],
"comment": "',comment,'"
"ebv_domain": [\n\t\t\t\t"', paste0(unlist(ebv_domain), collapse='",\n\t\t\t\t"'), '"\n\t\t\t],
"comment": "', comment, '"
}
]
}')
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6 changes: 3 additions & 3 deletions R/ebv_utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -916,8 +916,8 @@ ebv_i_check_url <- function(url){
#'
#' @return List with unique elements contained in both lists
#' @noRd
ebv_i_vector_intersect <- function(v,z) {
unlist(lapply(unique(v[v%in%z]), function(x) rep(x,min(sum(v==x),sum(z==x)))))
ebv_i_vector_intersect <- function(v, z) {
unlist(lapply(unique(v[v%in%z]), function(x) rep(x, min(sum(v==x), sum(z==x)))))
}

#' Checks if list 1 is contained in list 2
Expand All @@ -930,4 +930,4 @@ ebv_i_vector_intersect <- function(v,z) {
#'
#' @return Returns TRUE list 1 is contained in list 2, else FALSE
#' @noRd
ebv_i_contained <- function(v,z) {length(ebv_i_vector_intersect(v,z))==length(v)}
ebv_i_contained <- function(v, z) {length(ebv_i_vector_intersect(v, z))==length(v)}

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