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Revision 4080

Added by daigle over 16 years ago

Merge 1.9 changes into Head

View differences:

register-dataset.cgi
30 30

  
31 31
use Metacat;
32 32
use AppConfig qw(:expand :argcount);
33
use Config::Properties;
33 34
use XML::LibXML;
34 35
use XML::LibXSLT;
35 36
use Template;
......
42 43
use strict;
43 44

  
44 45
# Global configuration paramters
45
#my $cfgdir = "/usr/local/devtools/tomcat/webapps/knb/style/skins";
46
my $cfgdir = "@install-dir@@style-skins-relpath@";
47
my $tmpdir = "@temp-dir@";
48
my $templatesdir = "@install-dir@@style-common-relpath@/templates";
46
my $cgiUrl = $ENV{'SCRIPT_FILENAME'};
47
my $workingDirectory = dirname($cgiUrl);
48
my $metacatProps = "${workingDirectory}/../WEB-INF/metacat.properties";
49
my $properties = new Config::Properties();
50
unless (open (METACAT_PROPERTIES, $metacatProps)) {
51
    print "Content-type: text/html\n\n";
52
    print "Unable to locate Metacat properties. Working directory is set as '$workingDirectory', is this correct?";
53
    exit(0);
54
}
55

  
56
$properties->load(*METACAT_PROPERTIES);
57

  
58
# local directory configuration
59
my $configDir = $properties->getProperty('config-dir'); # skins directory
60
my $tmpDir = $properties->getProperty('temp-dir');
61
my $xslConvDir = "$configDir/lib/style";
62

  
63
# url configuration
64
my $metacatUrl = $properties->getProperty('metacatUrl');
65

  
49 66
my $now = time;
50 67
my $xslConvDir = "$cfgdir/lib/style/";
51 68

  
......
57 74
my $error = 0;
58 75
my @errorMessages;
59 76

  
60
# create a new AppConfig object and load our config parameters
61
# note that this requires the form submission to have a "cfg" paramter
62
# to determine which config file to load
63
my $config = AppConfig->new({
64
    GLOBAL => { ARGCOUNT => ARGCOUNT_ONE, } });
65

  
66
$config->define("metacatUrl");
67
$config->define("username");
68
$config->define("password");
69
$config->define("ldapUrl");
70
$config->define("defaultScope");
71
$config->define("organization");
72
$config->define("orgabbrev");
73
$config->define("orgurl");
74
$config->define("accesspubid");
75
$config->define("accesssysid");
76
$config->define("datasetpubid");
77
$config->define("datasetsysid");
78
$config->define("showSiteList", { DEFAULT => 'true'} );
79
$config->define("lsite", { DEFAULT => 'station'} );
80
$config->define("usite", { DEFAULT => 'Station'} );
81
$config->define("showWgList", { DEFAULT => 'true'} );
82
$config->define("showOrganization", { DEFAULT => 'true'} );
83
$config->define("hasKeyword", { DEFAULT => 'true'} );
84
$config->define("hasTemporal", { DEFAULT => 'true'} );
85
$config->define("hasSpatial", { DEFAULT => 'true'} );
86
$config->define("hasTaxonomic", { DEFAULT => 'true'} );
87
$config->define("hasMethod", { DEFAULT => 'true'} );
88
$config->define("hasUpload", { DEFAULT => 'false'} );
89
$config->define("temporalRequired", { DEFAULT => 'true'} );
90
$config->define("spatialRequired", { DEFAULT => 'true'} );
91
$config->define("contactEmailAddressRequired", { DEFAULT => 'false'} );
92
$config->define("publicReadable", { DEFAULT => 'true'} );
93
$config->define("adminIsDocOwner", { DEFAULT => 'false'} );
94
$config->define("moderators", { DEFAULT => ''} );
95
$config->define("mailhost");
96
$config->define("sender");
97
$config->define("recipient");
98
$config->define("adminname");
99
if ($FORM::cfg eq 'nceas') {
100
    $config->define("nceas_db");
101
    $config->define("nceas_db_user");
102
    $config->define("nceas_db_password");
103
}
104
$config->define("responseTemplate", { DEFAULT => 'crap.tmpl'} );
105
$config->define("entryFormTemplate", { DEFAULT => 'crap.tmpl'} );
106
$config->define("guideTemplate", { DEFAULT => 'crap.tmpl'} );
107
$config->define("loginFormTemplate", { DEFAULT => 'loginForm.tmpl'} );
108
$config->define("confirmDataTemplate", { DEFAULT => 'crap.tmpl'} );
109
$config->define("deleteDataTemplate", { DEFAULT => 'crap.tmpl'} );
110
$config->define("modEmailNotificationTemplate", { DEFAULT => 'crap.tmpl'} );
111
$config->define("modResultTemplate", { DEFAULT => 'crap.tmpl'} );
112
$config->define("getReviewsTemplate", { DEFAULT => 'crap.tmpl'} );
113
$config->define("debug", { DEFAULT => '0'} );
114
$config->define("lat", { ARGCOUNT => ARGCOUNT_HASH} );
115
$config->define("lon", { ARGCOUNT => ARGCOUNT_HASH} );
116

  
117

  
77
my $skinProperties = new Config::Properties();
118 78
if (! hasContent($FORM::cfg)) {
119 79
    $error = "Application misconfigured.  Please contact the administrator.";
120 80
    push(@errorMessages, $error);
121 81
} else {
122
    my $cfgfile = $cfgdir . "/" . $FORM::cfg . "/" . $FORM::cfg . ".cfg";
123
    $config->file($cfgfile);
82
    my $skinProps = "$configDir/$FORM::cfg/$FORM::cfg.properties";
83
    unless (open (SKIN_PROPERTIES, $skinProps)) {
84
        print "Content-type: text/html\n\n";
85
        print "Unable to locate skin properties at $skinProps.  Is this path correct?";
86
        exit(0);
87
    }
88
    $skinProperties->load(*SKIN_PROPERTIES);
124 89
}
125 90

  
126
my $metacatUrl = $config->metacatUrl();
127
my $username = $config->username();
128
my $password = $config->password();
129
my $ldapUrl = $config->ldapUrl();
130
my $defaultScope = $config->defaultScope();
131
my $organization = $config->organization();
132
my $orgabbrev = $config->orgabbrev();
133
my $orgurl = $config->orgurl();
134
my $orgfilter = $organization;
135
      $orgfilter =~ s/ /%20/g;
136
my $responseTemplate = $config->responseTemplate();
137
my $entryFormTemplate = $config->entryFormTemplate();
138
my $deleteDataTemplate = $config->deleteDataTemplate();
139
my $guideTemplate = $config->guideTemplate();
140
my $loginFormTemplate = $config->loginFormTemplate();
141
my $confirmDataTemplate = $config->confirmDataTemplate();
142
my $modEmailNotificationTemplate = $config->modEmailNotificationTemplate();
143
my $modResultTemplate = $config->modResultTemplate();
144
my $getReviewsTemplate = $config->getReviewsTemplate();
145
my $accesspubid = $config->accesspubid();
146
my $accesssysid = $config->accesssysid();
147
my $datasetpubid = $config->datasetpubid();
148
my $datasetsysid = $config->datasetsysid();
149
my $showSiteList = $config->showSiteList();
150
my $lsite = $config->lsite();
151
my $usite = $config->usite();
152
my $showWgList = $config->showWgList();
153
my $showOrganization = $config->showOrganization();
154
my $hasKeyword = $config->hasKeyword();
155
my $hasTemporal = $config->hasTemporal();
156
my $hasSpatial = $config->hasSpatial();
157
my $hasTaxonomic = $config->hasTaxonomic();
158
my $hasMethod = $config->hasMethod();
159
my $hasUpload = $config->hasUpload();
160
my $temporalRequired = $config->temporalRequired();
161
my $spatialRequired = $config->spatialRequired();
162
my $contactEmailAddressRequired = $config->contactEmailAddressRequired();
163
my $publicReadable = $config->publicReadable();
164
my $adminIsDocOwner = $config->adminIsDocOwner();
165
my $moderators = $config->moderators();
166
my $mailhost = $config->mailhost();
167
my $sender = $config->sender();
168
my $recipient = $config->recipient();
169
my $adminname = $config->adminname();
170
my $nceas_db;
171
my $nceas_db_user;
172
my $nceas_db_password;
173
if ($FORM::cfg eq 'nceas') {
174
    $nceas_db = $config->nceas_db();
175
    $nceas_db_user = $config->nceas_db_user();
176
    $nceas_db_password = $config->nceas_db_password();
91
# replacements for appconfig values using properties
92
my $metacatUrl = $properties->getProperty('metacatUrl');
93
my $moderators = $properties->getProperty('ldap.moderators');
94
my $config = $properties->splitToTree(qr/\./, 'registry.config');
95
my $templates = $properties->splitToTree(qr/\./, 'registry.templates');
96
my $modules = $properties->splitToTree(qr/\./, 'registry.modules');
97
my $required = $properties->splitToTree(qr/\./, 'registry.required');
98
my $spatial = $properties->splitToTree(qr/\./, 'registry.spatial');
99

