<?php

// Project: Web Reference Database (refbase) <http://www.refbase.net>

// Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's

// original author(s).

//

// This code is distributed in the hope that it will be useful,

// but WITHOUT ANY WARRANTY. Please see the GNU General Public

// License for more details.

//

// File: ./update.php

// Repository: $HeadURL: http://svn.code.sf.net/p/refbase/code/trunk/update.php $

// Author(s): Matthias Steffens <mailto:refbase@extracts.de>

//

// Created: 01-Mar-05, 20:47

// Modified: $Date: 2013-09-27 14:45:07 -0700 (Fri, 27 Sep 2013) $

// $Author: karnesky $

// $Revision: 1382 $

// This file will update any refbase MySQL database installation from v0.8.0 or greater to v0.9.6.

// (Note that this script currently doesn't offer any conversion from 'latin1' to 'utf8')

// CAUTION: YOU MUST REMOVE THIS SCRIPT FROM YOUR WEB DIRECTORY AFTER THE UPDATE!!

// Incorporate some include files:

include 'initialize/db.inc.php'; // 'db.inc.php' is included to hide username and password

include 'includes/header.inc.php'; // include header

include 'includes/footer.inc.php'; // include footer

include 'includes/include.inc.php'; // include common functions

include 'includes/install.inc.php'; // include install/update functions

include 'initialize/ini.inc.php'; // include common variables

// --------------------------------------------------------------------

// START A SESSION:

// call the 'start_session()' function (from 'include.inc.php') which will also read out available session variables:

start_session(false);

// --------------------------------------------------------------------

// Initialize preferred display language:

// (note that 'locales.inc.php' has to be included *after* the call to the 'start_session()' function)

include 'includes/locales.inc.php'; // include the locales

// --------------------------------------------------------------------

// This specifies the name of the database that handles the MySQL user access privileges.

// Unless you've fiddled with it, you shouldn't change the default value ('mysql'):

$adminDatabaseName = 'mysql';

// Extract any parameters passed to the script:

if (isset($_REQUEST['adminUserName']))

$adminUserName = $_REQUEST['adminUserName'];

else

$adminUserName = "";

if (isset($_REQUEST['adminPassword']))

$adminPassword = $_REQUEST['adminPassword'];

else

$adminPassword = "";

// --------------------------------------------------------------------

// Check the correct parameters have been passed:

if (empty($adminUserName) AND empty($adminPassword))

{

// if 'update.php' was called without any valid parameters:

// Display an update form:

if (isset($_SESSION['errors']))

{

$errors = $_SESSION['errors'];

// Note: though we clear the session variable, the current error message is still available to this script via '$errors':

deleteSessionVariable("errors"); // function 'deleteSessionVariable()' is defined in 'include.inc.php'

}

else

$errors = array(); // initialize the '$errors' variable in order to prevent 'Undefined variable...' messages

if (isset($_SESSION['formVars']))

{

$formVars = $_SESSION['formVars'];

// Note: though we clear the session variable, the current form variables are still available to this script via '$formVars':

deleteSessionVariable("formVars");

}

else

{

// Reset the '$formVars' variable (since we're providing the default values):

$formVars = array();

// provide the default values:

$formVars["adminUserName"] = "root";

$formVars["adminPassword"] = "";

}

// If there's no stored message available:

if (!isset($_SESSION['HeaderString']))

{

if (empty($errors)) // provide the default message:

$HeaderString = "To update refbase v0.8.0 or greater please fill out the form below and click the <em>Update</em> button:";

else // -> there were errors when validating the fields

$HeaderString = "<b><span class=\"warning\">There were validation errors regarding the details you entered. Please check the comments above the respective fields:</span></b>";

}

else

{

$HeaderString = $_SESSION['HeaderString']; // extract 'HeaderString' session variable (only necessary if register globals is OFF!)

