/**
 *	setup a default html page
 *
 *	see html.inc.php.
 *	@param bool $add_glue true for adding the glue code
 */
function default_html($add_glue)
{
    html_title(SITE_NAME);
    $favicon = FAVICON;
    if (!empty($favicon)) {
        if (is_url($favicon)) {
            html_favicon($favicon);
        } else {
            html_favicon(base_url() . $favicon);
        }
    }
    if (USE_MIN_FILES) {
        html_add_css(base_url() . 'css/reset.min.css', 1);
    } else {
        html_add_css(base_url() . 'css/reset.css', 1);
    }
    // 2 can be used for third-party components
    html_add_css(base_url() . 'css/main.css', 3);
    if ($add_glue) {
        html_add_css(base_url() . 'css/glue.css', 4);
    }
    if ($add_glue) {
        $jquery = JQUERY;
        if (is_url($jquery)) {
            html_add_js($jquery, 1);
        } else {
            html_add_js(base_url() . $jquery, 1);
        }
        // 2 can be used for third-party components
        if (USE_MIN_FILES) {
            html_add_js(base_url() . 'js/glue.min.js', 3);
        } else {
            html_add_js(base_url() . 'js/glue.js', 3);
        }
        html_add_js_var('$.glue.base_url', base_url());
        html_add_js_var('$.glue.conf.show_frontend_errors', SHOW_FRONTEND_ERRORS);
        html_add_js_var('$.glue.version', glue_version());
    }
}

function check_verify_bundle()
{
    $success = true;
    $repo = $_GET['p'];
    $what = $_FILES['bundle_file']['tmp_name'];
    $out1 = array();
    if ($success) {
        $success = $success && check_new_head_in_bundle($what, $out1);
    }
    if ($success) {
        $success = $success && save_bundle();
    }
    html_spacer();
    if ($success) {
        html_title("REGISTERED");
    } else {
        html_title("!!! ERROR !!!");
    }
    html_spacer();
    echo "<table>\n";
    foreach ($out1 as $out) {
        echo "<tr><td>{$out}</td></tr>\n";
    }
    echo "</table>\n";
    return $status;
}

                    $row_rsCheckPass = mysqli_fetch_assoc($rsCheckPass);
                    $totalRows_rsCheckPass = mysqli_num_rows($rsCheckPass);
                }
                // does posted password match current password
                if ($currentpass != $row_rsCheckPass[PASS_FLD]) {
                    $error = "Your current password was entered incorrectly.";
                }
                // if there are no users, or more than one, then return an error
                if ($totalRows_rsCheckPass != 1) {
                    $error = "Your current password was entered incorrectly.";
                }
            }
            if (empty($error)) {
                $loginmessage = change_password($_SESSION['user_id'], $newpass);
            } else {
                $loginmessage = $error;
            }
        }
        // text variables
        $pass_title = "Change Password Service";
        $pass_intro = "\n\t\t\t<p>Please complete this form to change your password. Once your password has been changed successfully you will need to log in again.</p>\n\t\t\t<p><strong>NOTE: Your new password must be between 6 - 10 characters.</strong></p>";
        $pass_form = "\n\t\t\t<form name=\"changepass\" method=\"post\" action=\"" . $_SERVER['PHP_SELF'] . "?" . $_SERVER['QUERY_STRING'] . "\">\n\t\t\t\t<p><label for=\"currentpass\">Current Password:</label><br/>\n\t\t\t\t\t<input name=\"currentpass\" type=\"password\" id=\"currentpass\" class=\"loginpass\"></p>\n\t\t\t\t<p><label for=\"newpass\">New Password:</label><br/>\n\t\t\t\t\t<input name=\"newpass\" id=\"newpass\" type=\"password\" class=\"loginpass\"></p>\n\t\t\t\t<p><label for=\"newpass2\">Re-enter New Password:</label><br/>\n\t\t\t\t\t<input name=\"newpass2\" type=\"password\" id=\"newpass2\" class=\"loginpass\"></p>\n\t\t\t\t<p><input type=\"submit\" class=\"button\" name=\"change\" value=\"Change\"></p>\n\t\t\t\t</form>\n\t\t\t";
        break;
    default:
        echo "not allowed";
        break;
}
// show html page framework
echo html_header($pass_title);
echo "<div id=\"page\">" . html_title() . "<div id=\"content\">\n\t\t\n\t\t<h1>" . $pass_title . "</h1>\n\t\t\n\t\t<p class=\"loginmessage\">" . $loginmessage . "</p>\n\n\t\t" . $pass_intro . $pass_form . "<p>If you experience any problems with this form please email " . AD_ADMIN_EMAIL . "</p>\n\n\t\t</div>\n\t</div>" . html_footer();

