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1 1929 brooke
#!/usr/bin/perl
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#
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#  '$RCSfile$'
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#  Copyright: 2000 Regents of the University of California
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#
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#   '$Author$'
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#     '$Date$'
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# '$Revision$'
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
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#
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#
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# This is a CGI application for inserting metadata documents into
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# the Metacat database.  It utilizes the Metacat.pm module for most work.
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# In this script, we process the form fields passed in from a POST, insert a
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# metadata document and an ACL document.
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use Metacat;
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use AppConfig qw(:expand :argcount);
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use XML::LibXML;
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use XML::LibXSLT;
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use Template;
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use Net::SMTP;
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use CGI qw/:standard :html3/;
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use strict;
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# Global configuration paramters
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#my $cfgdir = "@install-dir@";
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#my $cfgdir = "/usr/local/devtools/tomcat/webapps/knb/style/skins";
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my $cfgdir = "@install-dir@@style-skins-relpath@";
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my $tmpdir = "@temp-dir@";
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my $templatesdir = "@install-dir@@style-common-relpath@/templates";
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my $now = time;
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my $xslConvDir = "$cfgdir/lib/style/";
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# Import all of the HTML form fields as variables
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import_names('FORM');
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# Set up the hash for returning data to the HTML templates
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my $templateVars = { 'status' => 'success' };
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my $error = 0;
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my @errorMessages;
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# create a new AppConfig object and load our config parameters
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# note that this requires the form submission to have a "cfg" paramter
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# to determine which config file to load
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my $config = AppConfig->new({
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    GLOBAL => { ARGCOUNT => ARGCOUNT_ONE, } });
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$config->define("metacatUrl");
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$config->define("username");
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$config->define("password");
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$config->define("ldapUrl");
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$config->define("defaultScope");
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$config->define("organization");
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$config->define("orgabbrev");
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$config->define("orgurl");
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$config->define("accesspubid");
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$config->define("accesssysid");
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$config->define("datasetpubid");
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$config->define("datasetsysid");
75 2258 jones
$config->define("showSiteList", { DEFAULT => 'true'} );
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$config->define("lsite", { DEFAULT => 'station'} );
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$config->define("usite", { DEFAULT => 'Station'} );
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$config->define("showWgList", { DEFAULT => 'true'} );
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$config->define("showOrganization", { DEFAULT => 'true'} );
80 2138 sgarg
$config->define("hasKeyword", { DEFAULT => 'true'} );
81 2148 sgarg
$config->define("hasTemporal", { DEFAULT => 'true'} );
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$config->define("hasSpatial", { DEFAULT => 'true'} );
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$config->define("hasTaxonomic", { DEFAULT => 'true'} );
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$config->define("hasMethod", { DEFAULT => 'true'} );
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$config->define("temporalRequired", { DEFAULT => 'true'} );
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$config->define("spatialRequired", { DEFAULT => 'true'} );
87 2644 sgarg
$config->define("publicReadable", { DEFAULT => 'true'} );
88 2645 sgarg
$config->define("accessPrincipals", { DEFAULT => ''} );
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$config->define("accessType", { DEFAULT => ''} );
90 1929 brooke
$config->define("mailhost");
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$config->define("sender");
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$config->define("recipient");
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$config->define("adminname");
94 1973 jones
if ($FORM::cfg eq 'nceas') {
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    $config->define("nceas_db");
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    $config->define("nceas_db_user");
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    $config->define("nceas_db_password");
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}
99 1929 brooke
$config->define("responseTemplate", { DEFAULT => 'crap.tmpl'} );
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$config->define("entryFormTemplate", { DEFAULT => 'crap.tmpl'} );
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$config->define("guideTemplate", { DEFAULT => 'crap.tmpl'} );
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$config->define("confirmDataTemplate", { DEFAULT => 'crap.tmpl'} );
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$config->define("deleteDataTemplate", { DEFAULT => 'crap.tmpl'} );
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$config->define("debug", { DEFAULT => '0'} );
105 1929 brooke
$config->define("lat", { ARGCOUNT => ARGCOUNT_HASH} );
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$config->define("lon", { ARGCOUNT => ARGCOUNT_HASH} );
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if (! hasContent($FORM::cfg)) {
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    $error = "Application misconfigured.  Please contact the administrator.";
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    push(@errorMessages, $error);
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} else {
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    my $cfgfile = $cfgdir . "/" . $FORM::cfg . "/" . $FORM::cfg . ".cfg";
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    $config->file($cfgfile);
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}
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my $metacatUrl = $config->metacatUrl();
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my $username = $config->username();
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my $password = $config->password();
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my $ldapUrl = $config->ldapUrl();
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my $defaultScope = $config->defaultScope();
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my $organization = $config->organization();
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my $orgabbrev = $config->orgabbrev();
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my $orgurl = $config->orgurl();
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my $orgfilter = $organization;
125 2138 sgarg
      $orgfilter =~ s/ /%20/g;
126 1929 brooke
my $responseTemplate = $config->responseTemplate();
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my $entryFormTemplate = $config->entryFormTemplate();
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my $deleteDataTemplate = $config->deleteDataTemplate();
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my $guideTemplate = $config->guideTemplate();
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my $confirmDataTemplate = $config->confirmDataTemplate();
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my $accesspubid = $config->accesspubid();
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my $accesssysid = $config->accesssysid();
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my $datasetpubid = $config->datasetpubid();
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my $datasetsysid = $config->datasetsysid();
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my $showSiteList = $config->showSiteList();
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my $lsite = $config->lsite();
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my $usite = $config->usite();
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my $showWgList = $config->showWgList();
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my $showOrganization = $config->showOrganization();
140 2138 sgarg
my $hasKeyword = $config->hasKeyword();
141 2148 sgarg
my $hasTemporal = $config->hasTemporal();
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my $hasSpatial = $config->hasSpatial();
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my $hasTaxonomic = $config->hasTaxonomic();
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my $hasMethod = $config->hasMethod();
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my $temporalRequired = $config->temporalRequired();
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my $spatialRequired = $config->spatialRequired();
147 2644 sgarg
my $publicReadable = $config->publicReadable();
148 2645 sgarg
my $accessPrincipals = $config->accessPrincipals();
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my $accessType = $config->accessType();
150 1929 brooke
my $mailhost = $config->mailhost();
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my $sender = $config->sender();
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my $recipient = $config->recipient();
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my $adminname = $config->adminname();
154 1973 jones
my $nceas_db;
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my $nceas_db_user;
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my $nceas_db_password;
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if ($FORM::cfg eq 'nceas') {
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    $nceas_db = $config->nceas_db();
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    $nceas_db_user = $config->nceas_db_user();
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    $nceas_db_password = $config->nceas_db_password();
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}
162 1955 jones
my $debug = $config->debug();
163 1929 brooke
my $lat = $config->get('lat');
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my $lon = $config->get('lon');
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# Convert the lat and lon configs into usable data structures
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my @sitelist;
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my %siteLatDMS;
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my %siteLongDMS;
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foreach my $newsite (keys %$lat) {
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    my ($latd, $latm, $lats, $latdir) = split(':', $lat->{$newsite});
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    my ($lond, $lonm, $lons, $londir) = split(':', $lon->{$newsite});
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    push(@sitelist, $newsite);
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    $siteLatDMS{$newsite} = [ $latd, $latm, $lats, $latdir ];
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    $siteLongDMS{$newsite} = [ $lond, $lonm, $lons, $londir ];
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}
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# set some configuration options for the template object
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my $ttConfig = {
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             INCLUDE_PATH => $templatesdir,
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             INTERPOLATE  => 0,
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             POST_CHOMP   => 1,
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             };
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# create an instance of the template processor
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my $template = Template->new($ttConfig) || die $Template::ERROR, "\n";
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print "Content-type: text/html\n\n";
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# Set up the template information that is common to all forms
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$$templateVars{'cfg'} = $FORM::cfg;
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$$templateVars{'recipient'} = $recipient;
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$$templateVars{'adminname'} = $adminname;
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$$templateVars{'organization'} = $organization;
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$$templateVars{'orgabbrev'} = $orgabbrev;
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$$templateVars{'orgurl'} = $orgurl;
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$$templateVars{'orgfilter'} = $orgfilter;
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199 1983 jones
debug("Registry: Initialized");
200 1929 brooke
# Process the form based on stage parameter.
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if ($FORM::stage =~ "guide") {
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    # Send back the information on how to fill the form
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    $$templateVars{'section'} = "Guide on How to Complete Registry Entries";
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    $template->process( $guideTemplate, $templateVars);
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    exit(0);
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} elsif ($FORM::stage =~ "insert") {
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    # The user has entered the data. Do data validation and send back data
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    # to confirm the data that has been entered.
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    toConfirmData();
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    exit(0);
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213 2015 sgarg
}elsif ($FORM::dataWrong =~ "No, go back to editing" && $FORM::stage =~ "confirmed") {
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    # The user wants to correct the data that he has entered.
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    # Hence show the data again in entryData form.
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    confirmDataToReEntryData();
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    exit(0);
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}elsif ($FORM::stage =~ "modify") {
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    # Modification of a file has been requested.
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    # Show the form will all the values filled in.
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    my @sortedSites;
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    foreach my $site (sort @sitelist) {
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        push(@sortedSites, $site);
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    }
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    $$templateVars{'siteList'} = \@sortedSites;
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    $$templateVars{'section'} = "Modification Form";
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    $$templateVars{'docid'} = $FORM::docid;
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    modifyData();
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    exit(0);
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}elsif ($FORM::stage =~ "delete_confirm") {
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    # Result from deleteData form.
235 2415 sgarg
    if($FORM::deleteData =~ "Delete document"){
236 1977 jones
    # delete Data
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    deleteData(1);
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    exit(0);
239 1929 brooke
    } else {
240 2345 sgarg
    $$templateVars{'status'} = "Cancel";
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    $$templateVars{'function'} = "cancel";
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    $template->process( $responseTemplate, $templateVars);
243 1977 jones
    exit(0);
244 1929 brooke
    }
245
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}elsif ($FORM::stage =~ "delete") {
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    # Deletion of a file has been requested.
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    # Ask for username and password using deleteDataForm
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    $$templateVars{'docid'} = $FORM::docid;
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    $template->process( $deleteDataTemplate, $templateVars);
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    exit(0);
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}elsif ($FORM::stage !~ "confirmed") {
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    # None of the stages have been reached and data is not being confirmed.
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    # Hence, send back entry form for entry of data.
256 1983 jones
    debug("Registry: Sending form");
257 1929 brooke
    my @sortedSites;
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    foreach my $site (sort @sitelist) {
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        push(@sortedSites, $site);
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    }
261 1973 jones
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    if ($FORM::cfg eq 'nceas') {
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        my $projects = getProjectList();
264 1974 jones
        $$templateVars{'projects'} = $projects;
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        $$templateVars{'wg'} = \@FORM::wg;
266 1973 jones
    }
267 1974 jones
268 2258 jones
    $$templateVars{'showSiteList'} = $showSiteList;
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    $$templateVars{'lsite'} = $lsite;
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    $$templateVars{'usite'} = $usite;
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    $$templateVars{'showWgList'} = $showWgList;
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    $$templateVars{'showOrganization'} = $showOrganization;
273 2138 sgarg
    $$templateVars{'hasKeyword'} = $hasKeyword;
274 2148 sgarg
    $$templateVars{'hasTemporal'} = $hasTemporal;
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    $$templateVars{'hasSpatial'} = $hasSpatial;
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    $$templateVars{'hasTaxonomic'} = $hasTaxonomic;
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    $$templateVars{'hasMethod'} = $hasMethod;
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    $$templateVars{'temporalRequired'} = $temporalRequired;
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    $$templateVars{'spatialRequired'} = $spatialRequired;
280 2138 sgarg
281 1929 brooke
    $$templateVars{'siteList'} = \@sortedSites;
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    $$templateVars{'section'} = "Entry Form";
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    $$templateVars{'docid'} = "";
284 1983 jones
    debug("Registry: Sending form: ready to process template");
285 1929 brooke
    $template->process( $entryFormTemplate, $templateVars);
286 1983 jones
    debug("Registry: Sending form: template processed");
287 1929 brooke
    exit(0);
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}
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# Confirm stage has been reached. Enter the data into metacat.
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# Initialize some global vars
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my $latDeg1 = "";
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my $latMin1 = "";
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my $latSec1 = "";
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my $hemisphLat1 = "";
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my $longDeg1 = "";
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my $longMin1 = "";
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my $longSec1 = "";
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my $hemisphLong1 = "";
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my $latDeg2 = "";
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my $latMin2 = "";
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my $latSec2 = "";
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my $hemisphLat2 = "";
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my $longDeg2 = "";
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my $longMin2 = "";
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my $longSec2 = "";
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my $hemisphLong2 = "";
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# validate the input form parameters
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my $invalidParams;
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if (! $error) {
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    $invalidParams = validateParameters(1);
315
    if (scalar(@$invalidParams)) {
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        $$templateVars{'status'} = 'failure';
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        $$templateVars{'invalidParams'} = $invalidParams;
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        $error = 1;
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    }
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}
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my $metacat;
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my $docid;
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if (! $error) {
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    # Parameters have been validated and Create the XML document
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    my $xmldoc = createXMLDocument();
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    # Write out the XML file for debugging purposes
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    #my $testFile = $tmpdir . "/test.xml";
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    # Create a  metacat object
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    $metacat = Metacat->new();
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    if ($metacat) {
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        $metacat->set_options( metacatUrl => $metacatUrl );
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    } else {
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        #die "failed during metacat creation\n";
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        push(@errorMessages, "Failed during metacat creation.");
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    }
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    # Login to metacat
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    my $userDN = $FORM::username;
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    my $userOrg = $FORM::organization;
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    my $userPass = $FORM::password;
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    my $dname = "uid=$userDN,o=$userOrg,dc=ecoinformatics,dc=org";
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348 2057 sgarg
    my $xmldocWithDocID = $xmldoc;
349
350 1929 brooke
    my $errorMessage = "";
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    my $response = $metacat->login($dname, $userPass);
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    if (! $response) {
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        push(@errorMessages, $metacat->getMessage());
354
        push(@errorMessages, "Failed during login.\n");
355 2415 sgarg
        $$templateVars{'status'} = 'login_failure';
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        $$templateVars{'errorMessages'} = \@errorMessages;
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        $$templateVars{'docid'} = $docid;
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        $$templateVars{'cfg'} = $FORM::cfg;
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        $$templateVars{'function'} = "submitted";
360
        $$templateVars{'section'} = "Submission Status";
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        $template->process( $responseTemplate, $templateVars);
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        exit(0);
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    } else {
364 1929 brooke
365 2415 sgarg
        debug( "Registry: A");
366
        if ($FORM::docid eq "") {
367
            debug( "Registry: B1");
368
            # document is being inserted
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            my $notunique = "NOT_UNIQUE";
370
            while ($notunique eq "NOT_UNIQUE") {
371
                $docid = newAccessionNumber($defaultScope);
372
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                $xmldocWithDocID = $xmldoc;
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                $xmldocWithDocID =~ s/docid/$docid/;
375 1929 brooke
376 2415 sgarg
                # Code for testing the xml file being inserted####
377
                #my $testFile = "/tmp/test.xml";
378
                #open (TFILE,">$testFile") || die ("Cant open xml file...\n");
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                #print TFILE $xmldoc;
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                #close(TFILE);
381
                ####
382
383
                $notunique = insertMetadata($xmldocWithDocID, $docid);
384
                #  if (!$notunique) {
385
                # Write out the XML file for debugging purposes
386
                #my $testFile = $tmpdir . "/test-new.xml";
387
                #open (TFILE,">$testFile") || die ("Cant open xml file...\n");
388
                #print TFILE $newdoc;
389
                #close(TFILE);
390
                #   }
391
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                # The id wasn't unique, so update our lastid file
393
                if ($notunique eq "NOT_UNIQUE") {
394
                    debug( "Registry: Updating lastid (B1.1)");
395
                    updateLastId($defaultScope);
396
                }
397 1955 jones
            }
398 2415 sgarg
            debug("Registry: B2");
399
            if ($notunique ne "SUCCESS") {
400
                debug("Registry: NO SUCCESS");
401
                debug("Message is: $notunique");
402
                push(@errorMessages, $notunique);
403
            }
404 2056 sgarg
405 2415 sgarg
            debug("Registry: B3");
406
        } else {
407
            # document is being modified
408
            $docid = $FORM::docid;
409 1977 jones
410 2415 sgarg
            my $x;
411
            my $y;
412
            my $z;
413
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            ($x, $y, $z) = split(/\./, $docid);
415
            $z++;
416
            $docid = "$x.$y.$z";
417 1977 jones
418 2415 sgarg
            $xmldoc =~ s/docid/$docid/;
419 1929 brooke
420 2415 sgarg
            my $response = $metacat->update($docid, $xmldoc);
421 1929 brooke
422 2415 sgarg
            if (! $response) {
423
                push(@errorMessages, $metacat->getMessage());
424
                push(@errorMessages, "Failed while updating.\n");
425
            }
426 1929 brooke
427 2415 sgarg
            if (scalar(@errorMessages)) {
428
                debug("Registry: ErrorMessages defined in modify.");
429
430
                $$templateVars{'docid'} = $FORM::docid;
431
        	    copyFormToTemplateVars();
432
                $$templateVars{'status'} = 'failure';
433
                $$templateVars{'errorMessages'} = \@errorMessages;
434
                $error = 1;
435
            } else {
436
                $$templateVars{'docid'} = $docid;
437
        	$$templateVars{'cfg'} = $FORM::cfg;
438
            }
439 2024 sgarg
440 2415 sgarg
            #if (! $error) {
441
                #sendNotification($docid, $mailhost, $sender, $recipient);
442
            #}
443 1977 jones
444 2415 sgarg
            # Create our HTML response and send it back
445
            $$templateVars{'function'} = "modified";
446
            $$templateVars{'section'} = "Modification Status";
447
            $template->process( $responseTemplate, $templateVars);
448
449
            exit(0);
450
        }
451 1929 brooke
    }
452
}
453
454 1955 jones
debug("Registry: C");
455 1929 brooke
456
if (scalar(@errorMessages)) {
457 1955 jones
    debug("Registry: ErrorMessages defined.");
458 2024 sgarg
    $$templateVars{'docid'} = $FORM::docid;
459 2136 sgarg
    copyFormToTemplateVars();
460 1929 brooke
    $$templateVars{'status'} = 'failure';
461
    $$templateVars{'errorMessages'} = \@errorMessages;
462
    $error = 1;
463 2056 sgarg
} else {
464
    $$templateVars{'docid'} = $docid;
465
    $$templateVars{'cfg'} = $FORM::cfg;
466 1929 brooke
}
467
468 1936 jones
#if (! $error) {
469
#sendNotification($docid, $mailhost, $sender, $recipient);
470
#}
471 1929 brooke
472
# Create our HTML response and send it back
473
$$templateVars{'function'} = "submitted";
474
$$templateVars{'section'} = "Submission Status";
475 2056 sgarg
476 1929 brooke
$template->process( $responseTemplate, $templateVars);
477
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exit(0);
479
480
481
################################################################################
482
#
483 1955 jones
# Subroutine for updating a metacat id for a given scope to the highest value
484
#
485
################################################################################
486
sub updateLastId {
487
  my $scope = shift;
488
489
  my $errormsg = 0;
490
  my $docid = $metacat->getLastId($scope);
491
492
  if ($docid =~ /null/) {
493
      # No docids with this scope present, so do nothing
494
  } elsif ($docid) {
495
      # Update the lastid file for this scope
496
      (my $foundScope, my $id, my $rev) = split(/\./, $docid);
497
      debug("Docid is: $docid\n");
498
      debug("Lastid is: $id");
499
      my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
500 2478 sgarg
      open(LASTID, "+>$scopeFile") or
501 1955 jones
          die "Failed to open lastid file for writing!";
502
      print LASTID $id, "\n";
503
      close(LASTID);
504
  } else {
505
    $errormsg = $metacat->getMessage();
506
    debug("Error in getLastId: $errormsg");
507
  }
508
}
509
510
################################################################################
511
#
512 1929 brooke
# Subroutine for inserting a document to metacat
513
#
514
################################################################################
515
sub insertMetadata {
516
  my $xmldoc = shift;
517
  my $docid = shift;
518
519
  my $notunique = "SUCCESS";
520 1989 jones
  debug("Registry: Starting insert (D1)");
521 1929 brooke
  my $response = $metacat->insert($docid, $xmldoc);
522
  if (! $response) {
523 1989 jones
    debug("Registry: Response gotten (D2)");
524 1929 brooke
    my $errormsg = $metacat->getMessage();
525 1989 jones
    debug("Registry: Error is (D3): ".$errormsg);
526 1929 brooke
    if ($errormsg =~ /is already in use/) {
527
      $notunique = "NOT_UNIQUE";
528
      #print "Accession number already used: $docid\n";
529
    } elsif ($errormsg =~ /<login>/) {
530
      $notunique = "SUCCESS";
531
    } else {
532
      #print "<p>Dumping error on failure...</p>\n";
533
      #print "<p>", $errormsg, "</p>\n";
534
      #die "Failed during insert\n";
535
      #print "<p>Failed during insert</p>\n";
536
      $notunique = $errormsg;
537
    }
538
  }
539 1989 jones
  debug("Registry: Ending insert (D4)");
540 1929 brooke
541
  return $notunique;
542
}
543
544
################################################################################
545
#
546
# Subroutine for generating a new accession number
547
#  Note: this is not threadsafe, assumes only one running process at a time
548
#  Also: need to check metacat for max id # used in this scope already
549
################################################################################
550
sub newAccessionNumber {
551
  my $scope = shift;
552
553
  my $docrev = 1;
554
  my $lastid = 1;
555
556
  my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
557
  if (-e $scopeFile) {
558
    open(LASTID, "<$scopeFile") or die "Failed to generate accession number!";
559
    $lastid = <LASTID>;
560
    chomp($lastid);
561
    $lastid++;
562
    close(LASTID);
563
  }
564
  open(LASTID, ">$scopeFile") or die "Failed to open lastid file for writing!";
565
  print LASTID $lastid, "\n";
566
  close(LASTID);
567
568
  my $docroot = "$scope.$lastid.";
569
  my $docid = $docroot . $docrev;
570
  return $docid;
571
}
572
573
################################################################################
574
#
575
# Validate the parameters to make sure that required params are provided
576
#
577
################################################################################
578
sub validateParameters {
579
    my $chkUser = shift;
580
    my @invalidParams;
581
582 2612 sgarg
    push(@invalidParams, "Name of the Project is not selected in the form.")
