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#!/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: sgarg $'
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# '$Date: 2004-02-10 18:13:16 -0800 (Tue, 10 Feb 2004) $'
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# '$Revision: 2028 $'
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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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$config->define("datasetsysid");
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$config->define("mailhost");
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$config->define("sender");
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$config->define("recipient");
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$config->define("adminname");
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if ($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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$config->define("nceas_db_password");
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}
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$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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$config->define("debug", { DEFAULT => '0'} );
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$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 = $organization;
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$orgfilter =~ s/ /%20/g;
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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 $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();
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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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}
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my $debug = $config->debug();
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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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$$templateVars{'orgfilter'} = $orgfilter;
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debug("Registry: Initialized");
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# Process the form based on stage parameter.
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if ($FORM::stage =~ "guide") {
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# Send back the information on how to fill the form
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$$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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}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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$$templateVars{'docid'} = $FORM::docid;
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modifyData();
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exit(0);
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}elsif ($FORM::stage =~ "delete_confirm") {
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# Result from deleteData form.
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if($FORM::deleteData =~ "Delete data"){
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# delete Data
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deleteData(1);
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exit(0);
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} else {
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# go back to search page.
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exit(0);
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}
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}elsif ($FORM::stage =~ "delete") {
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# Deletion of a file has been requested.
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# Ask for username and password using deleteDataForm
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$$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.
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debug("Registry: Sending form");
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my @sortedSites;
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foreach my $site (sort @sitelist) {
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push(@sortedSites, $site);
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}
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if ($FORM::cfg eq 'nceas') {
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my $projects = getProjectList();
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$$templateVars{'projects'} = $projects;
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$$templateVars{'wg'} = \@FORM::wg;
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}
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$$templateVars{'siteList'} = \@sortedSites;
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$$templateVars{'section'} = "Entry Form";
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$$templateVars{'docid'} = "";
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debug("Registry: Sending form: ready to process template");
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$template->process( $entryFormTemplate, $templateVars);
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debug("Registry: Sending form: template processed");
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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);
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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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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());
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push(@errorMessages, "Failed during login.\n");
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}
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debug( "Registry: A");
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if ($FORM::docid eq "") {
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debug( "Registry: B1");
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# document is being inserted
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my $notunique = "NOT_UNIQUE";
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while ($notunique eq "NOT_UNIQUE") {
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$docid = newAccessionNumber($defaultScope);
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$xmldoc =~ s/docid/$docid/;
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#my $testFile = "/tmp/test.xml";
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#open (TFILE,">$testFile") || die ("Cant open xml file...\n");
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#print TFILE $xmldoc;
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#close(TFILE);
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$notunique = insertMetadata($xmldoc, $docid);
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# if (!$notunique) {
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# Write out the XML file for debugging purposes
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#my $testFile = $tmpdir . "/test-new.xml";
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#open (TFILE,">$testFile") || die ("Cant open xml file...\n");
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#print TFILE $newdoc;
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#close(TFILE);
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# }
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# The id wasn't unique, so update our lastid file
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if ($notunique eq "NOT_UNIQUE") {
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debug( "Registry: Updating lastid (B1.1)");
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updateLastId($defaultScope);
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}
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}
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debug("Registry: B2");
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if ($notunique ne "SUCCESS") {
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debug("Registry: NO SUCCESS");
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debug("Message is: $notunique");
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push(@errorMessages, $notunique);
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}
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debug("Registry: B3");
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} else {
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# document is being modified
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$docid = $FORM::docid;
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my $x;
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my $y;
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my $z;
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($x, $y, $z) = split(/\./, $docid);
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$z++;
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$docid = "$x.$y.$z";
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358
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$xmldoc =~ s/docid/$docid/;
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360
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361
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my $response = $metacat->update($docid, $xmldoc);
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|
362
|
|
|
363
|
if (! $response) {
|
|
364
|
push(@errorMessages, $metacat->getMessage());
|
|
365
|
push(@errorMessages, "Failed while updating.\n");
|
|
366
|
}
|
|
367
|
|
|
368
|
if (scalar(@errorMessages)) {
|
|
369
|
debug("Registry: ErrorMessages defined in modify.");
|
|
370
|
|
|
371
|
$$templateVars{'providerGivenName'} = $FORM::providerGivenName;
|
|
372
|
$$templateVars{'providerSurName'} = $FORM::providerSurName;
|
|
373
|
$$templateVars{'site'} = $FORM::site;
|
|
374
|
if ($FORM::cfg eq "nceas") {
|
|
375
|
my $projects = getProjectList();
|
|
376
|
$$templateVars{'projects'} = $projects;
|
|
377
|
$$templateVars{'wg'} = \@FORM::wg;
|
|
378
|
}
|
|
379
|
$$templateVars{'identifier'} = $FORM::identifier;
|
|
380
|
$$templateVars{'title'} = $FORM::title;
|
|
381
|
$$templateVars{'origNamefirst0'} = $FORM::origNamefirst0;
|
|
382
|
$$templateVars{'origNamelast0'} = $FORM::origNamelast0;
|
|
383
|
$$templateVars{'origNameOrg'} = $FORM::origNameOrg;
|
|
384
|
# $$templateVars{'origRole0'} = $FORM::origRole0;
|
|
385
|
$$templateVars{'origDelivery'} = $FORM::origDelivery;
|
|
386
|
$$templateVars{'origCity'} = $FORM::origCity;
|
|
387
|
$$templateVars{'origState'} = $FORM::origState;
|
|
388
|
$$templateVars{'origStateOther'} = $FORM::origStateOther;
|
|
389
|
$$templateVars{'origZIP'} = $FORM::origZIP;
|
|
390
|
$$templateVars{'origCountry'} = $FORM::origCountry;
|
|
391
|
$$templateVars{'origPhone'} = $FORM::origPhone;
|
|
392
|
$$templateVars{'origFAX'} = $FORM::origFAX;
|
|
393
|
$$templateVars{'origEmail'} = $FORM::origEmail;
|
|
394
|
if ($FORM::useSiteCoord ne "") {
|
|
395
|
$$templateVars{'useOrigAddress'} = "CHECKED";
|
|
396
|
}else{
|
|
397
|
$$templateVars{'useOrigAddress'} = $FORM::useOrigAddress;
|
|
398
|
}
|
|
399
|
$$templateVars{'origNamefirstContact'} = $FORM::origNamefirstContact;
|
|
400
|
$$templateVars{'origNamelastContact'} = $FORM::origNamelastContact;
|
|
401
|
$$templateVars{'origNameOrgContact'} = $FORM::origNameOrgContact;
|
|
402
|
$$templateVars{'origDeliveryContact'} = $FORM::origDeliveryContact;
|
|
403
|
$$templateVars{'origCityContact'} = $FORM::origCityContact;
|
|
404
|
$$templateVars{'origStateContact'} = $FORM::origStateContact;
|
|
405
|
$$templateVars{'origStateOtherContact'} = $FORM::origStateOtherContact;
|
|
406
|
$$templateVars{'origZIPContact'} = $FORM::origZIPContact;
|
|
407
|
$$templateVars{'origCountryContact'} = $FORM::origCountryContact;
|
|
408
|
$$templateVars{'origPhoneContact'} = $FORM::origPhoneContact;
|
|
409
|
$$templateVars{'origFAXContact'} = $FORM::origFAXContact;
|
|
410
|
$$templateVars{'origEmailContact'} = $FORM::origEmailContact;
|
|
411
|
$$templateVars{'origNamefirst1'} = $FORM::origNamefirst1;
|
|
412
|
$$templateVars{'origNamelast1'} = $FORM::origNamelast1;
|
|
413
|
$$templateVars{'origRole1'} = $FORM::origRole1;
|
|
414
|
$$templateVars{'origNamefirst2'} = $FORM::origNamefirst2;
|
|
415
|
$$templateVars{'origNamelast2'} = $FORM::origNamelast2;
|
|
416
|
$$templateVars{'origRole2'} = $FORM::origRole2;
|
|
417
|
$$templateVars{'origNamefirst3'} = $FORM::origNamefirst3;
|
|
418
|
$$templateVars{'origNamelast3'} = $FORM::origNamelast3;
|
|
419
|
$$templateVars{'origRole3'} = $FORM::origRole3;
|
|
420
|
$$templateVars{'origNamefirst4'} = $FORM::origNamefirst4;
|
|
421
|
$$templateVars{'origNamelast4'} = $FORM::origNamelast4;
|
|
422
|
$$templateVars{'origRole4'} = $FORM::origRole4;
|
|
423
|
$$templateVars{'origNamefirst5'} = $FORM::origNamefirst5;
|
|
424
|
$$templateVars{'origNamelast5'} = $FORM::origNamelast5;
|
|
425
|
$$templateVars{'origRole5'} = $FORM::origRole5;
|
|
426
|
$$templateVars{'origNamefirst6'} = $FORM::origNamefirst6;
|
|
427
|
$$templateVars{'origNamelast6'} = $FORM::origNamelast6;
|
|
428
|
$$templateVars{'origRole6'} = $FORM::origRole6;
|
|
429
|
$$templateVars{'origNamefirst7'} = $FORM::origNamefirst7;
|
|
430
|
$$templateVars{'origNamelast7'} = $FORM::origNamelast7;
|
|
431
|
$$templateVars{'origRole7'} = $FORM::origRole7;
|
|
432
|
$$templateVars{'origNamefirst8'} = $FORM::origNamefirst8;
|
|
433
|
$$templateVars{'origNamelast8'} = $FORM::origNamelast8;
|
|
434
|
$$templateVars{'origRole8'} = $FORM::origRole8;
|
|
435
|
$$templateVars{'origNamefirst9'} = $FORM::origNamefirst9;
|
|
436
|
$$templateVars{'origNamelast9'} = $FORM::origNamelast9;
|
|
437
|
$$templateVars{'origRole9'} = $FORM::origRole9;
|
|
438
|
$$templateVars{'origNamefirst10'} = $FORM::origNamefirst10;
|
|
439
|
$$templateVars{'origNamelast10'} = $FORM::origNamelast10;
|
|
440
|
$$templateVars{'origRole10'} = $FORM::origRole10;
|
|
441
|
$$templateVars{'abstract'} = $FORM::abstract;
|
|
442
|
$$templateVars{'keyCount'} = $FORM::keyCount;
|
|
443
|
foreach my $kyd (param()) {
|
|
444
|
if ($kyd =~ /keyword/) {
|
|
445
|
my $keyIndex = $kyd;
|
|
446
|
$keyIndex =~ s/keyword//; # get the index of the parameter 0, ..., 10
|
|
447
|
my $keyType = "kwType".$keyIndex;
|
|
448
|
my $keyTh = "kwTh".$keyIndex;
|
|
449
|
if ( $keyIndex =~ /[0-9]/ ){
|
|
450
|
if (hasContent(param($kyd)) && hasContent(param($keyType)) && hasContent(param($keyTh))) {
|
|
451
|
debug("Registry processing keyword: $kyd = ".param($kyd)." $keyType = ".param($keyType)." $keyTh = ".param($keyTh));
|
|
452
|
$$templateVars{$kyd} = param($kyd);
|
|
453
|
$$templateVars{$keyType} = param($keyType);
|
|
454
|
$$templateVars{$keyTh} = param($keyTh);
|
|
455
|
}
|
|
456
|
}
|
|
457
|
}
|
|
458
|
}
|
|
459
|
$$templateVars{'addComments'} = $FORM::addComments;
|
|
460
|
$$templateVars{'useConstraints'} = $FORM::useConstraints;
|
|
461
|
$$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
|
|
462
|
$$templateVars{'url'} = $FORM::url;
|
|
463
|
$$templateVars{'dataMedium'} = $FORM::dataMedium;
|
|
464
|
$$templateVars{'dataMediumOther'} = $FORM::dataMediumOther;
|
|
465
|
$$templateVars{'beginningYear'} = $FORM::beginningYear;
|
|
466
|
$$templateVars{'beginningMonth'} = $FORM::beginningMonth;
|
|
467
|
$$templateVars{'beginningDay'} = $FORM::beginningDay;
|
|
468
|
$$templateVars{'endingYear'} = $FORM::endingYear;
|
|
469
|
$$templateVars{'endingMonth'} = $FORM::endingMonth;
|
|
470
|
$$templateVars{'endingDay'} = $FORM::endingDay;
|
|
471
|
$$templateVars{'geogdesc'} = $FORM::geogdesc;
|
|
472
|
if($FORM::useSiteCoord ne ""){
|
|
473
|
$$templateVars{'useSiteCoord'} = "CHECKED";
|
|
474
|
}else{
|
|
475
|
$$templateVars{'useSiteCoord'} = "";
|
|
476
|
}
|
|
477
|
$$templateVars{'latDeg1'} = $FORM::latDeg1;
|
|
478
|
$$templateVars{'latMin1'} = $FORM::latMin1;
|
|
479
|
$$templateVars{'latSec1'} = $FORM::latSec1;
|
|
480
|
$$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
|
|
481
|
$$templateVars{'longDeg1'} = $FORM::longDeg1;
|
|
482
|
$$templateVars{'longMin1'} = $FORM::longMin1;
|
|
483
|
$$templateVars{'longSec1'} = $FORM::longSec1;
|
|
484
|
$$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
|
|
485
|
$$templateVars{'latDeg2'} = $FORM::latDeg2;
|
|
486
|
$$templateVars{'latMin2'} = $FORM::latMin2;
|
|
487
|
$$templateVars{'latSec2'} = $FORM::latSec2;
|
|
488
|
$$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
|
|
489
|
$$templateVars{'longDeg2'} = $FORM::longDeg2;
|
|
490
|
$$templateVars{'longMin2'} = $FORM::longMin2;
|
|
491
|
$$templateVars{'longSec2'} = $FORM::longSec2;
|
|
492
|
$$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
|
|
493
|
$$templateVars{'taxaCount'} = $FORM::taxaCount;
|
|
494
|
foreach my $trn (param()) {
|
|
495
|
if ($trn =~ /taxonRankName/) {
|
|
496
|
my $taxIndex = $trn;
|
|
497
|
$taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
|
|
498
|
my $trv = "taxonRankValue".$taxIndex;
|
|
499
|
if ( $taxIndex =~ /[0-9]/ ){
|
|
500
|
if (hasContent(param($trn)) && hasContent(param($trv))) {
|
|
501
|
debug("Registry processing taxon: $trn = ".param($trn)." $trv = ".param($trv));
|
|
502
|
$$templateVars{$trn} = param($trn);
|
|
503
|
$$templateVars{$trv} = param($trv);
|
|
504
|
}
|
|
505
|
}
|
|
506
|
}
|
|
507
|
}
|
|
508
|
$$templateVars{'taxaAuth'} = $FORM::taxaAuth;
|
|
509
|
$$templateVars{'methodTitle'} = $FORM::methodTitle;
|
|
510
|
$$templateVars{'methodPara'} = \@FORM::methodPara;
|
|
511
|
$$templateVars{'studyExtentDescription'} = $FORM::studyExtentDescription;
|
|
512
|
$$templateVars{'samplingDescription'} = $FORM::samplingDescription;
|
|
513
|
$$templateVars{'docid'} = $FORM::docid;
|
|
514
|
|
|
515
|
$$templateVars{'status'} = 'failure';
|
|
516
|
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
517
|
$error = 1;
|
|
518
|
}
|
|
519
|
|
|
520
|
#if (! $error) {
|
|
521
|
#sendNotification($docid, $mailhost, $sender, $recipient);
|
|
522
|
#}
|
|
523
|
|
|
524
|
# Create our HTML response and send it back
|
|
525
|
$$templateVars{'function'} = "modified";
|
|
526
|
$$templateVars{'section'} = "Modification Status";
|
|
527
|
$template->process( $responseTemplate, $templateVars);
|
|
528
|