}
# install_state
#   0 = no checks done
#   1 = server ok, get database information
#   2 = check the database information
#   3 = install the database
#   4 = get additional config file information
#   5 = write the config file
#	6 = post install checks
#	7 = done, link to login or db updater
$t_install_state = gpc_get_int('install', 0);
html_begin();
html_head_begin();
html_css_link('admin.css');
html_content_type();
html_title('Administration - Installation');
html_javascript_link('jquery-1.9.1.min.js');
html_javascript_link('install.js');
html_head_end();
?>

<body>
<table width="100%" cellspacing="0" cellpadding="0" bgcolor="#ffffff">
	<tr class="top-bar">
		<td class="links">
			[ <a href="index.php">Back to Administration</a> ]
		</td>
		<td class="title">
		<?php 
switch ($t_install_state) {
    case 6:

<?php

/**
 * @file zotero.php
 *
 * Explain how to use with Zotero
 *
 */
require_once '../config.inc.php';
require_once dirname(__FILE__) . '/html.php';
global $config;
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('Zotero - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(false);
?>
<div style="float:right;padding:10px;"><img src="static/zotero_z_32px.png" alt="zotero logo"/></div>
<h1>Using BioStor with Zotero</h1>


<p><a href="http://www.zotero.org">Zotero</a> is a Firefox extension for collecting and managing bibliographic references. You can use Zotero to capture citations from BioStor, and you can also link to references in BioStor from within Zotero using OpenURL. Note that the instructions below assume that you are using version 2.0 or Zotero.</p>

<h2>Storing citations</h2>
<p>Zotero can detect when a BioStor page contains bibliograpic information, and you can import that information into you Zotero library in the normal way (see the Zotero page <a href="http://www.zotero.org/support/getting_stuff_into_your_library">Getting stuff into your library</a>).</p>

<h2>Set up OpenURL linking</h2>
<p>To enable OpenURL linking go the <b>Actions</b> button in Zotero and click 
on the <b>Preferences</b> command:</p>

function display_bhl_result_html($referent, $hits)
{
    global $config;
    header("Content-type: text/html; charset=utf-8\n\n");
    echo html_html_open();
    echo html_head_open();
    echo html_title('Reference Finder - ' . $config['site_name']);
    echo html_include_css('css/main.css');
    echo html_include_css('css/lightbox.css');
    echo html_include_script('js/fadeup.js');
    echo html_include_script('js/prototype.js');
    echo html_include_script('js/scriptaculous.js?load=effects,builder');
    echo html_include_script('js/lightbox.js');
    // Handle user accepting a hit
    echo '<script type="text/javascript">';
    echo 'function store(form_id, page_id)
{
var form = $(form_id);
//alert($(form).serialize());