  
100
my $metacatUrl = $properties->getProperty('metacatUrl');
101
my $username = $config->{'username'};
102
my $password = $config->{'password'};
103

  
104
# XXX replace these with the proper array versions once the templates work correctly
105
my $showWgList = $required->{'wgList'};
106
my $showOrganization = $required->{'organization'};
107
my $hasKeyword = $required->{'keyword'};
108
my $hasTemporal = $required->{'temporal'};
109
my $hasSpatial = $required->{'spatial'};
110
my $hasTaxonomic = $required->{'taxonomic'};
111
my $hasMethod = $required->{'method'};
112
my $hasUpload = $required->{'upload'};
113

  
114
# contains sender, recipient, admin, mailhost
115
my $email = $properties->splitToTree(qr/\./, 'email');
116

  
117
# set stderr printing if configured
118
my $debug_enabled = $config->{'debug'};
119
if ($FORM::debug) {
120
    $debug_enabled = $FORM::debug;
177 121
}
178
my $debug = $config->debug();
122
my $lat = $config->get('lat');
123
my $lon = $config->get('lon');
124

  
125
my $metacatUrl = $properties->getProperty('metacatUrl');
126
my $username = $config->{'username'};
127
my $password = $config->{'password'};
128

  
129
# TODO SCW replace these with the proper array versions once the templates work correctly
130
my $showWgList = $required->{'wgList'};
131
my $showOrganization = $required->{'organization'};
132
my $hasKeyword = $required->{'keyword'};
133
my $hasTemporal = $required->{'temporal'};
134
my $hasSpatial = $required->{'spatial'};
135
my $hasTaxonomic = $required->{'taxonomic'};
136
my $hasMethod = $required->{'method'};
137
my $hasUpload = $required->{'upload'};
138

  
139
# contains sender, recipient, admin, mailhost
140
my $email = $properties->splitToTree(qr/\./, 'email');
141

  
142
# set stderr printing if configured
143
my $debug_enabled = $config->{'debug'};
179 144
if ($FORM::debug) {
180
    $debug = $FORM::debug;
145
    $debug_enabled = $FORM::debug;
181 146
}
182 147

  
183
# 1.8.1 temporary baseUrl fix
184
my $baseUrl = $metacatUrl;
185
$baseUrl =~ s/metacat$//;
148
# populate db parameters for NCEAS AdminDB
149
my $database = '';
150
if ($FORM::cfg eq 'nceas') {
151
    my $database = $properties->splitToTree(qr/\./, 'registry.db');
152
}
186 153

  
187
my $lat = $config->get('lat');
188
my $lon = $config->get('lon');
189

  
190
# Convert the lat and lon configs into usable data structures
154
#Convert the lat and lon configs into usable data structures
191 155
my @sitelist;
192 156
my %siteLatDMS;
193 157
my %siteLongDMS;
194
foreach my $newsite (keys %$lat) {
195
    my ($latd, $latm, $lats, $latdir) = split(':', $lat->{$newsite});
196
    my ($lond, $lonm, $lons, $londir) = split(':', $lon->{$newsite});
197
    push(@sitelist, $newsite);
198
    $siteLatDMS{$newsite} = [ $latd, $latm, $lats, $latdir ];
199
    $siteLongDMS{$newsite} = [ $lond, $lonm, $lons, $londir ];
158
while ( my ($key, $value) = each (%$spatial)) {
159
    my ($name, $lon, $lat) = split(",", $value);
160
    my ($latd, $latm, $lats, $latdir) = split(':', $lat);
161
    my ($lond, $lonm, $lons, $londir) = split(':', $lon);
162
    push(@sitelist, $name);
163
    $siteLatDMS{$name} = [ $latd, $latm, $lats, $latdir ];
164
    $siteLongDMS{$name} = [ $lond, $lonm, $lons, $londir ];
200 165
}
201 166

  
202 167
# set some configuration options for the template object
203 168
my $ttConfig = {
204
             INCLUDE_PATH => $templatesdir, 
169
             INCLUDE_PATH => $properties->getProperty('templates-dir'),
205 170
             INTERPOLATE  => 0,                    
206 171
             POST_CHOMP   => 1,
207 172
             #DEBUG        => 'all',
......
211 176
my $template = Template->new($ttConfig) || die $Template::ERROR, "\n";
212 177

  
213 178
# Set up the template information that is common to all forms
179
$$templateVars{'styleSkinsPath'} = $properties->getProperty('style-skins-path');
180
$$templateVars{'styleCommonPath'} = $properties->getProperty('style-common-path');
181
$$templateVars{'servletPath'} = $properties->getProperty('servlet-path');
182
$$templateVars{'metacatUrl'} = $metacatUrl;
183
$$templateVars{'cgiPrefix'} = $properties->getProperty('cgi-prefix');
214 184
$$templateVars{'cfg'} = $FORM::cfg;
215
$$templateVars{'recipient'} = $recipient;
216
$$templateVars{'adminname'} = $adminname;
217
$$templateVars{'organization'} = $organization;
218
$$templateVars{'orgabbrev'} = $orgabbrev;
219
$$templateVars{'orgurl'} = $orgurl;
220
$$templateVars{'orgfilter'} = $orgfilter;
221
$$templateVars{'baseUrl'} = $baseUrl;
185
$$templateVars{'email'} = $email;
186
$$templateVars{'templates'} = $templates;
187
$$templateVars{'required'} = $required;
188
$$templateVars{'config'} = $config;
222 189

  
223 190
debug("Registry: Initialized -- stage set: $FORM::stage");
224 191

  
......
227 194
    debug("Registry: No configuration set.");
228 195
    print "Content-type: text/html\n\n";
229 196
    $$templateVars{'message'} = 'Error: The registry requires a skin name to continue.';
230
    $template->process( $loginFormTemplate, $templateVars);
197
    $template->process( $templates->{'login'}, $templateVars);
231 198
    exit(0);
232 199
}
233 200

  
......
240 207
    exit(0);
241 208
}
242 209

  
243
# FIXME: temporary 1.8.1 fix to prevent missing upload directory from causing errors
244
if (not -W $tmpdir) {
245
    debug("Registry Error: Can't write files to $tmpdir, disabling file uploads");
246
    #push(@errorMessages, "Unable to write files to temporary folder. Email sysadmin.");
247
    $hasUpload = 'false';
248
}
249

  
250 210
# Process the form based on stage parameter. 
251 211
if ($FORM::stage =~ "loginform") {
252 212
    print "Content-type: text/html\n\n";
......
259 219

  
260 220
    if ( $session->is_empty ) {
261 221
	# no session found ... redirect to login page template
262
        $template->process( $loginFormTemplate, $templateVars);
222
        $template->process( $templates->{'login'}, $templateVars);
263 223
    } else {
264 224
	# session found ... delete the session....
265 225
	$session->delete();
266
	$template->process( $loginFormTemplate, $templateVars);
226
	$template->process( $templates->{'login'}, $templateVars);
267 227
    }
268 228
	exit(0);
269 229
} elsif ($FORM::stage =~ "logout") {
......
294 254
if ($FORM::stage =~ "guide") {
295 255
    # Send back the information on how to fill the form
296 256
    $$templateVars{'section'} = "Guide on How to Complete Registry Entries";
297
    $template->process( $guideTemplate, $templateVars);
257
    $template->process( $template->{'guide'}, $templateVars);
298 258
    exit(0);
299 259