583
        if (scalar(@FORM::wg) == 0 && $showWgList eq 'true');
584 2415 sgarg
    push(@invalidParams, "First name of person entering the form is missing.")
585 1929 brooke
        unless hasContent($FORM::providerGivenName);
586 2415 sgarg
    push(@invalidParams, "Last name of person entering the form is missing.")
587 1929 brooke
        unless hasContent($FORM::providerSurName);
588 2612 sgarg
    push(@invalidParams, "Dataset title is missing.")
589 2415 sgarg
        unless hasContent($FORM::title);
590 2636 sgarg
    push(@invalidParams, $usite." name is missing.")
591
        unless ((hasContent($FORM::site) && !($FORM::site =~ /^Select/)) ||
592 1974 jones
                $FORM::cfg eq "nceas");
593 2415 sgarg
    push(@invalidParams, "First name of principal data set owner is missing.")
594 1929 brooke
        unless hasContent($FORM::origNamefirst0);
595 2415 sgarg
    push(@invalidParams, "Last name of principal data set owner is missing.")
596 1929 brooke
        unless hasContent($FORM::origNamelast0);
597 2612 sgarg
    push(@invalidParams, "Dataset abstract is missing.")
598 1929 brooke
        unless hasContent($FORM::abstract);
599 2149 sgarg
    if($FORM::hasTemporal eq 'true'){
600 2415 sgarg
	push(@invalidParams, "Year of start date is missing.")
601 2149 sgarg
	    unless (hasContent($FORM::beginningYear) || $FORM::temporalRequired ne 'true');
602 2415 sgarg
	push(@invalidParams, "Year of stop date has been specified but year of start date is missing.")
603 2149 sgarg
	    if ((!hasContent($FORM::beginningYear)) && hasContent($FORM::endingYear));
604
    }
605 1983 jones
    push(@invalidParams, "Geographic description is missing.")
606 2148 sgarg
        unless (hasContent($FORM::geogdesc) || $FORM::spatialRequired ne 'true');
607 1929 brooke
608 2644 sgarg
    if($FORM::beginningMonth eq "MM"){
609
	#if (hasContent($FORM::beginningYear)){
610
	#    $FORM::beginningMonth = "01";
611
	#} else {
612 2149 sgarg
	    $FORM::beginningMonth = "";
613 2644 sgarg
	#}
614 2149 sgarg
    }
615 2644 sgarg
    if($FORM::beginningDay eq "DD"){
616
	#if (hasContent($FORM::beginningYear)){
617
	#    $FORM::beginningDay = "01";
618
	#} else {
619 2149 sgarg
	    $FORM::beginningDay = "";
620 2644 sgarg
	#}
621 2149 sgarg
    }
622 2644 sgarg
    if($FORM::endingMonth eq "MM"){
623
	#if (hasContent($FORM::endingYear)){
624
	#    $FORM::endingMonth = "01";
625
	#} else {
626 2149 sgarg
	    $FORM::endingMonth = "";
627 2644 sgarg
	#}
628 2149 sgarg
    }
629 2644 sgarg
    if($FORM::endingDay eq "DD"){
630
	#if (hasContent($FORM::endingYear)){
631
	#    $FORM::endingDay = "01";
632
	#} else {
633 2149 sgarg
	    $FORM::endingDay = "";
634 2644 sgarg
	#}
635 2149 sgarg
    }
636
637 2152 sgarg
    if (hasContent($FORM::beginningYear) && !($FORM::beginningYear =~ /[0-9][0-9][0-9][0-9]/)){
638 2415 sgarg
	push(@invalidParams, "Invalid year of start date specified.")
639 2152 sgarg
    }
640
641
    if (hasContent($FORM::endingYear) && !($FORM::endingYear =~ /[0-9][0-9][0-9][0-9]/)){
642 2415 sgarg
	push(@invalidParams, "Invalid year of stop date specified.")
643 2152 sgarg
    }
644
645 1929 brooke
    # If the "use site" coord. box is checked and if the site is in
646
    # the longitude hash ...  && ($siteLatDMS{$FORM::site})
647 2149 sgarg
648 2148 sgarg
    if($FORM::hasSpatial eq 'true'){
649
	if (($FORM::useSiteCoord) && ($siteLatDMS{$FORM::site}) ) {
650 1929 brooke
651 2148 sgarg
	    $latDeg1 = $siteLatDMS{$FORM::site}[0];
652
	    $latMin1 = $siteLatDMS{$FORM::site}[1];
653
	    $latSec1 = $siteLatDMS{$FORM::site}[2];
654
	    $hemisphLat1 = $siteLatDMS{$FORM::site}[3];
655
	    $longDeg1 = $siteLongDMS{$FORM::site}[0];
656
	    $longMin1 = $siteLongDMS{$FORM::site}[1];
657
	    $longSec1 = $siteLongDMS{$FORM::site}[2];
658
	    $hemisphLong1 = $siteLongDMS{$FORM::site}[3];
659
660
	}  else {
661
662
	    $latDeg1 = $FORM::latDeg1;
663
	    $latMin1 = $FORM::latMin1;
664
	    $latSec1 = $FORM::latSec1;
665
	    $hemisphLat1 = $FORM::hemisphLat1;
666
	    $longDeg1 = $FORM::longDeg1;
667
	    $longMin1 = $FORM::longMin1;
668
	    $longSec1 = $FORM::longSec1;
669
	    $hemisphLong1 = $FORM::hemisphLong1;
670
	}
671 2152 sgarg
672
	if($latDeg1 > 90 || $latDeg1 < 0){
673
	    push(@invalidParams, "Invalid first latitude degrees specified.");
674
	}
675
	if($latMin1 > 59 || $latMin1 < 0){
676
	    push(@invalidParams, "Invalid first latitude minutes specified.");
677
	}
678
	if($latSec1 > 59 || $latSec1 < 0){
679
	    push(@invalidParams, "Invalid first latitude seconds specified.");
680
	}
681
	if($longDeg1 > 180 || $longDeg1 < 0){
682
	    push(@invalidParams, "Invalid first longitude degrees specified.");
683
	}
684
	if($longMin1 > 59 || $longMin1 < 0){
685
	    push(@invalidParams, "Invalid first longitude minutes specified.");
686
	}
687
	if($longSec1 > 59 || $longSec1 < 0){
688
	    push(@invalidParams, "Invalid first longitude seconds specified.");
689
	}
690
691
	if(hasContent($FORM::latDeg2) && ($FORM::latDeg2 > 90 || $FORM::latDeg2 < 0)){
692
	    push(@invalidParams, "Invalid second latitude degrees specified.");
693
	}
694
	if(hasContent($FORM::latMin2) && ($FORM::latMin2 > 59 || $FORM::latMin2 < 0)){
695
	    push(@invalidParams, "Invalid second latitude minutes specified.");
696
	}
697
	if(hasContent($FORM::latSec2) && ($FORM::latSec2 > 59 || $FORM::latSec2 < 0)){
698
	    push(@invalidParams, "Invalid second latitude seconds specified.");
699
	}
700
	if(hasContent($FORM::latDeg2) && ($FORM::longDeg2 > 180 || $FORM::longDeg2 < 0)){
701
	    push(@invalidParams, "Invalid second longitude degrees specified.");
702
	}
703
	if(hasContent($FORM::latMin2) && ($FORM::longMin2 > 59 || $FORM::longMin2 < 0)){
704
	    push(@invalidParams, "Invalid second longitude minutes specified.");
705
	}
706
	if(hasContent($FORM::latSec2) && ($FORM::longSec2 > 59 || $FORM::longSec2 < 0)){
707
	    push(@invalidParams, "Invalid second longitude seconds specified.");
708
	}
709 1929 brooke
    }
710
711
    # Check if latDeg1 and longDeg1 has values if useSiteCoord is used.
712
    # This check is required because some of the sites dont have lat
713
    # and long mentioned in the config file.
714
715 2148 sgarg
716 2613 sgarg
    if($FORM::hasSpatial eq 'true' && $FORM::spatialRequired eq 'true'){
717 2148 sgarg
	if ($FORM::useSiteCoord ) {
718
	    push(@invalidParams, "The Data Registry doesn't have latitude and longitude information for the site that you chose. Please go back and enter the spatial information.")
719
		unless(hasContent($latDeg1) && hasContent($longDeg1));
720
	}else{
721
	    push(@invalidParams, "Latitude degrees are missing.")
722 2149 sgarg
		unless (hasContent($latDeg1) || $FORM::spatialRequired ne 'true');
723 2148 sgarg
	    push(@invalidParams, "Longitude degrees are missing.")
724 2149 sgarg
		unless (hasContent($longDeg1) || $FORM::spatialRequired ne 'true');
725 2148 sgarg
	}
726 2149 sgarg
	push(@invalidParams,
727
	     "You must provide a geographic description if you provide latitude and longitude information.")
728
	    if ((hasContent($latDeg1) || (hasContent($longDeg1))) && (!hasContent($FORM::geogdesc)));
729 1929 brooke
    }
730
731 2148 sgarg
    if($FORM::hasMethod eq 'true'){
732
	push(@invalidParams,
733
	     "You must provide a method description if you provide a method title.")
734
	    if (hasContent($FORM::methodTitle) && ( !(scalar(@FORM::methodPara) > 0)
735
						    || (! hasContent($FORM::methodPara[0]))));
736
	push(@invalidParams,
737 2415 sgarg
	     "You must provide a method description if you provide an extent of study description.")
738 2148 sgarg
	    if (hasContent($FORM::studyExtentDescription) && (!(scalar(@FORM::methodPara) > 0)
739
							      || (! hasContent($FORM::methodPara[0]))));
740
	push(@invalidParams,
741 2415 sgarg
	     "You must provide both an extent of study description and a sampling description, or neither.")
742 2148 sgarg
	    if (
743 1997 jones
                (hasContent($FORM::studyExtentDescription) && !hasContent($FORM::samplingDescription)) ||
744
                (!hasContent($FORM::studyExtentDescription) && hasContent($FORM::samplingDescription))
745 2148 sgarg
		);
746
    }
747 1989 jones
748 2415 sgarg
    push(@invalidParams, "First name of data set contact is missing.")
749 1977 jones
    unless (hasContent($FORM::origNamefirstContact) ||
750
        $FORM::useOrigAddress);
751 2415 sgarg
    push(@invalidParams, "Last name of data set contact is missing.")
752 1977 jones
    unless (hasContent($FORM::origNamelastContact) ||
753
        $FORM::useOrigAddress);
754 1929 brooke
    push(@invalidParams, "Data medium is missing.")
755 1977 jones
    unless (hasContent($FORM::dataMedium) || $FORM::dataMedium =~ /elect/);
756 2432 sgarg
    push(@invalidParams, "Usage rights are missing.")