// Update database
var success	= function(t){updateSuccess(t);}
var failure	= function(t){updateFailure(t);}

var url = "update.php";
var pars = $(form).serialize() + "&PageID=" + page_id;
var myAjax = new Ajax.Request(url, {method:"post", postBody:pars, onSuccess:success, onFailure:failure});
}

function updateSuccess (t)
{
var s = t.responseText.evalJSON();
//alert(t.responseText);
if (s.is_valid)
{
// we\'ve stored reference, so reload page, which will redirect us to page for reference
window.location.reload(true);
}
else
{
// User did not pass recaptcha so refresh it
Recaptcha.create("' . $config['recaptcha_publickey'] . '",
	"recaptcha_div", {
	theme: "clean",
	callback: Recaptcha.focus_response_field
});
//fadeUp($(recaptcha_div),255,255,153);
}
}

function updateFailure (t)
{
	var s = t.responseText.evalJSON();
	alert("Badness happened:\\n" + t.responseText);
}';
    // Based on http://ne0phyte.com/blog/2008/09/02/javascript-keypress-event/
    // and http://blog.evandavey.com/2008/02/how-to-capture-return-key-from-field.html
    // I want to capture enter key press in recaptcha to avoid submitting the form (user must click
    // on button for that). We listen for keypress and eat it. Note that we attach the listener after
    // the window has loaded.
    echo 'function onMyTextKeypress(event)
{
if (Event.KEY_RETURN == event.keyCode) 
{
// do something usefull
//alert(\'Enter key was pressed.\');		
Event.stop(event);
}
return;
}
Event.observe(window, \'load\', function() {
Event.observe(\'recaptcha_response_field\', \'keypress\', onMyTextKeypress);
});';
    echo '</script>';
    echo html_head_close();
    echo html_body_open();
    echo html_page_header(false);
    echo '<h1>Reference Finder results</h1>';
    if (count($hits) != 0) {
        echo '<form id="metadata_form" action=\'#\'>';
        // referent metadata (hidden). By populating form we can pass metadata to
        // update.php via Ajax call
        echo reference_hidden_form($referent);
        echo '<table border="0" cellpadding="10">';
        foreach ($hits as $hit) {
            echo '<tr>';
            // Thumbnail of page
            echo '<td valign="top">';
            echo '<a href="bhl_image.php?PageID=' . $hit->PageID . '" rel="lightbox">';
            echo '<img style="border:1px solid rgb(128,128,128);" src="bhl_image.php?PageID=' . $hit->PageID . '&amp;thumbnail" alt="page thumbnail"/>';
            echo '</a>';
            echo '</td>';
            // Details of match
            echo '<td valign="top">';
            echo '<div style="margin-bottom:4px;">' . $hit->snippet . '</div>';
            echo "<div><span>Title match score = " . $hit->score . "</span></div>";
            echo '<div><span>BHL PageID </span><a href="http://www.biodiversitylibrary.org/page/' . $hit->PageID . '">' . $hit->PageID . '</a></div>';
            // Action
            echo '<br/><span style="padding:2px;cursor:pointer;background-color:#2D7BB2;color:white;font-size:18px;font-family:Arial;text-align:center" onclick="store(\'metadata_form\', \'' . $hit->PageID . '\');">&nbsp;Click here to accept this match&nbsp;</span>';
            echo '</td>';
//.........这里部分代码省略.........