  
300 260
} elsif ($FORM::stage =~ "insert") {
......
316 276
    if ( $session->is_empty ) {
317 277
        # no session found ... redirect to login page template
318 278
    	$$templateVars{'message'} = 'You must login to modify your dataset.';
319
        $template->process( $loginFormTemplate, $templateVars);
279
        $template->process( $templates->{'login'}, $templateVars);
320 280
    } else {
321 281
    	# Show the form will all the values filled in.
322 282
    	my @sortedSites;
......
340 300
    } else {
341 301
    $$templateVars{'status'} = "Cancel";
342 302
    $$templateVars{'function'} = "cancel";
343
    $template->process( $responseTemplate, $templateVars);
303
    $template->process( $templates->{'response'}, $templateVars);
344 304
    exit(0);
345 305
    }
346 306

  
......
348 308
    # Deletion of a file has been requested. 
349 309
    # Ask for username and password using deleteDataForm
350 310
    $$templateVars{'docid'} = $FORM::docid;
351
    $template->process( $deleteDataTemplate, $templateVars);
311
    $template->process( $templates->{'deleteData'}, $templateVars);
352 312
    exit(0);
353 313

  
354 314
}elsif ($FORM::stage !~ "confirmed") {
......
360 320
        # no session found ... redirect to login page template
361 321
        $$templateVars{'showInstructions'} = 'true';
362 322
        $$templateVars{'message'} = 'You must login to register your dataset.';
363
        $template->process( $loginFormTemplate, $templateVars);
323
        $template->process( $templates->{'login'}, $templateVars);
364 324
    } else {
365 325

  
366 326
    	# Hence, send back entry form for entry of data.  
......
369 329
    	foreach my $site (sort @sitelist) {
370 330
        	push(@sortedSites, $site);
371 331
    	}
372
    
332

  
373 333
    	if ($FORM::cfg eq 'nceas') {
374
        	my $projects = getProjectList();
334
        	my $projects = getProjectList($database);
375 335
        	$$templateVars{'projects'} = $projects;
376 336
        	$$templateVars{'wg'} = \@FORM::wg;
377 337
    	}
378 338

  
379
    	$$templateVars{'showSiteList'} = $showSiteList;
380
    	$$templateVars{'lsite'} = $lsite;
381
    	$$templateVars{'usite'} = $usite;
382
    	$$templateVars{'showWgList'} = $showWgList;
383
    	$$templateVars{'showOrganization'} = $showOrganization;
384
    	$$templateVars{'hasKeyword'} = $hasKeyword;
385
    	$$templateVars{'hasTemporal'} = $hasTemporal;
386
    	$$templateVars{'hasSpatial'} = $hasSpatial;
387
    	$$templateVars{'hasTaxonomic'} = $hasTaxonomic;
388
    	$$templateVars{'hasMethod'} = $hasMethod;
389
      $$templateVars{'hasUpload'} = $hasUpload;
390
    	$$templateVars{'temporalRequired'} = $temporalRequired;
391
    	$$templateVars{'spatialRequired'} = $spatialRequired;
392
    	$$templateVars{'contactEmailAddressRequired'} = $contactEmailAddressRequired;
339
        #$$templateVars{'required'} = $required; 
340
        $$templateVars{'templates'} = $templates;
341
        $$templateVars{'showSiteList'} = $required->{'siteList'};
342
        $$templateVars{'site'} = $config->{'site'};
343
        $$templateVars{'showWgList'} = $showWgList;
344
        $$templateVars{'showOrganization'} = $showOrganization;
345
        $$templateVars{'hasKeyword'} = $hasKeyword;
346
        $$templateVars{'hasTemporal'} = $hasTemporal;
347
        $$templateVars{'hasSpatial'} = $hasSpatial;
348
        $$templateVars{'hasTaxonomic'} = $hasTaxonomic;
349
        $$templateVars{'hasMethod'} = $hasMethod;
350
        $$templateVars{'hasUpload'} = $hasUpload;
351
        $$templateVars{'temporalRequired'} = $required->{'temporalRequired'};
352
        $$templateVars{'spatialRequired'} = $required->{'spatialRequired'};
353
        $$templateVars{'contactEmailAddressRequired'} = $required->{'contactEmail'};
393 354

  
394
    	$$templateVars{'siteList'} = \@sortedSites;
395
    	$$templateVars{'section'} = "Entry Form";
396
    	$$templateVars{'docid'} = "";
397
    	debug("Registry: Sending form: ready to process template");
398
    	$template->process( $entryFormTemplate, $templateVars);
399
    	debug("Registry: Sending form: template processed");
355
        $$templateVars{'siteList'} = \@sortedSites;
356
        $$templateVars{'section'} = "Entry Form";
357
        $$templateVars{'docid'} = "";
358
        debug("Registry: Sending form: ready to process template");
359
        $template->process( $templates->{'entry'}, $templateVars);
360
        debug("Registry: Sending form: template processed");
400 361
   }
401 362
   exit(0);
402 363
}
......
444 405
    # Login to metacat
445 406
    my ($dname, $userPass) = getCredentials();
446 407
    my $response = $metacat->login($dname, $userPass);
408
    my $errorMessage = "";
447 409

  
448 410
    # Parameters have been validated and Create the XML document
449 411
    my $xmldoc = createXMLDocument();
450 412
    
451 413
    # Write out the XML file for debugging purposes
452
    #my $testFile = $tmpdir . "/test-file.xml";
414
    #my $testFile = $tmpDir . "/test-file.xml";
453 415
    #open (TFILE,">$testFile") || die ("Cant open xml file...\n");
454 416
    #print TFILE $xmldoc;
455 417
    #close(TFILE);
......
467 429
        $$templateVars{'cfg'} = $FORM::cfg;
468 430
        $$templateVars{'function'} = "submitted";
469 431
        $$templateVars{'section'} = "Submission Status";
470
        $template->process( $responseTemplate, $templateVars);
432
        $template->process( $templates->{'response'}, $templateVars);
471 433
        exit(0);
472 434
    } else {
473 435

  
474
    	if($adminIsDocOwner eq 'true'){
436
    	if($config->{'adminIsDocOwner'} eq 'true'){
475 437
    		$response = $metacat->login($username, $password);
476 438
   	 	if (! $response) {
477 439
        		push(@errorMessages, $metacat->getMessage());
......
482 444
        		$$templateVars{'cfg'} = $FORM::cfg;
483 445
        		$$templateVars{'function'} = "submitted";
484 446
        		$$templateVars{'section'} = "Submission Status";
485
        		$template->process( $responseTemplate, $templateVars);
447
        		$template->process( $templates->{'response'}, $templateVars);
486 448
        		exit(0);
487 449
    		}
488 450
    	} 
......
493 455
            # document is being inserted 
494 456
            my $notunique = "NOT_UNIQUE";
495 457
            while ($notunique eq "NOT_UNIQUE") {
496
                $docid = newAccessionNumber($defaultScope);
458
                $docid = newAccessionNumber($config->{'scope'});
497 459
                
498 460
                $xmldocWithDocID = $xmldoc;
499 461
                $xmldocWithDocID =~ s/docid/$docid/;
......
508 470
                $notunique = insertMetadata($xmldocWithDocID, $docid);
509 471
                #  if (!$notunique) {
510 472
                # Write out the XML file for debugging purposes
511
                #my $testFile = $tmpdir . "/test-new.xml";
473
                #my $testFile = $tmpDir . "/test-new.xml";
512 474
                #open (TFILE,">$testFile") || die ("Cant open xml file...\n");
513 475
                #print TFILE $newdoc;
514 476
                #close(TFILE);
......
517 479
                # The id wasn't unique, so update our lastid file
518 480
                if ($notunique eq "NOT_UNIQUE") {
519 481
                    debug( "Registry: Updating lastid (B1.1)");
520
                    updateLastId($defaultScope);
482
                    updateLastId($config->{'scope'});
521 483
                }
522 484
            }
523 485
            debug("Registry: B2");
......
569 531
            # Create our HTML response and send it back
570 532
            $$templateVars{'function'} = "modified";
571 533
            $$templateVars{'section'} = "Modification Status";
572
            $template->process( $responseTemplate, $templateVars);
534
            $template->process( $templates->{'response'}, $templateVars);
573 535
    