|
|
529
|
exit(0);
|
|
530
|
}
|
|
531
|
}
|
|
532
|
|
|
533
|
debug("Registry: C");
|
|
534
|
|
|
535
|
if (scalar(@errorMessages)) {
|
|
536
|
debug("Registry: ErrorMessages defined.");
|
|
537
|
$$templateVars{'providerGivenName'} = $FORM::providerGivenName;
|
|
538
|
$$templateVars{'providerSurName'} = $FORM::providerSurName;
|
|
539
|
$$templateVars{'site'} = $FORM::site;
|
|
540
|
if ($FORM::cfg eq "nceas") {
|
|
541
|
my $projects = getProjectList();
|
|
542
|
$$templateVars{'projects'} = $projects;
|
|
543
|
$$templateVars{'wg'} = \@FORM::wg;
|
|
544
|
}
|
|
545
|
$$templateVars{'identifier'} = $FORM::identifier;
|
|
546
|
$$templateVars{'title'} = $FORM::title;
|
|
547
|
$$templateVars{'origNamefirst0'} = $FORM::origNamefirst0;
|
|
548
|
$$templateVars{'origNamelast0'} = $FORM::origNamelast0;
|
|
549
|
$$templateVars{'origNameOrg'} = $FORM::origNameOrg;
|
|
550
|
# $$templateVars{'origRole0'} = $FORM::origRole0;
|
|
551
|
$$templateVars{'origDelivery'} = $FORM::origDelivery;
|
|
552
|
$$templateVars{'origCity'} = $FORM::origCity;
|
|
553
|
$$templateVars{'origState'} = $FORM::origState;
|
|
554
|
$$templateVars{'origStateOther'} = $FORM::origStateOther;
|
|
555
|
$$templateVars{'origZIP'} = $FORM::origZIP;
|
|
556
|
$$templateVars{'origCountry'} = $FORM::origCountry;
|
|
557
|
$$templateVars{'origPhone'} = $FORM::origPhone;
|
|
558
|
$$templateVars{'origFAX'} = $FORM::origFAX;
|
|
559
|
$$templateVars{'origEmail'} = $FORM::origEmail;
|
|
560
|
if ($FORM::useSiteCoord ne "") {
|
|
561
|
$$templateVars{'useOrigAddress'} = "CHECKED";
|
|
562
|
}else{
|
|
563
|
$$templateVars{'useOrigAddress'} = $FORM::useOrigAddress;
|
|
564
|
}
|
|
565
|
$$templateVars{'origNamefirstContact'} = $FORM::origNamefirstContact;
|
|
566
|
$$templateVars{'origNamelastContact'} = $FORM::origNamelastContact;
|
|
567
|
$$templateVars{'origNameOrgContact'} = $FORM::origNameOrgContact;
|
|
568
|
$$templateVars{'origDeliveryContact'} = $FORM::origDeliveryContact;
|
|
569
|
$$templateVars{'origCityContact'} = $FORM::origCityContact;
|
|
570
|
$$templateVars{'origStateContact'} = $FORM::origStateContact;
|
|
571
|
$$templateVars{'origStateOtherContact'} = $FORM::origStateOtherContact;
|
|
572
|
$$templateVars{'origZIPContact'} = $FORM::origZIPContact;
|
|
573
|
$$templateVars{'origCountryContact'} = $FORM::origCountryContact;
|
|
574
|
$$templateVars{'origPhoneContact'} = $FORM::origPhoneContact;
|
|
575
|
$$templateVars{'origFAXContact'} = $FORM::origFAXContact;
|
|
576
|
$$templateVars{'origEmailContact'} = $FORM::origEmailContact;
|
|
577
|
$$templateVars{'origNamefirst1'} = $FORM::origNamefirst1;
|
|
578
|
$$templateVars{'origNamelast1'} = $FORM::origNamelast1;
|
|
579
|
$$templateVars{'origRole1'} = $FORM::origRole1;
|
|
580
|
$$templateVars{'origNamefirst2'} = $FORM::origNamefirst2;
|
|
581
|
$$templateVars{'origNamelast2'} = $FORM::origNamelast2;
|
|
582
|
$$templateVars{'origRole2'} = $FORM::origRole2;
|
|
583
|
$$templateVars{'origNamefirst3'} = $FORM::origNamefirst3;
|
|
584
|
$$templateVars{'origNamelast3'} = $FORM::origNamelast3;
|
|
585
|
$$templateVars{'origRole3'} = $FORM::origRole3;
|
|
586
|
$$templateVars{'origNamefirst4'} = $FORM::origNamefirst4;
|
|
587
|
$$templateVars{'origNamelast4'} = $FORM::origNamelast4;
|
|
588
|
$$templateVars{'origRole4'} = $FORM::origRole4;
|
|
589
|
$$templateVars{'origNamefirst5'} = $FORM::origNamefirst5;
|
|
590
|
$$templateVars{'origNamelast5'} = $FORM::origNamelast5;
|
|
591
|
$$templateVars{'origRole5'} = $FORM::origRole5;
|
|
592
|
$$templateVars{'origNamefirst6'} = $FORM::origNamefirst6;
|
|
593
|
$$templateVars{'origNamelast6'} = $FORM::origNamelast6;
|
|
594
|
$$templateVars{'origRole6'} = $FORM::origRole6;
|
|
595
|
$$templateVars{'origNamefirst7'} = $FORM::origNamefirst7;
|
|
596
|
$$templateVars{'origNamelast7'} = $FORM::origNamelast7;
|
|
597
|
$$templateVars{'origRole7'} = $FORM::origRole7;
|
|
598
|
$$templateVars{'origNamefirst8'} = $FORM::origNamefirst8;
|
|
599
|
$$templateVars{'origNamelast8'} = $FORM::origNamelast8;
|
|
600
|
$$templateVars{'origRole8'} = $FORM::origRole8;
|
|
601
|
$$templateVars{'origNamefirst9'} = $FORM::origNamefirst9;
|
|
602
|
$$templateVars{'origNamelast9'} = $FORM::origNamelast9;
|
|
603
|
$$templateVars{'origRole9'} = $FORM::origRole9;
|
|
604
|
$$templateVars{'origNamefirst10'} = $FORM::origNamefirst10;
|
|
605
|
$$templateVars{'origNamelast10'} = $FORM::origNamelast10;
|
|
606
|
$$templateVars{'origRole10'} = $FORM::origRole10;
|
|
607
|
$$templateVars{'abstract'} = $FORM::abstract;
|
|
608
|
$$templateVars{'keyCount'} = $FORM::keyCount;
|
|
609
|
foreach my $kyd (param()) {
|
|
610
|
if ($kyd =~ /keyword/) {
|
|
611
|
my $keyIndex = $kyd;
|
|
612
|
$keyIndex =~ s/keyword//; # get the index of the parameter 0, ..., 10
|
|
613
|
my $keyType = "kwType".$keyIndex;
|
|
614
|
my $keyTh = "kwTh".$keyIndex;
|
|
615
|
if ( $keyIndex =~ /[0-9]/ ){
|
|
616
|
if (hasContent(param($kyd)) && hasContent(param($keyType)) && hasContent(param($keyTh))) {
|
|
617
|
debug("Registry processing keyword: $kyd = ".param($kyd)." $keyType = ".param($keyType)." $keyTh = ".param($keyTh));
|
|
618
|
$$templateVars{$kyd} = param($kyd);
|
|
619
|
$$templateVars{$keyType} = param($keyType);
|
|
620
|
$$templateVars{$keyTh} = param($keyTh);
|
|
621
|
}
|
|
622
|
}
|
|
623
|
}
|
|
624
|
}
|
|
625
|
$$templateVars{'addComments'} = $FORM::addComments;
|
|
626
|
$$templateVars{'useConstraints'} = $FORM::useConstraints;
|
|
627
|
$$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
|
|
628
|
$$templateVars{'url'} = $FORM::url;
|
|
629
|
$$templateVars{'dataMedium'} = $FORM::dataMedium;
|
|
630
|
$$templateVars{'dataMediumOther'} = $FORM::dataMediumOther;
|
|
631
|
$$templateVars{'beginningYear'} = $FORM::beginningYear;
|
|
632
|
$$templateVars{'beginningMonth'} = $FORM::beginningMonth;
|
|
633
|
$$templateVars{'beginningDay'} = $FORM::beginningDay;
|
|
634
|
$$templateVars{'endingYear'} = $FORM::endingYear;
|
|
635
|
$$templateVars{'endingMonth'} = $FORM::endingMonth;
|
|
636
|
$$templateVars{'endingDay'} = $FORM::endingDay;
|
|
637
|
$$templateVars{'geogdesc'} = $FORM::geogdesc;
|
|
638
|
if($FORM::useSiteCoord ne ""){
|
|
639
|
$$templateVars{'useSiteCoord'} = "CHECKED";
|
|
640
|
}else{
|
|
641
|
$$templateVars{'useSiteCoord'} = "";
|
|
642
|
}
|
|
643
|
$$templateVars{'latDeg1'} = $FORM::latDeg1;
|
|
644
|
$$templateVars{'latMin1'} = $FORM::latMin1;
|
|
645
|
$$templateVars{'latSec1'} = $FORM::latSec1;
|
|
646
|
$$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
|
|
647
|
$$templateVars{'longDeg1'} = $FORM::longDeg1;
|
|
648
|
$$templateVars{'longMin1'} = $FORM::longMin1;
|
|
649
|
$$templateVars{'longSec1'} = $FORM::longSec1;
|
|
650
|
$$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
|
|
651
|
$$templateVars{'latDeg2'} = $FORM::latDeg2;
|
|
652
|
$$templateVars{'latMin2'} = $FORM::latMin2;
|
|
653
|
$$templateVars{'latSec2'} = $FORM::latSec2;
|
|
654
|
$$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
|
|
655
|
$$templateVars{'longDeg2'} = $FORM::longDeg2;
|
|
656
|
$$templateVars{'longMin2'} = $FORM::longMin2;
|
|
657
|
$$templateVars{'longSec2'} = $FORM::longSec2;
|
|
658
|
$$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
|
|
659
|
$$templateVars{'taxaCount'} = $FORM::taxaCount;
|
|
660
|
foreach my $trn (param()) {
|
|
661
|
if ($trn =~ /taxonRankName/) {
|
|
662
|
my $taxIndex = $trn;
|
|
663
|
$taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
|
|
664
|
my $trv = "taxonRankValue".$taxIndex;
|
|
665
|
if ( $taxIndex =~ /[0-9]/ ){
|
|
666
|
if (hasContent(param($trn)) && hasContent(param($trv))) {
|
|
667
|
debug("Registry processing taxon: $trn = ".param($trn)." $trv = ".param($trv));
|
|
668
|
$$templateVars{$trn} = param($trn);
|
|
669
|
$$templateVars{$trv} = param($trv);
|
|
670
|
}
|
|
671
|
}
|
|
672
|
}
|
|
673
|
}
|
|
674
|
$$templateVars{'taxaAuth'} = $FORM::taxaAuth;
|
|
675
|
$$templateVars{'methodTitle'} = $FORM::methodTitle;
|
|
676
|
$$templateVars{'methodPara'} = \@FORM::methodPara;
|
|
677
|
$$templateVars{'studyExtentDescription'} = $FORM::studyExtentDescription;
|
|
678
|
$$templateVars{'samplingDescription'} = $FORM::samplingDescription;
|
|
679
|
$$templateVars{'docid'} = $FORM::docid;
|
|
680
|
|
|
681
|
$$templateVars{'status'} = 'failure';
|
|
682
|
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
683
|
$error = 1;
|
|
684
|
}
|
|
685
|
|
|
686
|
#if (! $error) {
|
|
687
|
#sendNotification($docid, $mailhost, $sender, $recipient);
|
|
688
|
#}
|
|
689
|
|
|
690
|
# Create our HTML response and send it back
|
|
691
|
$$templateVars{'function'} = "submitted";
|
|
692
|
$$templateVars{'section'} = "Submission Status";
|
|
693
|
$template->process( $responseTemplate, $templateVars);
|
|
694
|
|
|
695
|
exit(0);
|
|
696
|
|
|
697
|
|
|
698
|
################################################################################
|
|
699
|
#
|
|
700
|
# Subroutine for updating a metacat id for a given scope to the highest value
|
|
701
|
#
|
|
702
|
################################################################################
|
|
703
|
sub updateLastId {
|
|
704
|
my $scope = shift;
|
|
705
|
|
|
706
|
my $errormsg = 0;
|
|
707
|
my $docid = $metacat->getLastId($scope);
|
|
708
|
|
|
709
|
if ($docid =~ /null/) {
|
|
710
|
# No docids with this scope present, so do nothing
|
|
711
|
} elsif ($docid) {
|
|
712
|
# Update the lastid file for this scope
|
|
713
|
(my $foundScope, my $id, my $rev) = split(/\./, $docid);
|
|
714
|
debug("Docid is: $docid\n");
|
|
715
|
debug("Lastid is: $id");
|
|
716
|
my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
|
|
717
|
open(LASTID, ">$scopeFile") or
|
|
718
|
die "Failed to open lastid file for writing!";
|
|
719
|
print LASTID $id, "\n";
|
|
720
|
close(LASTID);
|
|
721
|
} else {
|
|
722
|
$errormsg = $metacat->getMessage();
|
|
723
|
debug("Error in getLastId: $errormsg");
|
|
724
|
}
|
|
725
|
}
|
|
726
|
|
|
727
|
################################################################################
|
|
728
|
#
|
|
729
|
# Subroutine for inserting a document to metacat
|
|
730
|
#
|
|
731
|
################################################################################
|
|
732
|
sub insertMetadata {
|
|
733
|
my $xmldoc = shift;
|
|
734
|
my $docid = shift;
|
|
735
|
|
|
736
|
my $notunique = "SUCCESS";
|
|
737
|
debug("Registry: Starting insert (D1)");
|
|
738
|
my $response = $metacat->insert($docid, $xmldoc);
|
|
739
|
if (! $response) {
|
|
740
|
debug("Registry: Response gotten (D2)");
|
|
741
|
my $errormsg = $metacat->getMessage();
|
|
742
|
debug("Registry: Error is (D3): ".$errormsg);
|
|
743
|
if ($errormsg =~ /is already in use/) {
|
|
744
|
$notunique = "NOT_UNIQUE";
|
|
745
|
#print "Accession number already used: $docid\n";
|
|
746
|
} elsif ($errormsg =~ /<login>/) {
|
|
747
|
$notunique = "SUCCESS";
|
|
748
|
} else {
|
|
749
|
#print "<p>Dumping error on failure...</p>\n";
|
|
750
|
#print "<p>", $errormsg, "</p>\n";
|
|
751
|
#die "Failed during insert\n";
|
|
752
|
#print "<p>Failed during insert</p>\n";
|
|
753
|
$notunique = $errormsg;
|
|
754
|
}
|
|
755
|
}
|
|
756
|
debug("Registry: Ending insert (D4)");
|
|
757
|
|
|
758
|
return $notunique;
|
|
759
|
}
|
|
760
|
|
|
761
|
################################################################################
|
|
762
|
#
|
|
763
|
# Subroutine for generating a new accession number
|
|
764
|
# Note: this is not threadsafe, assumes only one running process at a time
|
|
765
|
# Also: need to check metacat for max id # used in this scope already
|
|
766
|
################################################################################
|
|
767
|
sub newAccessionNumber {
|
|
768
|
my $scope = shift;
|
|
769
|
|
|
770
|
my $docrev = 1;
|
|
771
|
my $lastid = 1;
|
|
772
|
|
|
773
|
my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
|
|
774
|
if (-e $scopeFile) {
|
|
775
|
open(LASTID, "<$scopeFile") or die "Failed to generate accession number!";
|
|
776
|
$lastid = <LASTID>;
|
|
777
|
chomp($lastid);
|
|
778
|
$lastid++;
|
|
779
|
close(LASTID);
|
|
780
|
}
|
|
781
|
open(LASTID, ">$scopeFile") or die "Failed to open lastid file for writing!";
|
|
782
|
print LASTID $lastid, "\n";
|
|
783
|
close(LASTID);
|
|
784
|
|
|
785
|
my $docroot = "$scope.$lastid.";
|
|
786
|
my $docid = $docroot . $docrev;
|
|
787
|
return $docid;
|
|
788
|
}
|
|
789
|
|
|
790
|
################################################################################
|
|
791
|
#
|
|
792
|
# Subroutine for generating a new ACL document
|
|
793
|
#
|
|
794
|
################################################################################
|
|
795
|
sub newAccessDocument {
|
|
796
|
my $aclid = shift;
|
|
797
|
my $acl = "<?xml version=\"1.0\"?>\n";
|
|
798
|
$acl .= "<!DOCTYPE acl ";
|
|
799
|
$acl .= "PUBLIC \"$accesspubid\" \"$accesssysid\">\n";
|
|
800
|
$acl .= "<acl authSystem=\"ldap://ldap.ecoinformatics.org\" ";
|
|
801
|
$acl .= "order=\"denyFirst\">\n";
|
|
802
|
$acl .= "<identifier system=\"knb\">$aclid</identifier>\n";
|
|
803
|
#$acl .= "<identifier>$aclid</identifier>\n";
|
|
804
|
$acl .= "<allow><principal>$username</principal>" .
|
|
805
|
"<permission>all</permission></allow>\n";
|
|
806
|
#$acl .= "<allow><principal>public</principal>" .
|
|
807
|
# "<permission>read</permission></allow>\n";
|
|
808
|
$acl .= "</acl>\n";
|
|
809
|
|
|
810
|
return $acl;
|
|
811
|
}
|
|
812
|
|
|
813
|
################################################################################
|
|
814
|
#
|
|
815
|
# Subroutine for inserting identifers to the metadata document passed to us
|
|
816
|
#
|
|
817
|
################################################################################
|
|
818
|
sub insertIdentifiers {
|
|
819
|
my $docstring = shift;
|
|
820
|
my $aclid = shift;
|
|
821
|
my $docid = shift;
|
|
822
|
|
|
823
|
my $parser = XML::LibXML->new();
|
|
824
|
my $dom = $parser->parse_string($docstring);
|
|
825
|
|
|
826
|
my $root = $dom->documentElement;
|
|
827
|
my $name = $root->getName();
|
|
828
|
|
|
829
|
my $addedIdentifier = 0;
|
|
830
|
my $currentElement = $root->getFirstChild();
|
|
831
|
$name = $currentElement->getName();
|
|
832
|
while ("$name" !~ "triple" &&
|
|
833
|
"$name" !~ "temporalCov" &&
|
|
834
|
"$name" !~ "geographicCov" &&
|
|
835
|
"$name" !~ "taxonomicCov"
|
|
836
|
) {
|
|
837
|
if ("$name" =~ "identifier" ||
|
|
838
|
"$name" =~ "title") {
|
|
839
|
if (! $addedIdentifier) {
|
|
840
|
my $idelement = $dom->createElement( "identifier" );
|
|
841
|
$addedIdentifier = 1;
|
|
842
|
$idelement->setAttribute("system", "knb");
|
|
843
|
$idelement->appendTextNode($docid);
|
|
844
|
$root->insertBefore($idelement, $currentElement);
|
|
845
|
}
|
|
846
|
}
|
|
847
|
$currentElement = $currentElement->getNextSibling();
|
|
848
|
$name = $currentElement->getName();
|
|
849
|
}
|
|
850
|
# Link the document to the access doc
|
|
851
|
my $element = $dom->createElement( "triple" );
|
|
852
|
$element->appendTextChild( "subject", $aclid);
|
|
853
|
$element->appendTextChild( "relationship",
|
|
854
|
"describes access control rules for");
|
|
855
|
$element->appendTextChild( "object", $docid);
|
|
856
|
$root->insertBefore($element, $currentElement);
|
|
857
|
# Link the access doc to the access doc
|
|
858
|
$element = $dom->createElement( "triple" );
|
|
859
|
$element->appendTextChild( "subject", $aclid);
|
|
860
|
$element->appendTextChild( "relationship",
|
|
861
|
"describes access control rules for");
|
|
862
|
$element->appendTextChild( "object", $aclid);
|
|
863
|
$root->insertBefore($element, $currentElement);
|
|
864
|
|
|
865
|
return $dom->toString();
|
|
866
|
}
|
|
867
|
|
|
868
|
################################################################################
|
|
869
|
#
|
|
870
|
# Validate the parameters to make sure that required params are provided
|
|
871
|
#
|
|
872
|
################################################################################
|
|
873
|
sub validateParameters {
|
|
874
|
my $chkUser = shift;
|
|
875
|
my @invalidParams;
|
|
876
|
|
|
877
|
push(@invalidParams, "Provider's first name is missing.")
|
|
878
|
unless hasContent($FORM::providerGivenName);
|
|
879
|
push(@invalidParams, "Provider's last name is missing.")
|
|
880
|
unless hasContent($FORM::providerSurName);
|
|
881
|
push(@invalidParams, "Name of site is missing.")
|
|
882
|
unless (hasContent($FORM::site) || $FORM::site =~ /elect/ ||
|
|
883
|
$FORM::cfg eq "nceas");
|
|
884
|
push(@invalidParams, "Data set title is missing.")
|
|
885
|
unless hasContent($FORM::title);
|
|
886
|
push(@invalidParams, "Originator's first name is missing.")
|
|
887
|
unless hasContent($FORM::origNamefirst0);
|
|
888
|
push(@invalidParams, "Originator's last name is missing.")
|
|
889
|
unless hasContent($FORM::origNamelast0);
|
|
890
|
push(@invalidParams, "Abstract is missing.")
|
|
891
|
unless hasContent($FORM::abstract);
|
|
892
|
push(@invalidParams, "Beginning year of data set is missing.")
|
|
893
|
unless hasContent($FORM::beginningYear);
|
|
894
|
push(@invalidParams, "Geographic description is missing.")
|
|
895
|
unless (hasContent($FORM::geogdesc));
|
|
896
|
|
|
897
|
# If the "use site" coord. box is checked and if the site is in
|
|
898
|
# the longitude hash ... && ($siteLatDMS{$FORM::site})
|
|
899
|
|
|
900
|
if (($FORM::useSiteCoord) && ($siteLatDMS{$FORM::site}) ) {
|
|
901
|
|
|
902
|
$latDeg1 = $siteLatDMS{$FORM::site}[0];
|
|
903
|
$latMin1 = $siteLatDMS{$FORM::site}[1];
|
|
904
|
$latSec1 = $siteLatDMS{$FORM::site}[2];
|
|
905
|
$hemisphLat1 = $siteLatDMS{$FORM::site}[3];
|
|
906
|
$longDeg1 = $siteLongDMS{$FORM::site}[0];
|
|
907
|
$longMin1 = $siteLongDMS{$FORM::site}[1];
|
|
908
|
$longSec1 = $siteLongDMS{$FORM::site}[2];
|
|
909
|
$hemisphLong1 = $siteLongDMS{$FORM::site}[3];
|
|
910
|
|
|
911
|
} else {
|
|
912
|
|
|
913
|
$latDeg1 = $FORM::latDeg1;
|
|
914
|
$latMin1 = $FORM::latMin1;
|
|
915
|
$latSec1 = $FORM::latSec1;
|
|
916
|
$hemisphLat1 = $FORM::hemisphLat1;
|
|
917
|
$longDeg1 = $FORM::longDeg1;
|
|
918
|
$longMin1 = $FORM::longMin1;
|
|
919
|
$longSec1 = $FORM::longSec1;
|
|
920
|
$hemisphLong1 = $FORM::hemisphLong1;
|
|
921
|
}
|
|
922
|
|
|
923
|
# Check if latDeg1 and longDeg1 has values if useSiteCoord is used.
|
|
924
|
# This check is required because some of the sites dont have lat
|
|
925
|
# and long mentioned in the config file.
|
|
926
|
|
|
927
|
if ($FORM::useSiteCoord) {
|
|
928
|
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.")