//.........这里部分代码省略.........
        // genbank sequence
        if (in_array('http://purl.uniprot.org/core/Molecule', $type)) {
            $xsl_filename = 'xsl/genbank.xsl';
        }
        // taxon concept
        if (in_array('http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept', $type)) {
            $xsl_filename = 'xsl/taxonomy.xsl';
        }
        // Collection
        if (in_array('http://rs.tdwg.org/ontology/voc/Collection#Collection', $type)) {
            $xsl_filename = 'xsl/collection.xsl';
        }
        // Specimen (by itself)
        if (in_array('http://rs.tdwg.org/ontology/voc/TaxonOccurrence#TaxonOccurrence', $type) && !in_array('http://purl.uniprot.org/core/Molecule', $type)) {
            $xsl_filename = 'xsl/occurrence.xsl';
        }
        //------------------------------------------------------------------------------------------
        if ($xsl_filename != '') {
            $xp = new XsltProcessor();
            $xsl = new DomDocument();
            $xsl->load($xsl_filename);
            $xp->importStylesheet($xsl);
            $html = $xp->transformToXML($dom);
        } else {
            $html .= '<p/>';
            $html .= '<div style="padding:10px;background:white;-webkit-border-radius:10px;">';
            $html .= '<pre class="brush:xml">' . htmlentities($dom->saveXML(), ENT_COMPAT, 'UTF-8') . '</pre>';
            $html .= '</div>';
        }
        // Display...
        header("Content-type: text/html; charset=utf-8\n\n");
        echo html_html_open();
        echo html_head_open();
        echo html_title($topic_title);
        echo html_include_css('css/main.css');
        echo html_include_script('js/prototype.js');
        echo html_include_script('js/lookahead.js');
        echo html_include_script('js/browse.js');
        // RDF display
        echo html_include_script('js/shCore.js');
        echo html_include_script('js/shBrushXml.js');
        echo html_include_css('css/shCore.css');
        echo html_include_css('css/shThemeDefault.css');
        echo html_head_close();
        echo html_body_open();
        //echo html_page_header(true, $uri);
        echo '<div id="container">' . "\n";
        echo '   <div id="banner">' . "\n";
        echo html_page_header(true, $uri);
        echo '   </div>' . "\n";
        /*echo '<div id="nav">';
        		echo '   </div>' . "\n";
        		echo '<div id="content">';
        		echo 'xxxxxx';
        		echo '   </div>' . "\n"; */
        /*		echo '<div class="main">';
        		
        		echo '<div class="maincontent">';
        		echo '<div class="maincontent_border">'; */
        if (1) {
            echo $html;
        } else {
            ?>
<div id="nav">
  <div>
    <b>On the Web</b>

 function DisplayHtml()
 {
     global $config;
     header("Content-type: text/html; charset=utf-8\n\n");
     echo html_html_open();
     echo html_head_open();
     echo html_title($this->GetTitle() . ' - ' . $config['site_name']);
     $this->DisplayHtmlHead();
     echo html_head_close();
     $this->DisplayBodyOpen();
     $this->DisplayMicroformat();
     $this->DisplayHtmlContent();
     echo html_body_close($this->display_disqus);
     // true to show Disqus comments
     echo html_html_close();
 }

<?php

/**
 * @file referrer.php
 *
 * Explain how to use with Firefox
 *
 */
require_once '../config.inc.php';
require_once dirname(__FILE__) . '/html.php';
global $config;
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('OpenURL Referrer - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(false);
?>
<div style="float:right;padding:10px;"><img src="static/extensionItem.png" alt="extension logo"/></div>
<h1>Using BioStor with Firefox OpenURL Referrer Add-on</h1>

<p><a href="https://addons.mozilla.org/en-US/firefox/addon/4150">OpenURL Referrer</a> is a Firefox extension that converts bibliographic citations in the form of <a href="http://ocoins.info/">COinS</a> into URLs.</p>

<h2>Set up OpenURL linking</h2>
<p>Once you have installed OpenURL Referrer in Firefox, go to the <b>Tools</b> menu and choose the <b>Add-ons</b> command. This will display the list of installed Add-ons:</p>

<div style="text-align:center;"><img src="static/addons.png" width="400" alt="addons"/></div>

<p>Select <b>OpenURL Referrer</b> and click on the <b>Preferences</b> button to display the Preferences dialog box:</p>

