initial commit

.Rbuildignore

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+^EMLeditor\.Rproj$
+^\.Rproj\.user$

.Rhistory

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+library(devtools)
+install.packages("roxygen")
+library(roxygen)

.gitignore

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+.Rproj.user

DESCRIPTION

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+Package: EMLeditor
+Title: View and Edit EML
+Version: 0.0.0.9000
+Authors@R: 
+    person("Robert", "Baker", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-7591-5035"))
+Description: This package will be of most use to the U.S. National Park Service. EML-formatted .xml files are typically constructed using EDI's EMLassemblyline package and then imported as an R-object using the EML package. EMLeditor allows the user to view the contents of the R object and add aspects of metadata crucial for publication in the U.S. National Park Service DataStore repository. For instance, a user can view and edit a DOI, a link to a DRR, Park Unit connections, information about Confidential Unclassified Information (CUI), and more. EMLeditor allows the user to write a mockup of a README.txt to preview what the README automatically generated by DataStore upon upload will look like.
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
+    license
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.0
+Depends:
+    EML,
+    arcticdatautils,
+    magrittr,
+    stringr,
+    gdata,
+    stargazer
+Remotes: NCEAS/arcticdatautils

EMLeditor.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method(edit,DOI)
+export(eml_getNPS)
+export(eml_get_simpleNPS)
+export(get.CUI)
+export(get.DOI)
+export(get.DRRdoi)
+export(get.DSRefID)
+export(get.abstract)
+export(get.authorList)
+export(get.beginDate)
+export(get.citation)
+export(get.endDate)
+export(get.fileInfo)
+export(get.parkUnits)
+export(get.title)
+export(set.CUI)
+export(set.DOI)
+export(set.DRRdoi)
+export(set.parkUnits)