574 536
            exit(0);
575 537
        }
......
606 568
$$templateVars{'function'} = "submitted";
607 569
$$templateVars{'section'} = "Submission Status";
608 570

  
609
$template->process( $responseTemplate, $templateVars);
571
$template->process( $templates->{'response'}, $templateVars);
610 572

  
611 573
exit(0);
612 574

  
......
630 592
      (my $foundScope, my $id, my $rev) = split(/\./, $docid);
631 593
      debug("Docid is: $docid\n");
632 594
      debug("Lastid is: $id");
633
      my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
595
      my $scopeFile = $configDir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
634 596
      # FIXME: skins dir isn't generally writeable by the HTTP server, use tmp instead
635 597
      open(LASTID, "+>$scopeFile") or 
636 598
          die "Failed to open lastid file for writing!";
......
691 653
  my $docrev = 1;
692 654
  my $lastid = 1;
693 655

  
694
  my $scopeFile = $cfgdir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
656
  my $scopeFile = $configDir . "/" . $FORM::cfg . "/" . $scope . ".lastid";
695 657
  if (-e $scopeFile) {
696 658
    open(LASTID, "<$scopeFile") or die "Failed to generate accession number!";
697 659
    $lastid = <LASTID>;
......
719 681
    my @invalidParams;
720 682

  
721 683
    push(@invalidParams, "Name of the Project is not selected in the form.")
722
        if (scalar(@FORM::wg) == 0 && $showWgList eq 'true');
684
        if (scalar(@FORM::wg) == 0 && $required->{'wgList'} eq 'true');
723 685
    push(@invalidParams, "First name of person entering the form is missing.")
724 686
        unless hasContent($FORM::providerGivenName);
725 687
    push(@invalidParams, "Last name of person entering the form is missing.")
726 688
        unless hasContent($FORM::providerSurName);
727 689
    push(@invalidParams, "Dataset title is missing.")
728 690
        unless hasContent($FORM::title);
729
    push(@invalidParams, $usite." name is missing.")
691
    push(@invalidParams, ucfirst($config->{'site'})." name is missing.")
730 692
        unless ((hasContent($FORM::site) && !($FORM::site =~ /^Select/)) ||
731 693
                $FORM::cfg eq "nceas");
732 694
    push(@invalidParams, "First name of principal data set owner is missing.")
......
1051 1013
    my $fileNum = shift;
1052 1014
    my $fileHash = param("upload_$fileNum");
1053 1015
    my $fileName = param("uploadname_$fileNum");
1016
    my $contentType = param("uploadtype_$fileNum");
1054 1017
    my $filePerm = param("uploadperm_$fileNum");
1055
    my $contentType = param("uploadtype_$fileNum");
1056 1018
    my $cleanName = $fileName;
1057 1019

  
1058 1020
    # normalize input filenames; Windows filenames include full paths
1059 1021
    $cleanName =~ s/.*[\/\\](.*)/$1/;
1060 1022

  
1061
    my $outFile = $tmpdir . "/" . $cleanName;
1023
    my $outFile = $tmpDir . "/" . $cleanName;
1062 1024
    #debug("Reading file from disk: $outFile");
1063 1025

  
1064 1026
    my $fileSize = stat($outFile)->size;
......
1075 1037
        return 0;
1076 1038
    }
1077 1039

  
1078
    #my ($dname, $userPass) = getCredentials();
1079
    #debug("Logging in with $dname, $userPass");
1080
    #$metacat->login($username, $password);
1081

  
1082
    my $docid = newAccessionNumber($defaultScope);
1040
    my $docid = newAccessionNumber($config->{'scope'});
1083 1041
    my $unique = uploadData($outFile, $docid);
1084 1042
    if (!$unique) {
1085 1043
        debug( "Registry: Updating lastid file");
1086
        updateLastId($defaultScope);
1044
        updateLastId($config->{'scope'});
1087 1045
    }
1088 1046

  
1089 1047
    my $entityid = $fileHash."001";
......
1129 1087

  
1130 1088
    # file is in Metacat, generate the pertinent EML elements
1131 1089
    my $contentType = uploadInfo($fileName)->{'Content-Type'};
1132

  
1133 1090
    # occasionally CGI.pm doesn't get the file info.  In this case,
1134 1091
    # use a default MIME type of text/plain.  Seems fixed in the newer CGI.pm:
1135 1092
    # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=313141
......
1165 1122
    $ctx->add($fileData);
1166 1123
    my $digest = $ctx->hexdigest;
1167 1124

  
1168
    my $outputName = $tmpdir . "/" . $cleanName;
1125
    my $outputName = $tmpDir . "/" . $cleanName;
1169 1126
    open(OUT,">$outputName") or die "Could not open: $!";
1170 1127
    print OUT $fileData;
1171 1128
    close(OUT);
......
1176 1133

  
1177 1134
sub deleteFile {
1178 1135
    my $input = shift;
1179
    my $fileName = $tmpdir . "/" . $input;
1136
    my $fileName = $tmpDir . "/" . $input;
1180 1137

  
1181 1138
    if (-e $fileName) {
1182 1139
        unlink $fileName or
......
1310 1267
                  $roleName = $defaultRole;
1311 1268
                }
1312 1269

  
1270
                #debug("XXXXX role name: " . $roleName);
1313 1271
                push (@{$orig{$roleName}}, [$first, $last, $origRole]);
1314 1272
            }
1315 1273
        }
......
1439 1397
        foreach my $x (@$a_ref) {
1440 1398
            my ($kw, $kwType) = @$x;
1441 1399
            $kwElem .= "<keyword ";
1442
            if (hasContent($kwType) && $kwType ne "None") {
1400
            if (hasContent($kwType) && $kwType != "None") {
1443 1401
                 $kwElem.= "keywordType=\"".lc($kwType)."\"";
1444 1402
            }
1445 1403
            $kwElem .= ">$kw</keyword>\n";
......
1882 1840
        $access .= allowElement(getUsername(), 'read', 'write'); 
1883 1841
    }
1884 1842

  
1885
    if($publicReadable eq "true"){
1843
    if($config->{'publicReadable'} eq "true"){
1886 1844
        $access .= allowElement('public', 'read');
1887 1845
    }
1888 1846
    $access .= "</access>\n";
......
1906 1864
    my $username = '';
1907 1865
     
1908 1866
    if ($FORM::username ne '') {
1909
        $username = "uid=$FORM::username,o=$FORM::organization,dc=ecoinformatics,dc=org";
1867
        $username = "uid=$FORM::username,o=$FORM::organization,dc=ecoinformatics,dc=org";    
1910 1868
    } else {
1911 1869
        my $session = CGI::Session->load();
1912 1870
        if ( !$session->is_empty ) {
......
1955 1913
        push(@errorMessages, $error);
1956 1914
    } elsif ($doc=~ /<error/) {
1957 1915
    if ( $doc=~ /public/){
1958
        	$error ="Error in reading the eml document. Please check if you are logged in.";
1959
        	push(@errorMessages, $error);
1960
	} else {
1961
        	$error ="Error in reading the eml document. Please check if you have access to read the document";
1962
        	push(@errorMessages, $error);	
1963
	}
1916
          $error ="Error in reading the eml document. Please check if you are logged in.";
1917
          push(@errorMessages, $error);
1918
  } else {
1919
          $error ="Error in reading the eml document. Please check if you have access to read the document";
1920
          push(@errorMessages, $error); 
1921
  }
1964 1922
    } else {
1965 1923
        $findType = $xmldoc->findnodes('//dataset/identifier');
1966 1924
        if ($findType->size() > 0) {
......
1975 1933
                    # If the file is already in @fileArray then do not add it 
1976 1934
                    $alreadyInArray = 0;
1977 1935
                    foreach $element (@fileArray) {
1978
                        $tempfile = $tmpdir."/".$pushDoc;
1936
                        $tempfile = $tmpDir."/".$pushDoc;
1979 1937
                        if ($element eq $pushDoc) {
1980 1938
                            $alreadyInArray = 1;
1981 1939
                        }
1982 1940
                    }
1983 1941
            