 * @param integer $p_errors Whether to show all errors.
 * @return string url
 */
function mode_url($p_all, $p_errors)
{
    return basename(__FILE__) . '?' . http_build_query(array('show_all' => (int) $p_all, 'show_errors' => (int) $p_errors));
}
$t_link = '<a href="%s">%s %s</a>';
$t_show_all_mode_link = sprintf($t_link, mode_url(!$g_show_all, $g_show_errors), $g_show_all ? 'Hide' : 'Show', 'passed tests');
$t_show_errors_mode_link = sprintf($t_link, mode_url($g_show_all, !$g_show_errors), $g_show_errors ? 'Hide' : 'Show', 'verbose error messages');
http_content_headers();
html_begin();
html_head_begin();
html_css_link('admin.css');
html_content_type();
html_title('MantisBT Administration - Check Installation');
html_head_end();
?>

<body>

<?php 
html_top_banner();
?>

<p class="notice">Verbosity: <?php 
echo $t_show_all_mode_link;
?>
 | <?php 
echo $t_show_errors_mode_link;
?>

<?php

/**
 * @file mendeley.php
 *
 * Explain how to use with Mendeley
 *
 */
require_once '../config.inc.php';
require_once dirname(__FILE__) . '/html.php';
global $config;
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('Mendeley - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(false);
?>
<div style="float:right;padding:10px;"><img src="static/mendeleybox_bigger.png"  width="48" alt="mendeley logo"/></div>
<h1>Using BioStor with Mendeley</h1>

<p><a href="http://www.mendeley.com/">Mendeley</a> is social software for managing research papers. Because BioStor supports <a href="http://ocoins.info/">COinS</a>, the <a href="http://www.mendeley.com/import/">Mendeley Web Importer</a> can import bibliographic data from BioStor pages. If you are using Firefox and install the <a href="referrer.php">OpenURL Referrer Add-on</a> then if a reference in Mendeley doesn't have a URL, Mendeley will display a link (labelled "BioStor") next to each reference. Clicking on that link will take you to BioStor's OpenURL resolver.</p>

<?php 
echo html_body_close();
echo html_html_close();

<?php

/**
 * @file endnote.php
 *
 * Explain how to use with EndNote page
 *
 */
require_once '../config.inc.php';
require_once dirname(__FILE__) . '/html.php';
global $config;
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('EndNote - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(false);
?>
<div style="float:right;padding:10px;"><img src="static/endnote.png" width="48" height="48" alt="endnote logo"/></div><h1>Using BioStor with EndNote</h1>

<p>You can link to BioStor references from within <a href="http://www.endnote.com/">EndNote&reg;</a>.</p>

<h2>Set up OpenURL linking</h2>
<p>To enable OpenURL linking go to <b>EndNote Preferences</b> and click 
on <b>OpenURL</b>. You should see a dialog box similar to this one (the example is from EndNote 9 on Mac OS X):</p>

<div style="text-align:center;"><img src="static/endnote_openurl.png" width="400" alt="endnote openurl"/></div>

<p>Do the following:</p>
<ol>

/**
 * Print the part of the page that comes before meta redirect tags should be inserted
 * @param string $p_page_title Page title.
 * @return void
 */
function html_page_top1($p_page_title = null)
{
    html_begin();
    html_head_begin();
    html_content_type();
    $t_meta = config_get_global('meta_include_file');
    if (!is_blank($t_meta)) {
        include $t_meta;
    }
    global $g_robots_meta;
    if (!is_blank($g_robots_meta)) {
        echo "\t", '<meta name="robots" content="', $g_robots_meta, '" />', "\n";
    }
    html_title($p_page_title);
    html_css();
    html_rss_link();
    $t_favicon_image = config_get('favicon_image');
    if (!is_blank($t_favicon_image)) {
        echo "\t", '<link rel="shortcut icon" href="', helper_mantis_url($t_favicon_image), '" type="image/x-icon" />', "\n";
    }
    # Advertise the availability of the browser search plug-ins.
    $t_title = config_get('search_title');
    $t_searches = array('text', 'id');
    foreach ($t_searches as $t_type) {
        echo "\t", '<link rel="search" type="application/opensearchdescription+xml" ', 'title="' . sprintf(lang_get("opensearch_{$t_type}_description"), $t_title) . '" ', 'href="' . string_sanitize_url('browser_search_plugin.php?type=' . $t_type, true) . '"/>', "\n";
    }
    html_head_javascript();
}