R/editEMLfunctions.R

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+#' Check & set a DOI
+#'
+#' @details
+#' This function checks to see if there is a DOI in the <alternateIdentifier> tag. The EMLassemblyline package stores datapackage DOIs in this tag (although the official EML schema has the DOI in a different location). If there is no DOI in the <alternateIdentifier> tag, the function adds a DOI. If there is a DOI, the function alerts the users to this fact, reports the existing DOI, and suggests using a separate function to edit an existing DOI (edit.DOI()).
+#'
+#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param DOI is the same as the 7-digit reference code generated on DataStore when a draft reference is initiated. Don't worry about the https://wwww.doi.org and the datapackage prefix - those will all automatically be added in by the function.
+#' @returns an EML-formatted R object
+#' @export
+set.DOI<-function(emlObject, DOI){
+  doc<-arcticdatautils::eml_get_simple(emlObject, "alternateIdentifier") #where EMLassemblyline stores DOIs.
+  #if a DOI exists, report that it already exists and prompt to edit:
+  if(!is.null(doc)){
+    mylist<-NULL
+    #doc<-unlist(doc)
+    if(length(doc)>1){
+      for(i in 1:length(names(doc))){
+        if(stringr::str_detect(doc[i], "doi:" )){
+          mylist<-append(mylist, doc[i])
+        }
+      }
+    }
+    else{
+      mylist<-doc
+    }
+    doi<-mylist[[1]]
+    cat("Your EML already has a DOI specified in the <alternateIdentifier> tag:\n",  doi, "\n\nIf this is correct, no further action is needed. To edit your existing DOI, run \'edit.DOI()\'")
+  }
+  #if there is no DOI, add it directly:
+  else{
+    emlObject$dataset$alternateIdentifier<-paste0("doi: https://doi.org/10.57830", DOI)
+  }
+  return(emlObject)
+}
+
+#' Force-edits an existing DOI
+#'
+#' @description edit.DOI forces changes to an existing DOI
+#'
+#' @details
+#' If a DOI already exists in the <alternateidentifier> tag (get.DOI() to check), this allows the user to over-write the existing DOI.  WARNING: will cause loss of the system="https://doi.org" setting. So only use this if you really don't already have a DOI.
+#'
+#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param DOI is the same as the 7-digit reference code generated on DataStore when a draft reference is initiated. Don't worry about the https://wwww.doi.org and the datapackage prefix - those will all automatically be added in by the function.
+#' @returns an EML-formatted R object
+#' @export
+edit.DOI<-function(emlObject, DOI){
+  emlObject$dataset$alternateIdentifier<-paste0("doi:", DOI)
+  return(emlObject)
+}
+
+
+# Add Park Unit Connections to metadata
+#if geographic coverage exists, add to it.
+#if geographic coverage exists, doesn't yet add in id= attribute. Grr.
+
+#' Adds Park Unit Connections to metadata
+#'
+#' @details
+#' Add the Park Unit Connection(s) to a <geographicDescription> tag under <coverage>. Park Unit Connection(s) are the (typically) four-letter codes describing the park unit(s) where data were collected (e.g. ROMO, not ROMN). If there are already =items listed under geographicCoverage, Park Unit Connections will be inserted as the first item in the list of geographicCoverages and will be prefaced by the string "NPS Unit Connections:".
+#'
+#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param ParkUnits a string of comma-separated park unit codes
+#' @returns an EML-formatted R object
+#' @export
+#' @examples
+#' ParkUnits<-("ROMO, GRSD, TRYME")
+#' set.parkUnits(emlObject, ParkUnits)
+set.parkUnits<-function(emlObject, ParkUnits){
+  #get geographic coverage from emlObject
+  doc<-EML::eml_get(emlObject, "geographicCoverage")
+
+  #if there is no geo coverage, add it directly to emlObject
+  if(is.null(doc)){
+    emlObject$dataset$coverage$geographicCoverage$id<-"UnitConnections"
+    emlObject$dataset$coverage$geographicCoverage$geographicDescription<-paste0("NPS Unit Connections: ",ParkUnits)
+  }
+
+  #if there are already geographicCoverage(s)
+  #(unfortunately currently there is no way to ad id="UnitConnections" in this case)
+  else{
+    mylist<-NULL
+    #ditch the '@context' list from the goeCoverage:
+    for(i in 1:length(names(doc))){
+      if(!names(doc)[i]=='@context')
+        mylist<-append(mylist, doc[i])
+    }
+    #remove names from list (critical for writing back to xml)
+    names(mylist)<-NULL
+
+    #add text to indicate that these are park unit connections:
+    units<-paste0("NPS Unit Connections: ", ParkUnits)
+
+    #generate the new geographic coverage elements:
+    geocov2<-list(geographicDescription=units)
+
+    #combine new and old geo coverages (new always at the top!)
+    mylist<-append(list(geocov2), mylist)
+
+    #write over the existing geographic coverage
+    emlObject$dataset$coverage$geographicCoverage<-mylist
+  }
+  return(emlObject)
+}
+
+#' Adds CUI to metadata
+#'
+#' @description set.CUI adds CUI codes to EML metadata
+#'
+#' @details set.CUI adds a CUI code to the tag <CUI> under <additionalMetadata><metadata>.
+#'
+#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param CUI a string consisting of one of 5 potential CUI codes. Pay attention to the spaces:
+#' FED ONLY - Contains CUI. Only federal employees should have access (similar to "internal only" in DataStore)
+#' FEDCON - Contains CUI. Only federal employees and federal contractors should have access (also very much like current "internal only" setting in DataStore)
+#' DL ONLY - Contains CUI. Should only be available to a names list of individuals (where and how to list those individuals TBD)
+#' NOCON - Contains  CUI. Federal, state, local, or tribal employees may have access, but contractors cannot.
+#' PUBVER - Does NOT contain CUI. The original data contained CUI, but in this datapackage CUI have been obscured so that it no longer contains CUI.
+#' PUBFUL - Does NOT contain CUI. The original data contained no CUI. No data were obscured or altered to generate the data package
+#' @returns an EML-formatted R object
+#' @export
+#' @examples
+#' set.CUI(emlObject, "PUBFUL")
+set.CUI<-function(emlObject, CUI){
+  #add those random spaces in case people forget
+  if(CUI=="FEDONLY"){
+    CUI=="FED ONLY"
+  }
+  if(CUI=="DLONLY"){
+    CUI=="DL ONLY"
+  }
+  #add CUI to EML
+  emlObject$additionalMetadata$metadata$CUI<-CUI
+  return(emlObject)
+}
+
+
+
+#' adds DRR connection
+#'
+#' @description set.DRRdoi adds the DOI of an associated DRR
+#'
+#' @details adds uses the DataStore Reference ID for an associate DRR to the <useageCitation> as a properly formatted DOI (prefaced with "DRR: ") to the <useageCitation> tag. ####CAUTION: in the current implimentation this may overwrite any other useageCitation info.
+#'
+#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param DRRrefID a 7-digit string that is the DataStore Reference ID for the DRR associated with the datapackage.
+#' @returns an EML-formatted R object
+#' @export
+#' @examples
+#' set.DRRdoi(emlObject, "2293234")
+set.DRRdoi<-function(emlObject, DRRrefID){
+  doi<-paste0("DRR: https://doi.org/10.57830", DRRdoi)
+  emlObject$dataset$useageCitation<-doi
+  return(emlObject)
+}