757 2415 sgarg
    unless (hasContent($FORM::useConstraints));
758 1929 brooke
759
    return \@invalidParams;
760
}
761
762
################################################################################
763
#
764
# utility function to determine if a paramter is defined and not an empty string
765
#
766
################################################################################
767
sub hasContent {
768
    my $param = shift;
769
770
    my $paramHasContent;
771
    if (!defined($param) || $param eq '') {
772
        $paramHasContent = 0;
773
    } else {
774
        $paramHasContent = 1;
775
    }
776
    return $paramHasContent;
777
}
778
779 2032 sgarg
################################################################################
780
#
781
# Subroutine for replacing characters not recognizable by XML and otherwise.
782
#
783
################################################################################
784
sub normalize{
785
    my $val = shift;
786 1929 brooke
787 2032 sgarg
    $val =~ s/&/&amp;/g;
788
789
    $val =~ s/</&lt;/g;
790
    $val =~ s/>/&gt;/g;
791
    $val =~ s/\"/&quot;/g;
792 2348 sgarg
    $val =~ s/%/&#37;/g;
793
794 2032 sgarg
    my $returnVal = "";
795
796
    foreach (split(//,$val)){
797
	my $var = unpack "C*", $_;
798
799
	if($var<128 && $var>31){
800
	    $returnVal=$returnVal.$_;
801
	} elsif ($var<32){
802
	    if($var == 10){
803
		$returnVal=$returnVal.$_;
804
	    }
805
	    if($var == 13){
806
		$returnVal=$returnVal.$_;
807
	    }
808
	    if($var == 9){
809
		$returnVal=$returnVal.$_;
810
	    }
811
	} else {
812
	    $returnVal=$returnVal."&#".$var.";";
813
	}
814
    }
815
816
    $returnVal =~ s/&/%26/g;
817
    return $returnVal;
818
}
819
820 2037 sgarg
821 1929 brooke
################################################################################
822 2037 sgarg
#
823 2415 sgarg
# Subroutine for replacing characters not recognizable by XML and otherwise
824
# except for ", > amd <.
825
#
826
################################################################################
827
sub delNormalize{
828
    my $val = shift;
829
830
    $val =~ s/&/&amp;/g;
831
832
    $val =~ s/%/&#37;/g;
833
834
    my $returnVal = "";
835
836
    foreach (split(//,$val)){
837
        my $var = unpack "C*", $_;
838
839
        if($var<128 && $var>31){
840
            $returnVal=$returnVal.$_;
841
        } elsif ($var<32){
842
            if($var == 10){
843
                $returnVal=$returnVal.$_;
844
            }
845
            if($var == 13){
846
                $returnVal=$returnVal.$_;
847
            }
848
            if($var == 9){
849
                $returnVal=$returnVal.$_;
850
            }
851
        } else {
852
            $returnVal=$returnVal."&#".$var.";";
853
        }
854
    }
855
856
    $returnVal =~ s/&/%26/g;
857
    return $returnVal;
858
}
859
860
861
################################################################################
862
#
863 2037 sgarg
# Subroutine for replacing characters that might create problem in HTML.
864 2415 sgarg
# Specifically written for " being used in any text field. This creates a
865 2037 sgarg
# problem in confirmData template, when you specify input name value pair
866
# with value having a " in it.
867
#
868
################################################################################
869
sub normalizeCD{
870
    my $val = shift;
871
872
    $val =~ s/\"/&quot;/g;
873
874
    return $val;
875
}
876
877
878
################################################################################
879 1929 brooke
#
880
# Create the XML document from the HTML form input
881
# returns the XML document as a string
882
#
883
################################################################################
884
sub createXMLDocument {
885
886
    my $orig  = "";
887
    my $role  = "associatedParty";
888
    my $creat = "";
889
    my $metaP = "";
890
    my $apart = "";
891
    my $cont  = "";
892
    my $publ  = "";
893
    my $dso   = "";
894
    my $gmt = gmtime($now);
895 2032 sgarg
896
897 1929 brooke
    my $doc =  "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n";
898
899 2032 sgarg
    $doc .= "<eml:eml\n
900 1929 brooke
                     \t packageId=\"docid\" system=\"knb\"\n
901 2223 sgarg
                     \t xmlns:eml=\"eml://ecoinformatics.org/eml-2.0.1\"\n
902 1929 brooke
                     \t xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n
903 2223 sgarg
                     \t xmlns:ds=\"eml://ecoinformatics.org/dataset-2.0.1\"\n
904 1929 brooke
                     \t xmlns:stmml=\"http://www.xml-cml.org/schema/stmml\"\n
905 2223 sgarg
                     \t xsi:schemaLocation=\"eml://ecoinformatics.org/eml-2.0.1 eml.xsd\">\n";
906 1929 brooke
907
    $doc .= "<!-- Person who filled in the catalog entry form: ";
908 2032 sgarg
    $doc .= normalize($FORM::providerGivenName)." ".normalize($FORM::providerSurName)." -->\n";
909 1929 brooke
    $doc .= "<!-- Form filled out at $gmt GMT -->\n";
910
    $doc .= "<dataset>\n";
911
912
    if (hasContent($FORM::identifier)) {
913
        $doc .= "<alternateIdentifier system=\"$FORM::site\">";
914 2032 sgarg
        $doc .= normalize($FORM::identifier) . "</alternateIdentifier>\n";
915 1929 brooke
    }
916
917
    if (hasContent($FORM::title)) {
918 2032 sgarg
        $doc .= "<title>".normalize($FORM::title)."</title>\n";
919 1929 brooke
    }
920
921
    if (hasContent($FORM::origNamelast0)) {
922 1977 jones
    $role = "creator";
923 1929 brooke
        $orig .= "<individualName>\n";
924 2032 sgarg
        $orig .= "<givenName>".normalize($FORM::origNamefirst0)."</givenName>\n";
925
        $orig .= "<surName>".normalize($FORM::origNamelast0)."</surName>\n";
926 1929 brooke
        $orig .= "</individualName>\n";
927
    }
928
929
    if (hasContent($FORM::origNameOrg)) {
930 2032 sgarg
        $orig .= "<organizationName>".normalize($FORM::origNameOrg)."</organizationName>\n";
931 1929 brooke
    }
932
933
    if (hasContent($FORM::origDelivery) || hasContent($FORM::origCity) ||
934
        (hasContent($FORM::origState   ) &&
935
        ($FORM::origState !~ "Select state here.")) ||
936
        hasContent($FORM::origStateOther) ||
937
        hasContent($FORM::origZIP ) || hasContent($FORM::origCountry)) {
938
        $orig .= "<address>\n";
939
940
        if (hasContent($FORM::origDelivery)) {
941 2032 sgarg
            $orig .= "<deliveryPoint>".normalize($FORM::origDelivery)."</deliveryPoint>\n";
942 1929 brooke
        }
943
        if (hasContent($FORM::origCity)) {
944 2032 sgarg
            $orig .= "<city>".normalize($FORM::origCity)."</city>\n";
945 1929 brooke
        }
946
947 1977 jones
    if (hasContent($FORM::origState) &&
948 1929 brooke
            ($FORM::origState !~ "Select state here.")) {
949 2032 sgarg
            $orig .= "<administrativeArea>".normalize($FORM::origState);
950 1929 brooke
            $orig .= "</administrativeArea>\n";
951
        } elsif (hasContent($FORM::origStateOther)) {
952 2032 sgarg
            $orig .= "<administrativeArea>".normalize($FORM::origStateOther);
953 1929 brooke
            $orig .= "</administrativeArea>\n";
954
        }
955
        if (hasContent($FORM::origZIP)) {
956 2032 sgarg
            $orig .= "<postalCode>".normalize($FORM::origZIP)."</postalCode>\n";
957 1929 brooke
        }
958
        if (hasContent($FORM::origCountry)) {
959 2032 sgarg
            $orig .= "<country>".normalize($FORM::origCountry)."</country>\n";
960 1929 brooke
        }
961
        $orig .= "</address>\n";
962
    }
963
964
    if (hasContent($FORM::origPhone)) {
965 2032 sgarg
        $orig .= "<phone>".normalize($FORM::origPhone)."</phone>\n";
966 1929 brooke
    }
967
    if (hasContent($FORM::origFAX)) {
968 2032 sgarg
        $orig .= "<phone phonetype=\"Fax\">".normalize($FORM::origFAX)."</phone>\n";
969 1929 brooke
    }
970
    if (hasContent($FORM::origEmail)) {
971 2032 sgarg
        $orig .= "<electronicMailAddress>".normalize($FORM::origEmail);
972 1929 brooke
        $orig .= "</electronicMailAddress>\n";
973
    }
974
    $dso = "<$role>\n$orig</$role>\n";
975
976 2049 sgarg
    if ($FORM::cfg eq 'nceas') {
977
        for (my $i = 0; $i < scalar(@FORM::wg); $i++) {
978
            $creat .= "<creator>\n";
979
            $creat .= "<organizationName>".normalize($FORM::wg[$i])."</organizationName>\n";
980
            $creat .= "</creator>\n";
981
        }
982
    } else {
983
	    $creat .= "<creator>\n";
984
	    $creat .= "<organizationName>".normalize($FORM::site)."</organizationName>\n";
985
	    $creat .= "</creator>\n";
986
    }
987
988
    if ($FORM::cfg ne 'knb') {
989
        $creat .= "<creator>\n";
990
        $creat .= "<organizationName>".normalize($organization)."</organizationName>\n";
991
        $creat .= "</creator>\n";
992
    }
993
994 1929 brooke
    $creat .= $dso;
995
996
    if ($FORM::useOrigAddress) {
997
        # Add a contact originator like the original with a different role
998
            $cont .= "<contact>\n";
999 1977 jones
        $cont .= $orig;
1000
        $cont .= "</contact>\n";
1001 1929 brooke
    } else {
1002
        $cont .= "<contact>\n";
1003
1004
        $cont .= "<individualName>\n";
1005 2032 sgarg
        $cont .= "<givenName>".normalize($FORM::origNamefirstContact)."</givenName>\n";
1006
        $cont .= "<surName>".normalize($FORM::origNamelastContact)."</surName>\n";
1007 1929 brooke
        $cont .= "</individualName>\n";
1008
1009 1977 jones
    if (hasContent($FORM::origNameOrgContact)) {
1010 2032 sgarg
        $cont .= "<organizationName>".normalize($FORM::origNameOrgContact)."</organizationName>\n";
1011 1977 jones
    }
1012 1929 brooke
1013
        if (hasContent($FORM::origDeliveryContact) ||
1014
            hasContent($FORM::origCityContact) ||
1015
            (hasContent($FORM::origStateContact) &&
1016
            ($FORM::origStateContact !~ "Select state here.")) ||
1017
            hasContent($FORM::origStateOtherContact) ||
1018
            hasContent($FORM::origZIPContact) ||
1019
            hasContent($FORM::origCountryContact)) {
1020
            $cont .= "<address>\n";
1021
            if (hasContent($FORM::origDeliveryContact)) {
1022 2032 sgarg
                $cont .= "<deliveryPoint>".normalize($FORM::origDeliveryContact);
1023 1929 brooke
                $cont .= "</deliveryPoint>\n";
1024
            }
1025
            if (hasContent($FORM::origCityContact)) {
1026 2032 sgarg
                $cont .= "<city>".normalize($FORM::origCityContact)."</city>\n";
1027 1929 brooke
            }
1028
            if (hasContent($FORM::origStateContact) &&
1029
                ($FORM::origStateContact !~ "Select state here.")) {
1030 2032 sgarg
                $cont .= "<administrativeArea>".normalize($FORM::origStateContact);
1031 1929 brooke
                $cont .= "</administrativeArea>\n";
1032
            } elsif (hasContent($FORM::origStateOtherContact)) {
1033 2032 sgarg
                $cont .= "<administrativeArea>".normalize($FORM::origStateOtherContact);
1034 1929 brooke
                $cont .= "</administrativeArea>\n";
1035
            }
1036
            if (hasContent($FORM::origZIPContact)) {
1037 2032 sgarg
                $cont .= "<postalCode>".normalize($FORM::origZIPContact)."</postalCode>\n";
1038 1929 brooke
            }
1039
            if (hasContent($FORM::origCountryContact)) {
1040 2032 sgarg
                $cont .= "<country>".normalize($FORM::origCountryContact)."</country>\n";
1041 1929 brooke
            }
1042
            $cont .= "</address>\n";
1043
        }
1044
        if (hasContent($FORM::origPhoneContact)) {
1045 2032 sgarg
            $cont .= "<phone>".normalize($FORM::origPhoneContact)."</phone>\n";
1046 1929 brooke
        }
1047 1977 jones
    if (hasContent($FORM::origFAXContact)) {
1048 2032 sgarg
        $cont .= "<phone phonetype=\"Fax\">".normalize($FORM::origFAXContact)."</phone>\n";
1049 1977 jones
    }
1050 1929 brooke
        if (hasContent($FORM::origEmailContact)) {
1051 2032 sgarg
            $cont .= "<electronicMailAddress>".normalize($FORM::origEmailContact);
1052 1929 brooke
            $cont .= "</electronicMailAddress>\n";
1053
        }
1054 1977 jones
    $cont .= "</contact>\n";
1055 1929 brooke
    }
1056
1057
    $metaP .= "<metadataProvider>\n";
1058
    $metaP .= "<individualName>\n";
1059 2032 sgarg
    $metaP .= "<givenName>".normalize($FORM::providerGivenName)."</givenName>\n";
1060
    $metaP .= "<surName>".normalize($FORM::providerSurName)."</surName>\n";
1061 1929 brooke
    $metaP .= "</individualName>\n";
1062
    $metaP .= "</metadataProvider>\n";
1063
1064
    # Additional originators
1065
    foreach my $tmp (param()) {
1066
        if ($tmp =~ /origNamelast/){
1067
            my $tmp1 = $tmp;
1068
            $tmp1 =~ s/origNamelast//; # get the index of the parameter 0 to 10
1069
            if ( $tmp1 eq '1'
1070
                 || $tmp1 eq '2'
1071
                 || $tmp1 eq '3'
1072
                 || $tmp1 eq '4'
1073
                 || $tmp1 eq '5'
1074
                 || $tmp1 eq '6'
1075
                 || $tmp1 eq '7'
1076
                 || $tmp1 eq '8'
1077
                 || $tmp1 eq '9'
1078
                 || $tmp1 eq '10'
1079
                 ) {
1080
1081
                # do not generate XML for empty originator fields
1082
                if (hasContent(param("origNamefirst" . $tmp1))) {
1083
1084 1977 jones
            my $add = "";
1085
            $add .= "<individualName>\n";
1086
            $add .= "<givenName>";
1087 2032 sgarg
            $add .= normalize(param("origNamefirst" . $tmp1));
1088 1977 jones
            $add .= "</givenName>\n";
1089
            $add .= "<surName>";
1090 2032 sgarg
            $add .= normalize(param("origNamelast" . $tmp1));
1091 1977 jones
            $add .= "</surName>\n";
1092
            $add .= "</individualName>\n";
1093
1094
            if(param("origRole" . $tmp1) eq "Originator"){
1095
            $creat .= "<creator>\n";
1096
            $creat .= $add;
1097
            $creat .= "</creator>\n";
1098 1929 brooke
            }
1099 1977 jones
            elsif(param("origRole" . $tmp1) eq "Metadata Provider"){
1100
            $metaP .= "<metadataProvider>\n";
1101
            $metaP .= $add;
1102
            $metaP .= "</metadataProvider>\n";
1103
            }
1104
            elsif((param("origRole" . $tmp1) eq "Publisher")  && ($publ eq "")){
1105
            $publ .= "<publisher>\n";
1106
            $publ .= $add;
1107
            $publ .= "</publisher>\n";
1108
            }
1109
            else{
1110
            $apart .= "<associatedParty>\n";
1111
            $apart .= $add;
1112
            $apart .= "<role>";
1113
            $apart .= param("origRole" . $tmp1);
1114
            $apart .= "</role>\n";
1115
            $apart .= "</associatedParty>\n";
1116
            }
1117 1929 brooke
        }
1118 1977 jones
            }
1119
        }
1120 1929 brooke
    }
1121
1122
    $doc .= $creat;
1123
    $doc .= $metaP;
1124
    $doc .= $apart;
