Windows Script Component for Parsing XML with Perl. Perl Scripts can be invoked Via JavaScript by Invoking ActiveX Controls

input.xml

<?xml version="1.0" encoding="utf-8"?>
<order>
	<attributes>
		<attribute name="protocol" value ="PCR_Setup"/>
		<attribute name="samples_per_source" value ="0"/>
		<attribute name="plates_Sealed" value ="0"/>
		<attribute name ="Add_Sample" value ="1"/>
		<attribute name="Tip Box" value ="96 V11 LT250 Tip Box 19477.002"/>
	</attributes>

	<pcr_plates>
		<barcode master_mix_volume="40" sample_volume="20">PCR-001</barcode>
		<barcode master_mix_volume="20" sample_volume="10">PCR-002</barcode>
		<barcode master_mix_volume="30" sample_volume="20">PCR-003</barcode>
		<barcode master_mix_volume="30" sample_volume="20">PCR-004</barcode>
		<barcode master_mix_volume="30" sample_volume="20">PCR-005</barcode> 
	</pcr_plates>

	<sample_plates Labware ="96 Corning black FL assay" peel="false" seal ="true">
		<barcode>SP-A0294</barcode>
		<barcode>SP-A0316</barcode>
		<barcode>SP-B0916</barcode>
		<barcode>SP-C0815</barcode>
		<barcode>SP-C0915</barcode>
	</sample_plates>
	
</order>

InputParser.wsc

<?xml version="1.0"?>
<component>
   <registration   
    description="XML Inputfile Parser"
    progid="perl.inputparser"
    version="1.00"
    classid="{74bb1ba9-2e69-4ad6-b02c-c52f3cbe153b}"
    >
    </registration>

    <public>
		<method name="OpenInput"/>
		<method name="SaveInput"/>
		<method name="getPCR_PlateAttributes"/>
		<method name="getSamplePlateAttributes"/>
		<method name="getPCRbarcodeAttributes"/>
		<method name="getSampleBarcodeAttributes"/>
		<method name="getOrderAttributes"/>
		<method name="getNumberPCRplates"/>
		<method name="getNumberSamplePlates"/>
    </public>

	<script language="PerlScript">
		<![CDATA[
#!/usr/bin/perl
# InputParserClass

use XML::Simple;
use File::Copy;
my $xml = new XML::Simple;


my $doc;

my $inputFile;
# Load InputFile into Memmory
sub OpenInput{
	$inputFile =$_[0];
	$doc= $xml->XMLin($_[0], keyattr =>[]);

}

sub SaveInput{

copy($inputFile, $_[0]);

}


# getOrderAttributes(attribute);
sub getOrderAttributes{

my $node = $doc->{attributes}->{attribute};
#$nodeLength =  $#{$node};

my $itemFound = 0;

  foreach $item (@{$node}){

    if($item->{name} eq $_[0])
    {
      $itemFound = 1;
      return $item->{value};
    }


}

  if(!$itemFound)
  {

    return "Error: getOrderAttributes found $itemFound attributes named [$_[0]], expected to find 1";

  }


}

# getPCR_PlateAttributes(attribute);
sub getPCR_PlateAttributes{

my $node = $doc->{pcr_plates}->{$_[0]};


  if(!$node)
  {

    return "Error: getPCR_PlateAttributes found 0 attributes named [$_[0]], expected to find 1";

  }
  else
  {

    return $node;

  }


}

# getPCR_PlateAttributes(attribute);
sub getSamplePlateAttributes{

my $node = $doc->{sample_plates}->{$_[0]};


  if(!$node)
  {

    return "Error: getSamplePlateAttributes found 0 attributes named [$_[0]], expected to find 1";

  }
  else
  {

    return $node;

  }


}


#  getPCRplateAttributes(barcode, attribute);
sub getPCRbarcodeAttributes{

  my $node = $doc->{pcr_plates}->{barcode};
  my $barcodeFound = 0;
  my $attributeFound =0;

  foreach $item (@{$node}){

    my $bc = $item->{content};

    if($bc eq $_[0])
    {
      $barcodeFound = 1;

      my $barcodeAttribute = $item->{$_[1]};

      if($barcodeAttribute)
        {
          return $barcodeAttribute;
        }
        else
        {
          return "Error: getPCRplateAttributes found 0 attributes named [$_[1]], expected to find 1";

        }
    }
}

    if(!$barcodeFound)
    {

      return "Error: getOrderAttributes found $barcodeFound Barcodes named [$_[0]], expected to find 1";

    }
}
#  getSamplePlateAttributes(barcode, attribute);
sub getSampleBarcodeAttributes{

  my $node = $doc->{sample_plates}->{barcode};
  my $barcodeFound = 0;
  my $attributeFound =0;

  foreach $item (@{$node}){

    my $bc = $item->{content};

    if($bc eq $_[0])
    {
      $barcodeFound = 1;

      my $barcodeAttribute = $item->{$_[1]};

      if($barcodeAttribute)
        {
          return $barcodeAttribute;
        }
        else
        {
          return "Error: getSamplePlateAttributes found 0 attributes named [$_[1]], expected to find 1";

        }
    }
}

    if(!$barcodeFound)
    {

      return "Error: getSamplePlateAttributes found $barcodeFound Barcodes named [$_[0]], expected to find 1";

    }
}

#------------------------------------------------------------------------------
sub getNumberPCRplates{

   my $node = $doc->{pcr_plates}->{barcode};
   my $nodeLength =  $#{$node};

    return $nodeLength + 1;


}

sub getNumberSamplePlates{
    my $node = $doc->{sample_plates}->{barcode};
    my $nodeLength =  $#{$node};

    return $nodeLength + 1;




}
     

     


    ]]>
	</script>



</component>

main.js

print("Starting Watcher")

open("C:/VWorks Workspace/Scripts/Shared Scripts/FileUtilities.js")
open("C:/VWorks Workspace/Scripts/Shared Scripts/XML_files.js")
var VWorksFolder = "C:/VWorks Workspace/"
var WorkingFolder = VWorksFolder + "WorkingFolder/"
var OutputFolder = VWorksFolder + "Output/"
print("OutputFolder : [" + OutputFolder + "]")

function main(input_file_name) {

    var ip = new ActiveX("perl.inputparser")

    var pe = new ActiveX("protocol.editor")

    print("Opening Input File  [" + input_file_name + "]")


    ip.OpenInput(input_file_name)
    var time_string = getTimeString()
    var working_input_filename = WorkingFolder + time_string + "_" + StripPath(input_file_name)

    print(working_input_filename)
    ip.SaveInput(working_input_filename);
    print("Success")

    //--Edit Protocol

    print("Editing Protocol")
    pe.loadProtocol("C:\\VWorks Workspace\\Protocol Files\\Templates\\PCR.pro")

    var startupScripts = "var ip = new ActiveX(\"perl.inputparser\") \n" + "ip.OpenInput(\"" + working_input_filename + "\")"

    pe.findAndReplace("//startup_scripts", startupScripts);


    if(ip.getOrderAttributes("plates_Sealed") == "0")
        pe.deleteTask("Xpeel_task");


    if (ip.getOrderAttributes("Add_Sample") == "0") {
        
        pe.deleteSubProcess("Add Sample", "Bravo")
        pe.deleteProcess("Sample Tips");
        pe.deleteProcess("Sample Plate");
    
    
    }

    var protocolPath = pe.saveProtocol("C:\\VWorks Workspace\\WorkingFolder\\", "PCR", 1)


    DeleteFile(input_file_name);
    runset.appendProtocolFileToRunset(protocolPath, ip.getNumberPCRplates(), "", "")


}