|
|
929
|
unless(hasContent($latDeg1) && hasContent($longDeg1));
|
|
930
|
}else{
|
|
931
|
push(@invalidParams, "Latitude degrees are missing.")
|
|
932
|
unless hasContent($latDeg1);
|
|
933
|
push(@invalidParams, "Longitude degrees are missing.")
|
|
934
|
unless hasContent($longDeg1);
|
|
935
|
}
|
|
936
|
|
|
937
|
push(@invalidParams,
|
|
938
|
"You must provide a method description if you provide a method title.")
|
|
939
|
if (hasContent($FORM::methodTitle) && ( !(scalar(@FORM::methodPara) > 0)
|
|
940
|
|| (! hasContent($FORM::methodPara[0]))));
|
|
941
|
push(@invalidParams,
|
|
942
|
"You must provide a method description if you provide a study extent description.")
|
|
943
|
if (hasContent($FORM::studyExtentDescription) && (!(scalar(@FORM::methodPara) > 0)
|
|
944
|
|| (! hasContent($FORM::methodPara[0]))));
|
|
945
|
push(@invalidParams,
|
|
946
|
"You must provide both a study extent description and a sampling description, or neither.")
|
|
947
|
if (
|
|
948
|
(hasContent($FORM::studyExtentDescription) && !hasContent($FORM::samplingDescription)) ||
|
|
949
|
(!hasContent($FORM::studyExtentDescription) && hasContent($FORM::samplingDescription))
|
|
950
|
);
|
|
951
|
|
|
952
|
push(@invalidParams, "Contact first name is missing.")
|
|
953
|
unless (hasContent($FORM::origNamefirstContact) ||
|
|
954
|
$FORM::useOrigAddress);
|
|
955
|
push(@invalidParams, "Contact last name is missing.")
|
|
956
|
unless (hasContent($FORM::origNamelastContact) ||
|
|
957
|
$FORM::useOrigAddress);
|
|
958
|
push(@invalidParams, "Data medium is missing.")
|
|
959
|
unless (hasContent($FORM::dataMedium) || $FORM::dataMedium =~ /elect/);
|
|
960
|
|
|
961
|
return \@invalidParams;
|
|
962
|
}
|
|
963
|
|
|
964
|
################################################################################
|
|
965
|
#
|
|
966
|
# utility function to determine if a paramter is defined and not an empty string
|
|
967
|
#
|
|
968
|
################################################################################
|
|
969
|
sub hasContent {
|
|
970
|
my $param = shift;
|
|
971
|
|
|
972
|
my $paramHasContent;
|
|
973
|
if (!defined($param) || $param eq '') {
|
|
974
|
$paramHasContent = 0;
|
|
975
|
} else {
|
|
976
|
$paramHasContent = 1;
|
|
977
|
}
|
|
978
|
return $paramHasContent;
|
|
979
|
}
|
|
980
|
|
|
981
|
|
|
982
|
################################################################################
|
|
983
|
#
|
|
984
|
# Create the XML document from the HTML form input
|
|
985
|
# returns the XML document as a string
|
|
986
|
#
|
|
987
|
################################################################################
|
|
988
|
sub createXMLDocument {
|
|
989
|
|
|
990
|
my $orig = "";
|
|
991
|
my $role = "associatedParty";
|
|
992
|
my $creat = "";
|
|
993
|
my $metaP = "";
|
|
994
|
my $apart = "";
|
|
995
|
my $cont = "";
|
|
996
|
my $publ = "";
|
|
997
|
my $dso = "";
|
|
998
|
my $gmt = gmtime($now);
|
|
999
|
my $doc = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n";
|
|
1000
|
|
|
1001
|
$doc .= "<eml:eml\n
|
|
1002
|
\t packageId=\"docid\" system=\"knb\"\n
|
|
1003
|
\t xmlns:eml=\"eml://ecoinformatics.org/eml-2.0.0\"\n
|
|
1004
|
\t xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n
|
|
1005
|
\t xmlns:ds=\"eml://ecoinformatics.org/dataset-2.0.0\"\n
|
|
1006
|
\t xmlns:stmml=\"http://www.xml-cml.org/schema/stmml\"\n
|
|
1007
|
\t xsi:schemaLocation=\"eml://ecoinformatics.org/eml-2.0.0 eml.xsd\">\n";
|
|
1008
|
|
|
1009
|
$doc .= "<!-- Person who filled in the catalog entry form: ";
|
|
1010
|
$doc .= "$FORM::providerGivenName $FORM::providerSurName -->\n";
|
|
1011
|
$doc .= "<!-- Form filled out at $gmt GMT -->\n";
|
|
1012
|
$doc .= "<dataset>\n";
|
|
1013
|
|
|
1014
|
if (hasContent($FORM::identifier)) {
|
|
1015
|
$doc .= "<alternateIdentifier system=\"$FORM::site\">";
|
|
1016
|
$doc .= $FORM::identifier . "</alternateIdentifier>\n";
|
|
1017
|
}
|
|
1018
|
|
|
1019
|
if (hasContent($FORM::title)) {
|
|
1020
|
$doc .= "<title>$FORM::title</title>\n";
|
|
1021
|
}
|
|
1022
|
|
|
1023
|
if (hasContent($FORM::origNamelast0)) {
|
|
1024
|
$role = "creator";
|
|
1025
|
$orig .= "<individualName>\n";
|
|
1026
|
$orig .= "<givenName>$FORM::origNamefirst0</givenName>\n";
|
|
1027
|
$orig .= "<surName>$FORM::origNamelast0</surName>\n";
|
|
1028
|
$orig .= "</individualName>\n";
|
|
1029
|
}
|
|
1030
|
|
|
1031
|
if (hasContent($FORM::origNameOrg)) {
|
|
1032
|
$orig .= "<organizationName>$FORM::origNameOrg</organizationName>\n";
|
|
1033
|
}
|
|
1034
|
|
|
1035
|
if (hasContent($FORM::origDelivery) || hasContent($FORM::origCity) ||
|
|
1036
|
(hasContent($FORM::origState ) &&
|
|
1037
|
($FORM::origState !~ "Select state here.")) ||
|
|
1038
|
hasContent($FORM::origStateOther) ||
|
|
1039
|
hasContent($FORM::origZIP ) || hasContent($FORM::origCountry)) {
|
|
1040
|
$orig .= "<address>\n";
|
|
1041
|
|
|
1042
|
if (hasContent($FORM::origDelivery)) {
|
|
1043
|
$orig .= "<deliveryPoint>$FORM::origDelivery</deliveryPoint>\n";
|
|
1044
|
}
|
|
1045
|
if (hasContent($FORM::origCity)) {
|
|
1046
|
$orig .= "<city>$FORM::origCity</city>\n";
|
|
1047
|
}
|
|
1048
|
|
|
1049
|
if (hasContent($FORM::origState) &&
|
|
1050
|
($FORM::origState !~ "Select state here.")) {
|
|
1051
|
$orig .= "<administrativeArea>$FORM::origState";
|
|
1052
|
$orig .= "</administrativeArea>\n";
|
|
1053
|
} elsif (hasContent($FORM::origStateOther)) {
|
|
1054
|
$orig .= "<administrativeArea>$FORM::origStateOther";
|
|
1055
|
$orig .= "</administrativeArea>\n";
|
|
1056
|
}
|
|
1057
|
if (hasContent($FORM::origZIP)) {
|
|
1058
|
$orig .= "<postalCode>$FORM::origZIP</postalCode>\n";
|
|
1059
|
}
|
|
1060
|
if (hasContent($FORM::origCountry)) {
|
|
1061
|
$orig .= "<country>$FORM::origCountry</country>\n";
|
|
1062
|
}
|
|
1063
|
$orig .= "</address>\n";
|
|
1064
|
}
|
|
1065
|
|
|
1066
|
if (hasContent($FORM::origPhone)) {
|
|
1067
|
$orig .= "<phone>$FORM::origPhone</phone>\n";
|
|
1068
|
}
|
|
1069
|
if (hasContent($FORM::origFAX)) {
|
|
1070
|
$orig .= "<phone phonetype=\"Fax\">$FORM::origFAX</phone>\n";
|
|
1071
|
}
|
|
1072
|
if (hasContent($FORM::origEmail)) {
|
|
1073
|
$orig .= "<electronicMailAddress>$FORM::origEmail";
|
|
1074
|
$orig .= "</electronicMailAddress>\n";
|
|
1075
|
}
|
|
1076
|
$dso = "<$role>\n$orig</$role>\n";
|
|
1077
|
|
|
1078
|
$creat .= $dso;
|
|
1079
|
|
|
1080
|
if ($FORM::useOrigAddress) {
|
|
1081
|
# Add a contact originator like the original with a different role
|
|
1082
|
$cont .= "<contact>\n";
|
|
1083
|
$cont .= $orig;
|
|
1084
|
$cont .= "</contact>\n";
|
|
1085
|
} else {
|
|
1086
|
$cont .= "<contact>\n";
|
|
1087
|
|
|
1088
|
$cont .= "<individualName>\n";
|
|
1089
|
$cont .= "<givenName>$FORM::origNamefirstContact</givenName>\n";
|
|
1090
|
$cont .= "<surName>$FORM::origNamelastContact</surName>\n";
|
|
1091
|
$cont .= "</individualName>\n";
|
|
1092
|
|
|
1093
|
if (hasContent($FORM::origNameOrgContact)) {
|
|
1094
|
$cont .= "<organizationName>$FORM::origNameOrgContact</organizationName>\n";
|
|
1095
|
}
|
|
1096
|
|
|
1097
|
if (hasContent($FORM::origDeliveryContact) ||
|
|
1098
|
hasContent($FORM::origCityContact) ||
|
|
1099
|
(hasContent($FORM::origStateContact) &&
|
|
1100
|
($FORM::origStateContact !~ "Select state here.")) ||
|
|
1101
|
hasContent($FORM::origStateOtherContact) ||
|
|
1102
|
hasContent($FORM::origZIPContact) ||
|
|
1103
|
hasContent($FORM::origCountryContact)) {
|
|
1104
|
$cont .= "<address>\n";
|
|
1105
|
if (hasContent($FORM::origDeliveryContact)) {
|
|
1106
|
$cont .= "<deliveryPoint>$FORM::origDeliveryContact";
|
|
1107
|
$cont .= "</deliveryPoint>\n";
|
|
1108
|
}
|
|
1109
|
if (hasContent($FORM::origCityContact)) {
|
|
1110
|
$cont .= "<city>$FORM::origCityContact</city>\n";
|
|
1111
|
}
|
|
1112
|
if (hasContent($FORM::origStateContact) &&
|
|
1113
|
($FORM::origStateContact !~ "Select state here.")) {
|
|
1114
|
$cont .= "<administrativeArea>$FORM::origStateContact";
|
|
1115
|
$cont .= "</administrativeArea>\n";
|
|
1116
|
} elsif (hasContent($FORM::origStateOtherContact)) {
|
|
1117
|
$cont .= "<administrativeArea>$FORM::origStateOtherContact";
|
|
1118
|
$cont .= "</administrativeArea>\n";
|
|
1119
|
}
|
|
1120
|
if (hasContent($FORM::origZIPContact)) {
|
|
1121
|
$cont .= "<postalCode>$FORM::origZIPContact</postalCode>\n";
|
|
1122
|
}
|
|
1123
|
if (hasContent($FORM::origCountryContact)) {
|
|
1124
|
$cont .= "<country>$FORM::origCountryContact</country>\n";
|
|
1125
|
}
|
|
1126
|
$cont .= "</address>\n";
|
|
1127
|
}
|
|
1128
|
if (hasContent($FORM::origPhoneContact)) {
|
|
1129
|
$cont .= "<phone>$FORM::origPhoneContact</phone>\n";
|
|
1130
|
}
|
|
1131
|
if (hasContent($FORM::origFAXContact)) {
|
|
1132
|
$cont .= "<phone phonetype=\"Fax\">$FORM::origFAXContact</phone>\n";
|
|
1133
|
}
|
|
1134
|
if (hasContent($FORM::origEmailContact)) {
|
|
1135
|
$cont .= "<electronicMailAddress>$FORM::origEmailContact";
|
|
1136
|
$cont .= "</electronicMailAddress>\n";
|
|
1137
|
}
|
|
1138
|
$cont .= "</contact>\n";
|
|
1139
|
}
|
|
1140
|
|
|
1141
|
$metaP .= "<metadataProvider>\n";
|
|
1142
|
$metaP .= "<individualName>\n";
|
|
1143
|
$metaP .= "<givenName>$FORM::providerGivenName</givenName>\n";
|
|
1144
|
$metaP .= "<surName>$FORM::providerSurName</surName>\n";
|
|
1145
|
$metaP .= "</individualName>\n";
|
|
1146
|
$metaP .= "</metadataProvider>\n";
|
|
1147
|
|
|
1148
|
# Additional originators
|
|
1149
|
foreach my $tmp (param()) {
|
|
1150
|
if ($tmp =~ /origNamelast/){
|
|
1151
|
my $tmp1 = $tmp;
|
|
1152
|
$tmp1 =~ s/origNamelast//; # get the index of the parameter 0 to 10
|
|
1153
|
if ( $tmp1 eq '1'
|
|
1154
|
|| $tmp1 eq '2'
|
|
1155
|
|| $tmp1 eq '3'
|
|
1156
|
|| $tmp1 eq '4'
|
|
1157
|
|| $tmp1 eq '5'
|
|
1158
|
|| $tmp1 eq '6'
|
|
1159
|
|| $tmp1 eq '7'
|
|
1160
|
|| $tmp1 eq '8'
|
|
1161
|
|| $tmp1 eq '9'
|
|
1162
|
|| $tmp1 eq '10'
|
|
1163
|
) {
|
|
1164
|
|
|
1165
|
# do not generate XML for empty originator fields
|
|
1166
|
if (hasContent(param("origNamefirst" . $tmp1))) {
|
|
1167
|
|
|
1168
|
my $add = "";
|
|
1169
|
$add .= "<individualName>\n";
|
|
1170
|
$add .= "<givenName>";
|
|
1171
|
$add .= param("origNamefirst" . $tmp1);
|
|
1172
|
$add .= "</givenName>\n";
|
|
1173
|
$add .= "<surName>";
|
|
1174
|
$add .= param("origNamelast" . $tmp1);
|
|
1175
|
$add .= "</surName>\n";
|
|
1176
|
$add .= "</individualName>\n";
|
|
1177
|
|
|
1178
|
if(param("origRole" . $tmp1) eq "Originator"){
|
|
1179
|
$creat .= "<creator>\n";
|
|
1180
|
$creat .= $add;
|
|
1181
|
$creat .= "</creator>\n";
|
|
1182
|
}
|
|
1183
|
elsif(param("origRole" . $tmp1) eq "Metadata Provider"){
|
|
1184
|
$metaP .= "<metadataProvider>\n";
|
|
1185
|
$metaP .= $add;
|
|
1186
|
$metaP .= "</metadataProvider>\n";
|
|
1187
|
}
|
|
1188
|
elsif((param("origRole" . $tmp1) eq "Publisher") && ($publ eq "")){
|
|
1189
|
$publ .= "<publisher>\n";
|
|
1190
|
$publ .= $add;
|
|
1191
|
$publ .= "</publisher>\n";
|
|
1192
|
}
|
|
1193
|
else{
|
|
1194
|
$apart .= "<associatedParty>\n";
|
|
1195
|
$apart .= $add;
|
|
1196
|
$apart .= "<role>";
|
|
1197
|
$apart .= param("origRole" . $tmp1);
|
|
1198
|
$apart .= "</role>\n";
|
|
1199
|
$apart .= "</associatedParty>\n";
|
|
1200
|
}
|
|
1201
|
}
|
|
1202
|
}
|
|
1203
|
}
|
|
1204
|
}
|
|
1205
|
|
|
1206
|
$creat .= "<creator>\n";
|
|
1207
|
$creat .= "<organizationName>$FORM::site</organizationName>\n";
|
|
1208
|
$creat .= "</creator>\n";
|
|
1209
|
|
|
1210
|
$creat .= "<creator>\n";
|
|
1211
|
$creat .= "<organizationName>$organization</organizationName>\n";
|
|
1212
|
$creat .= "</creator>\n";
|
|
1213
|
|
|
1214
|
if ($FORM::cfg eq 'nceas') {
|
|
1215
|
for (my $i = 0; $i < scalar(@FORM::wg); $i++) {
|
|
1216
|
$creat .= "<creator>\n";
|
|
1217
|
$creat .= "<organizationName>$FORM::wg[$i]</organizationName>\n";
|
|
1218
|
$creat .= "</creator>\n";
|
|
1219
|
}
|
|
1220
|
}
|
|
1221
|
$doc .= $creat;
|
|
1222
|
$doc .= $metaP;
|
|
1223
|
$doc .= $apart;
|
|
1224
|
|
|
1225
|
$doc .= "<abstract>\n";
|
|
1226
|
$doc .= "<para>$FORM::abstract</para>\n";
|
|
1227
|
$doc .= "</abstract>\n";
|
|
1228
|
|
|
1229
|
# Keyword information
|
|
1230
|
foreach my $tmp (param()) {
|
|
1231
|
if ($tmp =~ /keyword/) {
|
|
1232
|
my $tmp1 = $tmp;
|
|
1233
|
$tmp1 =~ s/keyword//; # get the index of the parameter 0, ..., 10
|
|
1234
|
if ( $tmp1 =~ /[0-9]/ ){
|
|
1235
|
# don't generate xml for empty keyword fields
|
|
1236
|
# don't generate taxonomic keyword fields, those go in taxonomic coverage
|
|
1237
|
if (hasContent(param($tmp))) {
|
|
1238
|
$doc .= "<keywordSet>\n";
|
|
1239
|
$doc .= "<keyword ";
|
|
1240
|
if (hasContent(param("kwType" . $tmp1)) &&
|
|
1241
|
(param("kwType" . $tmp1) !~ "none") ) {
|
|
1242
|
$doc .= "keywordType=\"";
|
|
1243
|
$doc .= param("kwType" . $tmp1);
|
|
1244
|
$doc .= "\"";
|
|
1245
|
}
|
|
1246
|
$doc .= ">";
|
|
1247
|
$doc .= param("keyword" . $tmp1);
|
|
1248
|
$doc .= "</keyword>\n";
|
|
1249
|
$doc .= "<keywordThesaurus>";
|
|
1250
|
$doc .= param("kwTh" . $tmp1);
|
|
1251
|
$doc .= "</keywordThesaurus>\n";
|
|
1252
|
$doc .= "</keywordSet>\n";
|
|
1253
|
}
|
|
1254
|
}
|
|
1255
|
}
|
|
1256
|
}
|
|
1257
|
|
|
1258
|
if (hasContent($FORM::addComments)) {
|
|
1259
|
$doc .= "<additionalInfo>\n";
|
|
1260
|
$doc .= "<para>$FORM::addComments</para>\n";
|
|
1261
|
$doc .= "</additionalInfo>\n";
|
|
1262
|
}
|
|
1263
|
|
|
1264
|
if (hasContent($FORM::useConstraints) ||
|
|
1265
|
hasContent($FORM::useConstraintsOther)) {
|
|
1266
|
$doc .= "<intellectualRights>\n";
|
|
1267
|
if (hasContent($FORM::useConstraints)) {
|
|
1268
|
$doc .= "<para>$FORM::useConstraints</para>\n";
|
|
1269
|
}
|
|
1270
|
if (hasContent($FORM::useConstraintsOther)) {
|
|
1271
|
$doc .= "<para>$FORM::useConstraintsOther</para>\n";
|
|
1272
|
}
|
|
1273
|