1125
1126 2615 sgarg
    # add the publication Date to the eml document.
1127
    my $Second = "";
1128
    my $Minute = "";
1129
    my $Hour = "";
1130
    my $Day = "";
1131
    my $Month = "";
1132
    my $Year = "";
1133
    my $WeekDay = "";
1134
    my $DayOfYear = "";
1135
    my $IsDST = "";
1136
    ($Second, $Minute, $Hour, $Day, $Month, $Year, $WeekDay, $DayOfYear, $IsDST) = localtime(time) ;
1137
    $Month = $Month + 1;
1138
    if($Month < 10) {
1139
	$Month = "0".$Month;
1140
    }
1141
    if($Day < 10) {
1142
	$Day = "0".$Day;
1143
    }
1144
    $Year = $Year + 1900;
1145
1146
    $doc .= "<pubDate>\n";
1147
    $doc .= $Year."-".$Month."-".$Day;
1148
    $doc .= "</pubDate>\n";
1149
1150 1929 brooke
    $doc .= "<abstract>\n";
1151 2032 sgarg
    $doc .= "<para>".normalize($FORM::abstract)."</para>\n";
1152 1929 brooke
    $doc .= "</abstract>\n";
1153
1154
    # Keyword information
1155
    foreach my $tmp (param()) {
1156
        if ($tmp =~ /keyword/) {
1157
            my $tmp1 = $tmp;
1158
            $tmp1 =~ s/keyword//; # get the index of the parameter 0, ..., 10
1159
            if ( $tmp1 =~ /[0-9]/ ){
1160
                # don't generate xml for empty keyword fields
1161
                # don't generate taxonomic keyword fields, those go in taxonomic coverage
1162
                if (hasContent(param($tmp))) {
1163
                    $doc .= "<keywordSet>\n";
1164
                    $doc .= "<keyword ";
1165
                    if (hasContent(param("kwType" . $tmp1)) &&
1166 2415 sgarg
                       (param("kwType" . $tmp1) !~ "None") ) {
1167 1929 brooke
                         $doc .= "keywordType=\"";
1168 2403 sgarg
                         $doc .= lc(param("kwType" . $tmp1));
1169 1929 brooke
                         $doc .= "\"";
1170
                    }
1171
                    $doc .= ">";
1172 2032 sgarg
                    $doc .= normalize(param("keyword" . $tmp1));
1173 1929 brooke
                    $doc .= "</keyword>\n";
1174
                    $doc .= "<keywordThesaurus>";
1175 2032 sgarg
                    $doc .= normalize(param("kwTh" . $tmp1));
1176 1929 brooke
                    $doc .= "</keywordThesaurus>\n";
1177
                    $doc .= "</keywordSet>\n";
1178
                }
1179
            }
1180
        }
1181
    }
1182
1183
    if (hasContent($FORM::addComments)) {
1184
        $doc .= "<additionalInfo>\n";
1185 2032 sgarg
        $doc .= "<para>".normalize($FORM::addComments)."</para>\n";
1186 1929 brooke
        $doc .= "</additionalInfo>\n";
1187
    }
1188
1189
    if (hasContent($FORM::useConstraints) ||
1190
        hasContent($FORM::useConstraintsOther)) {
1191
        $doc .= "<intellectualRights>\n";
1192
        if (hasContent($FORM::useConstraints)) {
1193 2032 sgarg
            $doc .= "<para>".normalize($FORM::useConstraints)."</para>\n";
1194 1929 brooke
        }
1195
        if (hasContent($FORM::useConstraintsOther)) {
1196 2032 sgarg
            $doc .= "<para>".normalize($FORM::useConstraintsOther)."</para>\n";
1197 1929 brooke
        }
1198
        $doc .= "</intellectualRights>\n";
1199
    }
1200
1201
1202
    if (hasContent($FORM::url)) {
1203 1977 jones
    $doc .= "<distribution>\n";
1204 1929 brooke
        $doc .= "<online>\n";
1205 2032 sgarg
    $doc .= "<url>".normalize($FORM::url)."</url>\n";
1206 1977 jones
    $doc .= "</online>\n";
1207
    $doc .= "</distribution>\n";
1208 1929 brooke
    }
1209
1210
    $doc .= "<distribution>\n";
1211
    $doc .= "<offline>\n";
1212 2032 sgarg
    $doc .= "<mediumName>" . normalize($FORM::dataMedium)." ".normalize($FORM::dataMediumOther);
1213 1929 brooke
    $doc .= "</mediumName>\n";
1214
    $doc .= "</offline>\n";
1215
    $doc .= "</distribution>\n";
1216
1217 2148 sgarg
    my $cov = "";
1218 1929 brooke
1219
    if (hasContent($FORM::endingYear)) {
1220 2148 sgarg
	$cov .= "<temporalCoverage>\n";
1221
	$cov .= "<rangeOfDates>\n";
1222
	if (hasContent($FORM::beginningMonth)) {
1223
	    my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
1224
			 "JUL","AUG","SEP","OCT","NOV","DEC")
1225
		[$FORM::beginningMonth - 1];
1226 2644 sgarg
	    if (hasContent($FORM::beginningDay)) {
1227
	    	$cov .= "<beginDate>\n";
1228
	    	$cov .= "<calendarDate>";
1229
	    	$cov .= normalize($FORM::beginningYear)."-".normalize($FORM::beginningMonth)."-".normalize($FORM::beginningDay);
1230
	    	$cov .= "</calendarDate>\n";
1231
	    	$cov .= "</beginDate>\n";
1232
	    } else {
1233
	    	$cov .= "<beginDate>\n";
1234
	    	$cov .= "<calendarDate>";
1235
	    	$cov .= normalize($FORM::beginningYear)."-".normalize($FORM::beginningMonth)."-01";
1236
	    	$cov .= "</calendarDate>\n";
1237
	    	$cov .= "</beginDate>\n";
1238
	    }
1239 2148 sgarg
	} else {
1240
	    $cov .= "<beginDate>\n";
1241
	    $cov .= "<calendarDate>";
1242
	    $cov .= normalize($FORM::beginningYear);
1243
	    $cov .= "</calendarDate>\n";
1244
	    $cov .= "</beginDate>\n";
1245
	}
1246
1247
	if (hasContent($FORM::endingMonth)) {
1248
	    my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
1249
			 "JUL","AUG","SEP","OCT","NOV","DEC")
1250
		[$FORM::endingMonth - 1];
1251 2644 sgarg
1252
	    if (hasContent($FORM::endingDay)) {
1253
	    	$cov .= "<endDate>\n";
1254
	    	$cov .= "<calendarDate>";
1255
	    	$cov .= normalize($FORM::endingYear)."-".normalize($FORM::endingMonth)."-".normalize($FORM::endingDay);
1256
	    	$cov .= "</calendarDate>\n";
1257
	    	$cov .= "</endDate>\n";
1258
	    } else {
1259
	    	$cov .= "<endDate>\n";
1260
	    	$cov .= "<calendarDate>";
1261
	    	$cov .= normalize($FORM::endingYear)."-".normalize($FORM::endingMonth)."-01";
1262
	    	$cov .= "</calendarDate>\n";
1263
	    	$cov .= "</endDate>\n";
1264
	    }
1265 2148 sgarg
	} else {
1266
	    $cov .= "<endDate>\n";
1267
	    $cov .= "<calendarDate>";
1268
	    $cov .= normalize($FORM::endingYear);
1269
	    $cov .= "</calendarDate>\n";
1270
	    $cov .= "</endDate>\n";
1271
	}
1272
	$cov .= "</rangeOfDates>\n";
1273
	$cov .= "</temporalCoverage>\n";
1274 1977 jones
    } else {
1275 2148 sgarg
	if(hasContent($FORM::beginningYear)) {
1276
	    $cov .= "<temporalCoverage>\n";
1277
	    $cov .= "<singleDateTime>\n";
1278
	    if (hasContent($FORM::beginningMonth)) {
1279
		my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
1280
			     "JUL","AUG","SEP","OCT","NOV","DEC")
1281
		    [$FORM::beginningMonth - 1];
1282 2644 sgarg
1283
	    	if (hasContent($FORM::beginningDay)) {
1284
		   $cov .= "<calendarDate>";
1285
		   $cov .= normalize($FORM::beginningYear)."-".normalize($FORM::beginningMonth)."-".normalize($FORM::beginningDay);
1286
		   $cov .= "</calendarDate>\n";
1287
		} else {
1288
		   $cov .= "<calendarDate>";
1289
		   $cov .= normalize($FORM::beginningYear)."-".normalize($FORM::beginningMonth)."-01";
1290
		   $cov .= "</calendarDate>\n";
1291
		}
1292 2148 sgarg
	    } else {
1293
		$cov .= "<calendarDate>";
1294
		$cov .= normalize($FORM::beginningYear);
1295
		$cov .= "</calendarDate>\n";
1296
	    }
1297
	    $cov .= "</singleDateTime>\n";
1298
	    $cov .= "</temporalCoverage>\n";
1299
	}
1300 1977 jones
    }
1301 1929 brooke
1302 2613 sgarg
    if(hasContent($FORM::geogdesc) || ($FORM::latDeg1 < 91 && $FORM::latDeg1 > -1 && $FORM::longDeg1 < 181 && $FORM::longDeg1 > -1)) {
1303 2148 sgarg
	$cov .= "<geographicCoverage>\n";
1304 1929 brooke
1305 2149 sgarg
	if(hasContent($FORM::geogdesc)) {
1306 2148 sgarg
	    $cov .= "<geographicDescription>".normalize($FORM::geogdesc)."</geographicDescription>\n";
1307
	}
1308
1309 2613 sgarg
	if($latDeg1 < 91 && $latDeg1 > -1 && $longDeg1 < 181 && $longDeg1 > -1) {
1310 2148 sgarg
	    $cov .= "<boundingCoordinates>\n";
1311
	    # if the second latitude is missing, then set the second lat/long pair
1312
	    # equal to the first this makes a point appear like a rectangle
1313 2613 sgarg
	    if ($FORM::useSiteCoord || ($FORM::latDeg2 == "" && $FORM::latMin2 == "" && $FORM::latSec2 == "")) {
1314 2148 sgarg
1315
		$latDeg2 = $latDeg1;
1316
		$latMin2 = $latMin1;
1317
		$latSec2 = $latSec1;
1318
		$hemisphLat2 = $hemisphLat1;
1319
		$longDeg2 = $longDeg1;
1320
		$longMin2 = $longMin1;
1321
		$longSec2 = $longSec1;
1322
		$hemisphLong2 = $hemisphLong1;
1323
	    }
1324
	    else
1325
	    {
1326
		$latDeg2 = $FORM::latDeg2;
1327
		$latMin2 = $FORM::latMin2;
1328
		$latSec2 = $FORM::latSec2;
1329
		$hemisphLat2 = $FORM::hemisphLat2;
1330
		$longDeg2 = $FORM::longDeg2;
1331
		$longMin2 = $FORM::longMin2;
1332
		$longSec2 = $FORM::longSec2;
1333
		$hemisphLong2 = $FORM::hemisphLong2;
1334
	    }
1335
1336
1337
	    my $hemisph;
1338
	    $hemisph = ($hemisphLong1 eq "W") ? -1 : 1;
1339
	    $cov .= "<westBoundingCoordinate>";
1340 2152 sgarg
	    my $var = $hemisph * ($longDeg1 + (60*$longMin1+$longSec1)/3600);
1341
	    $cov .= sprintf("%.4f\n", $var);
1342 2148 sgarg
	    $cov .= "</westBoundingCoordinate>\n";
1343
1344
	    $hemisph = ($hemisphLong2 eq "W") ? -1 : 1;
1345
	    $cov .= "<eastBoundingCoordinate>";
1346 2152 sgarg
	    $var = $hemisph * ($longDeg2 + (60*$longMin2+$longSec2)/3600);
1347
	    $cov .= sprintf("%.4f\n", $var);
1348 2148 sgarg
	    $cov .= "</eastBoundingCoordinate>\n";
1349
1350
	    $hemisph = ($hemisphLat1 eq "S") ? -1 : 1;
1351
	    $cov .= "<northBoundingCoordinate>";
1352 2152 sgarg
	    $var = $hemisph * ($latDeg1 + (60*$latMin1+$latSec1)/3600);
1353
	    $cov .= sprintf("%.4f\n", $var);
1354 2148 sgarg
	    $cov .= "</northBoundingCoordinate>\n";
1355
1356
	    $hemisph = ($hemisphLat2 eq "S") ? -1 : 1;
1357
	    $cov .= "<southBoundingCoordinate>";
1358 2152 sgarg
	    $var = $hemisph * ($latDeg2 + (60*$latMin2+$latSec2)/3600);
1359
	    $cov .= sprintf("%.4f\n", $var);
1360 2148 sgarg
	    $cov .= "</southBoundingCoordinate>\n";
1361
1362
	    $cov .= "</boundingCoordinates>\n";
1363
	}
1364
	$cov .= "</geographicCoverage>\n";
1365 1929 brooke
    }
1366
1367 1984 jones
    # Write out the taxonomic coverage fields
1368
    my $foundFirstTaxon = 0;
1369
    foreach my $trn (param()) {
1370
        if ($trn =~ /taxonRankName/) {
1371
            my $taxIndex = $trn;
1372
            $taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
1373
            my $trv = "taxonRankValue".$taxIndex;
1374
            if ( $taxIndex =~ /[0-9]/ ){
1375
                if (hasContent(param($trn)) && hasContent(param($trv))) {
1376
                    if (! $foundFirstTaxon) {
1377 2148 sgarg
                        $cov .= "<taxonomicCoverage>\n";
1378 1984 jones
                        $foundFirstTaxon = 1;
1379 1985 jones
                        if (hasContent($FORM::taxaAuth)) {
1380 2148 sgarg
                            $cov .= "<generalTaxonomicCoverage>".normalize($FORM::taxaAuth)."</generalTaxonomicCoverage>\n";
1381 1985 jones
                        }
1382 1984 jones
                    }
1383 2148 sgarg
                    $cov .= "<taxonomicClassification>\n";
1384
                    $cov .= "  <taxonRankName>".normalize(param($trn))."</taxonRankName>\n";
1385
                    $cov .= "  <taxonRankValue>".normalize(param($trv))."</taxonRankValue>\n";
1386
                    $cov .= "</taxonomicClassification>\n";
1387 1984 jones
                }
1388
            }
1389
        }
1390
    }
1391
    if ($foundFirstTaxon) {
1392 2148 sgarg
        $cov .= "</taxonomicCoverage>\n";
1393 1984 jones
    }
1394 1929 brooke
1395 2149 sgarg
    if($cov ne "" ){
1396
	$doc .= "<coverage>".$cov."</coverage>";
1397
    }
1398 1929 brooke
    $doc .= $cont;
1399
    $doc .= $publ;
1400 1982 jones
1401 2151 sgarg
    if ((hasContent($FORM::methodTitle)) || scalar(@FORM::methodsPara) > 0 || ($FORM::methodPara[0] ne "")) {
1402 1982 jones
        my $methods = "<methods><methodStep><description><section>\n";
1403
        if (hasContent($FORM::methodTitle)) {
1404 2032 sgarg
            $methods .= "<title>".normalize($FORM::methodTitle)."</title>\n";
1405 1982 jones
        }
1406
        for (my $i = 0; $i < scalar(@FORM::methodPara); $i++) {
1407 2032 sgarg
            $methods .= "<para>".normalize($FORM::methodPara[$i])."</para>\n";
1408 1982 jones
        }
1409 1989 jones
        $methods .= "</section></description></methodStep>\n";
1410
        if (hasContent($FORM::studyExtentDescription)) {
1411
            $methods .= "<sampling><studyExtent><description>\n";
1412 2032 sgarg
            $methods .= "<para>".normalize($FORM::studyExtentDescription)."</para>\n";
1413 1989 jones
            $methods .= "</description></studyExtent>\n";
1414
            $methods .= "<samplingDescription>\n";
1415 2032 sgarg
            $methods .= "<para>".normalize($FORM::samplingDescription)."</para>\n";
1416 1989 jones
            $methods .= "</samplingDescription>\n";
1417
            $methods .= "</sampling>\n";
1418
        }
1419
        $methods .= "</methods>\n";
1420 1982 jones
        $doc .= $methods;
1421
    }
1422 1929 brooke
1423
    $doc .= "<access authSystem=\"knb\" order=\"denyFirst\">\n";
1424
    $doc .= "<allow>\n";
1425 2005 jones
    $doc .= "<principal>$username</principal>\n";
1426 1929 brooke
    $doc .= "<permission>all</permission>\n";
1427
    $doc .= "</allow>\n";
1428
    $doc .= "<allow>\n";
1429
    $doc .= "<principal>uid=$FORM::username,o=$FORM::organization,dc=ecoinformatics,dc=org</principal>\n";
1430
    $doc .= "<permission>all</permission>\n";
1431
    $doc .= "</allow>\n";
1432 2644 sgarg
    if($publicReadable eq "true"){
1433
    	$doc .= "<allow>\n";
1434
    	$doc .= "<principal>public</principal>\n";
1435
    	$doc .= "<permission>read</permission>\n";
1436
    	$doc .= "</allow>\n";
1437
    }
1438 2645 sgarg
    foreach(split(":",$accessPrincipals)){
1439
    	$doc .= "<allow>\n";
1440
    	$doc .= "<principal>".$_."</principal>\n";
1441
    	$doc .= "<permission>".$accessType."</permission>\n";
1442
    	$doc .= "</allow>\n";
1443
    }
1444 1929 brooke
    $doc .= "</access>\n";
1445
1446
    $doc .= "</dataset>\n</eml:eml>\n";
1447
1448
    return $doc;
1449
}
1450
1451
1452
################################################################################
1453
#
1454
# send an email message notifying the moderator of a new submission
1455
#
1456
################################################################################
1457
sub sendNotification {
1458
    my $identifier = shift;
1459
    my $mailhost = shift;
1460
    my $sender = shift;
1461
    my $recipient = shift;
1462
1463
    my $smtp = Net::SMTP->new($mailhost);
1464
    $smtp->mail($sender);
1465
    $smtp->to($recipient);
1466
1467
    my $message = <<"    ENDOFMESSAGE";
1468
    To: $recipient
1469
    From: $sender
1470
    Subject: New data submission
1471
1472
    Data was submitted to the data registry.
1473
    The identifying information for the new data set is:
1474
1475
    Identifier: $identifier
1476
    Title: $FORM::title
1477
    Submitter: $FORM::providerGivenName $FORM::providerSurName
1478
1479
    Please review the submmission and grant public read access if appropriate.
1480
    Thanks
1481
1482
    ENDOFMESSAGE
1483
    $message =~ s/^[ \t\r\f]+//gm;
1484
1485
    $smtp->data($message);
1486
    $smtp->quit;
1487
}
1488
1489
1490
################################################################################
1491
#
1492
# read the eml document and send back a form with values filled in.
1493
#
1494
################################################################################
1495
sub modifyData {
1496
1497
    # create metacat instance
1498
    my $metacat;
1499
    my $docid = $FORM::docid;
1500
    my $httpMessage;
1501
    my $doc;
1502
    my $xmldoc;
1503
    my $findType;
1504
    my $parser = XML::LibXML->new();
1505
    my @fileArray;
1506
    my $pushDoc;
1507
    my $alreadyInArray;
1508
    my $node;
1509
    my $response;
1510
    my $element;
1511
    my $tempfile;
1512
1513
    $metacat = Metacat->new();
1514
    if ($metacat) {
1515
        $metacat->set_options( metacatUrl => $metacatUrl );
1516
    } else {
1517
        #die "failed during metacat creation\n";
1518
        push(@errorMessages, "Failed during metacat creation.");
1519
    }
1520
1521
    $httpMessage = $metacat->read($docid);
1522
    $doc = $httpMessage->content();
1523
    $xmldoc = $parser->parse_string($doc);
1524
1525 1977 jones
    #$tempfile = $xslConvDir.$docid;
1526
    #push (@fileArray, $tempfile);
1527 1929 brooke
1528
    if ($xmldoc eq "") {
1529 1977 jones
        $error ="Error in parsing the eml document";
1530
        push(@errorMessages, $error);
1531 1929 brooke
    } else {
1532 1977 jones
        $findType = $xmldoc->findnodes('//dataset/identifier');
1533
        if ($findType->size() > 0) {
1534
            # This is a eml beta6 document
1535
            # Read the documents mentioned in triples also
1536
1537
            $findType = $xmldoc->findnodes('//dataset/triple');
1538
            if ($findType->size() > 0) {
1539
                foreach $node ($findType->get_nodelist) {
1540
                    $pushDoc = findValue($node, 'subject');
1541
1542
                    # If the file is already in @fileArray then do not add it
1543
                    $alreadyInArray = 0;
1544
                    foreach $element (@fileArray) {
1545
                        $tempfile = $tmpdir."/".$pushDoc;
1546
                        if ($element eq $pushDoc) {
1547
                            $alreadyInArray = 1;
1548
                        }
1549
                    }
1550
1551
                    if (!$alreadyInArray) {
1552
                        $tempfile = $tmpdir."/".$pushDoc;
1553
                        $response = "";
1554
                        $response = $metacat->read($pushDoc);
1555
                        if (! $response) {
1556
                            # could not read
1557
                            #push(@errorMessages, $response);
1558
                            push(@errorMessages, $metacat->getMessage());
1559
                            push(@errorMessages, "Failed during reading.\n");
1560
                        } else {
1561
                            my $xdoc = $response->content();
1562
                            #$tempfile = $xslConvDir.$pushDoc;
1563
                            open (TFILE,">$tempfile") ||
1564
                                die ("Cant open xml file... $tempfile\n");
1565
                            print TFILE $xdoc;
1566
                            close(TFILE);
1567
                            push (@fileArray, $tempfile);