// Note: though we clear the session variable, the current message is still available to this script via '$HeaderString':

deleteSessionVariable("HeaderString");

}

// Extract the view type requested by the user (either 'Mobile', 'Print', 'Web' or ''):

// ('' will produce the default 'Web' output style)

if (isset($_REQUEST['viewType']))

$viewType = $_REQUEST['viewType'];

else

$viewType = "";

// Show the login status:

showLogin(); // (function 'showLogin()' is defined in 'include.inc.php')

// DISPLAY header:

// call the 'displayHTMLhead()' and 'showPageHeader()' functions (which are defined in 'header.inc.php'):

displayHTMLhead(encodeHTML($officialDatabaseName) . " -- Update", "index,follow", "Update form for the " . encodeHTML($officialDatabaseName), "", false, "", $viewType, array());

showPageHeader($HeaderString);

// Start <form> and <table> holding the form elements:

?>

<form action="update.php" method="POST">

<input type="hidden" name="formType" value="update">

<input type="hidden" name="submit" value="Update"><?php // provide a default value for the 'submit' form tag. Otherwise, some browsers may not recognize the correct output format when a user hits <enter> within a form field (instead of clicking the "Update" button) ?>

<table align="center" border="0" cellpadding="0" cellspacing="12" width="95%" summary="This table holds the update form">

<tr>

<td colspan="3"><h3>refbase Update</h3></td>

</tr>

<tr>

<td width="190" valign="top"><b>Important Notes:</b></td>

<td valign="top" colspan="2">

It's important that you make a <span class="warning">backup</span> copy of your original files <em>db.inc.php</em> and <em>ini.inc.php</em> (which are located within the <em>initialize</em> subdirectory of your refbase base directory). We also strongly recommend to <a href="http://backup.refbase.net/" target="top" title="Instructions how to backup your refbase MySQL database">backup</a> your existing refbase MySQL database before proceeding.

<br>

<br>

Before executing this script, you <span class="warning">must edit</span> the updated include file <span class="warning"><em>initialize/db.inc.php</em></span> in a text editor and re-enter the values from your old <em>db.inc.php</em> file for the variables <em>$databaseName</em>, <em>$username</em> and <em>$password</em>. Then, proceed with this form:

</td>

</tr>

<tr>

<td valign="top"><b>MySQL Admin User:</b></td>

<td valign="top"><?php echo fieldError("adminUserName", $errors); ?>

<input type="text" name="adminUserName" value="<?php echo $formVars["adminUserName"]; ?>" size="30">

</td>

<td valign="top">Give the name of an administrative user that has full access to your MySQL database. Often, this is the <em>root</em> user.</td>

</tr>

<tr>

<td valign="top"><b>MySQL Admin Password:</b></td>

<td valign="top"><?php

// the form won't remember the password, so we'll ask the user to re-type it...

if (!empty($errors) AND !isset($errors["adminPassword"])) // ...if there were some validation errors but not with the password field

echo "\n\t\t\t<b>Please type your password again:</b>\n\t\t\t<br>";

else

echo fieldError("adminPassword", $errors);

?>

<input type="password" name="adminPassword" size="30">

</td>

<td valign="top">Please enter the password for the administrative user you've specified above.</td>

</tr>

<tr>

<td valign="top">&nbsp;</td>

<td valign="top" align="right">

<input type="submit" name="submit" value="Update">

</td>

<td valign="top">&nbsp;</td>

</tr>

</table>

</form><?php

// --------------------------------------------------------------------

// DISPLAY THE HTML FOOTER:

// call the 'showPageFooter()' and 'displayHTMLfoot()' functions (which are defined in 'footer.inc.php')

showPageFooter($HeaderString);

displayHTMLfoot();

// --------------------------------------------------------------------

}

else // some parameters have been passed, so let's validate the fields:

{

// --------------------------------------------------------------------

// Clear any errors that might have been found previously:

$errors = array();

// Write the (POST) form variables into an array:

foreach($_POST as $varname => $value)

$formVars[$varname] = $value;

// Validate the 'adminUserName' field:

if (empty($formVars["adminUserName"]))

// The 'adminUserName' field cannot be a null string

$errors["adminUserName"] = "This field cannot be blank:";