$sql = 'SELECT DISTINCT reference_id FROM rdmp_reference_specimen_joiner
INNER JOIN rdmp_specimen USING(occurrenceID)
WHERE datasetID = ' . $datasetID;
$ids = array();
$result = $db->Execute($sql);
if ($result == false) {
    die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
while (!$result->EOF) {
    $ids[] = $result->fields['reference_id'];
    $result->MoveNext();
}
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('GBIF dataset ' . $datasetID . ' - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(true);
$dataset = specimens_dataset($datasetID);
echo '<h1>' . count($ids) . ' references citing occurrences from GBIF dataset ' . $dataset->dataResourceName . ' (' . $dataset->providerName . ')' . '</h1>';
echo '<p><a href="gbif_data.php">View all GBIF datasets in BioStor</a></p>';
echo '<p><a href="http://data.gbif.org/datasets/resource/' . $datasetID . '/" target="_new">View ' . $dataset->dataResourceName . ' dataset at GBIF</a></p>';
echo '<table cellspacing="0" cellpadding="2" width="100%">';
foreach ($ids as $reference_id) {
    $reference = db_retrieve_reference($reference_id);
    echo '<tr';
    if (in_array($reference_id, $act_refs)) {
        echo ' style="background-color:#D8F3C9;"';
    }
    echo '>';

<?php

// to restrict guest access to this page set the $guest_access variable to match
// settings stored in the guest_areas field in the database
// $guest_access = 'pr';
$embedded_login = isset($_GET['embedded']) ? 1 : 0;
$login_type = isset($_GET['embedded']) ? "Embedded" : "Conventional";
include 'restrict.php';
echo html_header($login_type . ' login test page');
?>

<div id="page">
	<?php 
echo html_title();
?>
	
	<div id="content">
	<h1>Bouncer - <?php 
echo $login_type;
?>
 login test page</h1>
	
		<p>Unrestricted content - viewable by all users</p>
		<?php 
if (!empty($hidecontent)) {
    //echo $mini_login;
    echo mini_login();
} else {
    // this is the restricted content
    ?>
			<p><b>This is the restricted content.</b></p>

function html_pathlinks($proj, $cid, $path)
{
    $str = '';
    $str .= $path != '' ? html_ahref(array('p' => $proj, 'c' => $cid), $proj) : $proj;
    $dirs = explode('/', $path);
    $base = array_pop($dirs);
    $f = '';
    foreach ($dirs as $d) {
        $f .= $f == '' ? $d : "/{$d}";
        $str .= ' / ' . html_ahref(array('p' => $proj, 'c' => $cid, 'f' => $f), $d);
    }
    $str .= " / {$base}";
    return html_title($str);
}

/**
 * login_form
 * 
 * generates complete login form page
 *
 * @return $login_form - complete html code
 */
function login_form()
{
    global $bouncer_message;
    global $bouncer_page;
    // global $target_page;
    global $pre;
    $target = $_SERVER['HTTP_HOST'] . $_SERVER['REQUEST_URI'];
    $target = substr($target, 0, 7) != "http://" ? "http://" . $target : $target;
    // put together html
    $login_form = html_header("Login Page");
    $login_form .= "\n\t\t<div class=\"page_clear\"></div>\n\t\t<div id=\"page\">\n\t\t" . html_title() . "\n\t\t\t<div id=\"content\">";
    if (isset($bouncer_message['error'])) {
        $login_form .= "\n\t\t\t\t<div id=\"login_message\">" . $bouncer_message['error'] . "</div>";
    }
    if (!empty($bouncer_message['general'])) {
        $login_form .= "\n\t\t\t\t<div id=\"general_message\">" . $bouncer_message['general'] . "</div>";
    }
    $login_form .= '			
				<h2>Please enter your email address and password to login</h2>
				