1568
                        }
1569
                    }
1570
                }
1571
            }
1572 1929 brooke
1573 1977 jones
            # Read the main document.
1574 1929 brooke
1575 1977 jones
            $tempfile = $tmpdir."/".$docid; #= $xslConvDir.$docid;
1576
            open (TFILE,">$tempfile") || die ("Cant open xml file...\n");
1577
            print TFILE $doc;
1578
            close(TFILE);
1579
1580
            # Transforming beta6 to eml 2
1581
            my $xslt;
1582
            my $triplesheet;
1583
            my $results;
1584
            my $stylesheet;
1585
            my $resultsheet;
1586
1587
            $xslt = XML::LibXSLT->new();
1588
            #$tempfile = $xslConvDir."triple_info.xsl";
1589
            $tempfile = $tmpdir."/"."triple_info.xsl";
1590
1591
            $triplesheet = $xslt->parse_stylesheet_file($tempfile);
1592 1929 brooke
1593 1977 jones
            #$results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpdir/\'", packageName => "\'$docid\'");
1594
            $results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpdir/\'", packageName => "\'$docid\'");
1595 1929 brooke
1596 1977 jones
            #$tempfile = $xslConvDir."emlb6toeml2.xsl";
1597
            $tempfile = $tmpdir."/"."emlb6toeml2.xsl";
1598
            $stylesheet = $xslt->parse_stylesheet_file($tempfile);
1599
            $resultsheet = $stylesheet->transform($results);
1600
1601
            #$tempfile = "/usr/local/apache2/htdocs/xml/test.xml";;
1602
            #open (TFILE,">$tempfile") || die ("Cant open xml file...\n");
1603
            #print TFILE $stylesheet->output_string($resultsheet);
1604
            #close(TFILE);
1605 1929 brooke
1606 1977 jones
            getFormValuesFromEml2($resultsheet);
1607
1608
            # Delete the files written earlier.
1609
            unlink @fileArray;
1610 1929 brooke
1611 1977 jones
        } else {
1612
            getFormValuesFromEml2($xmldoc);
1613
        }
1614 1929 brooke
    }
1615
1616
    if (scalar(@errorMessages)) {
1617 1979 jones
        # if any errors, print them in the response template
1618 2334 sgarg
        $$templateVars{'status'} = 'failure_no_resubmit';
1619 1979 jones
        $$templateVars{'errorMessages'} = \@errorMessages;
1620
        $error = 1;
1621
        $$templateVars{'function'} = "modification";
1622
        $$templateVars{'section'} = "Modification Status";
1623
        $template->process( $responseTemplate, $templateVars);
1624 1929 brooke
    } else {
1625
        $$templateVars{'form'} = 're_entry';
1626 1977 jones
        $template->process( $entryFormTemplate, $templateVars);
1627 1929 brooke
    }
1628
}
1629
1630 1977 jones
################################################################################
1631
#
1632
# Parse an EML 2.0.0 file and extract the metadata into perl variables for
1633
# processing and returning to the template processor
1634
#
1635
################################################################################
1636 1929 brooke
sub getFormValuesFromEml2 {
1637
1638
    my $doc = shift;
1639
    my $results;
1640
    my $error;
1641
    my $node;
1642
    my $tempResult;
1643
    my $tempNode;
1644
    my $aoCount = 1;
1645
    my $foundDSO;
1646
1647 2138 sgarg
    # set variable values
1648 2258 jones
    $$templateVars{'showSiteList'} = $showSiteList;
1649
    $$templateVars{'lsite'} = $lsite;
1650
    $$templateVars{'usite'} = $usite;
1651
    $$templateVars{'showWgList'} = $showWgList;
1652
    $$templateVars{'showOrganization'} = $showOrganization;
1653 2138 sgarg
    $$templateVars{'hasKeyword'} = $hasKeyword;
1654 2148 sgarg
    $$templateVars{'hasTemporal'} = $hasTemporal;
1655
    $$templateVars{'hasSpatial'} = $hasSpatial;
1656
    $$templateVars{'hasTaxonomic'} = $hasTaxonomic;
1657
    $$templateVars{'hasMethod'} = $hasMethod;
1658
    $$templateVars{'spatialRequired'} = $spatialRequired;
1659
    $$templateVars{'temporalRequired'} = $temporalRequired;
1660
1661 1929 brooke
    # find out the tag <alternateIdentifier>.
1662
    $results = $doc->findnodes('//dataset/alternateIdentifier');
1663 1977 jones
    if ($results->size() > 1) {
1664
        errMoreThanOne("alternateIdentifier");
1665 1929 brooke
    } else {
1666 1977 jones
        foreach $node ($results->get_nodelist) {
1667
            $$templateVars{'identifier'} = findValue($node, '../alternateIdentifier');
1668
        }
1669 1929 brooke
    }
1670
1671
    # find out the tag <title>.
1672
    $results = $doc->findnodes('//dataset/title');
1673 1977 jones
    if ($results->size() > 1) {
1674
        errMoreThanOne("title");
1675
    } elsif ($results->size() < 1) {
1676
        $error ="Following tag not found: title. Please use Morpho to edit this document";
1677
        push(@errorMessages, $error."\n");
1678
        #if ($DEBUG == 1){ print $error;}
1679 1929 brooke
    } else {
1680 1977 jones
        foreach $node ($results->get_nodelist) {
1681
            $$templateVars{'title'} = findValue($node, '../title');
1682
        }
1683 1929 brooke
    }
1684
1685
    # find out the tag <creator>.
1686
    $results = $doc->findnodes('//dataset/creator/individualName');
1687 1979 jones
    debug("Registry: Creators: ".$results->size());
1688 2144 sgarg
     foreach $node ($results->get_nodelist) {
1689 1977 jones
            dontOccur($node, "../positionName|../onlineURL|../userId",
1690
              "positionName, onlineURL, userId");
1691
1692
            dontOccur($node, "./saluation", "saluation");
1693
1694 1979 jones
            debug("Registry: Checking a creator in loop 1...");
1695 1977 jones
            $tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
1696
            if($tempResult->size > 0) {
1697
                if($foundDSO == 0) {
1698
                    $foundDSO = 1;
1699 1929 brooke
1700 1979 jones
                    debug("Registry: Recording a creator in loop 1...");
1701 1977 jones
                    $$templateVars{'origNamefirst0'} = findValue($node, 'givenName');
1702
                    $$templateVars{'origNamelast0'} = findValue($node, 'surName');
1703
1704
                    my $tempResult2 = $node->findnodes('../address');
1705
                    if ($tempResult2->size > 1) {
1706
                        errMoreThanOne("address");
1707
                    } else {
1708
                        foreach my $tempNode2 ($tempResult2->get_nodelist) {
1709
                            $$templateVars{'origDelivery'} = findValue($tempNode2, 'deliveryPoint');
1710
                            $$templateVars{'origCity'} = findValue($tempNode2, 'city');
1711
                            $$templateVars{'origState'} = findValue($tempNode2, 'administrativeArea');
1712
                            $$templateVars{'origZIP'} = findValue($tempNode2, 'postalCode');
1713
                            $$templateVars{'origCountry'} = findValue($tempNode2, 'country');
1714
                        }
1715
                    }
1716
1717
                    my $tempResult3 = $node->findnodes('../phone');
1718
                    if ($tempResult3->size > 2) {
1719
                        errMoreThanN("phone");
1720
                    } else {
1721
                        foreach my $tempNode2 ($tempResult3->get_nodelist) {
1722
                            if ($tempNode2->hasAttributes()) {
1723
                                my @attlist = $tempNode2->attributes();
1724
                                if ($attlist[0]->value eq "Fax") {
1725
                                    $$templateVars{'origFAX'} = $tempNode2->textContent();
1726
                                } else {
1727
                                    $$templateVars{'origPhone'} = $tempNode2->textContent();
1728
                                }
1729
                            } else {
1730
                                $$templateVars{'origPhone'} = $tempNode2->textContent();
1731
                            }
1732
                        }
1733
                    }
1734
                    $$templateVars{'origEmail'} = findValue($node, '../electronicMailAddress');
1735
                    $$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
1736
                } else {
1737
                    errMoreThanN("address, phone and electronicMailAddress");
1738
                }
1739
            }
1740
        }
1741
        foreach $node ($results->get_nodelist) {
1742 1979 jones
            debug("Registry: Checking a creator in loop 2...");
1743
            $tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
1744 1977 jones
            if ($tempResult->size == 0) {
1745
                if ($foundDSO == 0) {
1746 1979 jones
                    debug("Registry: Recording a creator in loop 2 block A...");
1747 1977 jones
                    $foundDSO = 1;
1748
                    $$templateVars{'origNamefirst0'} = findValue($node, 'givenName');
1749
                    $$templateVars{'origNamelast0'} = findValue($node, 'surName');
1750
                    $$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
1751
                } else {
1752 1979 jones
                    debug("Registry: Recording a creator in loop 2 block B...");
1753 1977 jones
                    $$templateVars{"origNamefirst$aoCount"} =  findValue($node, './givenName');
1754
                    $$templateVars{"origNamelast$aoCount"} =  findValue($node, './surName');
1755
                    $$templateVars{"origRole$aoCount"} = "Originator";
1756
                    $aoCount++;
1757
                }
1758
            }
1759
        }
1760 1929 brooke
1761
    $results = $doc->findnodes('//dataset/creator/organizationName');
1762 1979 jones
    my $wgroups = $doc->findnodes("//dataset/creator/organizationName[contains(text(),'(NCEAS ')]");
1763
    debug("Registry: Number Org: ".$results->size());
1764
    debug("Registry:  Number WG: ".$wgroups->size());
1765
    if ($results->size() - $wgroups->size() > 3) {
1766 1977 jones
        errMoreThanN("creator/organizationName");
1767 1929 brooke
    } else {
1768 1977 jones
        foreach $node ($results->get_nodelist) {
1769
            my $tempValue = findValue($node,'../organizationName');
1770
            $tempResult = $node->findnodes('../individualName');
1771
            if ($tempResult->size == 0 && $tempValue ne $organization) {
1772
                $$templateVars{'site'} = $tempValue;
1773
            }
1774
        }
1775 2003 jones
        if ($FORM::cfg eq 'nceas') {
1776 1979 jones
            my @wg;
1777
            foreach $node ($results->get_nodelist) {
1778
                my $tempValue = findValue($node,'../organizationName');
1779
                $wg[scalar(@wg)] = $tempValue;
1780
            }
1781
            my $projects = getProjectList();
1782
            $$templateVars{'projects'} = $projects;
1783
            $$templateVars{'wg'} = \@wg;
1784
        }
1785 1929 brooke
    }
1786
1787
    $results = $doc->findnodes('//dataset/metadataProvider');
1788 2144 sgarg
    foreach $node ($results->get_nodelist) {
1789 1977 jones
            dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
1790
                "organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in metadataProvider");
1791
1792 2144 sgarg
	    $tempResult = $node->findnodes('./individualName');
1793 1977 jones
            if ($tempResult->size > 1) {
1794
                errMoreThanOne("metadataProvider/indvidualName");
1795
            } else {
1796
                foreach $tempNode ($tempResult->get_nodelist) {
1797
                    if ($$templateVars{'providerGivenName'} ne "") {
1798
                        $$templateVars{"origNamefirst$aoCount"} =  findValue($tempNode, './givenName');
1799
                        $$templateVars{"origNamelast$aoCount"} =  findValue($tempNode, './surName');
1800
                        $$templateVars{"origRole$aoCount"} = "Metadata Provider";
1801
                        $aoCount++;
1802
                    } else {
1803
                        $$templateVars{'providerGivenName'} =  findValue($tempNode, './givenName');
1804
                        $$templateVars{'providerSurName'} =  findValue($tempNode, './surName');
1805
                    }
1806
                }
1807
            }
1808
        }
1809 1929 brooke
1810
    $results = $doc->findnodes('//dataset/associatedParty');
1811 2144 sgarg
    foreach $node ($results->get_nodelist) {
1812 1977 jones
            dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
1813
                "organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in associatedParty");
1814
1815
            $tempResult = $node->findnodes('./individualName');
1816
            if ($tempResult->size > 1) {
1817
                errMoreThanOne("associatedParty/indvidualName");
1818
            } else {
1819
                foreach $tempNode ($tempResult->get_nodelist) {
1820
                    $$templateVars{"origNamefirst$aoCount"} =  findValue($tempNode, './givenName');
1821
                    $$templateVars{"origNamelast$aoCount"} =  findValue($tempNode, './surName');
1822
                    $$templateVars{"origRole$aoCount"} = findValue($tempNode, '../role');
1823
                    $aoCount++;
1824
                }
1825
            }
1826 2144 sgarg
     }
1827 1929 brooke
1828
    $results = $doc->findnodes('//dataset/publisher');
1829 2144 sgarg
#    if ($results->size() > 10) {
1830
 #       errMoreThanN("publisher");
1831
 #   } else {
1832 1977 jones
        foreach $node ($results->get_nodelist) {
1833
            dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
1834
                "organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in associatedParty");
1835
1836
            $tempResult = $node->findnodes('./individualName');
1837
            if ($tempResult->size > 1) {
1838
                errMoreThanOne("publisher/indvidualName");
1839
            } else {
1840
                foreach $tempNode ($tempResult->get_nodelist) {
1841
                    $$templateVars{"origNamefirst$aoCount"} =  findValue($tempNode, './givenName');
1842
                    $$templateVars{"origNamelast$aoCount"} =  findValue($tempNode, './surName');
1843
                    $$templateVars{"origRole$aoCount"} = "Publisher";
1844
                    $aoCount++;
1845
                }
1846
            }
1847
        }
1848 2144 sgarg
  #  }
1849 1929 brooke
1850 2144 sgarg
  #  if ($aoCount > 11) {
1851
  #      errMoreThanN("Additional Originators");
1852
 #   }
1853 1929 brooke
1854 2403 sgarg
    $$templateVars{'aoCount'} = $aoCount;
1855 2144 sgarg
1856 1929 brooke
    dontOccur($doc, "./pubDate", "pubDate");
1857
    dontOccur($doc, "./language", "language");
1858
    dontOccur($doc, "./series", "series");
1859
1860
    $results = $doc->findnodes('//dataset/abstract');
1861 1977 jones
    if ($results->size() > 1) {
1862
        errMoreThanOne("abstract");
1863 1929 brooke
    } else {
1864 1977 jones
        foreach my $node ($results->get_nodelist) {
1865
            dontOccur($node, "./section", "section");
1866
            $$templateVars{'abstract'} = findValueNoChild($node, "para");
1867
        }
1868 1929 brooke
    }
1869
1870
    $results = $doc->findnodes('//dataset/keywordSet');
1871 2028 sgarg
1872 2403 sgarg
    my $count = 1;
1873 2028 sgarg
    foreach $node ($results->get_nodelist) {
1874
	$tempResult = $node->findnodes('./keyword');
1875
	if ($tempResult->size() > 1) {
1876
	    errMoreThanOne("keyword");
1877
	} else {
1878
	    foreach $tempNode ($tempResult->get_nodelist) {
1879
		$$templateVars{"keyword$count"} = $tempNode->textContent();
1880
		if ($tempNode->hasAttributes()) {
1881
		    my @attlist = $tempNode->attributes();
1882 2403 sgarg
                    my $tmp = $attlist[0]->value;  #convert the first letter to upper case
1883
		    $tmp =~ s/\b(\w)/\U$1/g;
1884
		    $$templateVars{"kwType$count"} = $tmp;
1885 2028 sgarg
		}
1886 2042 sgarg
	    }
1887 2028 sgarg
	}
1888
	$$templateVars{"kwTh$count"} = findValue($node, "keywordThesaurus");
1889 2403 sgarg
        $count++;
1890 2028 sgarg
    }
1891 2042 sgarg
    $$templateVars{'keyCount'} = $count;
1892 2138 sgarg
    if($count > 0 ){
1893
       $$templateVars{'hasKeyword'} = "true";
1894
    }
1895 1929 brooke
1896
    $results = $doc->findnodes('//dataset/additionalInfo');
1897 1977 jones
    if ($results->size() > 1) {
1898
        errMoreThanOne("additionalInfo");
1899 1929 brooke
    } else {
1900 1977 jones
        foreach $node ($results->get_nodelist) {
1901
            dontOccur($node, "./section", "section");
1902
            $$templateVars{'addComments'} = findValueNoChild($node, "para");
1903
        }
1904 1929 brooke
    }
1905
1906
    $$templateVars{'useConstraints'} = "";
1907
    $results = $doc->findnodes('//dataset/intellectualRights');
1908 1977 jones
    if ($results->size() > 1) {
1909
        errMoreThanOne("intellectualRights");
1910 1929 brooke
    } else {
1911 1977 jones
        foreach $node ($results->get_nodelist) {
1912
            dontOccur($node, "./section", "section in intellectualRights");
1913 1929 brooke
1914 1977 jones
            $tempResult = $node->findnodes("para");
1915
            if ($tempResult->size > 2) {
1916
                   errMoreThanN("para");
1917
            } else {
1918
                foreach $tempNode ($tempResult->get_nodelist) {
1919
                    my $childNodes = $tempNode->childNodes;
1920
                    if ($childNodes->size() > 1) {
1921
                        $error ="The tag para in intellectualRights has children which cannot be shown using the form. Please use Morpho to edit this document";
1922
                        push(@errorMessages, $error);
1923
                        #if ($DEBUG == 1){ print $error."\n";}
1924
                    } else {
1925
                        #print $tempNode->nodeName().":".$tempNode->textContent();
1926
                        #print "\n";
1927
                        if ($$templateVars{'useConstraints'} eq "") {
1928
                            $$templateVars{'useConstraints'} = $tempNode->textContent();
1929
                        } else {
1930
                            $$templateVars{'useConstraintsOther'} = $tempNode->textContent();
1931
                        }
1932
                    }
1933
                }
1934
            }
1935
        }
1936 1929 brooke
    }
1937
1938
    $results = $doc->findnodes('//dataset/distribution/online');
1939 1977 jones