1984 1942
                    if (!$alreadyInArray) {
1985
                        $tempfile = $tmpdir."/".$pushDoc;
1943
                        $tempfile = $tmpDir."/".$pushDoc;
1986 1944
                        $response = "";
1987 1945
                        $response = $metacat->read($pushDoc);    
1988 1946
                        if (! $response) {
......
2005 1963

  
2006 1964
            # Read the main document. 
2007 1965

  
2008
            $tempfile = $tmpdir."/".$docid;
1966
            $tempfile = $tmpDir."/".$docid;
2009 1967
            open (TFILE,">$tempfile") || die ("Cant open xml file...\n");
2010 1968
            print TFILE $doc;
2011 1969
            close(TFILE);
......
2018 1976
            my $resultsheet;
2019 1977
        
2020 1978
            $xslt = XML::LibXSLT->new();
2021
            $tempfile = $tmpdir."/"."triple_info.xsl";
1979
            $tempfile = $tmpDir."/"."triple_info.xsl";
2022 1980
    
2023 1981
            $triplesheet = $xslt->parse_stylesheet_file($tempfile);
2024 1982

  
2025
            $results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpdir/\'", packageName => "\'$docid\'");
1983
            $results = $triplesheet->transform($xmldoc, packageDir => "\'$tmpDir/\'", packageName => "\'$docid\'");
2026 1984

  
2027
            $tempfile = $tmpdir."/"."emlb6toeml2.xsl";
1985
            $tempfile = $tmpDir."/"."emlb6toeml2.xsl";
2028 1986
            $stylesheet = $xslt->parse_stylesheet_file($tempfile);
2029 1987
            $resultsheet = $stylesheet->transform($results);
2030 1988
        
......
2051 2009
################################################################################
2052 2010
sub modifyData {
2053 2011

  
2054
    my $xmldoc = readDocumentFromMetacat();    	
2012
    my $xmldoc = readDocumentFromMetacat();     
2055 2013
    if (!scalar(@errorMessages)) {
2056
    	getFormValuesFromEml2($xmldoc);
2014
      getFormValuesFromEml2($xmldoc);
2057 2015
    }
2058 2016

  
2059 2017
    if (scalar(@errorMessages)) {
......
2063 2021
        $error = 1;
2064 2022
        $$templateVars{'function'} = "modification";
2065 2023
        $$templateVars{'section'} = "Modification Status";
2066
        $template->process( $responseTemplate, $templateVars); 
2024
        $template->process( $templates->{'response'}, $templateVars); 
2067 2025
    } else {
2068 2026
        $$templateVars{'form'} = 're_entry';
2069
        $template->process( $entryFormTemplate, $templateVars);
2027
        $template->process( $templates->{'entry'}, $templateVars);
2070 2028
    }
2071 2029
}
2072 2030

  
......
2088 2046
    my $foundDSO;
2089 2047

  
2090 2048
    # set variable values
2091
    $$templateVars{'showSiteList'} = $showSiteList;
2092
    $$templateVars{'lsite'} = $lsite;
2093
    $$templateVars{'usite'} = $usite;
2094
    $$templateVars{'showWgList'} = $showWgList;
2049
    $$templateVars{'required'} = $required;
2050
    $$templateVars{'showSiteList'} = $required->{'siteList'};
2051
    $$templateVars{'site'} = $config->{'site'};
2052
    #$$templateVars{'showWgList'} = $showWgList;
2095 2053
    $$templateVars{'showOrganization'} = $showOrganization;
2096 2054
    $$templateVars{'hasKeyword'} = $hasKeyword;
2097 2055
    $$templateVars{'hasTemporal'} = $hasTemporal;
2098 2056
    $$templateVars{'hasSpatial'} = $hasSpatial;
2099 2057
    $$templateVars{'hasTaxonomic'} = $hasTaxonomic;
2100 2058
    $$templateVars{'hasMethod'} = $hasMethod;
2101
    $$templateVars{'spatialRequired'} = $spatialRequired;
2102
    $$templateVars{'contactEmailAddressRequired'} = $contactEmailAddressRequired;
2103
    $$templateVars{'temporalRequired'} = $temporalRequired;
2059
    $$templateVars{'spatialRequired'} = $required->{'spatialRequired'};
2060
    $$templateVars{'contactEmailAddressRequired'} = $required->{'contactEmail'};
2061
    $$templateVars{'temporalRequired'} = $required->{'temporal'};
2104 2062

  
2105 2063
    # find out the tag <alternateIdentifier>. 
2106 2064
    $results = $doc->findnodes('//dataset/alternateIdentifier');
......
2200 2158
                    $aoCount++;
2201 2159
                }
2202 2160
            }
2203
            $$templateVars{'origEmail'} = findValue($node, '../electronicMailAddress');
2204
            $$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
2205 2161
        }
2206 2162

  
2207 2163
    $results = $doc->findnodes('//dataset/creator/organizationName');
......
2214 2170
        foreach $node ($results->get_nodelist) {
2215 2171
            my $tempValue = findValue($node,'../organizationName');
2216 2172
            $tempResult = $node->findnodes('../individualName');
2217
            if ($tempResult->size == 0 && $tempValue ne $organization) {
2173
            if ($tempResult->size == 0 && $tempValue ne $config->{'organization'}) {
2218 2174
                $$templateVars{'site'} = $tempValue;
2219 2175
            }
2220 2176
        }
......
2224 2180
                my $tempValue = findValue($node,'../organizationName');
2225 2181
                $wg[scalar(@wg)] = $tempValue;
2226 2182
            }
2227
            my $projects = getProjectList();
2183
            my $projects = getProjectList($database);
2228 2184
            $$templateVars{'projects'} = $projects;
2229 2185
            $$templateVars{'wg'} = \@wg;
2230 2186
        }
......
2266 2222
                    $$templateVars{"origNamefirst$aoCount"} =  findValue($tempNode, './givenName');
2267 2223
                    $$templateVars{"origNamelast$aoCount"} =  findValue($tempNode, './surName');
2268 2224
                    $$templateVars{"origRole$aoCount"} = findValue($tempNode, '../role');
2269
                    $aoCount++;
2225
                    $aoCount++;           
2270 2226
                }
2271 2227
            }
2272 2228
     }
......
2317 2273

  
2318 2274
    my $count = 1;
2319 2275
    foreach $node ($results->get_nodelist) {
2320
        $tempResult = $node->findnodes('./keyword');
2276
    $tempResult = $node->findnodes('./keyword');
2277
    if ($tempResult->size() > 1) {
2278
        errMoreThanOne("keyword");
2279
    } else {
2321 2280
        foreach $tempNode ($tempResult->get_nodelist) {
2322 2281
            $$templateVars{"keyword$count"} = $tempNode->textContent();
2323
            $$templateVars{"kwTh$count"} = findValue($node, "keywordThesaurus");
2324

  
2325 2282
            if ($tempNode->hasAttributes()) {
2326 2283
                my @attlist = $tempNode->attributes();
2327 2284
                my $tmp = $attlist[0]->value;  #convert the first letter to upper case
2328 2285
                $tmp =~ s/\b(\w)/\U$1/g;
2329 2286
                $$templateVars{"kwType$count"} = $tmp;
2330 2287
            }
2331
            $count++;
2332 2288
        }
2333 2289
    }
2290
    $$templateVars{"kwTh$count"} = findValue($node, "keywordThesaurus");
2291
        $count++;
2292
    }
2334 2293
    $$templateVars{'keyCount'} = $count;
2335 2294
    if($count > 0 ){
2336 2295
       $$templateVars{'hasKeyword'} = "true";
......
2550 2509
            dontOccur($node, "../positionName|../onlineURL|../userId", 
2551 2510
              "positionName, onlineURL, userId in contact tag");
2552 2511
            dontOccur($node, "./saluation", "saluation in contact tag");                
2553

  
2512
        
2554 2513
            $tempResult = $node->findnodes('../address|../phone|../electronicmailAddress|../organizationName');
2555 2514
            if ($tempResult->size > 0) {
2556 2515
                $$templateVars{'origNamefirstContact'} = findValue($node, 'givenName');
2557 2516
                $$templateVars{'origNamelastContact'} = findValue($node, 'surName');
2558

  
2517
    
2559 2518
                my $tempResult2 = $node->findnodes('../address');
2560 2519
                if ($tempResult2->size > 1) {
2561 2520
                    errMoreThanOne("address");
......
2568 2527
                        $$templateVars{'origCountryContact'} = findValue($tempNode2, 'country');
2569 2528
                    }
2570 2529
                }
2571