$doc .= "</intellectualRights>\n";
|
|
1274
|
}
|
|
1275
|
|
|
1276
|
|
|
1277
|
if (hasContent($FORM::url)) {
|
|
1278
|
$doc .= "<distribution>\n";
|
|
1279
|
$doc .= "<online>\n";
|
|
1280
|
$doc .= "<url>$FORM::url</url>\n";
|
|
1281
|
$doc .= "</online>\n";
|
|
1282
|
$doc .= "</distribution>\n";
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
$doc .= "<distribution>\n";
|
|
1286
|
$doc .= "<offline>\n";
|
|
1287
|
$doc .= "<mediumName>" . "$FORM::dataMedium $FORM::dataMediumOther";
|
|
1288
|
$doc .= "</mediumName>\n";
|
|
1289
|
$doc .= "</offline>\n";
|
|
1290
|
$doc .= "</distribution>\n";
|
|
1291
|
|
|
1292
|
$doc .= "<coverage>\n";
|
|
1293
|
$doc .= "<temporalCoverage>\n";
|
|
1294
|
|
|
1295
|
|
|
1296
|
if (hasContent($FORM::endingYear)) {
|
|
1297
|
$doc .= "<rangeOfDates>\n";
|
|
1298
|
if (hasContent($FORM::beginningMonth)) {
|
|
1299
|
my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
|
|
1300
|
"JUL","AUG","SEP","OCT","NOV","DEC")
|
|
1301
|
[$FORM::beginningMonth - 1];
|
|
1302
|
$doc .= "<beginDate>\n";
|
|
1303
|
$doc .= "<calendarDate>";
|
|
1304
|
$doc .= "$FORM::beginningYear-$FORM::beginningMonth-$FORM::beginningDay";
|
|
1305
|
$doc .= "</calendarDate>\n";
|
|
1306
|
$doc .= "</beginDate>\n";
|
|
1307
|
} else {
|
|
1308
|
$doc .= "<beginDate>\n";
|
|
1309
|
$doc .= "<calendarDate>";
|
|
1310
|
$doc .= "$FORM::beginningYear";
|
|
1311
|
$doc .= "</calendarDate>\n";
|
|
1312
|
$doc .= "</beginDate>\n";
|
|
1313
|
}
|
|
1314
|
|
|
1315
|
if (hasContent($FORM::endingMonth)) {
|
|
1316
|
my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
|
|
1317
|
"JUL","AUG","SEP","OCT","NOV","DEC")
|
|
1318
|
[$FORM::endingMonth - 1];
|
|
1319
|
$doc .= "<endDate>\n";
|
|
1320
|
$doc .= "<calendarDate>";
|
|
1321
|
$doc .= "$FORM::endingYear-$FORM::endingMonth-$FORM::endingDay";
|
|
1322
|
$doc .= "</calendarDate>\n";
|
|
1323
|
$doc .= "</endDate>\n";
|
|
1324
|
} else {
|
|
1325
|
$doc .= "<endDate>\n";
|
|
1326
|
$doc .= "<calendarDate>";
|
|
1327
|
$doc .= "$FORM::endingYear";
|
|
1328
|
$doc .= "</calendarDate>\n";
|
|
1329
|
$doc .= "</endDate>\n";
|
|
1330
|
}
|
|
1331
|
$doc .= "</rangeOfDates>\n";
|
|
1332
|
} else {
|
|
1333
|
$doc .= "<singleDateTime>\n";
|
|
1334
|
if (hasContent($FORM::beginningMonth)) {
|
|
1335
|
my $month = ("JAN","FEB","MAR","APR","MAY","JUN",
|
|
1336
|
"JUL","AUG","SEP","OCT","NOV","DEC")
|
|
1337
|
[$FORM::beginningMonth - 1];
|
|
1338
|
$doc .= "<calendarDate>";
|
|
1339
|
$doc .= "$FORM::beginningYear-$FORM::beginningMonth-$FORM::beginningDay";
|
|
1340
|
$doc .= "</calendarDate>\n";
|
|
1341
|
} else {
|
|
1342
|
$doc .= "<calendarDate>";
|
|
1343
|
$doc .= "$FORM::beginningYear";
|
|
1344
|
$doc .= "</calendarDate>\n";
|
|
1345
|
}
|
|
1346
|
$doc .= "</singleDateTime>\n";
|
|
1347
|
}
|
|
1348
|
|
|
1349
|
$doc .= "</temporalCoverage>\n";
|
|
1350
|
|
|
1351
|
$doc .= "<geographicCoverage>\n";
|
|
1352
|
$doc .= "<geographicDescription>$FORM::geogdesc</geographicDescription>\n";
|
|
1353
|
$doc .= "<boundingCoordinates>\n";
|
|
1354
|
|
|
1355
|
# if the second latitude is missing, then set the second lat/long pair
|
|
1356
|
# equal to the first this makes a point appear like a rectangle
|
|
1357
|
if ($FORM::latDeg2 == 0 && $FORM::latMin2 == 0 && $FORM::latSec2 == 0) {
|
|
1358
|
|
|
1359
|
$latDeg2 = $latDeg1;
|
|
1360
|
$latMin2 = $latMin1;
|
|
1361
|
$latSec2 = $latSec1;
|
|
1362
|
$hemisphLat2 = $hemisphLat1;
|
|
1363
|
$longDeg2 = $longDeg1;
|
|
1364
|
$longMin2 = $longMin1;
|
|
1365
|
$longSec2 = $longSec1;
|
|
1366
|
$hemisphLong2 = $hemisphLong1;
|
|
1367
|
}
|
|
1368
|
else
|
|
1369
|
{
|
|
1370
|
$latDeg2 = $FORM::latDeg2;
|
|
1371
|
$latMin2 = $FORM::latMin2;
|
|
1372
|
$latSec2 = $FORM::latSec2;
|
|
1373
|
$hemisphLat2 = $FORM::hemisphLat2;
|
|
1374
|
$longDeg2 = $FORM::longDeg2;
|
|
1375
|
$longMin2 = $FORM::longMin2;
|
|
1376
|
$longSec2 = $FORM::longSec2;
|
|
1377
|
$hemisphLong2 = $FORM::hemisphLong2;
|
|
1378
|
}
|
|
1379
|
|
|
1380
|
|
|
1381
|
my $hemisph;
|
|
1382
|
$hemisph = ($hemisphLong1 eq "W") ? -1 : 1;
|
|
1383
|
$doc .= "<westBoundingCoordinate>";
|
|
1384
|
$doc .= $hemisph * ($longDeg1 + (60*$longMin1+$longSec1)/3600);
|
|
1385
|
$doc .= "</westBoundingCoordinate>\n";
|
|
1386
|
|
|
1387
|
$hemisph = ($hemisphLong2 eq "W") ? -1 : 1;
|
|
1388
|
$doc .= "<eastBoundingCoordinate>";
|
|
1389
|
$doc .= $hemisph * ($longDeg2 + (60*$longMin2+$longSec2)/3600);
|
|
1390
|
$doc .= "</eastBoundingCoordinate>\n";
|
|
1391
|
|
|
1392
|
$hemisph = ($hemisphLat1 eq "S") ? -1 : 1;
|
|
1393
|
$doc .= "<northBoundingCoordinate>";
|
|
1394
|
$doc .= $hemisph * ($latDeg1 + (60*$latMin1+$latSec1)/3600);
|
|
1395
|
$doc .= "</northBoundingCoordinate>\n";
|
|
1396
|
|
|
1397
|
$hemisph = ($hemisphLat2 eq "S") ? -1 : 1;
|
|
1398
|
$doc .= "<southBoundingCoordinate>";
|
|
1399
|
$doc .= $hemisph * ($latDeg2 + (60*$latMin2+$latSec2)/3600);
|
|
1400
|
$doc .= "</southBoundingCoordinate>\n";
|
|
1401
|
|
|
1402
|
$doc .= "</boundingCoordinates>\n";
|
|
1403
|
$doc .= "</geographicCoverage>\n";
|
|
1404
|
|
|
1405
|
# Write out the taxonomic coverage fields
|
|
1406
|
my $foundFirstTaxon = 0;
|
|
1407
|
foreach my $trn (param()) {
|
|
1408
|
if ($trn =~ /taxonRankName/) {
|
|
1409
|
my $taxIndex = $trn;
|
|
1410
|
$taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
|
|
1411
|
my $trv = "taxonRankValue".$taxIndex;
|
|
1412
|
if ( $taxIndex =~ /[0-9]/ ){
|
|
1413
|
if (hasContent(param($trn)) && hasContent(param($trv))) {
|
|
1414
|
if (! $foundFirstTaxon) {
|
|
1415
|
$doc .= "<taxonomicCoverage>\n";
|
|
1416
|
$foundFirstTaxon = 1;
|
|
1417
|
if (hasContent($FORM::taxaAuth)) {
|
|
1418
|
$doc .= "<generalTaxonomicCoverage>".$FORM::taxaAuth."</generalTaxonomicCoverage>\n";
|
|
1419
|
}
|
|
1420
|
}
|
|
1421
|
$doc .= "<taxonomicClassification>\n";
|
|
1422
|
$doc .= " <taxonRankName>".param($trn)."</taxonRankName>\n";
|
|
1423
|
$doc .= " <taxonRankValue>".param($trv)."</taxonRankValue>\n";
|
|
1424
|
$doc .= "</taxonomicClassification>\n";
|
|
1425
|
}
|
|
1426
|
}
|
|
1427
|
}
|
|
1428
|
}
|
|
1429
|
if ($foundFirstTaxon) {
|
|
1430
|
$doc .= "</taxonomicCoverage>\n";
|
|
1431
|
}
|
|
1432
|
|
|
1433
|
$doc .= "</coverage>\n";
|
|
1434
|
|
|
1435
|
$doc .= $cont;
|
|
1436
|
$doc .= $publ;
|
|
1437
|
|
|
1438
|
if ((hasContent($FORM::methodTitle)) || scalar(@FORM::methodsPara) > 0) {
|
|
1439
|
my $methods = "<methods><methodStep><description><section>\n";
|
|
1440
|
if (hasContent($FORM::methodTitle)) {
|
|
1441
|
$methods .= "<title>$FORM::methodTitle</title>\n";
|
|
1442
|
}
|
|
1443
|
for (my $i = 0; $i < scalar(@FORM::methodPara); $i++) {
|
|
1444
|
$methods .= "<para>$FORM::methodPara[$i]</para>\n";
|
|
1445
|
}
|
|
1446
|
$methods .= "</section></description></methodStep>\n";
|
|
1447
|
if (hasContent($FORM::studyExtentDescription)) {
|
|
1448
|
$methods .= "<sampling><studyExtent><description>\n";
|
|
1449
|
$methods .= "<para>$FORM::studyExtentDescription</para>\n";
|
|
1450
|
$methods .= "</description></studyExtent>\n";
|
|
1451
|
$methods .= "<samplingDescription>\n";
|
|
1452
|
$methods .= "<para>$FORM::samplingDescription</para>\n";
|
|
1453
|
$methods .= "</samplingDescription>\n";
|
|
1454
|
$methods .= "</sampling>\n";
|
|
1455
|
}
|
|
1456
|
$methods .= "</methods>\n";
|
|
1457
|
$doc .= $methods;
|
|
1458
|
}
|
|
1459
|
|
|
1460
|
$doc .= "<access authSystem=\"knb\" order=\"denyFirst\">\n";
|
|
1461
|
$doc .= "<allow>\n";
|
|
1462
|
$doc .= "<principal>$username</principal>\n";
|
|
1463
|
$doc .= "<permission>all</permission>\n";
|
|
1464
|
$doc .= "</allow>\n";
|
|
1465
|
$doc .= "<allow>\n";
|
|
1466
|
$doc .= "<principal>uid=$FORM::username,o=$FORM::organization,dc=ecoinformatics,dc=org</principal>\n";
|
|
1467
|
$doc .= "<permission>all</permission>\n";
|
|
1468
|
$doc .= "</allow>\n";
|
|
1469
|
$doc .= "<allow>\n";
|
|
1470
|
$doc .= "<principal>public</principal>\n";
|
|
1471
|
$doc .= "<permission>read</permission>\n";
|
|
1472
|
$doc .= "</allow>\n";
|
|
1473
|
$doc .= "</access>\n";
|
|
1474
|
|
|
1475
|
$doc .= "</dataset>\n</eml:eml>\n";
|
|
1476
|
|
|
1477
|
return $doc;
|
|
1478
|
}
|
|
1479
|
|
|
1480
|
|
|
1481
|
################################################################################
|
|
1482
|
#
|
|
1483
|
# send an email message notifying the moderator of a new submission
|
|
1484
|
#
|
|
1485
|
################################################################################
|
|
1486
|
sub sendNotification {
|
|
1487
|
my $identifier = shift;
|
|
1488
|
my $mailhost = shift;
|
|
1489
|
my $sender = shift;
|
|
1490
|
my $recipient = shift;
|
|
1491
|
|
|
1492
|
my $smtp = Net::SMTP->new($mailhost);
|
|
1493
|
$smtp->mail($sender);
|
|
1494
|
$smtp->to($recipient);
|
|
1495
|
|
|
1496
|
my $message = <<" ENDOFMESSAGE";
|
|
1497
|
To: $recipient
|
|
1498
|
From: $sender
|
|
1499
|
Subject: New data submission
|
|
1500
|
|
|
1501
|
Data was submitted to the data registry.
|
|
1502
|
The identifying information for the new data set is:
|
|
1503
|
|
|
1504
|
Identifier: $identifier
|
|
1505
|
Title: $FORM::title
|
|
1506
|
Submitter: $FORM::providerGivenName $FORM::providerSurName
|
|
1507
|
|
|
1508
|
Please review the submmission and grant public read access if appropriate.
|
|
1509
|
Thanks
|
|
1510
|
|
|
1511
|
ENDOFMESSAGE
|
|
1512
|
$message =~ s/^[ \t\r\f]+//gm;
|
|
1513
|
|
|
1514
|
$smtp->data($message);
|
|
1515
|
$smtp->quit;
|
|
1516
|
}
|
|
1517
|
|
|
1518
|
|
|
1519
|
################################################################################
|
|
1520
|
#
|
|
1521
|
# read the eml document and send back a form with values filled in.
|
|
1522
|
#
|
|
1523
|
################################################################################
|
|
1524
|
sub modifyData {
|
|
1525
|
|
|
1526
|
# create metacat instance
|
|
1527
|
my $metacat;
|
|
1528
|
my $docid = $FORM::docid;
|
|
1529
|
my $httpMessage;
|
|
1530
|
my $doc;
|
|
1531
|
my $xmldoc;
|
|
1532
|
my $findType;
|
|
1533
|
my $parser = XML::LibXML->new();
|
|
1534
|
my @fileArray;
|
|
1535
|
my $pushDoc;
|
|
1536
|
my $alreadyInArray;
|
|
1537
|
my $node;
|
|
1538
|
my $response;
|
|
1539
|
my $element;
|
|
1540
|
my $tempfile;
|
|
1541
|
|
|
1542
|
$metacat = Metacat->new();
|
|
1543
|
if ($metacat) {
|
|
1544
|
$metacat->set_options( metacatUrl => $metacatUrl );
|
|
1545
|
} else {
|
|
1546
|
#die "failed during metacat creation\n";
|
|
1547
|
push(@errorMessages, "Failed during metacat creation.");
|
|
1548
|
}
|
|
1549
|
|
|
1550
|
$httpMessage = $metacat->read($docid);
|
|
1551
|
$doc = $httpMessage->content();
|
|
1552
|
$xmldoc = $parser->parse_string($doc);
|
|
1553
|
|
|
1554
|
#$tempfile = $xslConvDir.$docid;
|
|
1555
|
#push (@fileArray, $tempfile);
|
|
1556
|
|
|
1557
|
if ($xmldoc eq "") {
|
|
1558
|
$error ="Error in parsing the eml document";
|
|
1559
|
push(@errorMessages, $error);
|
|
1560
|
} else {
|
|
1561
|
$findType = $xmldoc->findnodes('//dataset/identifier');
|
|
1562
|
if ($findType->size() > 0) {
|
|
1563
|
# This is a eml beta6 document
|
|
1564
|
# Read the documents mentioned in triples also
|
|
1565
|
|
|
1566
|
$findType = $xmldoc->findnodes('//dataset/triple');
|
|
1567
|
if ($findType->size() > 0) {
|
|
1568
|
foreach $node ($findType->get_nodelist) {
|
|
1569
|
$pushDoc = findValue($node, 'subject');
|
|
1570
|
|
|
1571
|
# If the file is already in @fileArray then do not add it
|
|
1572
|
$alreadyInArray = 0;
|
|
1573
|
foreach $element (@fileArray) {
|
|
1574
|
$tempfile = $tmpdir."/".$pushDoc;
|
|
1575
|
if ($element eq $pushDoc) {
|
|
1576
|
$alreadyInArray = 1;
|
|
1577
|
}
|
|
1578
|
}
|
|
1579
|
|
|
1580
|
if (!$alreadyInArray) {
|
|
1581
|
$tempfile = $tmpdir."/".$pushDoc;
|
|
1582
|
$response = "";
|
|
1583
|
$response = $metacat->read($pushDoc);
|
|
1584
|
if (! $response) {
|
|
1585
|
# could not read
|
|
1586
|
#push(@errorMessages, $response);
|
|
1587
|
push(@errorMessages, $metacat->getMessage());
|
|
1588
|
push(@errorMessages, "Failed during reading.\n");
|
|
1589
|
} else {
|
|
1590
|
my $xdoc = $response->content();
|
|
1591
|
#$tempfile = $xslConvDir.$pushDoc;
|
|
1592
|
open (TFILE,">$tempfile") ||
|
|
1593
|
die ("Cant open xml file... $tempfile\n");
|
|
1594
|
print TFILE $xdoc;
|
|
1595
|
close(TFILE);
|
|
1596
|
push (@fileArray, $tempfile);
|
|
1597
|
}
|
|
1598
|
}
|
|
1599
|
}
|
|
1600
|
}
|
|
1601
|
|
|
1602
|
# Read the main document.
|
|
1603
|
|
|
1604
|
$tempfile = $tmpdir."/".$docid; #= $xslConvDir.$docid;
|
|
1605
|
open (TFILE,">$tempfile") || die ("Cant open xml file...\n");
|
|
1606
|
print TFILE $doc;
|
|
1607
|
close(TFILE);
|
|
1608
|
|
|
1609
|
# Transforming beta6 to eml 2
|
|
1610
|
my $xslt;
|
|
1611
|
my $triplesheet;
|
|
1612
|
my $results;
|
|
1613
|
my $stylesheet;
|
|
1614
|
my $resultsheet;
|
|
1615
|
|
|
1616
|
$xslt = XML::LibXSLT->new();
|
|
1617
|
#$tempfile = $xslConvDir."triple_info.xsl";
|
|
1618
|
$tempfile = $tmpdir."/"."triple_info.xsl";
|
|
1619
|
|
|
1620
|
$triplesheet = $xslt->parse_stylesheet_file($tempfile);
|
|
1621
|
|
|
1622
|
#$results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpdir/\'", packageName => "\'$docid\'");
|
|
1623
|
$results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpdir/\'", packageName => "\'$docid\'");
|
|
1624
|
|
|
1625
|
#$tempfile = $xslConvDir."emlb6toeml2.xsl";
|
|
1626
|
$tempfile = $tmpdir."/"."emlb6toeml2.xsl";
|
|
1627
|
$stylesheet = $xslt->parse_stylesheet_file($tempfile);
|
|
1628
|
$resultsheet = $stylesheet->transform($results);
|
|
1629
|
|
|
1630
|
#$tempfile = "/usr/local/apache2/htdocs/xml/test.xml";;
|
|
1631
|
#open (TFILE,">$tempfile") || die ("Cant open xml file...\n");
|
|
1632
|
#print TFILE $stylesheet->output_string($resultsheet);
|
|
1633
|
#close(TFILE);
|
|
1634
|
|
|
1635
|
getFormValuesFromEml2($resultsheet);