    if ($results->size() > 1) {
1940
        errMoreThanOne("distribution/online");
1941 1929 brooke
    } else {
1942 1977 jones
        foreach my $tempNode ($results->get_nodelist){
1943
            $$templateVars{'url'} = findValue($tempNode, "url");
1944
            dontOccur($tempNode, "./connection", "/distribution/online/connection");
1945
            dontOccur($tempNode, "./connectionDefinition", "/distribution/online/connectionDefinition");
1946
        }
1947 1929 brooke
    }
1948
1949
    $results = $doc->findnodes('//dataset/distribution/offline');
1950 1977 jones
    if ($results->size() > 1) {
1951
        errMoreThanOne("distribution/online");
1952 1929 brooke
    } else {
1953 1977 jones
        foreach my $tempNode ($results->get_nodelist) {
1954 2403 sgarg
            my $temp = findValue($tempNode, "mediumName");
1955
            if(substr($temp, 0, 5) eq "other"){
1956
                $$templateVars{'dataMedium'} = substr($temp, 0, 5);
1957
                $$templateVars{'dataMediumOther'} = substr($temp, 5);
1958
            } else {
1959
                $$templateVars{'dataMedium'} = $temp;
1960
            }
1961 1977 jones
            dontOccur($tempNode, "./mediumDensity", "/distribution/offline/mediumDensity");
1962
            dontOccur($tempNode, "./mediumDensityUnits", "/distribution/offline/mediumDensityUnits");
1963
            dontOccur($tempNode, "./mediumVolume", "/distribution/offline/mediumVolume");
1964
            dontOccur($tempNode, "./mediumFormat", "/distribution/offline/mediumFormat");
1965
            dontOccur($tempNode, "./mediumNote", "/distribution/offline/mediumNote");
1966
        }
1967 1929 brooke
    }
1968
1969
    dontOccur($doc, "./inline", "//dataset/distribution/inline");
1970
1971
    $results = $doc->findnodes('//dataset/coverage');
1972 1977 jones
    if ($results->size() > 1) {
1973
        errMoreThanOne("coverage");
1974 1929 brooke
    } else {
1975 1977 jones
        foreach $node ($results->get_nodelist) {
1976 1985 jones
            dontOccur($node, "./temporalCoverage/rangeOfDates/beginDate/time|./temporalCoverage/rangeOfDates/beginDate/alternativeTimeScale|./temporalCoverage/rangeOfDates/endDate/time|./temporalCoverage/rangeOfDates/endDate/alternativeTimeScale|./taxonomicCoverage/taxonomicSystem|./taxonomicCoverage/taxonomicClassification/commonName|./taxonomicCoverage/taxonomicClassification/taxonomicClassification|./geographicCoverage/datasetGPolygon|./geographicCoverage/boundingCoordinates/boundingAltitudes", "temporalCoverage/rangeOfDates/beginDate/time, /temporalCoverage/rangeOfDates/beginDate/alternativeTimeScale, /temporalCoverage/rangeOfDates/endDate/time, /temporalCoverage/rangeOfDates/endDate/alternativeTimeScale, /taxonomicCoverage/taxonomicSystem, /taxonomicCoverage/taxonomicClassification/commonName, /taxonomicCoverage/taxonomicClassification/taxonomicClassification, /geographicCoverage/datasetGPolygon, /geographicCoverage/boundingCoordinates/boundingAltitudes");
1977 1929 brooke
1978 1977 jones
            $tempResult = $node->findnodes('./temporalCoverage');
1979
            if ($tempResult->size > 1) {
1980
                   errMoreThanOne("temporalCoverage");
1981
            } else {
1982
                foreach $tempNode ($tempResult->get_nodelist) {
1983
                    my $x;
1984
                    my $y;
1985
                    my $z;
1986
                    my $tempdate = findValue($tempNode, "rangeOfDates/beginDate/calendarDate");
1987
                    ($x, $y, $z) = split("-", $tempdate);
1988
                    $$templateVars{'beginningYear'} = $x;
1989
                    $$templateVars{'beginningMonth'} = $y;
1990
                    $$templateVars{'beginningDay'} = $z;
1991
1992
                    $tempdate = findValue($tempNode, "rangeOfDates/endDate/calendarDate");
1993
                    ($x, $y, $z) = split("-", $tempdate);
1994
                    $$templateVars{'endingYear'} = $x;
1995
                    $$templateVars{'endingMonth'} = $y;
1996
                    $$templateVars{'endingDay'} = $z;
1997 2148 sgarg
1998 1977 jones
                    $tempdate = "";
1999
                    $tempdate = findValue($tempNode, "singleDateTime/calendarDate");
2000
                    if($tempdate ne ""){
2001
                        ($x, $y, $z) = split("-", $tempdate);
2002
                        $$templateVars{'beginningYear'} = $x;
2003
                        $$templateVars{'beginningMonth'} = $y;
2004
                        $$templateVars{'beginningDay'} = $z;
2005
                    }
2006 2148 sgarg
2007
		    $$templateVars{'hasTemporal'} = "true";
2008 1977 jones
                }
2009
            }
2010 1929 brooke
2011 1977 jones
            $tempResult = $node->findnodes('./geographicCoverage');
2012
            if ($tempResult->size > 1) {
2013
                errMoreThanOne("geographicCoverage");
2014
            } else {
2015
                foreach $tempNode ($tempResult->get_nodelist) {
2016 1983 jones
                    my $geogdesc = findValue($tempNode, "geographicDescription");
2017
                    debug("Registry: geogdesc from xml is: $geogdesc");
2018
                    $$templateVars{'geogdesc'} = $geogdesc;
2019
                    my $coord = findValue($tempNode, "boundingCoordinates/westBoundingCoordinate");
2020 1977 jones
                    if ($coord > 0) {
2021
                        #print "+";
2022
                        $$templateVars{'hemisphLong1'} = "E";
2023
                    } else {
2024
                        #print "-";
2025
                        eval($coord = $coord * -1);
2026
                        $$templateVars{'hemisphLong1'} = "W";
2027
                    }
2028
                    eval($$templateVars{'longDeg1'} = int($coord));
2029
                    eval($coord = ($coord - int($coord))*60);
2030
                    eval($$templateVars{'longMin1'} = int($coord));
2031
                    eval($coord = ($coord - int($coord))*60);
2032
                    eval($$templateVars{'longSec1'} = int($coord));
2033
2034
                    $coord = findValue($tempNode, "boundingCoordinates/southBoundingCoordinate");
2035
                    if ($coord > 0) {
2036
                        #print "+";
2037
                        $$templateVars{'hemisphLat2'} = "N";
2038
                    } else {
2039
                        #print "-";
2040
                        eval($coord = $coord * -1);
2041
                        $$templateVars{'hemisphLat2'} = "S";
2042
                    }
2043
                    eval($$templateVars{'latDeg2'} = int($coord));
2044
                    eval($coord = ($coord - int($coord))*60);
2045
                    eval($$templateVars{'latMin2'} = int($coord));
2046
                    eval($coord = ($coord - int($coord))*60);
2047
                    eval($$templateVars{'latSec2'} = int($coord));
2048
2049
                    $coord = findValue($tempNode, "boundingCoordinates/northBoundingCoordinate");
2050
                    if ($coord > 0) {
2051
                        #print "+";
2052
                        $$templateVars{'hemisphLat1'} = "N";
2053
                    } else {
2054
                        #print "-";
2055
                        eval($coord = $coord * -1);
2056
                        $$templateVars{'hemisphLat1'} = "S";
2057
                    }
2058
                    eval($$templateVars{'latDeg1'} = int($coord));
2059
                    eval($coord = ($coord - int($coord))*60);
2060
                    eval($$templateVars{'latMin1'} = int($coord));
2061
                    eval($coord = ($coord - int($coord))*60);
2062
                    eval($$templateVars{'latSec1'} = int($coord));
2063
2064
                    $coord = findValue($tempNode, "boundingCoordinates/eastBoundingCoordinate");
2065
                    if ($coord > 0) {
2066
                        #print "+";
2067
                        $$templateVars{'hemisphLong2'} = "E";
2068
                    } else {
2069
                        #print "-";
2070
                        eval($coord = $coord * -1);
2071
                        $$templateVars{'hemisphLong2'} = "W";
2072
                    }
2073
                    eval($$templateVars{'longDeg2'} = int($coord));
2074
                    eval($coord = ($coord - int($coord))*60);
2075
                    eval($$templateVars{'longMin2'} = int($coord));
2076
                    eval($coord = ($coord - int($coord))*60);
2077
                    eval($$templateVars{'longSec2'} = int($coord));
2078 2148 sgarg
2079 2258 jones
		            $$templateVars{'hasSpatial'} = "true";
2080 1977 jones
                }
2081
            }
2082 1984 jones
2083
            $tempResult = $node->findnodes('./taxonomicCoverage/taxonomicClassification');
2084
            my $taxonIndex = 0;
2085
            foreach $tempNode ($tempResult->get_nodelist) {
2086
                $taxonIndex++;
2087
                my $taxonRankName = findValue($tempNode, "taxonRankName");
2088
                my $taxonRankValue = findValue($tempNode, "taxonRankValue");
2089
                $$templateVars{"taxonRankName".$taxonIndex} = $taxonRankName;
2090
                $$templateVars{"taxonRankValue".$taxonIndex} = $taxonRankValue;
2091 2148 sgarg
2092
		$$templateVars{'hasTaxonomic'} = "true";
2093 1984 jones
            }
2094
            $$templateVars{'taxaCount'} = $taxonIndex;
2095 1985 jones
            my $taxaAuth = findValue($node, "./taxonomicCoverage/generalTaxonomicCoverage");
2096
            $$templateVars{'taxaAuth'} = $taxaAuth;
2097 1977 jones
        }
2098 1929 brooke
    }
2099
    dontOccur($doc, "./purpose", "purpose");
2100
    dontOccur($doc, "./maintenance", "maintnance");
2101
2102
    $results = $doc->findnodes('//dataset/contact/individualName');
2103 1977 jones
    if ($results->size() > 1) {
2104
        errMoreThanOne("contact/individualName");
2105 1929 brooke
    } else {
2106 1977 jones
        foreach $node ($results->get_nodelist) {
2107
            dontOccur($node, "../positionName|../onlineURL|../userId",
2108
              "positionName, onlineURL, userId in contact tag");
2109
            dontOccur($node, "./saluation", "saluation in contact tag");
2110
2111
            $tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
2112
            if ($tempResult->size > 0) {
2113
                $$templateVars{'origNamefirstContact'} = findValue($node, 'givenName');
2114
                $$templateVars{'origNamelastContact'} = findValue($node, 'surName');
2115
2116
                my $tempResult2 = $node->findnodes('../address');
2117
                if ($tempResult2->size > 1) {
2118
                    errMoreThanOne("address");
2119
                } else {
2120
                    foreach my $tempNode2 ($tempResult2->get_nodelist) {
2121
                        $$templateVars{'origDeliveryContact'} = findValue($tempNode2, 'deliveryPoint');
2122
                        $$templateVars{'origCityContact'} = findValue($tempNode2, 'city');
2123
                        $$templateVars{'origStateContact'} = findValue($tempNode2, 'administrativeArea');
2124
                        $$templateVars{'origZIPContact'} = findValue($tempNode2, 'postalCode');
2125
                        $$templateVars{'origCountryContact'} = findValue($tempNode2, 'country');
2126
                    }
2127
                }
2128
2129
                my $tempResult3 = $node->findnodes('../phone');
2130
                if ($tempResult3->size > 2) {
2131
                    errMoreThanN("phone");
2132
                } else {
2133
                    foreach my $tempNode2 ($tempResult3->get_nodelist) {
2134
                        if ($tempNode2->hasAttributes()) {
2135
                            my @attlist = $tempNode2->attributes();
2136
                            if ($attlist[0]->value eq "Fax") {
2137
                                $$templateVars{'origFAXContact'} = $tempNode2->textContent();
2138
                            } else {
2139
                                $$templateVars{'origPhoneContact'} = $tempNode2->textContent();
2140
                            }
2141
                        } else {
2142
                            $$templateVars{'origPhoneContact'} = $tempNode2->textContent();
2143
                        }
2144
                    }
2145
                }
2146
                $$templateVars{'origEmailContact'} = findValue($node, '../electronicMailAddress');
2147
                $$templateVars{'origNameOrgContact'} = findValue($node, '../organizationName');
2148
            } else {
2149
                $$templateVars{'origNamefirstContact'} = findValue($node, 'givenName');
2150
                $$templateVars{'origNamelastContact'} = findValue($node, 'surName');
2151
                $$templateVars{'origNameOrgContact'} = findValue($node, '../organizationName');
2152
            }
2153
        }
2154 1929 brooke
    }
2155
2156 1989 jones
    $results = $doc->findnodes(
2157
            '//dataset/methods/methodStep/description/section');
2158 1982 jones
    debug("Registry: Number methods: ".$results->size());
2159
    if ($results->size() > 1) {
2160
        errMoreThanN("methods/methodStep/description/section");
2161
    } else {
2162
2163
        my @methodPara;
2164
        foreach $node ($results->get_nodelist) {
2165
            my @children = $node->childNodes;
2166
            for (my $i = 0; $i < scalar(@children); $i++) {
2167
                debug("Registry: Method child loop ($i)");
2168
                my $child = $children[$i];
2169
                if ($child->nodeName eq 'title') {
2170
                    my $title = $child->textContent();
2171
                    debug("Registry: Method title ($title)");
2172
                    $$templateVars{'methodTitle'} = $title;
2173
                } elsif ($child->nodeName eq 'para') {
2174
                    my $para = $child->textContent();
2175
                    debug("Registry: Method para ($para)");
2176
                    $methodPara[scalar(@methodPara)] = $para;
2177
                }
2178
            }
2179 2148 sgarg
	    $$templateVars{'hasMethod'} = "true";
2180 1982 jones
        }
2181
        if (scalar(@methodPara) > 0) {
2182
            $$templateVars{'methodPara'} = \@methodPara;
2183
        }
2184
    }
2185
2186 1989 jones
    $results = $doc->findnodes(
2187
            '//dataset/methods/sampling/studyExtent/description/para');
2188
    if ($results->size() > 1) {
2189
        errMoreThanN("methods/sampling/studyExtent/description/para");
2190
    } else {
2191
        foreach $node ($results->get_nodelist) {
2192
            my $studyExtentDescription = $node->textContent();
2193
            $$templateVars{'studyExtentDescription'} = $studyExtentDescription;
2194 2148 sgarg
2195
	    $$templateVars{'hasMethod'} = "true";
2196 1989 jones
        }
2197
    }
2198
2199
    $results = $doc->findnodes(
2200
            '//dataset/methods/sampling/samplingDescription/para');
2201
    if ($results->size() > 1) {
2202
        errMoreThanN("methods/sampling/samplingDescription/para");
2203
    } else {
2204
        foreach $node ($results->get_nodelist) {
2205
            my $samplingDescription = $node->textContent();
2206
            $$templateVars{'samplingDescription'} = $samplingDescription;
2207 2148 sgarg
2208
	    $$templateVars{'hasMethod'} = "true";
2209 1989 jones
        }
2210
    }
2211
2212
    dontOccur($doc, "//methodStep/citation", "methodStep/citation");
2213
    dontOccur($doc, "//methodStep/protocol", "methodStep/protocol");
2214
    dontOccur($doc, "//methodStep/instrumentation", "methodStep/instrumentation");
2215
    dontOccur($doc, "//methodStep/software", "methodStep/software");
2216
    dontOccur($doc, "//methodStep/subStep", "methodStep/subStep");
2217
    dontOccur($doc, "//methodStep/dataSource", "methodStep/dataSource");
2218
    dontOccur($doc, "//methods/qualityControl", "methods/qualityControl");
2219
2220
    dontOccur($doc, "//methods/sampling/spatialSamplingUnits", "methods/sampling/spatialSamplingUnits");
2221
    dontOccur($doc, "//methods/sampling/citation", "methods/sampling/citation");
2222 1929 brooke
    dontOccur($doc, "./pubPlace", "pubPlace");
2223
    dontOccur($doc, "./project", "project");
2224
2225 2333 sgarg
    ############ Code for checking ACL #####################
2226
    dontOccur($doc, "//dataset/access/deny", "dataset/access/deny");
2227
2228
    $results = $doc->findnodes('//dataset/access/allow');
2229
    if ($results->size() != 3) {
2230
        errMoreThanN("dataset/access/allow");
2231
    } else {
2232
	my $accessError = 0;
2233
        foreach $node ($results->get_nodelist) {
2234
            my @children = $node->childNodes;
2235
	    my $principal = "";
2236
	    my $permission = "";
2237
            for (my $i = 0; $i < scalar(@children); $i++) {
2238
                my $child = $children[$i];
2239
                if ($child->nodeName eq 'principal') {
2240
                    $principal = $child->textContent();
2241
                } elsif ($child->nodeName eq 'permission') {
2242
                    $permission = $child->textContent();
2243
                }
2244
            }
2245
2246
	    if ($principal eq 'public' && $permission ne 'read') { $accessError = 1; }
2247
	    if ($principal eq $username && $permission ne 'all') { $accessError = 2; }
2248
	    if ($principal ne 'public' && $principal ne $username && $permission ne 'all') { $accessError = 3; }
2249
	}
2250
2251
	if ($accessError != 0) {
2252
	    my $error ="The ACL for this document has been changed outside the registry. Please use Morpho to edit this document";
2253
            push(@errorMessages, $error."\n");
2254
	}
2255
    }
2256
    ########################################################
2257
2258
2259 1929 brooke
    dontOccur($doc, "./dataTable", "dataTable");
2260
    dontOccur($doc, "./spatialRaster", "spatialRaster");
2261
    dontOccur($doc, "./spatialVector", "spatialVector");
2262
    dontOccur($doc, "./storedProcedure", "storedProcedure");
2263
    dontOccur($doc, "./view", "view");
2264
    dontOccur($doc, "./otherEntity", "otherEntity");
2265
    dontOccur($doc, "./references", "references");
2266
2267
    dontOccur($doc, "//citation", "citation");
2268
    dontOccur($doc, "//software", "software");
2269
    dontOccur($doc, "//protocol", "protocol");
2270
    dontOccur($doc, "//additionalMetadata", "additionalMetadata");