  
2530
            
2572 2531
                my $tempResult3 = $node->findnodes('../phone');
2573 2532
                if ($tempResult3->size > 2) {
2574 2533
                    errMoreThanN("phone");
......
2593 2552
                $$templateVars{'origNamelastContact'} = findValue($node, 'surName');
2594 2553
                $$templateVars{'origNameOrgContact'} = findValue($node, '../organizationName');
2595 2554
            }
2596
            $$templateVars{'origEmail'} = findValue($node, '../electronicMailAddress');
2597
            $$templateVars{'origNameOrg'} = findValue($node, '../organizationName');
2598

  
2599 2555
        }
2600 2556
    }
2601 2557
    
......
2708 2664
   
2709 2665
    ########################################################
2710 2666

  
2667

  
2711 2668
    dontOccur($doc, "./dataTable", "dataTable");
2712 2669
    dontOccur($doc, "./spatialRaster", "spatialRaster");
2713 2670
    dontOccur($doc, "./spatialVector", "spatialVector");
2714 2671
    dontOccur($doc, "./storedProcedure", "storedProcedure");
2715 2672
    dontOccur($doc, "./view", "view");
2716

  
2717 2673
    dontOccur($doc, "./otherEntity", "otherEntity");
2718 2674
    dontOccur($doc, "./references", "references");
2719 2675
    
......
2840 2796

  
2841 2797
    $$templateVars{'function'} = "deleted";
2842 2798
    $$templateVars{'section'} = "Deletion Status";
2843
    $template->process( $responseTemplate, $templateVars);
2799
    $template->process( $templates->{'response'}, $templateVars);
2844 2800
    }
2845 2801
}
2846 2802

  
......
2862 2818
        my $returnVal = $metacat->login($username,$password);
2863 2819
        debug("Registry: Login was $returnVal for login attempt to $metacatUrl, with $username");
2864 2820
        if($returnVal > 0){
2865
		# valid username and passwd
2866
		# create a new session and store username and passswd
2867
		$session = new CGI::Session();
2821
            # valid username and passwd
2822
            # create a new session and store username and passswd
2823
            $session = new CGI::Session();
2868 2824

  
2869
		$session->param('username', $username);
2870
		$session->param('password', $password);
2871
		
2872
		if($returnVal == 2 || $returnVal == 4){
2873
			# is a moderator. store this information in the session
2874
			$session->param('moderator', 'true');	
2875
		}
2825
            $session->param('username', $username);
2826
            $session->param('password', $password);
2827
    
2828
            if($returnVal == 2 || $returnVal == 4){
2829
                # is a moderator. store this information in the session
2830
                $session->param('moderator', 'true'); 
2831
            }
2876 2832

  
2877
		# send redirect to metacat and action = login
2878
		my $html = "<html><head>";
2879
    		$html .= "</head><body onload=\"document.loginForm.submit()\">";
2880
		$html .= "<form name=\"loginForm\" method=\"post\" action=\"@systemidserver@@servlet-path@\">";
2881
		$html .= "<input type=\"hidden\" name=\"action\" value=\"login\" />";
2882
		$html .= "<input type=\"hidden\" name=\"username\" value=\"".$FORM::username."\" />";
2883
		$html .= "<input type=\"hidden\" name=\"password\" value=\"".$FORM::password."\" />";
2884
		$html .= "<input type=\"hidden\" name=\"qformat\" value=\"".$FORM::cfg."\" />";
2885
		$html .= "</form></body></html>";
2886
		print $session->header();
2887
		print $html;
2888
	} else {
2889
		# send back the error template with error message as wrong username password
2890
		# push(@errorMessages, $metacat->getMessage());
2891
		print "Content-type: text/html\n\n";
2892
        	push(@errorMessages, "Failed during login.\n");
2893
        	$$templateVars{'status'} = 'login_failure';
2894
        	$$templateVars{'errorMessages'} = \@errorMessages;
2895
        	$$templateVars{'cfg'} = $FORM::cfg;
2896
        	$$templateVars{'section'} = "Login Status";
2897
        	$template->process( $responseTemplate, $templateVars);
2898
	}
2833
            # send redirect to metacat and action = login
2834
            my $html = "<html><head>";
2835
            $html .= "</head><body onload=\"document.loginForm.submit()\">";
2836
            $html .= "<form name=\"loginForm\" method=\"post\" action=\"". $metacatUrl ."\">";
2837
            $html .= "<input type=\"hidden\" name=\"action\" value=\"login\" />";
2838
            $html .= "<input type=\"hidden\" name=\"username\" value=\"".$FORM::username."\" />";
2839
            $html .= "<input type=\"hidden\" name=\"password\" value=\"".$FORM::password."\" />";
2840
            $html .= "<input type=\"hidden\" name=\"qformat\" value=\"".$FORM::cfg."\" />";
2841
            $html .= "</form></body></html>";
2842
            print $session->header();
2843
            print $html;
2844
        } else {
2845
            # send back the error template with error message as wrong username password
2846
            # push(@errorMessages, $metacat->getMessage());
2847
            print "Content-type: text/html\n\n";
2848
            push(@errorMessages, "Failed during login.\n");
2849
            $$templateVars{'status'} = 'login_failure';
2850
            $$templateVars{'errorMessages'} = \@errorMessages;
2851
            $$templateVars{'cfg'} = $FORM::cfg;
2852
            $$templateVars{'section'} = "Login Status";
2853
            $template->process( $templates->{'response'}, $templateVars);
2854
        }
2899 2855

  
2900
        exit(0);
2856
    exit(0);
2901 2857
    } else {
2902 2858
        # session found ... redirect to index page
2903
        my $url = "@systemidserver@@style-skins-path@/".$FORM::cfg."/index.html";
2904
	redirect($url);
2905
	exit(0);
2859
        my $url = "$configDir/$FORM::cfg/index.html";
2860
        redirect($url);
2861
        exit(0);
2906 2862
   }
2907 2863
}
2908 2864

  
......
2918 2874
    my $session = CGI::Session->load();
2919 2875
    if ( $session->is_empty || $session->is_expired) {
2920 2876
        # no session found ... send back to index.html page ... 
2921
	    debug("Session empty or not found");
2922
  	    my $url = "@systemidserver@@style-skins-path@/".$FORM::cfg."/index.html";
2923
	    redirect($url);
2877
        debug("Session empty or not found");
2878
        my $url = "$configDir/$FORM::cfg/index.html";
2879
        redirect($url);
2924 2880
        # should logout request be sent to metacat??? 
2925
	} else {
2926
	    # get the user name and delete the session
2927
	    debug("Session found");
2928
  	    my $uname = $session->param("username");
2929
	    $session->delete();
2930
	    # send redirect to metacat and action = login
2931
 	    my $html = "<html><head>";
2932
   	    $html .= "</head><body onload=\"document.loginForm.submit()\">";
2933
 	    $html .= "<form name=\"loginForm\" method=\"post\" action=\"@systemidserver@@servlet-path@\">";
2934
	    $html .= "<input type=\"hidden\" name=\"action\" value=\"logout\" />";
2935
	    $html .= "<input type=\"hidden\" name=\"username\" value=\"".$uname."\" />";
2936
	    $html .= "<input type=\"hidden\" name=\"qformat\" value=\"".$FORM::cfg."\" />";
2937
	    $html .= "</form></body></html>";
2938
	    print($html);
2939
	}
2881
    } else {
2882
        # get the user name and delete the session
2883
        debug("Session found");
2884
        my $uname = $session->param("username");
2885
        $session->delete();
2886
        # send redirect to metacat and action = login
2887
        my $html = "<html><head>";
2888
        $html .= "</head><body onload=\"document.loginForm.submit()\">";
2889
        $html .= "<form name=\"loginForm\" method=\"post\" action=\"". $metacatUrl ."\">";
2890
        $html .= "<input type=\"hidden\" name=\"action\" value=\"logout\" />";
2891
        $html .= "<input type=\"hidden\" name=\"username\" value=\"".$uname."\" />";
2892
        $html .= "<input type=\"hidden\" name=\"qformat\" value=\"".$FORM::cfg."\" />";
2893
        $html .= "</form></body></html>";
2894
        print($html);
2895
    }
2940 2896
}
2941 2897

