Metacat

#!/usr/bin/env perl

# eml_get_objectnames.pl

# Given a list of EML docids and dataids, generate a list of objectName elements

# present in the documents mapped to each dataid, and generate UPDATE SQL statements.

#

# This information is useful because both Morpho and the Metacat Registry historically 

# stored the dataid i n the 'docname' field within xml_documents.

use Metacat;

use Data::Dumper;

use XML::LibXML;

use LWP::UserAgent;

use strict;

############################################################################

#

# MAIN program block

#

############################################################################

# check that the correct number or parameters are passed from the commandline

if (($#ARGV + 1) < 1) {die "Usage: %./eml_get_objectnames.pl <metacat_url>\n\n";}

# Get the URL to the metacat server from the command line options

my $url = @ARGV; 

# Open a metacat connection

my $metacat = openMetacatConnection($url);

my @errorMessages;

my $error;

# requires an input CSV file containing two columns:

# the dataid and docid, which can be extracted from the database:

#   SELECT nodedata, docid FROM xml_nodes WHERE nodetype = 'TEXT' AND nodedata LIKE 'ecogrid%'

# and then trimming the ecogrid prefix from the dataid fields.

my $nameFile = 'docid-for-binaries.txt'; 

unless (open (FILE_LIST, $nameFile)) {

    print "file with docids required.\n";

    exit;

}

while (my $line = <FILE_LIST>) {

    my ($dataid, $docid) = split(',', trim($line));

    my $response = $metacat->read($docid);

    my $metadata = $response->content();

    # Now parse the metadata document, grabbing the objectName for the particular docid

    my $doc = getEMLDoc($metadata);

    my $objName = getObjectName($doc, $dataid);

    if ($objName ne $dataid && $objName ne "" && $objName !~ /deleteme/) {

        my $id = $dataid;

        $id =~ s/\.[0-9]+$//;

        print "UPDATE xml_documents SET docname = '$objName' WHERE docid = '$id';\n";

    }

}

exit;

############################################################################

#

# SUBROUTINES

#

############################################################################

#

# Create a connection to the metacat server

#

sub openMetacatConnection {

    my $url = shift;

    my $metacat = Metacat->new();

    if ($metacat) {

        $metacat->set_options( metacatUrl => $url );

    } else {

        die("Could not open connection to Metacat url: $url\n");

    }

    return $metacat;

}

#

# Retrieve EML documents and set up XML parser object

#

sub getEMLDoc {

    my $resultset = shift;

    my $parser = XML::LibXML->new();

    my $node;

    my $docid;

    my $doc = $parser->parse_string($resultset);

    if ($doc eq "") {

        $error ="Error in parsing the eml document";

        push(@errorMessages, $error);

    } elsif ($doc=~ /<error/) {

        if ($doc=~ /public/) {

            $error ="Error in reading the eml document. Please check if you are logged in.";

            push(@errorMessages, $error);

        } else {

          $error ="Error in reading the eml document. Please check if you have access to read the document";

          push(@errorMessages, $error);

        }

    } else {

        my $findType = $doc->findnodes('//dataset/identifier');

        if ($findType->size() > 0) {

            # This is a eml beta6 document

            # Read the documents mentioned in triples also

            push(@errorMessages, "EML2 beta6 support deprecated.");

        }

    }

    return $doc;

}

#

# Inspect an EML document for objectName elements, return the name if it differs from docid

#

sub getObjectName {

    my $doc = shift;

    my $docid = shift;

    # the five types of physical objects, though only dataTable and otherEntity appear to be used

    my @names = qw(dataTable otherEntity spatialRaster spatialVector storedProcedure);

    my $results;

    my $results_urls;

    my $dataid;

    my $objectName;

    my $offset = 0;

    foreach my $name (@names) {

        $results = $doc->findnodes("//$name/physical/objectName");

        $results_urls = $doc->findnodes("//$name/physical/distribution/online/url");

        foreach my $node ($results_urls->get_nodelist) {

            $offset++;

            $dataid = $node->textContent();

            $dataid =~ s/ecogrid:\/\/knb\///;

            # if the docid == docname, return the objectName

            if ($dataid eq $docid) {

                my $nameNode = $results->get_node($offset);

                if ($nameNode) {

                    $objectName = $nameNode->textContent();

                }

            }

        }

    }

    return $objectName;

}

#

# Remove whitespace from the start and end of the string

#

sub trim($)

{

  my $string = shift;

  $string =~ s/^\s+//;

  $string =~ s/\s+$//;

  return $string;

}