2271
}
2272
2273
################################################################################
2274
#
2275
# Delete the eml file that has been requested for deletion.
2276
#
2277
################################################################################
2278
sub deleteData {
2279
    my $deleteAll = shift;
2280
2281
    # create metacat instance
2282
    my $metacat;
2283
    my $docid = $FORM::docid;
2284
2285
    $metacat = Metacat->new();
2286
    if ($metacat) {
2287
        $metacat->set_options( metacatUrl => $metacatUrl );
2288
    } else {
2289
        #die "failed during metacat creation\n";
2290
        push(@errorMessages, "Failed during metacat creation.");
2291
    }
2292
2293
    # Login to metacat
2294
    my $userDN = $FORM::username;
2295
    my $userOrg = $FORM::organization;
2296
    my $userPass = $FORM::password;
2297
    my $dname = "uid=$userDN,o=$userOrg,dc=ecoinformatics,dc=org";
2298
2299
    my $errorMessage = "";
2300
    my $response = $metacat->login($dname, $userPass);
2301
2302
    if (! $response) {
2303 1977 jones
    # Could not login
2304 1929 brooke
        push(@errorMessages, $metacat->getMessage());
2305
        push(@errorMessages, "Failed during login.\n");
2306
2307
    } else {
2308 1977 jones
    #Able to login - try to delete the file
2309 1929 brooke
2310 1977 jones
    my $parser;
2311
    my @fileArray;
2312
    my $httpMessage;
2313
    my $xmldoc;
2314
    my $doc;
2315
    my $pushDoc;
2316
    my $alreadyInArray;
2317
    my $findType;
2318 1929 brooke
        my $node;
2319 1977 jones
    my $response;
2320
    my $element;
2321 1929 brooke
2322 1977 jones
    push (@fileArray, $docid);
2323
    $parser = XML::LibXML->new();
2324 1929 brooke
2325
        $httpMessage = $metacat->read($docid);
2326 1977 jones
    $doc = $httpMessage->content();
2327 2415 sgarg
    $doc = delNormalize($doc);
2328 1977 jones
    $xmldoc = $parser->parse_string($doc);
2329 1929 brooke
2330 1977 jones
    if ($xmldoc eq "") {
2331
        $error ="Error in parsing the eml document";
2332
        push(@errorMessages, $error);
2333
    } else {
2334 1929 brooke
2335 1977 jones
        $findType = $xmldoc->findnodes('//dataset/identifier');
2336
        if($findType->size() > 0){
2337
        # This is a eml beta6 document
2338
        # Delete the documents mentioned in triples also
2339
2340
        $findType = $xmldoc->findnodes('//dataset/triple');
2341
        if($findType->size() > 0){
2342
            foreach $node ($findType->get_nodelist){
2343
            $pushDoc = findValue($node, 'subject');
2344
2345
            # If the file is already in the @fileArray then do not add it
2346
            $alreadyInArray = 0;
2347
            foreach $element (@fileArray){
2348
                if($element eq $pushDoc){
2349
                $alreadyInArray = 1;
2350
                }
2351
            }
2352
2353
            if(!$alreadyInArray){
2354
                # If not already in array then delete the file.
2355
                push (@fileArray, $pushDoc);
2356
                $response = $metacat->delete($pushDoc);
2357
2358
                if (! $response) {
2359
                # Could not delete
2360
                #push(@errorMessages, $response);
2361
                push(@errorMessages, $metacat->getMessage());
2362
                push(@errorMessages, "Failed during deleting $pushDoc. Please check if you are authorized to delete this document.\n");
2363
                }
2364
            }
2365
            }
2366
        }
2367
        }
2368 1929 brooke
    }
2369
2370 1977 jones
    # Delete the main document.
2371
    if($deleteAll){
2372
        $response = $metacat->delete($docid);
2373
        if (! $response) {
2374
        # Could not delete
2375
        #push(@errorMessages, $response);
2376
        push(@errorMessages, $metacat->getMessage());
2377
        push(@errorMessages, "Failed during deleting $docid. Please check if you are authorized to delete this document.\n");
2378
        }
2379
    }
2380
    }
2381
2382 1929 brooke
    if (scalar(@errorMessages)) {
2383 1977 jones
    # If any errors, print them in the response template
2384
    $$templateVars{'status'} = 'failure';
2385
    $$templateVars{'errorMessages'} = \@errorMessages;
2386
    $error = 1;
2387 1929 brooke
    }
2388
2389
    # Process the response template
2390
    if($deleteAll){
2391
2392 1977 jones
    $$templateVars{'function'} = "deleted";
2393
    $$templateVars{'section'} = "Deletion Status";
2394
    $template->process( $responseTemplate, $templateVars);
2395 1929 brooke
    }
2396
}
2397
2398
2399
################################################################################
2400
#
2401
# Do data validation and send the data to confirm data template.
2402
#
2403
################################################################################
2404
sub toConfirmData{
2405
    # Check if any invalid parameters
2406
2407
    my $invalidParams;
2408
    if (! $error) {
2409 1977 jones
    $invalidParams = validateParameters(0);
2410
    if (scalar(@$invalidParams)) {
2411
        $$templateVars{'status'} = 'failure';
2412
        $$templateVars{'invalidParams'} = $invalidParams;
2413
        $error = 1;
2414 1929 brooke
    }
2415 1977 jones
    }
2416 1929 brooke
2417
2418 2037 sgarg
    $$templateVars{'providerGivenName'} = normalizeCD($FORM::providerGivenName);
2419
    $$templateVars{'providerSurName'} = normalizeCD($FORM::providerSurName);
2420 1977 jones
    if($FORM::site eq "Select your station here."){
2421
        $$templateVars{'site'} = "";
2422
    }else{
2423
        $$templateVars{'site'} = $FORM::site;
2424
    }
2425
    if($FORM::cfg eq "nceas"){
2426
        $$templateVars{'wg'} = \@FORM::wg;
2427
    }
2428 2037 sgarg
    $$templateVars{'identifier'} = normalizeCD($FORM::identifier);
2429
    $$templateVars{'title'} = normalizeCD($FORM::title);
2430
    $$templateVars{'origNamefirst0'} = normalizeCD($FORM::origNamefirst0);
2431
    $$templateVars{'origNamelast0'} = normalizeCD($FORM::origNamelast0);
2432
    $$templateVars{'origNameOrg'} = normalizeCD($FORM::origNameOrg);
2433 1977 jones
    # $$templateVars{'origRole0'} = $FORM::origRole0;
2434 2037 sgarg
    $$templateVars{'origDelivery'} = normalizeCD($FORM::origDelivery);
2435
    $$templateVars{'origCity'} = normalizeCD($FORM::origCity);
2436 1977 jones
    if($FORM::origState eq "Select State Here."){
2437
        $$templateVars{'origState'} = "";
2438
    }else{
2439
        $$templateVars{'origState'} = $FORM::origState;
2440
    }
2441 2037 sgarg
    $$templateVars{'origStateOther'} = normalizeCD($FORM::origStateOther);
2442
    $$templateVars{'origZIP'} = normalizeCD($FORM::origZIP);
2443
    $$templateVars{'origCountry'} = normalizeCD($FORM::origCountry);
2444
    $$templateVars{'origPhone'} = normalizeCD($FORM::origPhone);
2445
    $$templateVars{'origFAX'} = normalizeCD($FORM::origFAX);
2446
    $$templateVars{'origEmail'} = normalizeCD($FORM::origEmail);
2447
    $$templateVars{'useOrigAddress'} = normalizeCD($FORM::useOrigAddress);
2448 1977 jones
    if($FORM::useOrigAddress eq "on"){
2449 2037 sgarg
        $$templateVars{'origNamefirstContact'} = normalizeCD($FORM::origNamefirst0);
2450
        $$templateVars{'origNamelastContact'} = normalizeCD($FORM::origNamelast0);
2451
        $$templateVars{'origNameOrgContact'} = normalizeCD($FORM::origNameOrg);
2452
        $$templateVars{'origDeliveryContact'} = normalizeCD($FORM::origDelivery);
2453
        $$templateVars{'origCityContact'} = normalizeCD($FORM::origCity);
2454 1977 jones
        if($FORM::origState eq "Select State Here."){
2455
        $$templateVars{'origStateContact'} = "";
2456
        }else{
2457
        $$templateVars{'origStateContact'} = $FORM::origState;
2458
        }
2459 2037 sgarg
        $$templateVars{'origStateOtherContact'} = normalizeCD($FORM::origStateOther);
2460
        $$templateVars{'origZIPContact'} = normalizeCD($FORM::origZIP);
2461
        $$templateVars{'origCountryContact'} = normalizeCD($FORM::origCountry);
2462
        $$templateVars{'origPhoneContact'} = normalizeCD($FORM::origPhone);
2463
        $$templateVars{'origFAXContact'} = normalizeCD($FORM::origFAX);
2464
        $$templateVars{'origEmailContact'} = normalizeCD($FORM::origEmail);
2465 1977 jones
    }else{
2466 2037 sgarg
        $$templateVars{'origNamefirstContact'} = normalizeCD($FORM::origNamefirstContact);
2467
        $$templateVars{'origNamelastContact'} = normalizeCD($FORM::origNamelastContact);
2468
        $$templateVars{'origNameOrgContact'} = normalizeCD($FORM::origNameOrgContact);
2469
        $$templateVars{'origDeliveryContact'} = normalizeCD($FORM::origDeliveryContact);
2470
        $$templateVars{'origCityContact'} = normalizeCD($FORM::origCityContact);
2471 1977 jones
        if($FORM::origStateContact eq "Select State Here."){
2472
        $$templateVars{'origStateContact'} = "";
2473
        }else{
2474
        $$templateVars{'origStateContact'} = $FORM::origStateContact;
2475
        }
2476 2037 sgarg
        $$templateVars{'origStateOtherContact'} = normalizeCD($FORM::origStateOtherContact);
2477
        $$templateVars{'origZIPContact'} = normalizeCD($FORM::origZIPContact);
2478
        $$templateVars{'origCountryContact'} = normalizeCD($FORM::origCountryContact);
2479
        $$templateVars{'origPhoneContact'} = normalizeCD($FORM::origPhoneContact);
2480
        $$templateVars{'origFAXContact'} = normalizeCD($FORM::origFAXContact);
2481
        $$templateVars{'origEmailContact'} = normalizeCD($FORM::origEmailContact);
2482 1977 jones
    }
2483 2144 sgarg
2484 2403 sgarg
    my $aoFNArray = \@FORM::aoFirstName;
2485
    my $aoLNArray = \@FORM::aoLastName;
2486
    my $aoRoleArray = \@FORM::aoRole;
2487
    my $aoCount = 1;
2488
2489
    for(my $i = 0; $i <= $#$aoRoleArray; $i++){
2490
        if (hasContent($aoFNArray->[$i]) && hasContent($aoLNArray->[$i])) {
2491
            debug("Registry processing Associated Party: origName = ".$aoFNArray->[$i]
2492
                  ." origNamelast = ".$aoLNArray->[$i]." origRole = "
2493
                  .$aoRoleArray->[$i]);
2494
            $$templateVars{"origNamefirst".$aoCount} = normalizeCD($aoFNArray->[$i]);
2495
            $$templateVars{"origNamelast".$aoCount} = normalizeCD($aoLNArray->[$i]);
2496
            $$templateVars{"origRole".$aoCount} = normalizeCD($aoRoleArray->[$i]);
2497
            $aoCount++;
2498
	}
2499 1977 jones
    }
2500 2144 sgarg
2501 2403 sgarg
    $$templateVars{'aoCount'} = $aoCount;
2502 2037 sgarg
    $$templateVars{'abstract'} = normalizeCD($FORM::abstract);
2503 2403 sgarg
2504
2505
    my $keywordArray = \@FORM::keyword;
2506
    my $keywordTypeArray = \@FORM::keywordType;
2507
    my $keywordThArray = \@FORM::keywordTh;
2508
    my $keyCount = 1;
2509
2510
    for(my $i = 0; $i <= $#$keywordArray; $i++){
2511
        if (hasContent($keywordArray->[$i])) {
2512
            debug("Registry processing keyword: keyword = ".$keywordArray->[$i]."
2513
                  keywordType = ".$keywordTypeArray->[$i]."
2514
                  keywordTh = ".$keywordThArray->[$i]);
2515
            $$templateVars{"keyword".$keyCount} = normalizeCD($keywordArray->[$i]);
2516
            $$templateVars{"kwType".$keyCount} = normalizeCD($keywordTypeArray->[$i]);
2517
            $$templateVars{"kwTh".$keyCount} = normalizeCD($keywordThArray->[$i]);
2518
            $keyCount++;
2519
	}
2520
    }
2521
    $$templateVars{'keyCount'} = $keyCount;
2522
2523 2037 sgarg
    $$templateVars{'addComments'} = normalizeCD($FORM::addComments);
2524 1977 jones
    $$templateVars{'useConstraints'} = $FORM::useConstraints;
2525 2403 sgarg
    if($FORM::useConstraints eq "other"){
2526
        $$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
2527
    }
2528 1977 jones
    $$templateVars{'url'} = $FORM::url;
2529 2403 sgarg
    $$templateVars{'dataMedium'} = $FORM::dataMedium;
2530
    if($FORM::dataMedium eq "other"){
2531
        $$templateVars{'dataMediumOther'} = normalizeCD($FORM::dataMediumOther);
2532
    }
2533 1977 jones
    $$templateVars{'beginningYear'} = $FORM::beginningYear;
2534
    $$templateVars{'beginningMonth'} = $FORM::beginningMonth;
2535
    $$templateVars{'beginningDay'} = $FORM::beginningDay;
2536
    $$templateVars{'endingYear'} = $FORM::endingYear;
2537
    $$templateVars{'endingMonth'} = $FORM::endingMonth;
2538
    $$templateVars{'endingDay'} = $FORM::endingDay;
2539 2037 sgarg
    $$templateVars{'geogdesc'} = normalizeCD($FORM::geogdesc);
2540 1977 jones
    $$templateVars{'useSiteCoord'} = $FORM::useSiteCoord;
2541
    $$templateVars{'latDeg1'} = $FORM::latDeg1;
2542
    $$templateVars{'latMin1'} = $FORM::latMin1;
2543
    $$templateVars{'latSec1'} = $FORM::latSec1;
2544
    $$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
2545
    $$templateVars{'longDeg1'} = $FORM::longDeg1;
2546
    $$templateVars{'longMin1'} = $FORM::longMin1;
2547
    $$templateVars{'longSec1'} = $FORM::longSec1;
2548
    $$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
2549
    $$templateVars{'latDeg2'} = $FORM::latDeg2;
2550
    $$templateVars{'latMin2'} = $FORM::latMin2;
2551
    $$templateVars{'latSec2'} = $FORM::latSec2;
2552
    $$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
2553
    $$templateVars{'longDeg2'} = $FORM::longDeg2;
2554
    $$templateVars{'longMin2'} = $FORM::longMin2;
2555
    $$templateVars{'longSec2'} = $FORM::longSec2;
2556
    $$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
2557 1984 jones
2558 2403 sgarg
    my $taxonRankArray = \@FORM::taxonRank;
2559
    my $taxonNameArray = \@FORM::taxonName;
2560
    my $taxonCount = 1;
2561
2562
    for(my $i = 0; $i <= $#$taxonNameArray; $i++){
2563
        if (hasContent($taxonRankArray->[$i]) && hasContent($taxonNameArray->[$i])) {
2564
            debug("Registry processing keyword: trv = ".$taxonRankArray->[$i]
2565
                    ." trn = ".$taxonNameArray->[$i]);
2566
            $$templateVars{"taxonRankName".$taxonCount} = normalizeCD($taxonNameArray->[$i]);
2567
            $$templateVars{"taxonRankValue".$taxonCount} = normalizeCD($taxonRankArray->[$i]);
2568
            $taxonCount++;
2569
	}
2570 1984 jones
    }
2571 2403 sgarg
2572
    $$templateVars{'taxaCount'} = $taxonCount-1;
2573 2037 sgarg
    $$templateVars{'taxaAuth'} = normalizeCD($FORM::taxaAuth);
2574 1984 jones
2575 2037 sgarg
    $$templateVars{'methodTitle'} = normalizeCD($FORM::methodTitle);
2576 2403 sgarg
2577 2037 sgarg
    my @tempMethodPara;
2578
    for (my $i = 0; $i < scalar(@FORM::methodPara); $i++) {
2579
	$tempMethodPara[$i] = normalizeCD($FORM::methodPara[$i]);
2580
    }
2581
    $$templateVars{'methodPara'} = \@tempMethodPara;
2582
    $$templateVars{'studyExtentDescription'} = normalizeCD($FORM::studyExtentDescription);
2583
    $$templateVars{'samplingDescription'} = normalizeCD($FORM::samplingDescription);
2584 2138 sgarg
    $$templateVars{'origStateContact'} = $FORM::origState;
2585
2586 2258 jones
    $$templateVars{'showSiteList'} = $FORM::showSiteList;
2587
    $$templateVars{'lsite'} = $FORM::lsite;
2588
    $$templateVars{'usite'} = $FORM::usite;
2589
    $$templateVars{'showWgList'} = $FORM::showWgList;
2590
    $$templateVars{'showOrganization'} = $FORM::showOrganization;
2591 2138 sgarg
    $$templateVars{'hasKeyword'} = $FORM::hasKeyword;
2592 2148 sgarg
    $$templateVars{'hasTemporal'} = $FORM::hasTemporal;
2593
    $$templateVars{'hasSpatial'} = $FORM::hasSpatial;
2594
    $$templateVars{'hasTaxonomic'} = $FORM::hasTaxonomic;
2595
    $$templateVars{'hasMethod'} = $FORM::hasMethod;
2596
    $$templateVars{'spatialRequired'} = $FORM::spatialRequired;
2597
    $$templateVars{'temporalRequired'} = $FORM::temporalRequired;
2598
2599 1977 jones
    $$templateVars{'docid'} = $FORM::docid;
2600 1929 brooke
2601 2024 sgarg
    if (! $error) {
2602
	# If no errors, then print out data in confirm Data template
2603 1929 brooke
2604 2024 sgarg
	$$templateVars{'section'} = "Confirm Data";
2605
	$template->process( $confirmDataTemplate, $templateVars);
2606
2607 1977 jones
    } else{
2608
    # Errors from validation function. print the errors out using the response template
2609
    if (scalar(@errorMessages)) {
2610
        $$templateVars{'status'} = 'failure';
2611
        $$templateVars{'errorMessages'} = \@errorMessages;
2612
        $error = 1;
2613
    }
2614 1929 brooke
        # Create our HTML response and send it back
2615 1977 jones
    $$templateVars{'function'} = "submitted";
2616
    $$templateVars{'section'} = "Submission Status";
2617
    $template->process( $responseTemplate, $templateVars);