|
|
1636
|
|
|
1637
|
# Delete the files written earlier.
|
|
1638
|
unlink @fileArray;
|
|
1639
|
|
|
1640
|
} else {
|
|
1641
|
getFormValuesFromEml2($xmldoc);
|
|
1642
|
}
|
|
1643
|
}
|
|
1644
|
|
|
1645
|
if (scalar(@errorMessages)) {
|
|
1646
|
# if any errors, print them in the response template
|
|
1647
|
$$templateVars{'status'} = 'failure';
|
|
1648
|
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
1649
|
$error = 1;
|
|
1650
|
$$templateVars{'function'} = "modification";
|
|
1651
|
$$templateVars{'section'} = "Modification Status";
|
|
1652
|
$template->process( $responseTemplate, $templateVars);
|
|
1653
|
} else {
|
|
1654
|
$$templateVars{'form'} = 're_entry';
|
|
1655
|
$template->process( $entryFormTemplate, $templateVars);
|
|
1656
|
}
|
|
1657
|
}
|
|
1658
|
|
|
1659
|
################################################################################
|
|
1660
|
#
|
|
1661
|
# Parse an EML 2.0.0 file and extract the metadata into perl variables for
|
|
1662
|
# processing and returning to the template processor
|
|
1663
|
#
|
|
1664
|
################################################################################
|
|
1665
|
sub getFormValuesFromEml2 {
|
|
1666
|
|
|
1667
|
my $doc = shift;
|
|
1668
|
my $results;
|
|
1669
|
my $error;
|
|
1670
|
my $node;
|
|
1671
|
my $tempResult;
|
|
1672
|
my $tempNode;
|
|
1673
|
my $aoCount = 1;
|
|
1674
|
my $foundDSO;
|
|
1675
|
|
|
1676
|
# find out the tag <alternateIdentifier>.
|
|
1677
|
$results = $doc->findnodes('//dataset/alternateIdentifier');
|
|
1678
|
if ($results->size() > 1) {
|
|
1679
|
errMoreThanOne("alternateIdentifier");
|
|
1680
|
} else {
|
|
1681
|
foreach $node ($results->get_nodelist) {
|
|
1682
|
$$templateVars{'identifier'} = findValue($node, '../alternateIdentifier');
|
|
1683
|
}
|
|
1684
|
}
|
|
1685
|
|
|
1686
|
# find out the tag <title>.
|
|
1687
|
$results = $doc->findnodes('//dataset/title');
|
|
1688
|
if ($results->size() > 1) {
|
|
1689
|
errMoreThanOne("title");
|
|
1690
|
} elsif ($results->size() < 1) {
|
|
1691
|
$error ="Following tag not found: title. Please use Morpho to edit this document";
|
|
1692
|
push(@errorMessages, $error."\n");
|
|
1693
|
#if ($DEBUG == 1){ print $error;}
|
|
1694
|
} else {
|
|
1695
|
foreach $node ($results->get_nodelist) {
|
|
1696
|
$$templateVars{'title'} = findValue($node, '../title');
|
|
1697
|
}
|
|
1698
|
}
|
|
1699
|
|
|
1700
|
# find out the tag <creator>.
|
|
1701
|
$results = $doc->findnodes('//dataset/creator/individualName');
|
|
1702
|
debug("Registry: Creators: ".$results->size());
|
|
1703
|
if ($results->size() > 11) {
|
|
1704
|
errMoreThanN("creator/individualName");
|
|
1705
|
} else {
|
|
1706
|
foreach $node ($results->get_nodelist) {
|
|
1707
|
dontOccur($node, "../positionName|../onlineURL|../userId",
|
|
1708
|
"positionName, onlineURL, userId");
|
|
1709
|
|
|
1710
|
dontOccur($node, "./saluation", "saluation");
|
|
1711
|
|
|
1712
|
debug("Registry: Checking a creator in loop 1...");
|
|
1713
|
$tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
|
|
1714
|
if($tempResult->size > 0) {
|
|
1715
|
if($foundDSO == 0) {
|
|
1716
|
$foundDSO = 1;
|
|
1717
|
|
|
1718
|
debug("Registry: Recording a creator in loop 1...");
|
|
1719
|
$$templateVars{'origNamefirst0'} = findValue($node, 'givenName');
|
|
1720
|
$$templateVars{'origNamelast0'} = findValue($node, 'surName');
|
|
1721
|
|
|
1722
|
my $tempResult2 = $node->findnodes('../address');
|
|
1723
|
if ($tempResult2->size > 1) {
|
|
1724
|
errMoreThanOne("address");
|
|
1725
|
} else {
|
|
1726
|
foreach my $tempNode2 ($tempResult2->get_nodelist) {
|
|
1727
|
$$templateVars{'origDelivery'} = findValue($tempNode2, 'deliveryPoint');
|
|
1728
|
$$templateVars{'origCity'} = findValue($tempNode2, 'city');
|
|
1729
|
$$templateVars{'origState'} = findValue($tempNode2, 'administrativeArea');
|
|
1730
|
$$templateVars{'origZIP'} = findValue($tempNode2, 'postalCode');
|
|
1731
|
$$templateVars{'origCountry'} = findValue($tempNode2, 'country');
|
|
1732
|
}
|
|
1733
|
}
|
|
1734
|
|
|
1735
|
my $tempResult3 = $node->findnodes('../phone');
|
|
1736
|
if ($tempResult3->size > 2) {
|
|
1737
|
errMoreThanN("phone");
|
|
1738
|
} else {
|
|
1739
|
foreach my $tempNode2 ($tempResult3->get_nodelist) {
|
|
1740
|
if ($tempNode2->hasAttributes()) {
|
|
1741
|
my @attlist = $tempNode2->attributes();
|
|
1742
|
if ($attlist[0]->value eq "Fax") {
|
|
1743
|
$$templateVars{'origFAX'} = $tempNode2->textContent();
|
|
1744
|
} else {
|
|
1745
|
$$templateVars{'origPhone'} = $tempNode2->textContent();
|
|
1746
|
}
|
|
1747
|
} else {
|
|
1748
|
$$templateVars{'origPhone'} = $tempNode2->textContent();
|
|
1749
|
}
|
|
1750
|
}
|
|
1751
|
}
|
|
1752
|
$$templateVars{'origEmail'} = findValue($node, '../electronicMailAddress');
|
|
1753
|
$$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
|
|
1754
|
} else {
|
|
1755
|
errMoreThanN("address, phone and electronicMailAddress");
|
|
1756
|
}
|
|
1757
|
}
|
|
1758
|
}
|
|
1759
|
foreach $node ($results->get_nodelist) {
|
|
1760
|
debug("Registry: Checking a creator in loop 2...");
|
|
1761
|
$tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
|
|
1762
|
if ($tempResult->size == 0) {
|
|
1763
|
if ($foundDSO == 0) {
|
|
1764
|
debug("Registry: Recording a creator in loop 2 block A...");
|
|
1765
|
$foundDSO = 1;
|
|
1766
|
$$templateVars{'origNamefirst0'} = findValue($node, 'givenName');
|
|
1767
|
$$templateVars{'origNamelast0'} = findValue($node, 'surName');
|
|
1768
|
$$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
|
|
1769
|
} else {
|
|
1770
|
debug("Registry: Recording a creator in loop 2 block B...");
|
|
1771
|
$$templateVars{"origNamefirst$aoCount"} = findValue($node, './givenName');
|
|
1772
|
$$templateVars{"origNamelast$aoCount"} = findValue($node, './surName');
|
|
1773
|
$$templateVars{"origRole$aoCount"} = "Originator";
|
|
1774
|
$aoCount++;
|
|
1775
|
}
|
|
1776
|
}
|
|
1777
|
}
|
|
1778
|
}
|
|
1779
|
|
|
1780
|
$results = $doc->findnodes('//dataset/creator/organizationName');
|
|
1781
|
my $wgroups = $doc->findnodes("//dataset/creator/organizationName[contains(text(),'(NCEAS ')]");
|
|
1782
|
debug("Registry: Number Org: ".$results->size());
|
|
1783
|
debug("Registry: Number WG: ".$wgroups->size());
|
|
1784
|
if ($results->size() - $wgroups->size() > 3) {
|
|
1785
|
errMoreThanN("creator/organizationName");
|
|
1786
|
} else {
|
|
1787
|
foreach $node ($results->get_nodelist) {
|
|
1788
|
my $tempValue = findValue($node,'../organizationName');
|
|
1789
|
$tempResult = $node->findnodes('../individualName');
|
|
1790
|
if ($tempResult->size == 0 && $tempValue ne $organization) {
|
|
1791
|
$$templateVars{'site'} = $tempValue;
|
|
1792
|
}
|
|
1793
|
}
|
|
1794
|
if ($FORM::cfg eq 'nceas') {
|
|
1795
|
my @wg;
|
|
1796
|
foreach $node ($results->get_nodelist) {
|
|
1797
|
my $tempValue = findValue($node,'../organizationName');
|
|
1798
|
$wg[scalar(@wg)] = $tempValue;
|
|
1799
|
}
|
|
1800
|
my $projects = getProjectList();
|
|
1801
|
$$templateVars{'projects'} = $projects;
|
|
1802
|
$$templateVars{'wg'} = \@wg;
|
|
1803
|
}
|
|
1804
|
}
|
|
1805
|
|
|
1806
|
$results = $doc->findnodes('//dataset/metadataProvider');
|
|
1807
|
if ($results->size() > 11) {
|
|
1808
|
errMoreThanN("metadataProvider");
|
|
1809
|
} else {
|
|
1810
|
foreach $node ($results->get_nodelist) {
|
|
1811
|
dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
|
|
1812
|
"organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in metadataProvider");
|
|
1813
|
|
|
1814
|
$tempResult = $node->findnodes('./individualName');
|
|
1815
|
if ($tempResult->size > 1) {
|
|
1816
|
errMoreThanOne("metadataProvider/indvidualName");
|
|
1817
|
} else {
|
|
1818
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1819
|
if ($$templateVars{'providerGivenName'} ne "") {
|
|
1820
|
$$templateVars{"origNamefirst$aoCount"} = findValue($tempNode, './givenName');
|
|
1821
|
$$templateVars{"origNamelast$aoCount"} = findValue($tempNode, './surName');
|
|
1822
|
$$templateVars{"origRole$aoCount"} = "Metadata Provider";
|
|
1823
|
$aoCount++;
|
|
1824
|
} else {
|
|
1825
|
$$templateVars{'providerGivenName'} = findValue($tempNode, './givenName');
|
|
1826
|
$$templateVars{'providerSurName'} = findValue($tempNode, './surName');
|
|
1827
|
}
|
|
1828
|
}
|
|
1829
|
}
|
|
1830
|
}
|
|
1831
|
}
|
|
1832
|
|
|
1833
|
$results = $doc->findnodes('//dataset/associatedParty');
|
|
1834
|
if ($results->size() > 10) {
|
|
1835
|
errMoreThanN("associatedParty");
|
|
1836
|
} else {
|
|
1837
|
foreach $node ($results->get_nodelist) {
|
|
1838
|
dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
|
|
1839
|
"organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in associatedParty");
|
|
1840
|
|
|
1841
|
$tempResult = $node->findnodes('./individualName');
|
|
1842
|
if ($tempResult->size > 1) {
|
|
1843
|
errMoreThanOne("associatedParty/indvidualName");
|
|
1844
|
} else {
|
|
1845
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1846
|
$$templateVars{"origNamefirst$aoCount"} = findValue($tempNode, './givenName');
|
|
1847
|
$$templateVars{"origNamelast$aoCount"} = findValue($tempNode, './surName');
|
|
1848
|
$$templateVars{"origRole$aoCount"} = findValue($tempNode, '../role');
|
|
1849
|
$aoCount++;
|
|
1850
|
}
|
|
1851
|
}
|
|
1852
|
}
|
|
1853
|
}
|
|
1854
|
|
|
1855
|
$results = $doc->findnodes('//dataset/publisher');
|
|
1856
|
if ($results->size() > 10) {
|
|
1857
|
errMoreThanN("publisher");
|
|
1858
|
} else {
|
|
1859
|
foreach $node ($results->get_nodelist) {
|
|
1860
|
dontOccur($node, "./organizationName|./positionName|./onlineURL|./userId|./electronicMailAddress|./phone|./address",
|
|
1861
|
"organizationName, positionName, onlineURL, userId, electronicMailAddress, phone, address in associatedParty");
|
|
1862
|
|
|
1863
|
$tempResult = $node->findnodes('./individualName');
|
|
1864
|
if ($tempResult->size > 1) {
|
|
1865
|
errMoreThanOne("publisher/indvidualName");
|
|
1866
|
} else {
|
|
1867
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1868
|
$$templateVars{"origNamefirst$aoCount"} = findValue($tempNode, './givenName');
|
|
1869
|
$$templateVars{"origNamelast$aoCount"} = findValue($tempNode, './surName');
|
|
1870
|
$$templateVars{"origRole$aoCount"} = "Publisher";
|
|
1871
|
$aoCount++;
|
|
1872
|
}
|
|
1873
|
}
|
|
1874
|
}
|
|
1875
|
}
|
|
1876
|
|
|
1877
|
if ($aoCount > 11) {
|
|
1878
|
errMoreThanN("Additional Originators");
|
|
1879
|
}
|
|
1880
|
|
|
1881
|
dontOccur($doc, "./pubDate", "pubDate");
|
|
1882
|
dontOccur($doc, "./language", "language");
|
|
1883
|
dontOccur($doc, "./series", "series");
|
|
1884
|
|
|
1885
|
$results = $doc->findnodes('//dataset/abstract');
|
|
1886
|
if ($results->size() > 1) {
|
|
1887
|
errMoreThanOne("abstract");
|
|
1888
|
} else {
|
|
1889
|
foreach my $node ($results->get_nodelist) {
|
|
1890
|
dontOccur($node, "./section", "section");
|
|
1891
|
$$templateVars{'abstract'} = findValueNoChild($node, "para");
|
|
1892
|
}
|
|
1893
|
}
|
|
1894
|
|
|
1895
|
$results = $doc->findnodes('//dataset/keywordSet');
|
|
1896
|
|
|
1897
|
my $count = 0;
|
|
1898
|
foreach $node ($results->get_nodelist) {
|
|
1899
|
$tempResult = $node->findnodes('./keyword');
|
|
1900
|
if ($tempResult->size() > 1) {
|
|
1901
|
errMoreThanOne("keyword");
|
|
1902
|
} else {
|
|
1903
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1904
|
$$templateVars{"keyword$count"} = $tempNode->textContent();
|
|
1905
|
if ($tempNode->hasAttributes()) {
|
|
1906
|
my @attlist = $tempNode->attributes();
|
|
1907
|
$$templateVars{"kwType$count"} = $attlist[0]->value;
|
|
1908
|
}
|
|
1909
|
}
|
|
1910
|
}
|
|
1911
|
$$templateVars{"kwTh$count"} = findValue($node, "keywordThesaurus");
|
|
1912
|
$count++;
|
|
1913
|
}
|
|
1914
|
|
|
1915
|
|
|
1916
|
$results = $doc->findnodes('//dataset/additionalInfo');
|
|
1917
|
if ($results->size() > 1) {
|
|
1918
|
errMoreThanOne("additionalInfo");
|
|
1919
|
} else {
|
|
1920
|
foreach $node ($results->get_nodelist) {
|
|
1921
|
dontOccur($node, "./section", "section");
|
|
1922
|
$$templateVars{'addComments'} = findValueNoChild($node, "para");
|
|
1923
|
}
|
|
1924
|
}
|
|
1925
|
|
|
1926
|
$$templateVars{'useConstraints'} = "";
|
|
1927
|
$results = $doc->findnodes('//dataset/intellectualRights');
|
|
1928
|
if ($results->size() > 1) {
|
|
1929
|
errMoreThanOne("intellectualRights");
|
|
1930
|
} else {
|
|
1931
|
foreach $node ($results->get_nodelist) {
|
|
1932
|
dontOccur($node, "./section", "section in intellectualRights");
|
|
1933
|
|
|
1934
|
$tempResult = $node->findnodes("para");
|
|
1935
|
if ($tempResult->size > 2) {
|
|
1936
|
errMoreThanN("para");
|
|
1937
|
} else {
|
|
1938
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1939
|
my $childNodes = $tempNode->childNodes;
|
|
1940
|
if ($childNodes->size() > 1) {
|
|
1941
|
$error ="The tag para in intellectualRights has children which cannot be shown using the form. Please use Morpho to edit this document";
|
|
1942
|
push(@errorMessages, $error);
|
|
1943
|
#if ($DEBUG == 1){ print $error."\n";}
|
|
1944
|
} else {
|
|
1945
|
#print $tempNode->nodeName().":".$tempNode->textContent();
|
|
1946
|
#print "\n";
|
|
1947
|
if ($$templateVars{'useConstraints'} eq "") {
|
|
1948
|
$$templateVars{'useConstraints'} = $tempNode->textContent();
|
|
1949
|
} else {
|
|
1950
|
$$templateVars{'useConstraintsOther'} = $tempNode->textContent();
|
|
1951
|
}
|
|
1952
|
}
|
|
1953
|
}
|
|
1954
|
}
|
|
1955
|
}
|
|
1956
|
}
|
|
1957
|
|
|
1958
|
$results = $doc->findnodes('//dataset/distribution/online');
|
|
1959
|
if ($results->size() > 1) {
|
|
1960
|
errMoreThanOne("distribution/online");
|
|
1961
|
} else {
|
|
1962
|
foreach my $tempNode ($results->get_nodelist){
|
|
1963
|
$$templateVars{'url'} = findValue($tempNode, "url");
|
|
1964
|
dontOccur($tempNode, "./connection", "/distribution/online/connection");
|
|
1965
|
dontOccur($tempNode, "./connectionDefinition", "/distribution/online/connectionDefinition");
|
|
1966
|
}
|
|
1967
|
}
|
|
1968
|
|
|
1969
|
$results = $doc->findnodes('//dataset/distribution/offline');
|
|
1970
|
if ($results->size() > 1) {
|
|
1971
|
errMoreThanOne("distribution/online");
|
|
1972
|
} else {
|
|
1973
|
foreach my $tempNode ($results->get_nodelist) {
|
|
1974
|
$$templateVars{'dataMedium'} = findValue($tempNode, "mediumName");
|
|
1975
|
dontOccur($tempNode, "./mediumDensity", "/distribution/offline/mediumDensity");
|
|
1976
|
dontOccur($tempNode, "./mediumDensityUnits", "/distribution/offline/mediumDensityUnits");
|
|
1977
|
dontOccur($tempNode, "./mediumVolume", "/distribution/offline/mediumVolume");
|
|
1978
|
dontOccur($tempNode, "./mediumFormat", "/distribution/offline/mediumFormat");
|
|
1979
|
dontOccur($tempNode, "./mediumNote", "/distribution/offline/mediumNote");
|
|
1980
|
}
|
|
1981
|
}
|
|
1982
|
|
|
1983
|