// Validate the 'adminPassword' field:

if (empty($formVars["adminPassword"]))

// The 'adminPassword' field cannot be a null string

$errors["adminPassword"] = "This field cannot be blank:";

// --------------------------------------------------------------------

// Now the script has finished the validation, check if there were any errors:

if (count($errors) > 0)

{

// Write back session variables:

saveSessionVariable("errors", $errors); // function 'saveSessionVariable()' is defined in 'include.inc.php'

saveSessionVariable("formVars", $formVars);

// There are errors. Relocate back to the update form:

header("Location: update.php");

exit; // >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !EXIT! <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

}

// --------------------------------------------------------------------

// If we made it here, then the data is considered valid!

// (0) CLOSE EXISTING CONNECTION

// we have to close the existing connection since we need to establish a new connection with admin permissions

disconnectFromMySQLDatabase(); // function 'disconnectFromMySQLDatabase()' is defined in 'include.inc.php'

// (1) OPEN ADMIN CONNECTION, (2) SELECT DATABASE

connectToMySQLDatabaseAsAdmin($adminUserName, $adminPassword); // function 'connectToMySQLDatabaseAsAdmin()' is defined in 'install.inc.php'

// --------------------------------------------------------------------

// (2) RUN the SQL queries on the database through the admin connection:

// NOTE: many simple, brain-dead UPDATE queries follow below

// (we should probably have a SQL function and/or make this an array and process that)

$resultArray = array();

// Alter table specification for table 'deleted'

// TODO: create a new function 'changeColumn()' that only modifies the column spec if the new column spec is different from the old one

$query = "ALTER table " . $tableDeleted . " MODIFY edition varchar(50) default NULL";

$result = queryMySQLDatabase($query);

$resultArray["Table 'deleted': altered table specification. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0); // get the number of rows that were modified (or return 0 if an error occurred)

$query = "ALTER table " . $tableDeleted . " MODIFY thesis enum('Bachelor''s thesis','Honours thesis','Master''s thesis','Ph.D. thesis','Diploma thesis','Doctoral thesis','Habilitation thesis') default NULL";

$result = queryMySQLDatabase($query);

$resultArray["Table 'deleted': altered table specification. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Alter table specification for table 'refs'

$query = "ALTER table " . $tableRefs . " MODIFY edition varchar(50) default NULL";

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': altered table specification. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "ALTER table " . $tableRefs . " MODIFY thesis enum('Bachelor''s thesis','Honours thesis','Master''s thesis','Ph.D. thesis','Diploma thesis','Doctoral thesis','Habilitation thesis') default NULL";

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': altered table specification. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Add field 'version' to table 'deleted'

$properties = "MEDIUMINT(8) UNSIGNED DEFAULT 1 AFTER modified_by";

$resultArray["Table 'deleted': added field 'version'"] = addColumnIfNotExists("version", $tableDeleted, $properties); // function 'addColumnIfNotExists()' is defined in 'install.inc.php'

// Add field 'version' to table 'refs'

$properties = "MEDIUMINT(8) UNSIGNED DEFAULT 1 AFTER modified_by";

$resultArray["Table 'refs': added field 'version'"] = addColumnIfNotExists("version", $tableRefs, $properties);

// Update table 'refs'

$query = "UPDATE " . $tableRefs . " SET thesis = NULL WHERE thesis = ''"; // this fix is required to ensure correct sorting when outputting citations with '$citeOrder="type"' or '$citeOrder="type-year"'

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'thesis' field (replaced empty string with NULL). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableRefs . " SET type = 'Conference Article' WHERE type RLIKE '^(Unsupported: )?Conference Proceeding$'"; // this may not be perfect since some items of type "Conference Proceeding" may be actually a "Conference Volume"

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'type' field ('Conference Proceeding' => 'Conference Article'). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableRefs . " SET type = 'Miscellaneous' WHERE type RLIKE '^(Unsupported: )?Generic$'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'type' field ('Generic' => 'Miscellaneous'). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableRefs . " SET type = 'Newspaper Article' WHERE type RLIKE '^(Unsupported: )?Newspaper$'"; // this may not be perfect since some items of type "Newspaper" may be actually a "Newspaper Volume"

