set_producing_units bug fix (#17)

* add testthat for unit testing

* add testthat for unit testing

* update function names to tidyverse style guide: public functions in snake case. Private functions prefixed by .

* update function name and documentation conform to tidyverse snake case style guide

* remove old function name man files

* initial commit snake case function naming

* snake case function naming initial commit

* remove old function name man files

* initial commit snake case function names

* set_DOI to set_doi

* set_DOI to set_doi

* write.readMe to write_readme

* arguments to snake case

* arguments to snake case

* arguments to snake case

* set_DOI to set_doi

* delete man file for old read me function name

* write_readme initial commit

* Version to 0.0.1.1 - all function and argument names changed to snake case.

* delete this random file

* rename internal function objects using snake_case

* enforce tidyverse style via styler

* add pkgdown

* add pkdown files

* add github.io url

* update examples for snake case function names

* snake case function names via knit

* initial commit

* remove blank spaces

* remove 'docs'

* initial commit via pkgdown

* initial commit via pkgdown

* docs added via pkgdown

* fix For_or_by_nps

* set_park_units now works if there are no previous geographic coverage elements, if there is 1 or if there are more than 1 pre-existing geographic coverages.

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 R/EML_editor.R
 .Rhistory
+docs

DESCRIPTION

@@ -28,3 +28,4 @@ Imports:
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+URL: https://roblbaker.github.io/EMLeditor/

R/editEMLfunctions.R

@@ -72,21 +72,21 @@ set_doi<-function(eml_object, ds_ref, NPS=TRUE){
 
   #If there is a DOI, find the correct doi by searching for the text "doi: ".
   else{
-    mylist<-NULL
+    my_list<-NULL
 
     #hopefully deals with case when there are multiple DOIs specified under alternateIdentifier tags. Haven't run into this yet and so this remains untested.
     if(length(doc)>1){
       for(i in seq_along(doc)){
         if(stringr::str_detect(doc[i], "doi:" )){
-          mylist<-append(mylist, doc[i])
+          my_list<-append(my_list, doc[i])
         }
       }
     }
     #if there is only one alternateIdentifier:
     else{
-      mylist<-doc
+      my_list<-doc
     }
-    doi<-mylist[[1]]
+    doi<-my_list[[1]]
 
     #If a DOI exists, ask the user what to do about it:
     var1<-readline(prompt=cat("Your EML already has a DOI specified in the <alternateIdentifier> tag:\n\n",  doi, "\n\nEnter 1 to retain this DOI\nEnter 2 to overwrite this DOI"))
@@ -203,21 +203,41 @@ set_park_units<-function(eml_object, park_units, NPS=TRUE){
 
   #if there are already geographicCoverage(s)
   else{
-    mylist<-NULL
-    #ditch the '@context' list from the geographicCoverage:
-    for(i in seq_along(names(doc))){
-      if(!names(doc)[i]=='@context'){
-        mylist<-append(mylist, doc[i])
-      }
-    }
+
+    #remove @context from list
+    my_list<-within(doc, rm("@context"))
+
     #remove names from list (critical for writing back to xml)
-    names(mylist)<-NULL
+    names(my_list)<-NULL
+
+    #if there is more than 1 geo coverage:
+    if(length(my_list>2)){
 
-    #combine new and old geo coverages (new always at the top!)
-    mylist<-append(unit_list, mylist)
+      #combine new and old geo coverages (new always at the top!)
+      my_list<-append(unit_list, my_list)
 
-    #write over the existing geographic coverage
-    eml_object$dataset$coverage$geographicCoverage<-mylist
+      #write over the existing geographic coverage
+      eml_object$dataset$coverage$geographicCoverage<-my_list
+    }
+
+    #if there is only one geo coverage:
+    if(length(my_list==2)){
+
+      geocov2 <- EML::eml$geographicCoverage(geographicDescription =
+                        doc$geographicDescription,
+                        boundingCoordinates = EML::eml$boundingCoordinates(
+                          northBoundingCoordinate =
+                            doc$boundingCoordinates$northBoundingCoordinate,
+                          eastBoundingCoordinate =
+                            doc$boundingCoordinates$eastBoundingCoordinate,
+                          southBoundingCoordinate =
+                            doc$boundingCoordinates$southBoundingCoordinate,
+                          westBoundingCoordinate =
+                            doc$boundingCoordinates$westBoundingCoordinate))
+
+      #add park unit connections and existing geo coverage (park units always on top!)
+      eml_object$dataset$coverage$geographicCoverage <- list(geocov, geocov2)
+    }
   }
 
   #Set NPS publisher, if it doesn't already exist
@@ -259,46 +279,46 @@ set_cui<-function(eml_object, cui_code=c("PUBFUL", "PUBVER", "NOCON", "DL ONLY",
   cui_code<-match.arg(cui_code)
 
   #Generate new CUI element for additionalMetadata
-  myCUI<-list(metadata=list(CUI=cui_code), id="CUI")
+  my_cui<-list(metadata=list(CUI=cui_code), id="CUI")
 
   #get existing additionalMetadata elements:
   doc<-EML::eml_get(eml_object, "additionalMetadata")
 
   #if no prior additionalMetadata elements, add CUI to additionalMetadata:
   if(sum(names(doc)!="@context")==0){
-    eml_object$additionalMetadata<-myCUI
+    eml_object$additionalMetadata<-my_cui
   }
 