dontOccur($doc, "./inline", "//dataset/distribution/inline");
|
|
1984
|
|
|
1985
|
$results = $doc->findnodes('//dataset/coverage');
|
|
1986
|
if ($results->size() > 1) {
|
|
1987
|
errMoreThanOne("coverage");
|
|
1988
|
} else {
|
|
1989
|
foreach $node ($results->get_nodelist) {
|
|
1990
|
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");
|
|
1991
|
|
|
1992
|
$tempResult = $node->findnodes('./temporalCoverage');
|
|
1993
|
if ($tempResult->size > 1) {
|
|
1994
|
errMoreThanOne("temporalCoverage");
|
|
1995
|
} else {
|
|
1996
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
1997
|
my $x;
|
|
1998
|
my $y;
|
|
1999
|
my $z;
|
|
2000
|
my $tempdate = findValue($tempNode, "rangeOfDates/beginDate/calendarDate");
|
|
2001
|
($x, $y, $z) = split("-", $tempdate);
|
|
2002
|
$$templateVars{'beginningYear'} = $x;
|
|
2003
|
$$templateVars{'beginningMonth'} = $y;
|
|
2004
|
$$templateVars{'beginningDay'} = $z;
|
|
2005
|
|
|
2006
|
$tempdate = findValue($tempNode, "rangeOfDates/endDate/calendarDate");
|
|
2007
|
($x, $y, $z) = split("-", $tempdate);
|
|
2008
|
$$templateVars{'endingYear'} = $x;
|
|
2009
|
$$templateVars{'endingMonth'} = $y;
|
|
2010
|
$$templateVars{'endingDay'} = $z;
|
|
2011
|
|
|
2012
|
$tempdate = "";
|
|
2013
|
$tempdate = findValue($tempNode, "singleDateTime/calendarDate");
|
|
2014
|
if($tempdate ne ""){
|
|
2015
|
($x, $y, $z) = split("-", $tempdate);
|
|
2016
|
$$templateVars{'beginningYear'} = $x;
|
|
2017
|
$$templateVars{'beginningMonth'} = $y;
|
|
2018
|
$$templateVars{'beginningDay'} = $z;
|
|
2019
|
}
|
|
2020
|
}
|
|
2021
|
}
|
|
2022
|
|
|
2023
|
$tempResult = $node->findnodes('./geographicCoverage');
|
|
2024
|
if ($tempResult->size > 1) {
|
|
2025
|
errMoreThanOne("geographicCoverage");
|
|
2026
|
} else {
|
|
2027
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
2028
|
my $geogdesc = findValue($tempNode, "geographicDescription");
|
|
2029
|
debug("Registry: geogdesc from xml is: $geogdesc");
|
|
2030
|
$$templateVars{'geogdesc'} = $geogdesc;
|
|
2031
|
my $coord = findValue($tempNode, "boundingCoordinates/westBoundingCoordinate");
|
|
2032
|
if ($coord > 0) {
|
|
2033
|
#print "+";
|
|
2034
|
$$templateVars{'hemisphLong1'} = "E";
|
|
2035
|
} else {
|
|
2036
|
#print "-";
|
|
2037
|
eval($coord = $coord * -1);
|
|
2038
|
$$templateVars{'hemisphLong1'} = "W";
|
|
2039
|
}
|
|
2040
|
eval($$templateVars{'longDeg1'} = int($coord));
|
|
2041
|
eval($coord = ($coord - int($coord))*60);
|
|
2042
|
eval($$templateVars{'longMin1'} = int($coord));
|
|
2043
|
eval($coord = ($coord - int($coord))*60);
|
|
2044
|
eval($$templateVars{'longSec1'} = int($coord));
|
|
2045
|
|
|
2046
|
$coord = findValue($tempNode, "boundingCoordinates/southBoundingCoordinate");
|
|
2047
|
if ($coord > 0) {
|
|
2048
|
#print "+";
|
|
2049
|
$$templateVars{'hemisphLat2'} = "N";
|
|
2050
|
} else {
|
|
2051
|
#print "-";
|
|
2052
|
eval($coord = $coord * -1);
|
|
2053
|
$$templateVars{'hemisphLat2'} = "S";
|
|
2054
|
}
|
|
2055
|
eval($$templateVars{'latDeg2'} = int($coord));
|
|
2056
|
eval($coord = ($coord - int($coord))*60);
|
|
2057
|
eval($$templateVars{'latMin2'} = int($coord));
|
|
2058
|
eval($coord = ($coord - int($coord))*60);
|
|
2059
|
eval($$templateVars{'latSec2'} = int($coord));
|
|
2060
|
|
|
2061
|
$coord = findValue($tempNode, "boundingCoordinates/northBoundingCoordinate");
|
|
2062
|
if ($coord > 0) {
|
|
2063
|
#print "+";
|
|
2064
|
$$templateVars{'hemisphLat1'} = "N";
|
|
2065
|
} else {
|
|
2066
|
#print "-";
|
|
2067
|
eval($coord = $coord * -1);
|
|
2068
|
$$templateVars{'hemisphLat1'} = "S";
|
|
2069
|
}
|
|
2070
|
eval($$templateVars{'latDeg1'} = int($coord));
|
|
2071
|
eval($coord = ($coord - int($coord))*60);
|
|
2072
|
eval($$templateVars{'latMin1'} = int($coord));
|
|
2073
|
eval($coord = ($coord - int($coord))*60);
|
|
2074
|
eval($$templateVars{'latSec1'} = int($coord));
|
|
2075
|
|
|
2076
|
$coord = findValue($tempNode, "boundingCoordinates/eastBoundingCoordinate");
|
|
2077
|
if ($coord > 0) {
|
|
2078
|
#print "+";
|
|
2079
|
$$templateVars{'hemisphLong2'} = "E";
|
|
2080
|
} else {
|
|
2081
|
#print "-";
|
|
2082
|
eval($coord = $coord * -1);
|
|
2083
|
$$templateVars{'hemisphLong2'} = "W";
|
|
2084
|
}
|
|
2085
|
eval($$templateVars{'longDeg2'} = int($coord));
|
|
2086
|
eval($coord = ($coord - int($coord))*60);
|
|
2087
|
eval($$templateVars{'longMin2'} = int($coord));
|
|
2088
|
eval($coord = ($coord - int($coord))*60);
|
|
2089
|
eval($$templateVars{'longSec2'} = int($coord));
|
|
2090
|
}
|
|
2091
|
}
|
|
2092
|
|
|
2093
|
$tempResult = $node->findnodes('./taxonomicCoverage/taxonomicClassification');
|
|
2094
|
my $taxonIndex = 0;
|
|
2095
|
foreach $tempNode ($tempResult->get_nodelist) {
|
|
2096
|
$taxonIndex++;
|
|
2097
|
my $taxonRankName = findValue($tempNode, "taxonRankName");
|
|
2098
|
my $taxonRankValue = findValue($tempNode, "taxonRankValue");
|
|
2099
|
$$templateVars{"taxonRankName".$taxonIndex} = $taxonRankName;
|
|
2100
|
$$templateVars{"taxonRankValue".$taxonIndex} = $taxonRankValue;
|
|
2101
|
}
|
|
2102
|
$$templateVars{'taxaCount'} = $taxonIndex;
|
|
2103
|
my $taxaAuth = findValue($node, "./taxonomicCoverage/generalTaxonomicCoverage");
|
|
2104
|
$$templateVars{'taxaAuth'} = $taxaAuth;
|
|
2105
|
}
|
|
2106
|
}
|
|
2107
|
dontOccur($doc, "./purpose", "purpose");
|
|
2108
|
dontOccur($doc, "./maintenance", "maintnance");
|
|
2109
|
|
|
2110
|
$results = $doc->findnodes('//dataset/contact/individualName');
|
|
2111
|
if ($results->size() > 1) {
|
|
2112
|
errMoreThanOne("contact/individualName");
|
|
2113
|
} else {
|
|
2114
|
foreach $node ($results->get_nodelist) {
|
|
2115
|
dontOccur($node, "../positionName|../onlineURL|../userId",
|
|
2116
|
"positionName, onlineURL, userId in contact tag");
|
|
2117
|
dontOccur($node, "./saluation", "saluation in contact tag");
|
|
2118
|
|
|
2119
|
$tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
|
|
2120
|
if ($tempResult->size > 0) {
|
|
2121
|
$$templateVars{'origNamefirstContact'} = findValue($node, 'givenName');
|
|
2122
|
$$templateVars{'origNamelastContact'} = findValue($node, 'surName');
|
|
2123
|
|
|
2124
|
my $tempResult2 = $node->findnodes('../address');
|
|
2125
|
if ($tempResult2->size > 1) {
|
|
2126
|
errMoreThanOne("address");
|
|
2127
|
} else {
|
|
2128
|
foreach my $tempNode2 ($tempResult2->get_nodelist) {
|
|
2129
|
$$templateVars{'origDeliveryContact'} = findValue($tempNode2, 'deliveryPoint');
|
|
2130
|
$$templateVars{'origCityContact'} = findValue($tempNode2, 'city');
|
|
2131
|
$$templateVars{'origStateContact'} = findValue($tempNode2, 'administrativeArea');
|
|
2132
|
$$templateVars{'origZIPContact'} = findValue($tempNode2, 'postalCode');
|
|
2133
|
$$templateVars{'origCountryContact'} = findValue($tempNode2, 'country');
|
|
2134
|
}
|
|
2135
|
}
|
|
2136
|
|
|
2137
|
my $tempResult3 = $node->findnodes('../phone');
|
|
2138
|
if ($tempResult3->size > 2) {
|
|
2139
|
errMoreThanN("phone");
|
|
2140
|
} else {
|
|
2141
|
foreach my $tempNode2 ($tempResult3->get_nodelist) {
|
|
2142
|
if ($tempNode2->hasAttributes()) {
|
|
2143
|
my @attlist = $tempNode2->attributes();
|
|
2144
|
if ($attlist[0]->value eq "Fax") {
|
|
2145
|
$$templateVars{'origFAXContact'} = $tempNode2->textContent();
|
|
2146
|
} else {
|
|
2147
|
$$templateVars{'origPhoneContact'} = $tempNode2->textContent();
|
|
2148
|
}
|
|
2149
|
} else {
|
|
2150
|
$$templateVars{'origPhoneContact'} = $tempNode2->textContent();
|
|
2151
|
}
|
|
2152
|
}
|
|
2153
|
}
|
|
2154
|
$$templateVars{'origEmailContact'} = findValue($node, '../electronicMailAddress');
|
|
2155
|
$$templateVars{'origNameOrgContact'} = findValue($node, '../organizationName');
|
|
2156
|
} else {
|
|
2157
|
$$templateVars{'origNamefirstContact'} = findValue($node, 'givenName');
|
|
2158
|
$$templateVars{'origNamelastContact'} = findValue($node, 'surName');
|
|
2159
|
$$templateVars{'origNameOrgContact'} = findValue($node, '../organizationName');
|
|
2160
|
}
|
|
2161
|
}
|
|
2162
|
}
|
|
2163
|
|
|
2164
|
$results = $doc->findnodes(
|
|
2165
|
'//dataset/methods/methodStep/description/section');
|
|
2166
|
debug("Registry: Number methods: ".$results->size());
|
|
2167
|
if ($results->size() > 1) {
|
|
2168
|
errMoreThanN("methods/methodStep/description/section");
|
|
2169
|
} else {
|
|
2170
|
|
|
2171
|
my @methodPara;
|
|
2172
|
foreach $node ($results->get_nodelist) {
|
|
2173
|
my @children = $node->childNodes;
|
|
2174
|
for (my $i = 0; $i < scalar(@children); $i++) {
|
|
2175
|
debug("Registry: Method child loop ($i)");
|
|
2176
|
my $child = $children[$i];
|
|
2177
|
if ($child->nodeName eq 'title') {
|
|
2178
|
my $title = $child->textContent();
|
|
2179
|
debug("Registry: Method title ($title)");
|
|
2180
|
$$templateVars{'methodTitle'} = $title;
|
|
2181
|
} elsif ($child->nodeName eq 'para') {
|
|
2182
|
my $para = $child->textContent();
|
|
2183
|
debug("Registry: Method para ($para)");
|
|
2184
|
$methodPara[scalar(@methodPara)] = $para;
|
|
2185
|
}
|
|
2186
|
}
|
|
2187
|
}
|
|
2188
|
if (scalar(@methodPara) > 0) {
|
|
2189
|
$$templateVars{'methodPara'} = \@methodPara;
|
|
2190
|
}
|
|
2191
|
}
|
|
2192
|
|
|
2193
|
$results = $doc->findnodes(
|
|
2194
|
'//dataset/methods/sampling/studyExtent/description/para');
|
|
2195
|
if ($results->size() > 1) {
|
|
2196
|
errMoreThanN("methods/sampling/studyExtent/description/para");
|
|
2197
|
} else {
|
|
2198
|
foreach $node ($results->get_nodelist) {
|
|
2199
|
my $studyExtentDescription = $node->textContent();
|
|
2200
|
$$templateVars{'studyExtentDescription'} = $studyExtentDescription;
|
|
2201
|
}
|
|
2202
|
}
|
|
2203
|
|
|
2204
|
$results = $doc->findnodes(
|
|
2205
|
'//dataset/methods/sampling/samplingDescription/para');
|
|
2206
|
if ($results->size() > 1) {
|
|
2207
|
errMoreThanN("methods/sampling/samplingDescription/para");
|
|
2208
|
} else {
|
|
2209
|
foreach $node ($results->get_nodelist) {
|
|
2210
|
my $samplingDescription = $node->textContent();
|
|
2211
|
$$templateVars{'samplingDescription'} = $samplingDescription;
|
|
2212
|
}
|
|
2213
|
}
|
|
2214
|
|
|
2215
|
dontOccur($doc, "//methodStep/citation", "methodStep/citation");
|
|
2216
|
dontOccur($doc, "//methodStep/protocol", "methodStep/protocol");
|
|
2217
|
dontOccur($doc, "//methodStep/instrumentation", "methodStep/instrumentation");
|
|
2218
|
dontOccur($doc, "//methodStep/software", "methodStep/software");
|
|
2219
|
dontOccur($doc, "//methodStep/subStep", "methodStep/subStep");
|
|
2220
|
dontOccur($doc, "//methodStep/dataSource", "methodStep/dataSource");
|
|
2221
|
dontOccur($doc, "//methods/qualityControl", "methods/qualityControl");
|
|
2222
|
|
|
2223
|
dontOccur($doc, "//methods/sampling/spatialSamplingUnits", "methods/sampling/spatialSamplingUnits");
|
|
2224
|
dontOccur($doc, "//methods/sampling/citation", "methods/sampling/citation");
|
|
2225
|
dontOccur($doc, "./pubPlace", "pubPlace");
|
|
2226
|
dontOccur($doc, "./project", "project");
|
|
2227
|
|
|
2228
|
dontOccur($doc, "./dataTable", "dataTable");
|
|
2229
|
dontOccur($doc, "./spatialRaster", "spatialRaster");
|
|
2230
|
dontOccur($doc, "./spatialVector", "spatialVector");
|
|
2231
|
dontOccur($doc, "./storedProcedure", "storedProcedure");
|
|
2232
|
dontOccur($doc, "./view", "view");
|
|
2233
|
dontOccur($doc, "./otherEntity", "otherEntity");
|
|
2234
|
dontOccur($doc, "./references", "references");
|
|
2235
|
|
|
2236
|
dontOccur($doc, "//citation", "citation");
|
|
2237
|
dontOccur($doc, "//software", "software");
|
|
2238
|
dontOccur($doc, "//protocol", "protocol");
|
|
2239
|
dontOccur($doc, "//additionalMetadata", "additionalMetadata");
|
|
2240
|
}
|
|
2241
|
|
|
2242
|
################################################################################
|
|
2243
|
#
|
|
2244
|
# Delete the eml file that has been requested for deletion.
|
|
2245
|
#
|
|
2246
|
################################################################################
|
|
2247
|
sub deleteData {
|
|
2248
|
my $deleteAll = shift;
|
|
2249
|
|
|
2250
|
# create metacat instance
|
|
2251
|
my $metacat;
|
|
2252
|
my $docid = $FORM::docid;
|
|
2253
|
|
|
2254
|
$metacat = Metacat->new();
|
|
2255
|
if ($metacat) {
|
|
2256
|
$metacat->set_options( metacatUrl => $metacatUrl );
|
|
2257
|
} else {
|
|
2258
|
#die "failed during metacat creation\n";
|
|
2259
|
push(@errorMessages, "Failed during metacat creation.");
|
|
2260
|
}
|
|
2261
|
|
|
2262
|
# Login to metacat
|
|
2263
|
my $userDN = $FORM::username;
|
|
2264
|
my $userOrg = $FORM::organization;
|
|
2265
|
my $userPass = $FORM::password;
|
|
2266
|
my $dname = "uid=$userDN,o=$userOrg,dc=ecoinformatics,dc=org";
|
|
2267
|
|
|
2268
|
my $errorMessage = "";
|
|
2269
|
my $response = $metacat->login($dname, $userPass);
|
|
2270
|
|
|
2271
|
if (! $response) {
|
|
2272
|
# Could not login
|
|
2273
|
push(@errorMessages, $metacat->getMessage());
|
|
2274
|
push(@errorMessages, "Failed during login.\n");
|
|
2275
|
|
|
2276
|
} else {
|
|
2277
|
#Able to login - try to delete the file
|
|
2278
|
|
|
2279
|
my $parser;
|
|
2280
|
my @fileArray;
|
|
2281
|
my $httpMessage;
|
|
2282
|
my $xmldoc;
|
|
2283
|
my $doc;
|
|
2284
|
my $pushDoc;
|
|
2285
|
my $alreadyInArray;
|
|
2286
|
my $findType;
|
|
2287
|
my $node;
|
|
2288
|
my $response;
|
|
2289
|
my $element;
|
|
2290
|
|
|
2291
|
push (@fileArray, $docid);
|
|
2292
|
$parser = XML::LibXML->new();
|
|
2293
|
|
|
2294
|
$httpMessage = $metacat->read($docid);
|
|
2295
|
$doc = $httpMessage->content();
|
|
2296
|
$xmldoc = $parser->parse_string($doc);
|
|
2297
|
|
|
2298
|
if ($xmldoc eq "") {
|
|
2299
|
$error ="Error in parsing the eml document";
|
|
2300
|
push(@errorMessages, $error);
|
|
2301
|
} else {
|
|
2302
|
|
|
2303
|
$findType = $xmldoc->findnodes('//dataset/identifier');
|
|
2304
|
if($findType->size() > 0){
|
|
2305
|
# This is a eml beta6 document
|
|
2306
|
# Delete the documents mentioned in triples also
|
|
2307
|
|
|
2308
|
$findType = $xmldoc->findnodes('//dataset/triple');
|
|
2309
|
if($findType->size() > 0){
|
|
2310
|
foreach $node ($findType->get_nodelist){
|
|
2311
|
$pushDoc = findValue($node, 'subject');
|
|
2312
|
|
|
2313
|
# If the file is already in the @fileArray then do not add it
|
|
2314
|
$alreadyInArray = 0;
|
|
2315
|
foreach $element (@fileArray){
|
|
2316
|
if($element eq $pushDoc){
|
|
2317
|
$alreadyInArray = 1;
|
|
2318
|
}
|
|
2319
|
}
|
|
2320
|
|
|
2321
|
if(!$alreadyInArray){
|
|
2322
|
# If not already in array then delete the file.
|
|
2323
|
push (@fileArray, $pushDoc);
|
|
2324
|
$response = $metacat->delete($pushDoc);
|
|
2325
|
|
|
2326
|
if (! $response) {
|
|
2327
|
# Could not delete
|
|
2328
|
#push(@errorMessages, $response);
|
|
2329
|
push(@errorMessages, $metacat->getMessage());
|
|
2330
|
push(@errorMessages, "Failed during deleting $pushDoc. Please check if you are authorized to delete this document.\n");