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'type' field ('Newspaper' => 'Newspaper Article'). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableRefs . " SET type = 'Software' WHERE type RLIKE '^(Unsupported: )?Computer Program$'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'type' field ('Computer Program' => 'Software'). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableRefs . " SET type = REPLACE(type,'Unsupported: ','') WHERE type RLIKE '^Unsupported: (Abstract|Conference (Article|Volume)|Magazine Article|Manual|Miscellaneous|Newspaper Article|Patent|Report|Software)$'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'refs': updated 'type' field (removed 'Unsupported' label for all newly supported types). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Add new utilities to table 'depends'

$values = "(NULL, 'pdftotext', 'true', NULL)";

$resultArray["Table 'depends': inserted entry for 'pdftotext' utility"] = insertIfNotExists(array("depends_external" => "pdftotext"), $tableDepends, $values);

// Create new MySQL table 'user_options'

$properties = "(option_id MEDIUMINT(8) UNSIGNED NOT NULL AUTO_INCREMENT PRIMARY KEY, "

. "user_id MEDIUMINT(8) UNSIGNED NOT NULL DEFAULT '0', "

. "export_cite_keys ENUM('yes','no') NOT NULL DEFAULT 'yes', "

. "autogenerate_cite_keys ENUM('yes','no') NOT NULL DEFAULT 'yes', "

. "prefer_autogenerated_cite_keys ENUM('no','yes') NOT NULL DEFAULT 'no', "

. "use_custom_cite_key_format ENUM('no','yes') NOT NULL DEFAULT 'no', "

. "cite_key_format VARCHAR(255) DEFAULT NULL, "

. "uniquify_duplicate_cite_keys ENUM('yes','no') NOT NULL DEFAULT 'yes', "

. "nonascii_chars_in_cite_keys ENUM('transliterate','strip','keep') DEFAULT NULL, "

. "use_custom_text_citation_format ENUM('no','yes') NOT NULL DEFAULT 'no', "

. "text_citation_format VARCHAR(255) DEFAULT NULL, "

. "records_per_page SMALLINT(5) UNSIGNED DEFAULT NULL, "

. "show_auto_completions ENUM('yes','no') NOT NULL DEFAULT 'yes', "

. "main_fields TEXT, "

. "INDEX (user_id))";

$resultArray["Created table 'user_options'"] = addTableIfNotExists($tableUserOptions, $properties); // function 'addTableIfNotExists()' is defined in 'install.inc.php'

// Insert default user options for anyone who's not logged in

$values = "(NULL, 0, 'yes', 'yes', 'no', 'no', '<:authors:><:year:>', 'yes', NULL, 'no', '<:authors[2| & | et al.]:>< :year:>< {:recordIdentifier:}>', NULL, 'author, title, publication, keywords, abstract')";

$resultArray["Table 'user_options': inserted default options for anyone who's not logged in"] = insertIfNotExists(array("user_id" => 0), $tableUserOptions, $values); // function 'insertIfNotExists()' is defined in 'install.inc.php'

// Insert default user options for all users

// First, check how many users are contained in table 'users':

$query = "SELECT user_id, first_name, last_name FROM " . $tableUsers;

$result = queryMySQLDatabase($query); // function 'queryMySQLDatabase()' is defined in 'include.inc.php'

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0) // If there were rows (= user IDs) found ...

