R/buildJabRefConfigFiles.r

In Matherion/metabefor: Facilitating systematic review and meta-analyses

buildJabRefConfigFiles <- function(screeners = c("a", "b"),
                                   screenerFieldsPrefix = "screener",
                                   screenerFieldsSuffix = "status",
                                   fields = (c("title", "abstract")),
                                   duplicateField = NULL,
                                   sortField = "title",
                                   sortDesc = FALSE,
                                   screeningType = "screening",
                                   jabrefVersion = "2.10",
                                   outputPath = getwd(),
                                   jabrefXML = NULL,
                                   batFile = NULL,
                                   generateSettingRemovalBatchFile = FALSE,
                                   screenerSuffixInFilename = FALSE) {

  res <- list(input = c(list(call = sys.call()),
                        as.list(environment()),
                        list(sysCall = as.list(sys.call()))),
              intermediate = list(batFile = batFile),
              output = list());
                           
  res$intermediate$screenerFields = paste0(screenerFieldsPrefix, screeners, screenerFieldsSuffix);
  
  if (!is.null(duplicateField)) {
    res$intermediate$fields <- fields <- c(fields, duplicateField);
  }
  
  if (is.null(res$intermediate$batFile)) {
    res$intermediate$batFile <- paste0('java -jar JabRef-', jabrefVersion, '.jar --primp "SYSREV_XMLFILENAME"');
  }
  
  if (!is.null(jabrefXML)) {
    jabrefXML <- readLines(jabrefXML);
  }
  else {
    ### Generate basic Jabref configuration file
    if (jabrefVersion == "2.10") {
      jabrefXML <- '<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE preferences SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<preferences EXTERNAL_XML_VERSION="1.0">
  <root type="user">
    <map/>
    <node name="net">
      <map/>
      <node name="sf">
        <map/>
        <node name="jabref">
          <map>
            <entry key="memoryStickMode" value="true"/>
            <entry key="windowMaximised" value="true"/>
            <entry key="dialogWarningForDuplicateKey" value="false"/>
            <entry key="dialogWarningForEmptyKey" value="false"/>
            <entry key="useImportInspectionDialog" value="false"/>
            <entry key="useImportInspectionDialogForSingle" value="false"/>
            <entry key="enforceLegalBibtexKey" value="false"/>
            <entry key="confirmDelete" value="true"/>
            <entry key="allowTableEditing" value="false"/>
            <entry key="timeStampFormat" value="yyyy.MM.dd"/>
            <entry key="timeStampField" value="timestamp"/>
            <entry key="allowTableEditing" value="true"/>
            <entry key="defaultEncoding" value="UTF8"/>
            <entry key="backup" value="true"/>
            <entry key="autoSave" value="true"/>
            <entry key="autoSaveInterval" value="5"/>
            <entry key="defaultShowSource" value="false"/>
            <entry key="autoComplete" value="true"/>
            <entry key="autoCompleteFields" value="author;editor;title;journal;publisher;keywords;crossref;SYSREV_SCREENERFIELD"/>
            <entry key="fileColumn" value="false"/>
            <entry key="pdfColumn" value="false"/>
            <entry key="urlColumn" value="false"/>
            <entry key="citeseerColumn" value="false"/>
            <entry key="arxivColumn" value="false"/>
            <entry key="showSource" value="false"/>
            <entry key="preview0" value="\\begin{title} \\format[HTMLChars]{\\title} \\end{title}&lt;BR&gt;"/>
            <entry key="preview1" value="\\begin{title} \\format[HTMLChars]{\\title} \\end{title}&lt;BR&gt;"/>
            <entry key="customTabName_0" value="Screening"/>
            <entry key="customTabFields_0" value="SYSREV_FIELDS;SYSREV_SCREENERFIELD"/>
            <entry key="columnNames" value="SYSREV_FIELDS;SYSREV_SCREENERFIELD"/>
            <entry key="columnWidths" value="SYSREV_FIELDWIDTHS"/>
            <entry key="numberColWidth" value="50"/>
            <entry key="priSort" value="SYSREV_SORTFIELD"/>
            <entry key="priDescending" value="SYSREV_SORTDESCENDING"/>
            <entry key="entryEditorHeight" value="600"/>
            <entry key="previewPanelHeight" value="0"/>
            <entry key="customTypeName_0" value="SYSREV_SCREENINGTYPE"/>
            <entry key="customTypeReq_0" value=""/>
            <entry key="customTypeOpt_0" value="SYSREV_FIELDS"/>
            <entry key="customTypePriOpt_0" value="SYSREV_FIELDS"/>
          </map>
          <node name="labelPattern">
            <map/>
          </node>
        </node>
      </node>
    </node>
  </root>
</preferences>';
    }
    else {
      stop("The basic configuration file for this version of JabRef is not yet implemented!");
    }
  }
  
  res$intermediate$screenerXML <- list()
  for (currentScreener in 1:length(screeners)) {
    
    res$intermediate$screenerXML[[currentScreener]] <- jabrefXML;
    
    ### Replace screenerfield for this screener
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_SCREENERFIELD", res$intermediate$screenerFields[currentScreener], res$intermediate$screenerXML[[currentScreener]]);
    
    ### Replace fields to screen
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_FIELDS", paste0(fields, collapse=";"), res$intermediate$screenerXML[[currentScreener]]);
    
    ### Replace field widths
    fieldWidths <- paste0(paste(round(rep(1000/length(fields), length(fields))), collapse=";"), ";100");
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_FIELDWIDTHS", fieldWidths, res$intermediate$screenerXML[[currentScreener]]);
    
    ### Replace fields to screen
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_SCREENINGTYPE", screeningType, res$intermediate$screenerXML[[currentScreener]]);

    ### Replace field to sort on and direction of sorting
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_SORTFIELD", sortField, res$intermediate$screenerXML[[currentScreener]]);
    res$intermediate$screenerXML[[currentScreener]] <- gsub("SYSREV_SORTDESCENDING", tolower(as.character(sortDesc)), res$intermediate$screenerXML[[currentScreener]]);
    
    if (screenerSuffixInFilename) {
      filenameSuffix <- paste0(" - ", screeners[currentScreener]);
    }
    else {
      filenameSuffix <- "";
    }
    ### Write config file
    writeLines(res$intermediate$screenerXML[[currentScreener]],
               paste0(outputPath, "/jabref", filenameSuffix, ".xml"));
    ### Write batch file to open JabRef with config file
    writeLines(gsub("SYSREV_XMLFILENAME", paste0("jabref", filenameSuffix, ".xml"), res$intermediate$batFile),
               paste0(outputPath, "/screen", filenameSuffix, ".bat"));
    
    ### Is requested, write registry file and batch file to remove settings
    if (generateSettingRemovalBatchFile) {
      writeLines("REGEDIT4\n[-HKEY_CURRENT_USER\\Software\\JavaSoft\\Prefs\\net\\sf\\jabref]",
                 paste0(outputPath, "/remove jabref settings (windows only).reg"));
      writeLines('regedit /S "remove jabref settings (windows only).reg"',
                 paste0(outputPath, "/remove jabref settings (windows only).bat"));
    }
  }
  
  return(res);

}