|
|
2331
|
}
|
|
2332
|
}
|
|
2333
|
}
|
|
2334
|
}
|
|
2335
|
}
|
|
2336
|
}
|
|
2337
|
|
|
2338
|
# Delete the main document.
|
|
2339
|
if($deleteAll){
|
|
2340
|
$response = $metacat->delete($docid);
|
|
2341
|
if (! $response) {
|
|
2342
|
# Could not delete
|
|
2343
|
#push(@errorMessages, $response);
|
|
2344
|
push(@errorMessages, $metacat->getMessage());
|
|
2345
|
push(@errorMessages, "Failed during deleting $docid. Please check if you are authorized to delete this document.\n");
|
|
2346
|
}
|
|
2347
|
}
|
|
2348
|
}
|
|
2349
|
|
|
2350
|
if (scalar(@errorMessages)) {
|
|
2351
|
# If any errors, print them in the response template
|
|
2352
|
$$templateVars{'status'} = 'failure';
|
|
2353
|
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
2354
|
$error = 1;
|
|
2355
|
}
|
|
2356
|
|
|
2357
|
# Process the response template
|
|
2358
|
if($deleteAll){
|
|
2359
|
|
|
2360
|
$$templateVars{'function'} = "deleted";
|
|
2361
|
$$templateVars{'section'} = "Deletion Status";
|
|
2362
|
$template->process( $responseTemplate, $templateVars);
|
|
2363
|
}
|
|
2364
|
}
|
|
2365
|
|
|
2366
|
|
|
2367
|
################################################################################
|
|
2368
|
#
|
|
2369
|
# Do data validation and send the data to confirm data template.
|
|
2370
|
#
|
|
2371
|
################################################################################
|
|
2372
|
sub toConfirmData{
|
|
2373
|
# Check if any invalid parameters
|
|
2374
|
|
|
2375
|
my $invalidParams;
|
|
2376
|
if (! $error) {
|
|
2377
|
$invalidParams = validateParameters(0);
|
|
2378
|
if (scalar(@$invalidParams)) {
|
|
2379
|
$$templateVars{'status'} = 'failure';
|
|
2380
|
$$templateVars{'invalidParams'} = $invalidParams;
|
|
2381
|
$error = 1;
|
|
2382
|
}
|
|
2383
|
}
|
|
2384
|
|
|
2385
|
|
|
2386
|
$$templateVars{'providerGivenName'} = $FORM::providerGivenName;
|
|
2387
|
$$templateVars{'providerSurName'} = $FORM::providerSurName;
|
|
2388
|
if($FORM::site eq "Select your station here."){
|
|
2389
|
$$templateVars{'site'} = "";
|
|
2390
|
}else{
|
|
2391
|
$$templateVars{'site'} = $FORM::site;
|
|
2392
|
}
|
|
2393
|
if($FORM::cfg eq "nceas"){
|
|
2394
|
$$templateVars{'wg'} = \@FORM::wg;
|
|
2395
|
}
|
|
2396
|
$$templateVars{'identifier'} = $FORM::identifier;
|
|
2397
|
$$templateVars{'title'} = $FORM::title;
|
|
2398
|
$$templateVars{'origNamefirst0'} = $FORM::origNamefirst0;
|
|
2399
|
$$templateVars{'origNamelast0'} = $FORM::origNamelast0;
|
|
2400
|
$$templateVars{'origNameOrg'} = $FORM::origNameOrg;
|
|
2401
|
# $$templateVars{'origRole0'} = $FORM::origRole0;
|
|
2402
|
$$templateVars{'origDelivery'} = $FORM::origDelivery;
|
|
2403
|
$$templateVars{'origCity'} = $FORM::origCity;
|
|
2404
|
if($FORM::origState eq "Select State Here."){
|
|
2405
|
$$templateVars{'origState'} = "";
|
|
2406
|
}else{
|
|
2407
|
$$templateVars{'origState'} = $FORM::origState;
|
|
2408
|
}
|
|
2409
|
$$templateVars{'origStateOther'} = $FORM::origStateOther;
|
|
2410
|
$$templateVars{'origZIP'} = $FORM::origZIP;
|
|
2411
|
$$templateVars{'origCountry'} = $FORM::origCountry;
|
|
2412
|
$$templateVars{'origPhone'} = $FORM::origPhone;
|
|
2413
|
$$templateVars{'origFAX'} = $FORM::origFAX;
|
|
2414
|
$$templateVars{'origEmail'} = $FORM::origEmail;
|
|
2415
|
$$templateVars{'useOrigAddress'} = $FORM::useOrigAddress;
|
|
2416
|
if($FORM::useOrigAddress eq "on"){
|
|
2417
|
$$templateVars{'origNamefirstContact'} = $FORM::origNamefirst0;
|
|
2418
|
$$templateVars{'origNamelastContact'} = $FORM::origNamelast0;
|
|
2419
|
$$templateVars{'origNameOrgContact'} = $FORM::origNameOrg;
|
|
2420
|
$$templateVars{'origDeliveryContact'} = $FORM::origDelivery;
|
|
2421
|
$$templateVars{'origCityContact'} = $FORM::origCity;
|
|
2422
|
if($FORM::origState eq "Select State Here."){
|
|
2423
|
$$templateVars{'origStateContact'} = "";
|
|
2424
|
}else{
|
|
2425
|
$$templateVars{'origStateContact'} = $FORM::origState;
|
|
2426
|
}
|
|
2427
|
$$templateVars{'origStateOtherContact'} = $FORM::origStateOther;
|
|
2428
|
$$templateVars{'origZIPContact'} = $FORM::origZIP;
|
|
2429
|
$$templateVars{'origCountryContact'} = $FORM::origCountry;
|
|
2430
|
$$templateVars{'origPhoneContact'} = $FORM::origPhone;
|
|
2431
|
$$templateVars{'origFAXContact'} = $FORM::origFAX;
|
|
2432
|
$$templateVars{'origEmailContact'} = $FORM::origEmail;
|
|
2433
|
}else{
|
|
2434
|
$$templateVars{'origNamefirstContact'} = $FORM::origNamefirstContact;
|
|
2435
|
$$templateVars{'origNamelastContact'} = $FORM::origNamelastContact;
|
|
2436
|
$$templateVars{'origNameOrgContact'} = $FORM::origNameOrgContact;
|
|
2437
|
$$templateVars{'origDeliveryContact'} = $FORM::origDeliveryContact;
|
|
2438
|
$$templateVars{'origCityContact'} = $FORM::origCityContact;
|
|
2439
|
if($FORM::origStateContact eq "Select State Here."){
|
|
2440
|
$$templateVars{'origStateContact'} = "";
|
|
2441
|
}else{
|
|
2442
|
$$templateVars{'origStateContact'} = $FORM::origStateContact;
|
|
2443
|
}
|
|
2444
|
$$templateVars{'origStateOtherContact'} = $FORM::origStateOtherContact;
|
|
2445
|
$$templateVars{'origZIPContact'} = $FORM::origZIPContact;
|
|
2446
|
$$templateVars{'origCountryContact'} = $FORM::origCountryContact;
|
|
2447
|
$$templateVars{'origPhoneContact'} = $FORM::origPhoneContact;
|
|
2448
|
$$templateVars{'origFAXContact'} = $FORM::origFAXContact;
|
|
2449
|
$$templateVars{'origEmailContact'} = $FORM::origEmailContact;
|
|
2450
|
}
|
|
2451
|
$$templateVars{'origNamefirst1'} = $FORM::origNamefirst1;
|
|
2452
|
$$templateVars{'origNamelast1'} = $FORM::origNamelast1;
|
|
2453
|
if($FORM::origNamefirst1 eq "" && $FORM::origNamelast1 eq ""){
|
|
2454
|
$$templateVars{'origRole1'} = "";
|
|
2455
|
}else{
|
|
2456
|
$$templateVars{'origRole1'} = $FORM::origRole1;
|
|
2457
|
}
|
|
2458
|
$$templateVars{'origNamefirst2'} = $FORM::origNamefirst2;
|
|
2459
|
$$templateVars{'origNamelast2'} = $FORM::origNamelast2;
|
|
2460
|
if($FORM::origNamefirst2 eq "" && $FORM::origNamelast2 eq ""){
|
|
2461
|
$$templateVars{'origRole2'} = "";
|
|
2462
|
}else{
|
|
2463
|
$$templateVars{'origRole2'} = $FORM::origRole2;
|
|
2464
|
}
|
|
2465
|
$$templateVars{'origNamefirst3'} = $FORM::origNamefirst3;
|
|
2466
|
$$templateVars{'origNamelast3'} = $FORM::origNamelast3;
|
|
2467
|
if($FORM::origNamefirst3 eq "" && $FORM::origNamelast3 eq ""){
|
|
2468
|
$$templateVars{'origRole3'} = "";
|
|
2469
|
}else{
|
|
2470
|
$$templateVars{'origRole3'} = $FORM::origRole3;
|
|
2471
|
}
|
|
2472
|
$$templateVars{'origNamefirst4'} = $FORM::origNamefirst4;
|
|
2473
|
$$templateVars{'origNamelast4'} = $FORM::origNamelast4;
|
|
2474
|
if($FORM::origNamefirst4 eq "" && $FORM::origNamelast4 eq ""){
|
|
2475
|
$$templateVars{'origRole4'} = "";
|
|
2476
|
}else{
|
|
2477
|
$$templateVars{'origRole4'} = $FORM::origRole4;
|
|
2478
|
}
|
|
2479
|
$$templateVars{'origNamefirst5'} = $FORM::origNamefirst5;
|
|
2480
|
$$templateVars{'origNamelast5'} = $FORM::origNamelast5;
|
|
2481
|
if($FORM::origNamefirst5 eq "" && $FORM::origNamelast5 eq ""){
|
|
2482
|
$$templateVars{'origRole5'} = "";
|
|
2483
|
}else{
|
|
2484
|
$$templateVars{'origRole5'} = $FORM::origRole5;
|
|
2485
|
}
|
|
2486
|
$$templateVars{'origNamefirst6'} = $FORM::origNamefirst6;
|
|
2487
|
$$templateVars{'origNamelast6'} = $FORM::origNamelast6;
|
|
2488
|
if($FORM::origNamefirst6 eq "" && $FORM::origNamelast6 eq ""){
|
|
2489
|
$$templateVars{'origRole6'} = "";
|
|
2490
|
}else{
|
|
2491
|
$$templateVars{'origRole6'} = $FORM::origRole6;
|
|
2492
|
}
|
|
2493
|
$$templateVars{'origNamefirst7'} = $FORM::origNamefirst7;
|
|
2494
|
$$templateVars{'origNamelast7'} = $FORM::origNamelast7;
|
|
2495
|
if($FORM::origNamefirst7 eq "" && $FORM::origNamelast7 eq ""){
|
|
2496
|
$$templateVars{'origRole7'} = "";
|
|
2497
|
}else{
|
|
2498
|
$$templateVars{'origRole7'} = $FORM::origRole7;
|
|
2499
|
}
|
|
2500
|
$$templateVars{'origNamefirst8'} = $FORM::origNamefirst8;
|
|
2501
|
$$templateVars{'origNamelast8'} = $FORM::origNamelast8;
|
|
2502
|
if($FORM::origNamefirst8 eq "" && $FORM::origNamelast8 eq ""){
|
|
2503
|
$$templateVars{'origRole8'} = "";
|
|
2504
|
}else{
|
|
2505
|
$$templateVars{'origRole8'} = $FORM::origRole8;
|
|
2506
|
}
|
|
2507
|
$$templateVars{'origNamefirst9'} = $FORM::origNamefirst9;
|
|
2508
|
$$templateVars{'origNamelast9'} = $FORM::origNamelast9;
|
|
2509
|
if($FORM::origNamefirst9 eq "" && $FORM::origNamelast9 eq ""){
|
|
2510
|
$$templateVars{'origRole9'} = "";
|
|
2511
|
}else{
|
|
2512
|
$$templateVars{'origRole9'} = $FORM::origRole9;
|
|
2513
|
}
|
|
2514
|
$$templateVars{'origNamefirst10'} = $FORM::origNamefirst10;
|
|
2515
|
$$templateVars{'origNamelast10'} = $FORM::origNamelast10;
|
|
2516
|
if($FORM::origNamefirst10 eq "" && $FORM::origNamelast10 eq ""){
|
|
2517
|
$$templateVars{'origRole10'} = "";
|
|
2518
|
}else{
|
|
2519
|
$$templateVars{'origRole10'} = $FORM::origRole10;
|
|
2520
|
}
|
|
2521
|
$$templateVars{'abstract'} = $FORM::abstract;
|
|
2522
|
$$templateVars{'keyCount'} = $FORM::keyCount;
|
|
2523
|
foreach my $kyd (param()) {
|
|
2524
|
if ($kyd =~ /keyword/) {
|
|
2525
|
my $keyIndex = $kyd;
|
|
2526
|
$keyIndex =~ s/keyword//; # get the index of the parameter 0, ..., 10
|
|
2527
|
my $keyType = "kwType".$keyIndex;
|
|
2528
|
my $keyTh = "kwTh".$keyIndex;
|
|
2529
|
if ( $keyIndex =~ /[0-9]/ ){
|
|
2530
|
if (hasContent(param($kyd)) && hasContent(param($keyType)) && hasContent(param($keyTh))) {
|
|
2531
|
debug("Registry processing keyword: $kyd = ".param($kyd)." $keyType = ".param($keyType)." $keyTh = ".param($keyTh));
|
|
2532
|
$$templateVars{$kyd} = param($kyd);
|
|
2533
|
$$templateVars{$keyType} = param($keyType);
|
|
2534
|
$$templateVars{$keyTh} = param($keyTh);
|
|
2535
|
}
|
|
2536
|
}
|
|
2537
|
}
|
|
2538
|
}
|
|
2539
|
$$templateVars{'addComments'} = $FORM::addComments;
|
|
2540
|
$$templateVars{'useConstraints'} = $FORM::useConstraints;
|
|
2541
|
$$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
|
|
2542
|
$$templateVars{'url'} = $FORM::url;
|
|
2543
|
if($FORM::dataMedium eq "Select type of medium here."){
|
|
2544
|
$$templateVars{'dataMedium'} = "";
|
|
2545
|
}else{
|
|
2546
|
$$templateVars{'dataMedium'} = $FORM::dataMedium;
|
|
2547
|
}
|
|
2548
|
$$templateVars{'dataMediumOther'} = $FORM::dataMediumOther;
|
|
2549
|
$$templateVars{'beginningYear'} = $FORM::beginningYear;
|
|
2550
|
$$templateVars{'beginningMonth'} = $FORM::beginningMonth;
|
|
2551
|
$$templateVars{'beginningDay'} = $FORM::beginningDay;
|
|
2552
|
$$templateVars{'endingYear'} = $FORM::endingYear;
|
|
2553
|
$$templateVars{'endingMonth'} = $FORM::endingMonth;
|
|
2554
|
$$templateVars{'endingDay'} = $FORM::endingDay;
|
|
2555
|
$$templateVars{'geogdesc'} = $FORM::geogdesc;
|
|
2556
|
$$templateVars{'useSiteCoord'} = $FORM::useSiteCoord;
|
|
2557
|
$$templateVars{'latDeg1'} = $FORM::latDeg1;
|
|
2558
|
$$templateVars{'latMin1'} = $FORM::latMin1;
|
|
2559
|
$$templateVars{'latSec1'} = $FORM::latSec1;
|
|
2560
|
$$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
|
|
2561
|
$$templateVars{'longDeg1'} = $FORM::longDeg1;
|
|
2562
|
$$templateVars{'longMin1'} = $FORM::longMin1;
|
|
2563
|
$$templateVars{'longSec1'} = $FORM::longSec1;
|
|
2564
|
$$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
|
|
2565
|
$$templateVars{'latDeg2'} = $FORM::latDeg2;
|
|
2566
|
$$templateVars{'latMin2'} = $FORM::latMin2;
|
|
2567
|
$$templateVars{'latSec2'} = $FORM::latSec2;
|
|
2568
|
$$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
|
|
2569
|
$$templateVars{'longDeg2'} = $FORM::longDeg2;
|
|
2570
|
$$templateVars{'longMin2'} = $FORM::longMin2;
|
|
2571
|
$$templateVars{'longSec2'} = $FORM::longSec2;
|
|
2572
|
$$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
|
|
2573
|
|
|
2574
|
$$templateVars{'taxaCount'} = $FORM::taxaCount;
|
|
2575
|
foreach my $trn (param()) {
|
|
2576
|
if ($trn =~ /taxonRankName/) {
|
|
2577
|
my $taxIndex = $trn;
|
|
2578
|
$taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
|
|
2579
|
my $trv = "taxonRankValue".$taxIndex;
|
|
2580
|
if ( $taxIndex =~ /[0-9]/ ){
|
|
2581
|
if (hasContent(param($trn)) && hasContent(param($trv))) {
|
|
2582
|
debug("Registry processing taxon: $trn = ".param($trn)." $trv = ".param($trv));
|
|
2583
|
$$templateVars{$trn} = param($trn);
|
|
2584
|
$$templateVars{$trv} = param($trv);
|
|
2585
|
}
|
|
2586
|
}
|
|
2587
|
}
|
|
2588
|
}
|
|
2589
|
$$templateVars{'taxaAuth'} = $FORM::taxaAuth;
|
|
2590
|
|
|
2591
|
$$templateVars{'methodTitle'} = $FORM::methodTitle;
|
|
2592
|
$$templateVars{'methodPara'} = \@FORM::methodPara;
|
|
2593
|
$$templateVars{'studyExtentDescription'} = $FORM::studyExtentDescription;
|
|
2594
|
$$templateVars{'samplingDescription'} = $FORM::samplingDescription;
|
|
2595
|
$$templateVars{'docid'} = $FORM::docid;
|
|
2596
|
|
|
2597
|
if (! $error) {
|
|
2598
|
# If no errors, then print out data in confirm Data template
|
|
2599
|
|
|
2600
|
$$templateVars{'section'} = "Confirm Data";
|
|
2601
|
$template->process( $confirmDataTemplate, $templateVars);
|
|
2602
|
|
|
2603
|
} else{
|
|
2604
|
# Errors from validation function. print the errors out using the response template
|
|
2605
|
if (scalar(@errorMessages)) {
|
|
2606
|
$$templateVars{'status'} = 'failure';
|
|
2607
|
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
2608
|
$error = 1;
|
|
2609
|
}
|
|
2610
|
# Create our HTML response and send it back
|
|
2611
|
$$templateVars{'function'} = "submitted";
|
|
2612
|
$$templateVars{'section'} = "Submission Status";
|
|
2613
|
$template->process( $responseTemplate, $templateVars);