{

while ($row = @ mysql_fetch_array($result))

{

$values = "(NULL, " . $row['user_id'] . ", 'yes', 'yes', 'no', 'yes', '<:authors[2|+|++]:><:year:>', 'yes', 'transliterate', 'no', '<:authors[2| & | et al.]:>< :year:>< {:recordIdentifier:}>', NULL, 'author, title, publication, keywords, abstract')";

$resultArray["Table 'user_options': inserted default options for user " . $row['user_id'] . " (" . $row['first_name'] . " " . $row['last_name'] . ")"] = insertIfNotExists(array("user_id" => $row['user_id']), $tableUserOptions, $values);

}

}

// Add field 'records_per_page' to table 'user_options'

$properties = "SMALLINT(5) UNSIGNED DEFAULT NULL AFTER text_citation_format";

$resultArray["Table 'user_options': added field 'records_per_page'"] = addColumnIfNotExists("records_per_page", $tableUserOptions, $properties);

// Add field 'show_auto_completions' to table 'user_options'

$properties = "ENUM('yes','no') NOT NULL DEFAULT 'yes' AFTER records_per_page";

$resultArray["Table 'user_options': added field 'show_auto_completions'"] = addColumnIfNotExists("show_auto_completions", $tableUserOptions, $properties);

// Add field 'main_fields' to table 'user_options'

$properties = "TEXT AFTER show_auto_completions";

$resultArray["Table 'user_options': added field 'main_fields'"] = addColumnIfNotExists("main_fields", $tableUserOptions, $properties);

// Add field 'allow_browse_view' to table 'user_permissions'

$properties = "ENUM('yes','no') NOT NULL DEFAULT 'yes' AFTER allow_print_view";

$resultArray["Table 'user_permissions': added field 'allow_browse_view'"] = addColumnIfNotExists("allow_browse_view", $tableUserPermissions, $properties);

// Add field 'allow_list_view' to table 'user_permissions'

$properties = "ENUM('yes','no') NOT NULL DEFAULT 'yes' AFTER allow_upload";

$resultArray["Table 'user_permissions': added field 'allow_list_view'"] = addColumnIfNotExists("allow_list_view", $tableUserPermissions, $properties);

// Disable the Browse view feature (which isn't done yet) for all users

$query= "UPDATE " . $tableUserPermissions . " SET allow_browse_view = 'no'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'user_permissions': disabled the Browse view feature (which isn't done yet). Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Enable the Export feature for anyone who's not logged in ('$userID = 0'):

$query= "UPDATE " . $tableUserPermissions . " SET allow_export = 'yes', allow_batch_export = 'yes' WHERE user_id = 0";

$result = queryMySQLDatabase($query);

$resultArray["Table 'user_permissions': enabled the export feature for anyone who's not logged in. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Update table 'styles'

$query = "UPDATE " . $tableStyles . " SET style_spec = REPLACE(style_spec,'cite_','styles/cite_') WHERE style_spec RLIKE '^cite_'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'style_spec' field. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$values = "(NULL, 'Ann Glaciol', 'true', 'styles/cite_AnnGlaciol_JGlaciol.php', 'B010', '1')";

$resultArray["Table 'styles': inserted style 'Ann Glaciol'"] = insertIfNotExists(array("style_name" => "Ann Glaciol"), $tableStyles, $values);

$values = "(NULL, 'J Glaciol', 'true', 'styles/cite_AnnGlaciol_JGlaciol.php', 'B030', '1')";

$resultArray["Table 'styles': inserted style 'J Glaciol'"] = insertIfNotExists(array("style_name" => "J Glaciol"), $tableStyles, $values);

$values = "(NULL, 'APA', 'true', 'styles/cite_APA.php', 'A010', '1')";

$resultArray["Table 'styles': inserted style 'APA'"] = insertIfNotExists(array("style_name" => "APA"), $tableStyles, $values);

$values = "(NULL, 'AMA', 'true', 'styles/cite_AMA.php', 'A020', '1')";

$resultArray["Table 'styles': inserted style 'AMA'"] = insertIfNotExists(array("style_name" => "AMA"), $tableStyles, $values);

$values = "(NULL, 'MLA', 'true', 'styles/cite_MLA.php', 'A030', '1')";

$resultArray["Table 'styles': inserted style 'MLA'"] = insertIfNotExists(array("style_name" => "MLA"), $tableStyles, $values);

$values = "(NULL, 'Chicago', 'true', 'styles/cite_Chicago.php', 'A070', '1')";