				<form id="bouncer_loginform" name ="bouncer_loginform" method="post" action="' . $target . '">
				
				<p><label for="email">Email address:</label><br/>
					<input name="email" type="email" id="email" /></p>
				
				<p><label for="pass">Password:</label><br/>
					<input name="pass" id="pass" type="password" /></p>
				
				<p><label for="remember">Remember Me:</label>
					<input name="remember" type="checkbox" id="remember" /></p>
				
				<p><input type="hidden" name="bounce" value="' . md5(constant($pre . 'BOUNCE_WEB_ROOT')) . '" />
					<input type="submit" name="login" value="Login" /></p>
				</form>
				
				<h2>
				<a href="' . $bouncer_page['password_email'] . '">Forgotten your password?</a>
				</h2>
		
			</div>
		</div>
		';
    $login_form .= html_footer();
    return $login_form;
}

function display_outlet($outlet)
{
    global $couch;
    global $config;
    // clean
    $outlet = stripcslashes($outlet);
    echo html_html_open();
    echo html_head_open();
    echo html_title($outlet . ' - ' . $config['site_name']);
    echo html_include_css('css/main.css');
    echo html_include_script('js/jquery-1.4.4.min.js');
    echo html_head_close();
    echo html_body_open();
    echo '<div style="padding:10px;">';
    //----------------------------------------------------------------------------------------------
    // Home
    echo '<span><a href="' . $config['web_root'] . '">' . $config['site_name'] . '</a></span>';
    echo html_search_box();
    //----------------------------------------------------------------------------------------------
    // Outlet
    echo '<h1>' . $outlet . '</h1>';
    //http://localhost:5984/afd/_design/publication/_view/outlet_year_volume?startkey=[%22Annals%20And%20Magazine%20of%20Natural%20History%22]&endkey=[%22Annals%20And%20Magazine%20of%20Natural%20History\ufff0%22]
    $startkey = array($outlet);
    $endkey = array($outlet . '\\ufff0');
    $resp = $couch->send("GET", "/" . $config['couchdb'] . "/_design/publication/_view/outlet_year_volume?startkey=" . urlencode(json_encode($startkey)) . "&endkey=" . urlencode(json_encode($endkey)));
    $articles = json_decode($resp);
    //print_r($articles);
    $num_articles = count($articles->rows);
    if (count($articles) == 0) {
    } else {
        echo '<h2>Articles in this publication (' . $num_articles . ')</h2>';
        if ($num_articles < 20) {
            // list view
            echo '<ul>';
            foreach ($articles->rows as $row) {
                $resp = $couch->send("GET", "/" . $config['couchdb'] . "/" . $row->value);
                $publication = json_decode($resp);
                if (isset($publication->error)) {
                    // We don't have this reference
                } else {
                    echo '<li style="list-style-type:none;">' . display_one_publication($publication) . '</li>';
                }
            }
            echo '</ul>';
        } else {
            // treemap view (should do this with a CouchDB index...)
            $years = array();
            foreach ($articles->rows as $row) {
                $resp = $couch->send("GET", "/" . $config['couchdb'] . "/" . $row->value);
                $publication = json_decode($resp);
                if (isset($publication->error)) {
                    // We don't have this reference
                } else {
                    $year = 'YYYY';
                    if (isset($publication->year)) {
                        $year = $publication->year;
                    }
                    if (!isset($years[$publication->year])) {
                        $years[$publication->year] = array();
                    }
                    $years[$publication->year][] = $row->value;
                }
            }
            // Get sizes of categories
            $size = array();
            foreach ($years as $p) {
                $sizes[] = count($p);
            }
            // Get size of rectangle we want to draw this in
            $r = new Rectangle(0, 0, 400, 500);
            // Construct quantum treemap
            $qt = new QuantumTreemap($sizes, 1.0, $r);
            $qt->quantumLayout();
            $json = $qt->export2json();
            $obj = json_decode($json);
            // Add category labels and list of object ids to each cell in treemap
            $i = 0;
            foreach ($years as $k => $v) {
                $obj->rects[$i]->label = $k;
                $obj->rects[$i]->ids = array();
                foreach ($v as $id) {
                    $obj->rects[$i]->ids[] = $id;
                }
                $i++;
            }
            // Treemap
            echo "\n";
            echo '<div style="position:relative">';
            draw($obj);
            echo '</div>' . "\n";
        }
    }
    echo '<div>';
    echo html_body_close(false);
    echo html_html_close();
}