  
2942 2898
################################################################################
......
2976 2932
    my $session = CGI::Session->load();
2977 2933
    if ( $session->is_empty || $session->is_expired) {
2978 2934
        # no session found ... send back to index.html page ... 
2979
	processResultTemplate($stage, 'failure', "Moderator is not logged in.\n");		
2980
	$returnValue = -1;
2935
        processResultTemplate($stage, 'failure', "Moderator is not logged in.\n");
2936
        $returnValue = -1;
2981 2937
    } 
2982 2938

  
2983 2939
    # check if logged in user is moderator
2984 2940
    my $moderator = $session->param("moderator");
2985 2941
    if ( $moderator ne 'true') {
2986 2942
        # no session found ... send back to index.html page ... 
2987
	debug("Logged in user is not moderator");
2988
	processResultTemplate($stage, 'failure', "Logged in user is not moderator.\n");		
2989
	$returnValue = -1;
2943
        debug("Logged in user is not moderator");
2944
        processResultTemplate($stage, 'failure', "Logged in user is not moderator.\n");
2945
        $returnValue = -1;
2990 2946
    } 
2991 2947

  
2992 2948
    if($returnValue eq 1){
2993
    	$modUsername = $session->param("username");
2994
    	$modPassword = $session->param("password");
2949
        $modUsername = $session->param("username");
2950
        $modPassword = $session->param("password");
2995 2951
    }
2996 2952

  
2997 2953
    return $returnValue;
2998 2954
}
2999 2955

  
3000 2956
sub handleRead {
3001
	my $docid = $FORM::docid;
3002
	my $errorMessage;
3003
	
3004
    	print "Content-type: text/html\n\n";
3005
		
3006
	# Check if the session exists
3007
	my $session = CGI::Session->load();
3008
    	if ( $session->is_empty || $session->is_expired) {
3009
        	# no session found ... send back the regular read page ...
3010
       		my $url = "@systemidserver@@style-skins-path@/".$FORM::cfg."/index.html";
3011
	        redirect($url);
3012
    	} else {
3013
		my $htmldoc = "";
3014
		$htmldoc .= "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">";
3015
		$htmldoc .= "<html><head><title>Dataset Description: ".$docid."</title><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"></head>";
3016
		$htmldoc .= "<frameset rows=\"150,*\" cols=\"*\" frameborder=\"NO\" border=\"0\" framespacing=\"0\">";
3017
		$htmldoc .= "<frame src=\"@systemidserver@@style-skins-path@/".$FORM::cfg."/header.jsp\" marginwidth=\"40\" name=\"topFrame\" scrolling=\"NO\" noresize>";
3018
		$htmldoc .= "<frameset cols=\"200,*\" frameborder=\"NO\" border=\"0\" framespacing=\"0\">";
3019
        	$htmldoc .= "<body></body><frame src=\"@cgi-prefix@/register-dataset.cgi?cfg=".$FORM::cfg."&stage=review_frame&docid=".$docid."\" name=\"rightFrame\" scrolling=\"NO\" noresize></frame>";
3020
        	$htmldoc .= "<frame src=\"@systemidserver@@servlet-path@?action=read&qformat=".$FORM::cfg."&docid=".$docid."&insertTemplate=0\" name=\"mainFrame\">";
3021
  		$htmldoc .= "</frameset></frameset></html>";
2957
    my $docid = $FORM::docid;
2958
    my $errorMessage;
3022 2959

  
3023
       		print $htmldoc;	
2960
    print "Content-type: text/html\n\n";
2961

  
2962
    # Check if the session exists
2963
    my $session = CGI::Session->load();
2964
        if ( $session->is_empty || $session->is_expired) {
2965
            # no session found ... send back the regular read page ...
2966
       	    my $url = "$configDir/$FORM::cfg/index.html";
2967
       	    redirect($url);
2968
        } else {
2969
       	    my $htmldoc = "";
2970
       	    $htmldoc .= "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">";
2971
       	    $htmldoc .= "<html><head><title>Dataset Description: ".$docid."</title><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"></head>";
2972
       	    $htmldoc .= "<frameset rows=\"150,*\" cols=\"*\" frameborder=\"NO\" border=\"0\" framespacing=\"0\">";
2973
       	    $htmldoc .= "<frame src=\"$configDir/$FORM::cfg/header.jsp\" marginwidth=\"40\" name=\"topFrame\" scrolling=\"NO\" noresize>";
2974
       	    $htmldoc .= "<frameset cols=\"200,*\" frameborder=\"NO\" border=\"0\" framespacing=\"0\">";
2975
       	    $htmldoc .= "<body></body><frame src=\"$cgiUrl?cfg=$FORM::cfg&stage=review_frame&docid=".$docid."\" name=\"rightFrame\" scrolling=\"NO\" noresize></frame>";
2976
       	    $htmldoc .= "<frame src=\"". $metacatUrl ."?action=read&qformat=".$FORM::cfg."&docid=".$docid."&insertTemplate=0\" name=\"mainFrame\">";
2977
            $htmldoc .= "</frameset></frameset></html>";
2978

  
2979
       	    print $htmldoc;	
3024 2980
	}
3025 2981
} 
3026 2982

  
......
3038 2994
	if ( $moderator eq 'true') {
3039 2995
		$$templateVars{'isModerator'} = "true";
3040 2996
	}
3041
	$template->process( $getReviewsTemplate, $templateVars);
2997
	$template->process( $templates->{'getReviews'}, $templateVars);
3042 2998
}
3043 2999

  
3044 3000
sub getReviewHistoryHTML {
......
3596 3552
#
3597 3553
################################################################################
3598 3554
sub mod_sendNotification {
3599
    my $title = shift;
3600
    my $contactEmailAddress = shift;
3601
    my $contactName = shift;
3602
    my $subject = shift;
3555
	my $title = shift;
3556
	my $contactEmailAddress = shift;
3557
	my $contactName = shift;
3558
	my $subject = shift;
3603 3559

  
3604
    debug($subject);
3560
	debug($subject);
3605 3561
    # send notification to the user and the moderator
3606
    my $templateVars = { 'stage' => $FORM::stage };
3607
    $$templateVars{'recipient'} = $recipient;
3608
    $$templateVars{'sender'} = $sender;
3609
    # form doesn't handle edit without revision; append
3610
    #my ($x, $y, $z) = split(/\./, $FORM::docid);
3611
    #my $docidWithoutRev = $x.".".$y;
3612
    #$$templateVars{'docid'} = $docidWithoutRev;
3613
    $$templateVars{'docid'} = $FORM::docid;
3614
    $$templateVars{'comment'} = $FORM::review;
3615
    $$templateVars{'contactName'} = $contactName;
3616
    $$templateVars{'dpTitle'} = $title;
3562
	my $templateVars = { 'stage' => $FORM::stage };
3563
	my ($x, $y, $z) = split(/\./, $FORM::docid);
3564
        my $docidWithoutRev = $x.".".$y;
3565
	$$templateVars{'docid'} = $docidWithoutRev;
3566
	$$templateVars{'comment'} = $FORM::review;
3567
	$$templateVars{'contactName'} = $contactName;
3568
	$$templateVars{'dpTitle'} = $title;
3617 3569

  
3618
    $$templateVars{'recipient_status'} = 'moderator';
3619
    sendNotification($mailhost, $sender, $recipient, $subject, 
3620
                            $modEmailNotificationTemplate, $templateVars);
3621
    if($contactEmailAddress ne ''){
3622
        # send notification to contact email address specified in cfg   
3623
        $$templateVars{'recipient'} = $contactEmailAddress;
3624
        $$templateVars{'recipient_status'} = 'user';
3625
        sendNotification($mailhost, $sender, $contactEmailAddress, 
3626
                $subject, $modEmailNotificationTemplate, $templateVars);
3627
    }
3570
	$$templateVars{'recipient_status'} = 'moderator';
3571
	sendNotification($email->{'sender'}, $email->{'recipient'}, $subject, 
3572
							$templates->{'modEmailNotification'}, $templateVars);
3573
	if($contactEmailAddress ne ''){
3574
		# send notification to contact email address specified in cfg   
3575
		$$templateVars{'recipient_status'} = 'user';
3576
		sendNotification($email->{'sender'}, $contactEmailAddress, 
3577
				$subject, $templates->{'modEmailNotification'}, $templateVars);
3578
	}
3628 3579
}
3629 3580