$resultArray["Table 'styles': inserted style 'Chicago'"] = insertIfNotExists(array("style_name" => "Chicago"), $tableStyles, $values);

$values = "(NULL, 'Harvard 1', 'true', 'styles/cite_Harvard_1.php', 'A090', '1')";

$resultArray["Table 'styles': inserted style 'Harvard 1'"] = insertIfNotExists(array("style_name" => "Harvard 1"), $tableStyles, $values);

$values = "(NULL, 'Harvard 2', 'true', 'styles/cite_Harvard_2.php', 'A093', '1')";

$resultArray["Table 'styles': inserted style 'Harvard 2'"] = insertIfNotExists(array("style_name" => "Harvard 2"), $tableStyles, $values);

$values = "(NULL, 'Harvard 3', 'true', 'styles/cite_Harvard_3.php', 'A096', '1')";

$resultArray["Table 'styles': inserted style 'Harvard 3'"] = insertIfNotExists(array("style_name" => "Harvard 3"), $tableStyles, $values);

$values = "(NULL, 'Vancouver', 'true', 'styles/cite_Vancouver.php', 'A110', '1')";

$resultArray["Table 'styles': inserted style 'Vancouver'"] = insertIfNotExists(array("style_name" => "Vancouver"), $tableStyles, $values);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B010' WHERE style_name = 'Ann Glaciol'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'Ann Glaciol' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B020' WHERE style_name = 'Deep Sea Res'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'Deep Sea Res' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B030' WHERE style_name = 'J Glaciol'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'J Glaciol' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B040' WHERE style_name = 'Mar Biol'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'Mar Biol' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B050' WHERE style_name = 'MEPS'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'MEPS' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'B060' WHERE style_name = 'Polar Biol'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'Polar Biol' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableStyles . " SET order_by = 'C010' WHERE style_name = 'Text Citation'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'styles': updated 'Text Citation' style. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Update table 'types'

$query = "UPDATE " . $tableTypes . " SET order_by = '01' WHERE type_name = 'Journal Article'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Journal Article' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '02' WHERE type_name = 'Abstract'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Abstract' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '03' WHERE type_name = 'Book Chapter'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Book Chapter' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '04' WHERE type_name = 'Book Whole'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Book Whole' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '05' WHERE type_name = 'Conference Article'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Conference Article' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '06' WHERE type_name = 'Conference Volume'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Conference Volume' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '07' WHERE type_name = 'Journal'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Journal' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '08' WHERE type_name = 'Magazine Article'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Magazine Article' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '09' WHERE type_name = 'Manual'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Manual' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '10' WHERE type_name = 'Manuscript'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Manuscript' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '11' WHERE type_name = 'Map'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Map' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '12' WHERE type_name = 'Miscellaneous'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Miscellaneous' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '13' WHERE type_name = 'Newspaper Article'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Newspaper Article' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '14' WHERE type_name = 'Patent'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Patent' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '15' WHERE type_name = 'Report'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Report' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableTypes . " SET order_by = '16' WHERE type_name = 'Software'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'types': updated 'Software' type. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$values = "(NULL, 'Abstract', 'true', 2, '02')";

$resultArray["Table 'types': inserted type 'Abstract'"] = insertIfNotExists(array("type_name" => "Abstract"), $tableTypes, $values);

$values = "(NULL, 'Conference Article', 'true', 2, '05')";

$resultArray["Table 'types': inserted type 'Conference Article'"] = insertIfNotExists(array("type_name" => "Conference Article"), $tableTypes, $values);

$values = "(NULL, 'Conference Volume', 'true', 3, '06')";

$resultArray["Table 'types': inserted type 'Conference Volume'"] = insertIfNotExists(array("type_name" => "Conference Volume"), $tableTypes, $values);

$values = "(NULL, 'Magazine Article', 'true', 1, '08')";

$resultArray["Table 'types': inserted type 'Magazine Article'"] = insertIfNotExists(array("type_name" => "Magazine Article"), $tableTypes, $values);

$values = "(NULL, 'Manual', 'true', 3, '09')";