<?php

/**
 * @file guide.php
 *
 * Tutorial page
 *
 */
require_once '../config.inc.php';
require_once dirname(__FILE__) . '/html.php';
global $config;
header("Content-type: text/html; charset=utf-8\n\n");
echo html_html_open();
echo html_head_open();
echo html_title('Guide to using BioStor - ' . $config['site_name']);
echo html_head_close();
echo html_body_open();
echo html_page_header(false);
echo '<h1>Guide to using Biostor</h1>
<p>This page provides a guide to using BioStor to find a reference. At its heart BioStor is an OpenURL resolver, wich you can use either from within bibliographic software and web sites, or through BioStor\'s web interface.</p>

<h2>Using BioStor as a service</h2>
<p>You can use BioStor to find references from within <a href="endnote.php">EndNote</a> and <a href="zotero.php">Zotero</a>. If you use the Firefox web browser you could install the <a href="referrer.php">OpenURL Referrer add on</a>, which will add the same functionality to sites that support support COinS, such as <a href="mendeley.php">Mendeley</a>.</p>
<p>If you are using BioStor in this way, you can skip the next ahead to...</p>

<h2>Using the web interface</h2>
<p>BioStor\'s OpenURL resolver provides a <a href="openurl.php">query form</a> for entering the bibliographic details of the reference you are searching for. You can enter these details directly, or have BioStor parse the citation for you.</p>

<h3>Citation parser</h3>
<p>BioStor has a simple citation parser:</p>
<div style="text-align:center;"><img src="static/citation.png" alt="citation"/></div>

function display_form()
{
    global $config;
    header("Content-type: text/html; charset=utf-8\n\n");
    echo html_html_open();
    echo html_head_open();
    echo html_title($config['site_name']);
    echo html_include_css('css/main.css');
    echo html_head_close();
    echo html_body_open();
    echo '<div style="padding:10px;">';
    echo '<h1>OpenURL resolver</h1>';
    // Stuff to go here...
    echo '<h1>' . $config['site_name'] . '</h1>';
    echo '<p>This is a simple OpenURL resolver for </p>';
    echo '<h2>COinS support</h2>';
    echo '<p>If you have a web browser that has extensions that support COinS (e.g., Chrome, Firefox) then set the OpenURL resolver to <b>' . $config['web_server'] . $config['web_root'] . 'openurl' . '</b></p>';
    echo '<p>Otherwise you can drag this bookmarklet ';
    echo '<a href="' . "javascript:(function(){var%20co_d=document;var%20co_s=co_d.getElementsByTagName('span');for(i%20in%20co_s){var%20co_c=co_s[i];var%20co_n=co_c.className;if(co_n%20&&%20co_n.indexOf('Z3988')!=-1){var%20co_a=co_d.createElement('a');co_a.setAttribute('href','http://iphylo.org/~rpage/afd/openurl?'+co_c.getAttribute('title'));co_text=co_d.createTextNode('OpenURL');co_a.appendChild(co_text);co_c.appendChild(co_a);}}})();" . '">AFD OpenURL</a>';
    echo ' to your bookmarks:</p>';
    echo '</div>';
    echo html_body_close(true);
    echo html_html_close();
}