2618 1929 brooke
    }
2619
}
2620
2621
2622
################################################################################
2623
#
2624
# From confirm Data template - user wants to make some changes.
2625
#
2626
################################################################################
2627
sub confirmDataToReEntryData{
2628
    my @sortedSites;
2629
    foreach my $site (sort @sitelist) {
2630
        push(@sortedSites, $site);
2631
    }
2632
2633
    $$templateVars{'siteList'} = \@sortedSites;
2634
    $$templateVars{'section'} = "Re-Entry Form";
2635 2136 sgarg
    copyFormToTemplateVars();
2636
    $$templateVars{'docid'} = $FORM::docid;
2637 1929 brooke
2638 2136 sgarg
    $$templateVars{'form'} = 're_entry';
2639
    $template->process( $entryFormTemplate, $templateVars);
2640
}
2641
2642
2643
################################################################################
2644
#
2645
# Copy form data to templateVars.....
2646
#
2647
################################################################################
2648
sub copyFormToTemplateVars{
2649 1929 brooke
    $$templateVars{'providerGivenName'} = $FORM::providerGivenName;
2650
    $$templateVars{'providerSurName'} = $FORM::providerSurName;
2651
    $$templateVars{'site'} = $FORM::site;
2652 1982 jones
    if ($FORM::cfg eq "nceas") {
2653 1977 jones
        my $projects = getProjectList();
2654
        $$templateVars{'projects'} = $projects;
2655
        $$templateVars{'wg'} = \@FORM::wg;
2656
    }
2657 1929 brooke
    $$templateVars{'identifier'} = $FORM::identifier;
2658
    $$templateVars{'title'} = $FORM::title;
2659
    $$templateVars{'origNamefirst0'} = $FORM::origNamefirst0;
2660
    $$templateVars{'origNamelast0'} = $FORM::origNamelast0;
2661
    $$templateVars{'origNameOrg'} = $FORM::origNameOrg;
2662
 #   $$templateVars{'origRole0'} = $FORM::origRole0;
2663
    $$templateVars{'origDelivery'} = $FORM::origDelivery;
2664
    $$templateVars{'origCity'} = $FORM::origCity;
2665
    $$templateVars{'origState'} = $FORM::origState;
2666
    $$templateVars{'origStateOther'} = $FORM::origStateOther;
2667
    $$templateVars{'origZIP'} = $FORM::origZIP;
2668
    $$templateVars{'origCountry'} = $FORM::origCountry;
2669
    $$templateVars{'origPhone'} = $FORM::origPhone;
2670
    $$templateVars{'origFAX'} = $FORM::origFAX;
2671
    $$templateVars{'origEmail'} = $FORM::origEmail;
2672 1977 jones
    if ($FORM::useSiteCoord ne "") {
2673
        $$templateVars{'useOrigAddress'} = "CHECKED";
2674 1929 brooke
    }else{
2675 1977 jones
        $$templateVars{'useOrigAddress'} = $FORM::useOrigAddress;
2676 1929 brooke
    }
2677
    $$templateVars{'origNamefirstContact'} = $FORM::origNamefirstContact;
2678
    $$templateVars{'origNamelastContact'} = $FORM::origNamelastContact;
2679
    $$templateVars{'origNameOrgContact'} = $FORM::origNameOrgContact;
2680
    $$templateVars{'origDeliveryContact'} = $FORM::origDeliveryContact;
2681
    $$templateVars{'origCityContact'} = $FORM::origCityContact;
2682
    $$templateVars{'origStateContact'} = $FORM::origStateContact;
2683
    $$templateVars{'origStateOtherContact'} = $FORM::origStateOtherContact;
2684
    $$templateVars{'origZIPContact'} = $FORM::origZIPContact;
2685
    $$templateVars{'origCountryContact'} = $FORM::origCountryContact;
2686
    $$templateVars{'origPhoneContact'} = $FORM::origPhoneContact;
2687
    $$templateVars{'origFAXContact'} = $FORM::origFAXContact;
2688
    $$templateVars{'origEmailContact'} = $FORM::origEmailContact;
2689 2144 sgarg
2690
    $$templateVars{'aoCount'} = $FORM::aoCount;
2691
    foreach my $origName (param()) {
2692
	if ($origName =~ /origNamefirst/) {
2693
	    my $origNameIndex = $origName;
2694
	    $origNameIndex =~ s/origNamefirst//; # get the index of the parameter 0, ..., 10
2695
	    my $origNamelast = "origNamelast".$origNameIndex;
2696
	    my $origRole = "origRole".$origNameIndex;
2697
	    if ( $origNameIndex =~ /[0-9]/  && $origNameIndex > 0){
2698
		if (hasContent(param($origName)) && hasContent(param($origNamelast)) && hasContent(param($origRole))) {
2699
		    debug("Registry processing keyword: $origName = ".param($origName)." $origNamelast = ".param($origNamelast)." $origRole = ".param($origRole));
2700
		    $$templateVars{$origName} = normalizeCD(param($origName));
2701
		    $$templateVars{$origNamelast} = normalizeCD(param($origNamelast));
2702
		    $$templateVars{$origRole} = normalizeCD(param($origRole));
2703
		}
2704
	    }
2705
	}
2706
    }
2707
2708 1929 brooke
    $$templateVars{'abstract'} = $FORM::abstract;
2709 2028 sgarg
    $$templateVars{'keyCount'} = $FORM::keyCount;
2710
    foreach my $kyd (param()) {
2711
	if ($kyd =~ /keyword/) {
2712
	    my $keyIndex = $kyd;
2713
	    $keyIndex =~ s/keyword//; # get the index of the parameter 0, ..., 10
2714
	    my $keyType = "kwType".$keyIndex;
2715
	    my $keyTh = "kwTh".$keyIndex;
2716
	    if ( $keyIndex =~ /[0-9]/ ){
2717
		if (hasContent(param($kyd)) && hasContent(param($keyType)) && hasContent(param($keyTh))) {
2718
		    debug("Registry processing keyword: $kyd = ".param($kyd)." $keyType = ".param($keyType)." $keyTh = ".param($keyTh));
2719 2403 sgarg
		    $$templateVars{$kyd} = param($kyd);
2720
                    my $tmp = param($keyType);  #convert the first letter to upper case
2721
		    $tmp =~ s/\b(\w)/\U$1/g;
2722
                    $$templateVars{$keyType} = $tmp;
2723 2028 sgarg
		    $$templateVars{$keyTh} = param($keyTh);
2724
		}
2725
	    }
2726
	}
2727
    }
2728 1929 brooke
    $$templateVars{'addComments'} = $FORM::addComments;
2729
    $$templateVars{'useConstraints'} = $FORM::useConstraints;
2730
    $$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
2731
    $$templateVars{'url'} = $FORM::url;
2732
    $$templateVars{'dataMedium'} = $FORM::dataMedium;
2733
    $$templateVars{'dataMediumOther'} = $FORM::dataMediumOther;
2734
    $$templateVars{'beginningYear'} = $FORM::beginningYear;
2735
    $$templateVars{'beginningMonth'} = $FORM::beginningMonth;
2736
    $$templateVars{'beginningDay'} = $FORM::beginningDay;
2737
    $$templateVars{'endingYear'} = $FORM::endingYear;
2738
    $$templateVars{'endingMonth'} = $FORM::endingMonth;
2739
    $$templateVars{'endingDay'} = $FORM::endingDay;
2740 1983 jones
    $$templateVars{'geogdesc'} = $FORM::geogdesc;
2741 1929 brooke
    if($FORM::useSiteCoord ne ""){
2742 1977 jones
    $$templateVars{'useSiteCoord'} = "CHECKED";
2743 1929 brooke
    }else{
2744 1977 jones
    $$templateVars{'useSiteCoord'} = "";
2745 1929 brooke
    }
2746
    $$templateVars{'latDeg1'} = $FORM::latDeg1;
2747
    $$templateVars{'latMin1'} = $FORM::latMin1;
2748
    $$templateVars{'latSec1'} = $FORM::latSec1;
2749
    $$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
2750
    $$templateVars{'longDeg1'} = $FORM::longDeg1;
2751
    $$templateVars{'longMin1'} = $FORM::longMin1;
2752
    $$templateVars{'longSec1'} = $FORM::longSec1;
2753
    $$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
2754
    $$templateVars{'latDeg2'} = $FORM::latDeg2;
2755
    $$templateVars{'latMin2'} = $FORM::latMin2;
2756
    $$templateVars{'latSec2'} = $FORM::latSec2;
2757
    $$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
2758
    $$templateVars{'longDeg2'} = $FORM::longDeg2;
2759
    $$templateVars{'longMin2'} = $FORM::longMin2;
2760
    $$templateVars{'longSec2'} = $FORM::longSec2;
2761
    $$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
2762 1985 jones
    $$templateVars{'taxaCount'} = $FORM::taxaCount;
2763
    foreach my $trn (param()) {
2764
        if ($trn =~ /taxonRankName/) {
2765
            my $taxIndex = $trn;
2766
            $taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
2767
            my $trv = "taxonRankValue".$taxIndex;
2768
            if ( $taxIndex =~ /[0-9]/ ){
2769
                if (hasContent(param($trn)) && hasContent(param($trv))) {
2770
                    debug("Registry processing taxon: $trn = ".param($trn)." $trv = ".param($trv));
2771
                    $$templateVars{$trn} = param($trn);
2772
                    $$templateVars{$trv} = param($trv);
2773
                }
2774
            }
2775
        }
2776 1982 jones
    }
2777 1985 jones
    $$templateVars{'taxaAuth'} = $FORM::taxaAuth;
2778
    $$templateVars{'methodTitle'} = $FORM::methodTitle;
2779
    $$templateVars{'methodPara'} = \@FORM::methodPara;
2780 1989 jones
    $$templateVars{'studyExtentDescription'} = $FORM::studyExtentDescription;
2781
    $$templateVars{'samplingDescription'} = $FORM::samplingDescription;
2782 2138 sgarg
2783 2258 jones
    $$templateVars{'showSiteList'} = $FORM::showSiteList;
2784
    $$templateVars{'lsite'} = $FORM::lsite;
2785
    $$templateVars{'usite'} = $FORM::usite;
2786
    $$templateVars{'showWgList'} = $FORM::showWgList;
2787
    $$templateVars{'showOrganization'} = $FORM::showOrganization;
2788 2148 sgarg
    $$templateVars{'hasKeyword'} = $FORM::hasKeyword;
2789
    $$templateVars{'hasTemporal'} = $FORM::hasTemporal;
2790
    $$templateVars{'hasSpatial'} = $FORM::hasSpatial;
2791
    $$templateVars{'hasTaxonomic'} = $FORM::hasTaxonomic;
2792
    $$templateVars{'hasMethod'} = $FORM::hasMethod;
2793
    $$templateVars{'spatialRequired'} = $FORM::spatialRequired;
2794
    $$templateVars{'temporalRequired'} = $FORM::temporalRequired;
2795 1929 brooke
}
2796
2797
################################################################################
2798
#
2799
# check if there is multiple occurence of the given tag and find its value.
2800
#
2801
################################################################################
2802
2803
sub findValue {
2804
    my $node = shift;
2805
    my $value = shift;
2806
    my $result;
2807
    my $tempNode;
2808
2809
    $result = $node->findnodes("./$value");
2810 1977 jones
    if ($result->size > 1) {
2811
        errMoreThanOne("$value");
2812 1929 brooke
    } else {
2813 1977 jones
        foreach $tempNode ($result->get_nodelist){
2814
            #print $tempNode->nodeName().":".$tempNode->textContent();
2815
            #print "\n";
2816
            return $tempNode->textContent();
2817
        }
2818 1929 brooke
    }
2819
}
2820
2821
2822
################################################################################
2823
#
2824
# check if given tags has any children. if not return the value
2825
#
2826
################################################################################
2827
sub findValueNoChild {
2828
    my $node = shift;
2829
    my $value = shift;
2830
    my $tempNode;
2831
    my $childNodes;
2832
    my $result;
2833
    my $error;
2834
2835
    $result = $node->findnodes("./$value");
2836 1977 jones
    if($result->size > 1){
2837
       errMoreThanOne("$value");
2838
    } else {
2839
        foreach $tempNode ($result->get_nodelist) {
2840
            $childNodes = $tempNode->childNodes;
2841
            if ($childNodes->size() > 1) {
2842
                $error ="The tag $value has children which cannot be shown using the form. Please use Morpho to edit this document";
2843
                push(@errorMessages, $error);
2844
                #if ($DEBUG == 1){ print $error."\n";}
2845
            } else {
2846
                #print $tempNode->nodeName().":".$tempNode->textContent();
2847
                #print "\n";
2848
                return $tempNode->textContent();
2849
            }
2850
        }
2851
    }
2852 1929 brooke
}
2853
2854
2855
################################################################################
2856
#
2857
# check if given tags are children of given node.
2858
#
2859
################################################################################
2860
sub dontOccur {
2861
    my $node = shift;
2862
    my $value = shift;
2863
    my $errVal = shift;
2864
2865
    my $result = $node->findnodes("$value");
2866
    if($result->size > 0){
2867 1977 jones
        $error ="One of the following tags found: $errVal. Please use Morpho to edit this document";
2868
        push(@errorMessages, $error."\n");
2869
        #if ($DEBUG == 1){ print $error;}
2870 1929 brooke
    }
2871
}
2872
2873
2874
################################################################################
2875
#
2876
# print out error for more than one occurence of a given tag
2877
#
2878
################################################################################
2879
sub errMoreThanOne {
2880
    my $value = shift;
2881
    my $error ="More than one occurence of the tag $value found. Please use Morpho to edit this document";
2882
    push(@errorMessages, $error."\n");
2883
    # if ($DEBUG == 1){ print $error;}
2884
}
2885
2886
2887
################################################################################
2888
#
2889
# print out error for more than given number of occurences of a given tag
2890
#
2891
################################################################################
2892
sub errMoreThanN {
2893
    my $value = shift;
2894
    my $error ="More occurences of the tag $value found than that can be shown in the form. Please use Morpho to edit this document";
2895
    push(@errorMessages, $error);
2896
    #if ($DEBUG == 1){ print $error."\n";}
2897
}
2898
2899
2900
################################################################################
2901
#
2902
# convert coord to degrees, minutes and seconds form.
2903
#
2904
################################################################################
2905
#sub convertCoord {
2906
#    my $wx = shift;
2907
#    print $deg." ".$min." ".$sec;
2908
#    print "\n";
2909
#}
2910
2911
2912 1955 jones
################################################################################
2913
#
2914
# print debugging messages to stderr
2915
#
2916
################################################################################
2917
sub debug {
2918
    my $msg = shift;
2919
2920
    if ($debug) {
2921
        print STDERR "$msg\n";
2922
    }
2923
}
2924 1973 jones
2925
################################################################################
2926
#
2927
# get the list of projects
2928
#
2929
################################################################################
2930
sub getProjectList {
2931
2932 2478 sgarg
    #use NCEAS::AdminDB;
2933
    #my $admindb = NCEAS::AdminDB->new();
2934
    #$admindb->connect($nceas_db, $nceas_db_user, $nceas_db_password);
2935
    #my $projects = $admindb->getProjects();
2936
    my $projects = getTestProjectList();
2937 1993 jones
    return $projects;
2938
}
2939 1973 jones
2940 1993 jones
################################################################################
2941
#
2942
# get a test list of projects for use only in testing where the NCEAS
2943
# admin db is not available.
2944
#
2945
################################################################################
2946
sub getTestProjectList {
2947 1973 jones
    # This block is for testing only!  Remove for production use
2948
    my @row1;
2949 1974 jones
    $row1[0] = 6000; $row1[1] = 'Andelman'; $row1[2] = 'Sandy'; $row1[3] = 'The very long and windy path to an apparent ecological conclusion: statistics lie';
2950 1973 jones
    my @row2;
2951 1974 jones
    $row2[0] = 7000; $row2[1] = 'Bascompte'; $row2[2] = 'Jordi'; $row2[3] = 'Postdoctoral Fellow';
2952 1980 jones
    my @row3;
2953
    $row3[0] = 7001; $row3[1] = 'Hackett'; $row3[2] = 'Edward'; $row3[3] = 'Sociology rules the world';
2954
    my @row4;
2955
    $row4[0] = 7002; $row4[1] = 'Jones'; $row4[2] = 'Matthew'; $row4[3] = 'Informatics rules the world';
2956
    my @row5;
2957
    $row5[0] = 7003; $row5[1] = 'Schildhauer'; $row5[2] = 'Mark'; $row5[3] = 'Excel rocks my world, assuming a, b, and c';
2958
    my @row6;
2959
    $row6[0] = 7004; $row6[1] = 'Rogers'; $row6[2] = 'Bill'; $row6[3] = 'Graduate Intern';
2960
    my @row7;
2961
    $row7[0] = 7005; $row7[1] = 'Zedfried'; $row7[2] = 'Karl'; $row7[3] = 'A multivariate analysis of thing that go bump in the night';
2962 1973 jones
    my @projects;
2963
    $projects[0] = \@row1;
2964
    $projects[1] = \@row2;
2965 1980 jones
    $projects[2] = \@row3;
2966
    $projects[3] = \@row4;
2967
    $projects[4] = \@row5;
2968
    $projects[5] = \@row6;
2969
    $projects[6] = \@row7;
2970 1973 jones
    return \@projects;
2971
}