$resultArray["Table 'types': inserted type 'Manual'"] = insertIfNotExists(array("type_name" => "Manual"), $tableTypes, $values);

$values = "(NULL, 'Miscellaneous', 'true', 3, '12')";

$resultArray["Table 'types': inserted type 'Miscellaneous'"] = insertIfNotExists(array("type_name" => "Miscellaneous"), $tableTypes, $values);

$values = "(NULL, 'Newspaper Article', 'true', 1, '13')";

$resultArray["Table 'types': inserted type 'Newspaper Article'"] = insertIfNotExists(array("type_name" => "Newspaper Article"), $tableTypes, $values);

$values = "(NULL, 'Patent', 'true', 3, '14')";

$resultArray["Table 'types': inserted type 'Patent'"] = insertIfNotExists(array("type_name" => "Patent"), $tableTypes, $values);

$values = "(NULL, 'Report', 'true', 3, '15')";

$resultArray["Table 'types': inserted type 'Report'"] = insertIfNotExists(array("type_name" => "Report"), $tableTypes, $values);

$values = "(NULL, 'Software', 'true', 3, '16')";

$resultArray["Table 'types': inserted type 'Software'"] = insertIfNotExists(array("type_name" => "Software"), $tableTypes, $values);

// Add new language options to table 'languages'

$values = "(NULL, 'fr', 'true', '3')";

$resultArray["Table 'languages': inserted French language option"] = insertIfNotExists(array("language_name" => "fr"), $tableLanguages, $values);

$values = "(NULL, 'es', 'false', '4')";

$resultArray["Table 'languages': inserted Spanish language option"] = insertIfNotExists(array("language_name" => "es"), $tableLanguages, $values);

$values = "(NULL, 'cn', 'true', '5')";

$resultArray["Table 'languages': inserted Chinese language option"] = insertIfNotExists(array("language_name" => "cn"), $tableLanguages, $values);

$values = "(NULL, 'ru', 'true', '6')";

$resultArray["Table 'languages': inserted Russian language option"] = insertIfNotExists(array("language_name" => "ru"), $tableLanguages, $values);

$values = "(NULL, 'ja', 'true', '7')";

$resultArray["Table 'languages': inserted Japanese language option"] = insertIfNotExists(array("language_name" => "ja"), $tableLanguages, $values);

// Enable disabled localizations

$query = "UPDATE " . $tableLanguages . " SET language_enabled = 'true' WHERE language_name = 'de'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'languages': enabled German language option. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Alter table specification for table 'formats'

$query = "ALTER table " . $tableFormats . " MODIFY format_type enum('export','import','cite') NOT NULL default 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': altered table specification. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Update existing formats in table 'formats'

$query = "UPDATE " . $tableFormats . " SET format_name = 'BibTeX' WHERE format_name = 'Bibtex'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': renamed format name 'Bibtex' to 'BibTeX'. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Update existing import formats in table 'formats'

$query = "UPDATE " . $tableFormats . " SET format_spec = 'bibutils/import_bib2refbase.php', order_by = 'A010' WHERE format_name = 'BibTeX' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'BibTeX' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A020' WHERE format_name = 'Copac' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Copac' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A030' WHERE format_name = 'CSA' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'CSA' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_spec = 'bibutils/import_end2refbase.php', order_by = 'A040' WHERE format_name = 'Endnote' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Endnote' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A045' WHERE format_name = 'Endnote XML' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Endnote XML' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_name = 'ISI', format_spec = 'import_isi2refbase.php', order_by = 'A050', depends_id = 1 WHERE (format_name = 'RIS (ISI)' OR format_name = 'ISI') AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'ISI' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A060' WHERE format_name = 'Pubmed Medline' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Pubmed Medline' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_spec = 'bibutils/import_med2refbase.php', order_by = 'A065' WHERE format_name = 'Pubmed XML' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Pubmed XML' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A070' WHERE format_name = 'RefWorks' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'RefWorks' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_spec = 'import_ris2refbase.php', order_by = 'A080', depends_id = 1 WHERE format_name = 'RIS' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'RIS' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A090' WHERE format_name = 'SciFinder' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'SciFinder' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A100' WHERE format_name = 'Text (Tab-Delimited)' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Text (Tab-Delimited)' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A150' WHERE format_name = 'CrossRef XML' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'CrossRef XML' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_spec = 'bibutils/import_modsxml2refbase.php', order_by = 'A160', depends_id = 2 WHERE format_name = 'MODS XML' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'MODS XML' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'A170' WHERE format_name = 'OAI_DC XML' AND format_type = 'import'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'OAI_DC XML' import format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Add new import formats in table 'formats'