   #if additionalMetadata already exists:
   if(sum(names(doc)!="@context")>0){
-    mylist<-NULL
+    my_list<-NULL
     #ditch the '@context' list from doc:
     for(i in seq_along(names(doc))){
       if(!names(doc)[i]=='@context' && !names(doc)[i]=="id"){
-        mylist<-append(mylist, doc[i])
+        my_list<-append(my_list, doc[i])
       }
-    x<-length(mylist)
+    x<-length(my_list)
     }
 
     #Is CUI already specified?
-    existCUI<-NULL
+    exist_cui<-NULL
     for(i in seq_along(doc)){
       if(suppressWarnings(stringr::str_detect(doc[i], "CUI"))){
-        existCUI<-"CUI"
+        exist_cui<-"CUI"
       }
     }
 
     #If existing CUI, stop.
-    if(!is.null(existCUI)){
+    if(!is.null(exist_cui)){
       stop("CUI has already been specified")
     }
     #If no existing CUI, add it in:
-    if(is.null(existCUI)){
+    if(is.null(exist_cui)){
       if(x==1){
-        eml_object$additionalMetadata<-list(myCUI, eml_object$additionalMetadata)
+        eml_object$additionalMetadata<-list(my_cui, eml_object$additionalMetadata)
       }
       if(x>1){
-        eml_object$additionalMetadata[[x+1]]<-myCUI
+        eml_object$additionalMetadata[[x+1]]<-my_cui
       }
     }
   }
@@ -463,10 +483,8 @@ set_lit<-function(eml_object, bibtex_file, NPS=TRUE){
 #' @examples
 #' \dontrun{
 #' prod_units<-c("ABCD", "EFGH")
-#' set_producing_units(eml_object, prod_units
-#'
+#' set_producing_units(eml_object, prod_units)
 #' set_producing_units(eml_object, c("ABCD", "EFGH"))
-#'
 #' set_producing_units(eml_object, "ABCD")
 #' }
 set_producing_units<-function(eml_object, prod_units, NPS=TRUE){
@@ -575,8 +593,8 @@ set_language<-function(eml_object, lang, NPS=TRUE){
   #if the language is already specified in the metadata:
   else{
     if(nchar(lng)==3){
-      fulllang<-dplyr::filter(langcodes, Alpha_3_B==lng)[[4]]
-      cat("The current language is set to ", crayon::blue$bold(lng),", the ISO 639-2 code for ", fulllang, ".", sep="")
+      full_lang<-dplyr::filter(langcodes, Alpha_3_B==lng)[[4]]
+      cat("The current language is set to ", crayon::blue$bold(lng),", the ISO 639-2 code for ", full_lang, ".", sep="")
     }
     else{
       cat("The current language is set to ", crayon::blue$bold(lng),".", sep="")
@@ -616,7 +634,7 @@ set_language<-function(eml_object, lang, NPS=TRUE){
 #' @details set_protocol requires that you have your protocols and projects organized in a specific fashion in DataStore. Errors generated by this function my stem from either a protocol that has not been published (or is not publicly available) or an obsolete protocol/project organization within DataStore.
 #'
 #' @param eml_object is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
-#' @param protocol_ID a string. The 7-digit number identifying the protocol in DataStore under which the data were collected.
+#' @param protocol_id a string. The 7-digit number identifying the DataStore reference number for the Project that describes your inventory or monitoring project.
 #' @param NPS Logical. Checks EML for NPS publisher info and injects it if publisher is empty. If publisher already exists, does nothing. If you are not publishing with NPS, set to FALSE. If NPS=TRUE, the originatingAgency will be set to NPS and the field that maps to DataStore's "by or for NPS" will be set to TRUE.
 #'
 #' @return
@@ -627,32 +645,32 @@ set_language<-function(eml_object, lang, NPS=TRUE){
 #' set_protocol(eml_object, 2222140)
 #' }
 #'
-set_protocol<-function(eml_object, protocol_ID, NPS=TRUE){
+set_protocol<-function(eml_object, protocol_id, NPS=TRUE){
 
   #get data to construct project:
 
   #get protocol profile via rest services:
-  ds_reference <- httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/",protocol_ID)))
+  ds_reference <- httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/",protocol_id)))
 
   #extract project title
-  projTitle<-ds_reference$bibliography$title
+  proj_title<-ds_reference$bibliography$title
 
   #generate URL for the DataStore landing page:
-  URL<-paste0("https://irma.nps.gov/DataStore/Reference/Profile/", protocol_ID)
+  url<-paste0("https://irma.nps.gov/DataStore/Reference/Profile/", protocol_id)
 
   #get DataStore ref number for the organization Name:
   ref<-ds_reference$series$referenceId
 
   #rest services call to get organization name info:
-  orgName<-httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/", ref)))$bibliography$title
+  org_name<-httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/", ref)))$bibliography$title
 
   #Construct a project to inject into EML. Note 'role' is required but not sure what to put there.
   #Also i find it confusing that onlineURL references projTitle not orgName but hopefully we will hash that out soon.
 
-  proj<-list(title=projTitle,
-             personnel=list(organizationName=orgName,
-                            onlineUrl=URL,
-                            role="contentContainer"))
+  proj<-list(title=proj_title,
+             personnel=list(organizationName=org_name,
+                            onlineUrl=url,
+                            role="originator"))
 
   #get existing project (if any)
   doc<-eml_object$dataset$project