  
3630 3581
################################################################################
......
3633 3584
#
3634 3585
################################################################################
3635 3586
sub sendNotification {
3636
    my $mailhost = shift;
3637 3587
    my $sender = shift;
3638 3588
    my $recipient = shift;
3639 3589
    my $subject = shift;
3640 3590
    my $templateForm = shift;
3641 3591
    my $templateVars = shift;
3642 3592

  
3643
    my $smtp = Net::SMTP->new($mailhost);
3593
    my $smtp = Net::SMTP->new($email->{'mailhost'});
3644 3594
    $smtp->mail($sender);
3645 3595
    $smtp->to($recipient);
3646 3596

  
......
3686 3636
	}
3687 3637
    }
3688 3638
    $$templateVars{'message'} = $message;
3689
    $template->process($modResultTemplate, $templateVars);
3639
    $template->process($templates->{'modResult'}, $templateVars);
3690 3640
}
3691 3641

  
3692 3642

  
......
3697 3647
################################################################################
3698 3648
sub toConfirmData{
3699 3649
    # Check if any invalid parameters
3700

  
3650
 
3701 3651
    my $invalidParams;
3702 3652
    if (! $error) {
3703
        $invalidParams = validateParameters(0);
3704
        if (scalar(@$invalidParams)) {
3705
            $$templateVars{'status'} = 'failure';
3706
            $$templateVars{'invalidParams'} = $invalidParams;
3707
            $error = 1;
3708
        }
3653
    	$invalidParams = validateParameters(0);
3654
    	if (scalar(@$invalidParams)) {
3655
        	$$templateVars{'status'} = 'failure';
3656
        	$$templateVars{'invalidParams'} = $invalidParams;
3657
        	$error = 1;
3658
    	}
3709 3659
    }
3710 3660

  
3711 3661
    $$templateVars{'providerGivenName'} = normalizeCD($FORM::providerGivenName);
......
3809 3759
            $$templateVars{"kwType".$keyCount} = normalizeCD($keywordTypeArray->[$i]);
3810 3760
            $$templateVars{"kwTh".$keyCount} = normalizeCD($keywordThArray->[$i]);
3811 3761
            $keyCount++;
3812
        }
3813
    }
3762
	}    
3763
    }    
3814 3764
    $$templateVars{'keyCount'} = $keyCount;
3815

  
3765
    
3816 3766
    $$templateVars{'addComments'} = normalizeCD($FORM::addComments);
3817 3767
    $$templateVars{'useConstraints'} = $FORM::useConstraints;
3818 3768
    if($FORM::useConstraints eq "other"){
......
3852 3802
    my $taxonNameArray = \@FORM::taxonName;
3853 3803
    my $taxonCount = 1;
3854 3804

  
3855
    for (my $i = 0; $i <= $#$taxonNameArray; $i++) {
3805
    for(my $i = 0; $i <= $#$taxonNameArray; $i++){
3856 3806
        if (hasContent($taxonRankArray->[$i]) && hasContent($taxonNameArray->[$i])) {
3857 3807
            debug("Registry processing keyword: trv = ".$taxonRankArray->[$i]
3858 3808
                    ." trn = ".$taxonNameArray->[$i]);
3859 3809
            $$templateVars{"taxonRankName".$taxonCount} = normalizeCD($taxonRankArray->[$i]);
3860 3810
            $$templateVars{"taxonRankValue".$taxonCount} = normalizeCD($taxonNameArray->[$i]);
3861 3811
            $taxonCount++;
3862
        }
3812
	}    
3863 3813
    }
3864 3814

  
3865 3815
    $$templateVars{'taxaCount'} = $taxonCount-1;
......
3877 3827
                $$templateVars{"uploadname_$upNum"} = param("uploadname_$upNum");
3878 3828
                $$templateVars{"uploadtype_$upNum"} = param("uploadtype_$upNum");
3879 3829
                $$templateVars{"uploadperm_$upNum"} = param("uploadperm_$upNum");
3830
                  
3880 3831
            }
3881 3832
        }
3882 3833
    }
......
3895 3846
            $$templateVars{"upload_$totalFileNum"} = $fileInfo->{'fileHash'};
3896 3847
            $$templateVars{"uploadname_$totalFileNum"} = $fileInfo->{'fileName'};
3897 3848
            $$templateVars{"uploadtype_$totalFileNum"} = $fileInfo->{'contentType'};
3898
            $$templateVars{"uploadperm_$totalFileNum"} = param("uploadperm_$totalFileNum");
3899 3849
            $uploadCount++;
3900 3850
        }
3901 3851
    }
......
3913 3863
    $$templateVars{'origStateContact'} = $FORM::origState;
3914 3864

  
3915 3865
    $$templateVars{'showSiteList'} = $FORM::showSiteList;
3916
    $$templateVars{'lsite'} = $FORM::lsite;
3917
    $$templateVars{'usite'} = $FORM::usite;
3866
    $$templateVars{'site'} = $FORM::site;
3918 3867
    $$templateVars{'showWgList'} = $FORM::showWgList;
3919 3868
    $$templateVars{'showOrganization'} = $FORM::showOrganization;
3920 3869
    $$templateVars{'hasKeyword'} = $FORM::hasKeyword;
......
3938 3887
    if (! $error) {
3939 3888
	# If no errors, then print out data in confirm Data template
3940 3889
	$$templateVars{'section'} = "Confirm Data";
3941
	$template->process( $confirmDataTemplate, $templateVars);
3890
	$template->process( $templates->{'confirmData'}, $templateVars);
3942 3891

  
3943 3892
    } else{    
3944 3893
    # Errors from validation function. print the errors out using the response template
......
3950 3899
        # Create our HTML response and send it back
3951 3900
    $$templateVars{'function'} = "submitted";
3952 3901
    $$templateVars{'section'} = "Submission Status";
3953
    $template->process( $responseTemplate, $templateVars);
3902
    $template->process( $templates->{'response'}, $templateVars);
3954 3903
    }
3955 3904
}
3956 3905

  
......
3972 3921
    $$templateVars{'docid'} = $FORM::docid;
3973 3922

  
3974 3923
    $$templateVars{'form'} = 're_entry';
3975
    $template->process( $entryFormTemplate, $templateVars);
3924
    $template->process( $templates->{'entry'}, $templateVars);
3976 3925
}
3977 3926

  
3978 3927

  
......
3986 3935
    $$templateVars{'providerSurName'} = $FORM::providerSurName;
3987 3936
    $$templateVars{'site'} = $FORM::site;
3988 3937
    if ($FORM::cfg eq "nceas") {
3989
        my $projects = getProjectList();
3938
        my $projects = getProjectList($database);
3990 3939
        $$templateVars{'projects'} = $projects;
3991 3940
        $$templateVars{'wg'} = \@FORM::wg;
3992 3941
    }
......
4116 4065
    $$templateVars{'samplingDescription'} = $FORM::samplingDescription;
4117 4066
    
4118 4067
    $$templateVars{'showSiteList'} = $FORM::showSiteList;
4119
    $$templateVars{'lsite'} = $FORM::lsite;
4120
    $$templateVars{'usite'} = $FORM::usite;
4068
    $$templateVars{'site'} = $FORM::site;
4121 4069
    $$templateVars{'showWgList'} = $FORM::showWgList;
4122 4070
    $$templateVars{'showOrganization'} = $FORM::showOrganization;
4123 4071
    $$templateVars{'hasKeyword'} = $FORM::hasKeyword;
......
4289 4237
sub debug {
4290 4238
    my $msg = shift;
4291 4239
    
4292
    if ($debug) {
4240
    if ($debug_enabled) {
4293 4241
        print STDERR "$msg\n";
4294 4242
    }
4295 4243
    else {
......
4306 4254
#
4307 4255
################################################################################
4308 4256
sub getProjectList {
4257
    my $database = shift;
4309 4258
    my $projects;
4310 4259

  
4311 4260
    # Check for availability AdminDB.pm, for accessing NCEAS projects

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