|
|
2614
|
}
|
|
2615
|
}
|
|
2616
|
|
|
2617
|
|
|
2618
|
################################################################################
|
|
2619
|
#
|
|
2620
|
# From confirm Data template - user wants to make some changes.
|
|
2621
|
#
|
|
2622
|
################################################################################
|
|
2623
|
sub confirmDataToReEntryData{
|
|
2624
|
my @sortedSites;
|
|
2625
|
foreach my $site (sort @sitelist) {
|
|
2626
|
push(@sortedSites, $site);
|
|
2627
|
}
|
|
2628
|
|
|
2629
|
$$templateVars{'siteList'} = \@sortedSites;
|
|
2630
|
$$templateVars{'section'} = "Re-Entry Form";
|
|
2631
|
|
|
2632
|
$$templateVars{'providerGivenName'} = $FORM::providerGivenName;
|
|
2633
|
$$templateVars{'providerSurName'} = $FORM::providerSurName;
|
|
2634
|
$$templateVars{'site'} = $FORM::site;
|
|
2635
|
if ($FORM::cfg eq "nceas") {
|
|
2636
|
my $projects = getProjectList();
|
|
2637
|
$$templateVars{'projects'} = $projects;
|
|
2638
|
$$templateVars{'wg'} = \@FORM::wg;
|
|
2639
|
}
|
|
2640
|
$$templateVars{'identifier'} = $FORM::identifier;
|
|
2641
|
$$templateVars{'title'} = $FORM::title;
|
|
2642
|
$$templateVars{'origNamefirst0'} = $FORM::origNamefirst0;
|
|
2643
|
$$templateVars{'origNamelast0'} = $FORM::origNamelast0;
|
|
2644
|
$$templateVars{'origNameOrg'} = $FORM::origNameOrg;
|
|
2645
|
# $$templateVars{'origRole0'} = $FORM::origRole0;
|
|
2646
|
$$templateVars{'origDelivery'} = $FORM::origDelivery;
|
|
2647
|
$$templateVars{'origCity'} = $FORM::origCity;
|
|
2648
|
$$templateVars{'origState'} = $FORM::origState;
|
|
2649
|
$$templateVars{'origStateOther'} = $FORM::origStateOther;
|
|
2650
|
$$templateVars{'origZIP'} = $FORM::origZIP;
|
|
2651
|
$$templateVars{'origCountry'} = $FORM::origCountry;
|
|
2652
|
$$templateVars{'origPhone'} = $FORM::origPhone;
|
|
2653
|
$$templateVars{'origFAX'} = $FORM::origFAX;
|
|
2654
|
$$templateVars{'origEmail'} = $FORM::origEmail;
|
|
2655
|
if ($FORM::useSiteCoord ne "") {
|
|
2656
|
$$templateVars{'useOrigAddress'} = "CHECKED";
|
|
2657
|
}else{
|
|
2658
|
$$templateVars{'useOrigAddress'} = $FORM::useOrigAddress;
|
|
2659
|
}
|
|
2660
|
$$templateVars{'origNamefirstContact'} = $FORM::origNamefirstContact;
|
|
2661
|
$$templateVars{'origNamelastContact'} = $FORM::origNamelastContact;
|
|
2662
|
$$templateVars{'origNameOrgContact'} = $FORM::origNameOrgContact;
|
|
2663
|
$$templateVars{'origDeliveryContact'} = $FORM::origDeliveryContact;
|
|
2664
|
$$templateVars{'origCityContact'} = $FORM::origCityContact;
|
|
2665
|
$$templateVars{'origStateContact'} = $FORM::origStateContact;
|
|
2666
|
$$templateVars{'origStateOtherContact'} = $FORM::origStateOtherContact;
|
|
2667
|
$$templateVars{'origZIPContact'} = $FORM::origZIPContact;
|
|
2668
|
$$templateVars{'origCountryContact'} = $FORM::origCountryContact;
|
|
2669
|
$$templateVars{'origPhoneContact'} = $FORM::origPhoneContact;
|
|
2670
|
$$templateVars{'origFAXContact'} = $FORM::origFAXContact;
|
|
2671
|
$$templateVars{'origEmailContact'} = $FORM::origEmailContact;
|
|
2672
|
$$templateVars{'origNamefirst1'} = $FORM::origNamefirst1;
|
|
2673
|
$$templateVars{'origNamelast1'} = $FORM::origNamelast1;
|
|
2674
|
$$templateVars{'origRole1'} = $FORM::origRole1;
|
|
2675
|
$$templateVars{'origNamefirst2'} = $FORM::origNamefirst2;
|
|
2676
|
$$templateVars{'origNamelast2'} = $FORM::origNamelast2;
|
|
2677
|
$$templateVars{'origRole2'} = $FORM::origRole2;
|
|
2678
|
$$templateVars{'origNamefirst3'} = $FORM::origNamefirst3;
|
|
2679
|
$$templateVars{'origNamelast3'} = $FORM::origNamelast3;
|
|
2680
|
$$templateVars{'origRole3'} = $FORM::origRole3;
|
|
2681
|
$$templateVars{'origNamefirst4'} = $FORM::origNamefirst4;
|
|
2682
|
$$templateVars{'origNamelast4'} = $FORM::origNamelast4;
|
|
2683
|
$$templateVars{'origRole4'} = $FORM::origRole4;
|
|
2684
|
$$templateVars{'origNamefirst5'} = $FORM::origNamefirst5;
|
|
2685
|
$$templateVars{'origNamelast5'} = $FORM::origNamelast5;
|
|
2686
|
$$templateVars{'origRole5'} = $FORM::origRole5;
|
|
2687
|
$$templateVars{'origNamefirst6'} = $FORM::origNamefirst6;
|
|
2688
|
$$templateVars{'origNamelast6'} = $FORM::origNamelast6;
|
|
2689
|
$$templateVars{'origRole6'} = $FORM::origRole6;
|
|
2690
|
$$templateVars{'origNamefirst7'} = $FORM::origNamefirst7;
|
|
2691
|
$$templateVars{'origNamelast7'} = $FORM::origNamelast7;
|
|
2692
|
$$templateVars{'origRole7'} = $FORM::origRole7;
|
|
2693
|
$$templateVars{'origNamefirst8'} = $FORM::origNamefirst8;
|
|
2694
|
$$templateVars{'origNamelast8'} = $FORM::origNamelast8;
|
|
2695
|
$$templateVars{'origRole8'} = $FORM::origRole8;
|
|
2696
|
$$templateVars{'origNamefirst9'} = $FORM::origNamefirst9;
|
|
2697
|
$$templateVars{'origNamelast9'} = $FORM::origNamelast9;
|
|
2698
|
$$templateVars{'origRole9'} = $FORM::origRole9;
|
|
2699
|
$$templateVars{'origNamefirst10'} = $FORM::origNamefirst10;
|
|
2700
|
$$templateVars{'origNamelast10'} = $FORM::origNamelast10;
|
|
2701
|
$$templateVars{'origRole10'} = $FORM::origRole10;
|
|
2702
|
$$templateVars{'abstract'} = $FORM::abstract;
|
|
2703
|
$$templateVars{'keyCount'} = $FORM::keyCount;
|
|
2704
|
foreach my $kyd (param()) {
|
|
2705
|
if ($kyd =~ /keyword/) {
|
|
2706
|
my $keyIndex = $kyd;
|
|
2707
|
$keyIndex =~ s/keyword//; # get the index of the parameter 0, ..., 10
|
|
2708
|
my $keyType = "kwType".$keyIndex;
|
|
2709
|
my $keyTh = "kwTh".$keyIndex;
|
|
2710
|
if ( $keyIndex =~ /[0-9]/ ){
|
|
2711
|
if (hasContent(param($kyd)) && hasContent(param($keyType)) && hasContent(param($keyTh))) {
|
|
2712
|
debug("Registry processing keyword: $kyd = ".param($kyd)." $keyType = ".param($keyType)." $keyTh = ".param($keyTh));
|
|
2713
|
$$templateVars{$kyd} = param($kyd);
|
|
2714
|
$$templateVars{$keyType} = param($keyType);
|
|
2715
|
$$templateVars{$keyTh} = param($keyTh);
|
|
2716
|
}
|
|
2717
|
}
|
|
2718
|
}
|
|
2719
|
}
|
|
2720
|
|
|
2721
|
$$templateVars{'addComments'} = $FORM::addComments;
|
|
2722
|
$$templateVars{'useConstraints'} = $FORM::useConstraints;
|
|
2723
|
$$templateVars{'useConstraintsOther'} = $FORM::useConstraintsOther;
|
|
2724
|
$$templateVars{'url'} = $FORM::url;
|
|
2725
|
$$templateVars{'dataMedium'} = $FORM::dataMedium;
|
|
2726
|
$$templateVars{'dataMediumOther'} = $FORM::dataMediumOther;
|
|
2727
|
$$templateVars{'beginningYear'} = $FORM::beginningYear;
|
|
2728
|
$$templateVars{'beginningMonth'} = $FORM::beginningMonth;
|
|
2729
|
$$templateVars{'beginningDay'} = $FORM::beginningDay;
|
|
2730
|
$$templateVars{'endingYear'} = $FORM::endingYear;
|
|
2731
|
$$templateVars{'endingMonth'} = $FORM::endingMonth;
|
|
2732
|
$$templateVars{'endingDay'} = $FORM::endingDay;
|
|
2733
|
$$templateVars{'geogdesc'} = $FORM::geogdesc;
|
|
2734
|
if($FORM::useSiteCoord ne ""){
|
|
2735
|
$$templateVars{'useSiteCoord'} = "CHECKED";
|
|
2736
|
}else{
|
|
2737
|
$$templateVars{'useSiteCoord'} = "";
|
|
2738
|
}
|
|
2739
|
$$templateVars{'latDeg1'} = $FORM::latDeg1;
|
|
2740
|
$$templateVars{'latMin1'} = $FORM::latMin1;
|
|
2741
|
$$templateVars{'latSec1'} = $FORM::latSec1;
|
|
2742
|
$$templateVars{'hemisphLat1'} = $FORM::hemisphLat1;
|
|
2743
|
$$templateVars{'longDeg1'} = $FORM::longDeg1;
|
|
2744
|
$$templateVars{'longMin1'} = $FORM::longMin1;
|
|
2745
|
$$templateVars{'longSec1'} = $FORM::longSec1;
|
|
2746
|
$$templateVars{'hemisphLong1'} = $FORM::hemisphLong1;
|
|
2747
|
$$templateVars{'latDeg2'} = $FORM::latDeg2;
|
|
2748
|
$$templateVars{'latMin2'} = $FORM::latMin2;
|
|
2749
|
$$templateVars{'latSec2'} = $FORM::latSec2;
|
|
2750
|
$$templateVars{'hemisphLat2'} = $FORM::hemisphLat2;
|
|
2751
|
$$templateVars{'longDeg2'} = $FORM::longDeg2;
|
|
2752
|
$$templateVars{'longMin2'} = $FORM::longMin2;
|
|
2753
|
$$templateVars{'longSec2'} = $FORM::longSec2;
|
|
2754
|
$$templateVars{'hemisphLong2'} = $FORM::hemisphLong2;
|
|
2755
|
$$templateVars{'taxaCount'} = $FORM::taxaCount;
|
|
2756
|
foreach my $trn (param()) {
|
|
2757
|
if ($trn =~ /taxonRankName/) {
|
|
2758
|
my $taxIndex = $trn;
|
|
2759
|
$taxIndex =~ s/taxonRankName//; # get the index of the parameter 0, ..., 10
|
|
2760
|
my $trv = "taxonRankValue".$taxIndex;
|
|
2761
|
if ( $taxIndex =~ /[0-9]/ ){
|
|
2762
|
if (hasContent(param($trn)) && hasContent(param($trv))) {
|
|
2763
|
debug("Registry processing taxon: $trn = ".param($trn)." $trv = ".param($trv));
|
|
2764
|
$$templateVars{$trn} = param($trn);
|
|
2765
|
$$templateVars{$trv} = param($trv);
|
|
2766
|
}
|
|
2767
|
}
|
|
2768
|
}
|
|
2769
|
}
|
|
2770
|
$$templateVars{'taxaAuth'} = $FORM::taxaAuth;
|
|
2771
|
$$templateVars{'methodTitle'} = $FORM::methodTitle;
|
|
2772
|
$$templateVars{'methodPara'} = \@FORM::methodPara;
|
|
2773
|
$$templateVars{'studyExtentDescription'} = $FORM::studyExtentDescription;
|
|
2774
|
$$templateVars{'samplingDescription'} = $FORM::samplingDescription;
|
|
2775
|
$$templateVars{'docid'} = $FORM::docid;
|
|
2776
|
|
|
2777
|
$$templateVars{'form'} = 're_entry';
|
|
2778
|
$template->process( $entryFormTemplate, $templateVars);
|
|
2779
|
}
|
|
2780
|
|
|
2781
|
|
|
2782
|
################################################################################
|
|
2783
|
#
|
|
2784
|
# check if there is multiple occurence of the given tag and find its value.
|
|
2785
|
#
|
|
2786
|
################################################################################
|
|
2787
|
|
|
2788
|
sub findValue {
|
|
2789
|
my $node = shift;
|
|
2790
|
my $value = shift;
|
|
2791
|
my $result;
|
|
2792
|
my $tempNode;
|
|
2793
|
|
|
2794
|
$result = $node->findnodes("./$value");
|
|
2795
|
if ($result->size > 1) {
|
|
2796
|
errMoreThanOne("$value");
|
|
2797
|
} else {
|
|
2798
|
foreach $tempNode ($result->get_nodelist){
|
|
2799
|
#print $tempNode->nodeName().":".$tempNode->textContent();
|
|
2800
|
#print "\n";
|
|
2801
|
return $tempNode->textContent();
|
|
2802
|
}
|
|
2803
|
}
|
|
2804
|
}
|
|
2805
|
|
|
2806
|
|
|
2807
|
################################################################################
|
|
2808
|
#
|
|
2809
|
# check if given tags has any children. if not return the value
|
|
2810
|
#
|
|
2811
|
################################################################################
|
|
2812
|
sub findValueNoChild {
|
|
2813
|
my $node = shift;
|
|
2814
|
my $value = shift;
|
|
2815
|
my $tempNode;
|
|
2816
|
my $childNodes;
|
|
2817
|
my $result;
|
|
2818
|
my $error;
|
|
2819
|
|
|
2820
|
$result = $node->findnodes("./$value");
|
|
2821
|
if($result->size > 1){
|
|
2822
|
errMoreThanOne("$value");
|
|
2823
|
} else {
|
|
2824
|
foreach $tempNode ($result->get_nodelist) {
|
|
2825
|
$childNodes = $tempNode->childNodes;
|
|
2826
|
if ($childNodes->size() > 1) {
|
|
2827
|
$error ="The tag $value has children which cannot be shown using the form. Please use Morpho to edit this document";
|
|
2828
|
push(@errorMessages, $error);
|
|
2829
|
#if ($DEBUG == 1){ print $error."\n";}
|
|
2830
|
} else {
|
|
2831
|
#print $tempNode->nodeName().":".$tempNode->textContent();
|
|
2832
|
#print "\n";
|
|
2833
|
return $tempNode->textContent();
|
|
2834
|
}
|
|
2835
|
}
|
|
2836
|
}
|
|
2837
|
}
|
|
2838
|
|
|
2839
|
|
|
2840
|
################################################################################
|
|
2841
|
#
|
|
2842
|
# check if given tags are children of given node.
|
|
2843
|
#
|
|
2844
|
################################################################################
|
|
2845
|
sub dontOccur {
|
|
2846
|
my $node = shift;
|
|
2847
|
my $value = shift;
|
|
2848
|
my $errVal = shift;
|
|
2849
|
|
|
2850
|
my $result = $node->findnodes("$value");
|
|
2851
|
if($result->size > 0){
|
|
2852
|
$error ="One of the following tags found: $errVal. Please use Morpho to edit this document";
|
|
2853
|
push(@errorMessages, $error."\n");
|
|
2854
|
#if ($DEBUG == 1){ print $error;}
|
|
2855
|
}
|
|
2856
|
}
|
|
2857
|
|
|
2858
|
|
|
2859
|
################################################################################
|
|
2860
|
#
|
|
2861
|
# print out error for more than one occurence of a given tag
|
|
2862
|
#
|
|
2863
|
################################################################################
|
|
2864
|
sub errMoreThanOne {
|
|
2865
|
my $value = shift;
|
|
2866
|
my $error ="More than one occurence of the tag $value found. Please use Morpho to edit this document";
|
|
2867
|
push(@errorMessages, $error."\n");
|
|
2868
|
# if ($DEBUG == 1){ print $error;}
|
|
2869
|
}
|
|
2870
|
|
|
2871
|
|
|
2872
|
################################################################################
|
|
2873
|
#
|
|
2874
|
# print out error for more than given number of occurences of a given tag
|
|
2875
|
#
|
|
2876
|
################################################################################
|
|
2877
|
sub errMoreThanN {
|
|
2878
|
my $value = shift;
|
|
2879
|
my $error ="More occurences of the tag $value found than that can be shown in the form. Please use Morpho to edit this document";
|
|
2880
|
push(@errorMessages, $error);
|
|
2881
|
#if ($DEBUG == 1){ print $error."\n";}
|
|
2882
|
}
|
|
2883
|
|
|
2884
|
|
|
2885
|
################################################################################
|
|
2886
|
#
|
|
2887
|
# convert coord to degrees, minutes and seconds form.
|
|
2888
|
#
|
|
2889
|
################################################################################
|
|
2890
|
#sub convertCoord {
|
|
2891
|
# my $wx = shift;
|
|
2892
|
# print $deg." ".$min." ".$sec;
|
|
2893
|
# print "\n";
|
|
2894
|
#}
|
|
2895
|
|
|
2896
|
|
|
2897
|
################################################################################
|
|
2898
|
#
|
|
2899
|
# print debugging messages to stderr
|
|
2900
|
#
|
|
2901
|
################################################################################
|
|
2902
|
sub debug {
|
|
2903
|
my $msg = shift;
|
|
2904
|
|
|
2905
|
if ($debug) {
|
|
2906
|
print STDERR "$msg\n";
|
|
2907
|
}
|
|
2908
|
}
|
|
2909
|
|
|
2910
|
################################################################################
|
|
2911
|
#
|
|
2912
|
# get the list of projects
|
|
2913
|
#
|
|
2914
|
################################################################################
|
|
2915
|
sub getProjectList {
|
|
2916
|
|
|
2917
|
use NCEAS::AdminDB;
|
|
2918
|
my $admindb = NCEAS::AdminDB->new();
|
|
2919
|
$admindb->connect($nceas_db, $nceas_db_user, $nceas_db_password);
|
|
2920
|
my $projects = $admindb->getProjects();
|
|
2921
|
#my $projects = getTestProjectList();
|
|
2922
|
return $projects;
|
|
2923
|
}
|
|
2924
|
|
|
2925
|
################################################################################
|
|
2926
|
#
|
|
2927
|
# get a test list of projects for use only in testing where the NCEAS
|
|
2928
|
# admin db is not available.
|
|
2929
|
#
|
|
2930
|
################################################################################
|
|
2931
|
sub getTestProjectList {
|
|
2932
|
# This block is for testing only! Remove for production use
|
|
2933
|
my @row1;
|
|
2934
|
$row1[0] = 6000; $row1[1] = 'Andelman'; $row1[2] = 'Sandy'; $row1[3] = 'The very long and windy path to an apparent ecological conclusion: statistics lie';
|
|
2935
|
my @row2;
|
|
2936
|
$row2[0] = 7000; $row2[1] = 'Bascompte'; $row2[2] = 'Jordi'; $row2[3] = 'Postdoctoral Fellow';
|
|
2937
|
my @row3;
|
|
2938
|
$row3[0] = 7001; $row3[1] = 'Hackett'; $row3[2] = 'Edward'; $row3[3] = 'Sociology rules the world';
|
|
2939
|
my @row4;
|
|
2940
|
$row4[0] = 7002; $row4[1] = 'Jones'; $row4[2] = 'Matthew'; $row4[3] = 'Informatics rules the world';
|
|
2941
|
my @row5;
|
|
2942
|
$row5[0] = 7003; $row5[1] = 'Schildhauer'; $row5[2] = 'Mark'; $row5[3] = 'Excel rocks my world, assuming a, b, and c';
|
|
2943
|
my @row6;
|
|
2944
|
$row6[0] = 7004; $row6[1] = 'Rogers'; $row6[2] = 'Bill'; $row6[3] = 'Graduate Intern';
|
|
2945
|
my @row7;
|
|
2946
|
$row7[0] = 7005; $row7[1] = 'Zedfried'; $row7[2] = 'Karl'; $row7[3] = 'A multivariate analysis of thing that go bump in the night';
|
|
2947
|
my @projects;
|
|
2948
|
$projects[0] = \@row1;
|
|
2949
|
$projects[1] = \@row2;
|
|
2950
|
$projects[2] = \@row3;
|
|
2951
|
$projects[3] = \@row4;
|
|
2952
|
$projects[4] = \@row5;
|
|
2953
|
$projects[5] = \@row6;
|
|
2954
|
$projects[6] = \@row7;
|
|
2955
|
return \@projects;
|
|
2956
|
}
|