$values = "(NULL, 'Copac', 'import', 'true', 'bibutils/import_copac2refbase.php', 'A020', 2)";

$resultArray["Table 'formats': inserted 'Copac' import format"] = insertIfNotExists(array("format_name" => "Copac", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'CSA', 'import', 'true', 'import_csa2refbase.php', 'A030', 1)";

$resultArray["Table 'formats': inserted 'CSA' import format"] = insertIfNotExists(array("format_name" => "CSA", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'Endnote XML', 'import', 'true', 'bibutils/import_endx2refbase.php', 'A045', 2)";

$resultArray["Table 'formats': inserted 'Endnote XML' import format"] = insertIfNotExists(array("format_name" => "Endnote XML", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'Pubmed Medline', 'import', 'true', 'import_medline2refbase.php', 'A060', 1)";

$resultArray["Table 'formats': inserted 'Pubmed Medline' import format"] = insertIfNotExists(array("format_name" => "Pubmed Medline", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'RefWorks', 'import', 'true', 'import_refworks2refbase.php', 'A070', 1)";

$resultArray["Table 'formats': inserted 'RefWorks' import format"] = insertIfNotExists(array("format_name" => "RefWorks", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'SciFinder', 'import', 'true', 'import_scifinder2refbase.php', 'A090', 1)";

$resultArray["Table 'formats': inserted 'SciFinder' import format"] = insertIfNotExists(array("format_name" => "SciFinder", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'Text (Tab-Delimited)', 'import', 'true', 'import_tabdelim2refbase.php', 'A100', 1)";

$resultArray["Table 'formats': inserted 'Text (Tab-Delimited)' import format"] = insertIfNotExists(array("format_name" => "Text (Tab-Delimited)", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'arXiv XML', 'import', 'true', 'import_arxiv2refbase.php', 'A130', 1)";

$resultArray["Table 'formats': inserted 'arXiv XML' import format"] = insertIfNotExists(array("format_name" => "arXiv XML", "format_type" => "import"), $tableFormats, $values);

$values = "(NULL, 'CrossRef XML', 'import', 'true', 'import_crossref2refbase.php', 'A150', 1)";

$resultArray["Table 'formats': inserted 'CrossRef XML' import format"] = insertIfNotExists(array("format_name" => "CrossRef XML", "format_type" => "import"), $tableFormats, $values);

// Update existing export formats in table 'formats'

$query = "UPDATE " . $tableFormats . " SET order_by = 'B010' WHERE format_name = 'BibTeX' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'BibTeX' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B040' WHERE format_name = 'Endnote' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Endnote' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B050' WHERE format_name = 'ISI' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'ISI' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B080' WHERE format_name = 'RIS' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'RIS' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B105' WHERE format_name = 'Text (CSV)' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Text (CSV)' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_name = 'Atom XML', format_enabled = 'true', format_spec ='export_atomxml.php', order_by = 'B140' WHERE format_name = 'OpenSearch RSS' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'OpenSearch RSS' export format, and renamed it to 'Atom XML'. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B160' WHERE format_name = 'MODS XML' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'MODS XML' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B170' WHERE format_name = 'OAI_DC XML' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'OAI_DC XML' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B180' WHERE format_name = 'ODF XML' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'ODF XML' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET format_name = 'SRW_MODS XML', order_by = 'B195' WHERE format_name = 'SRW XML' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'SRW XML' export format, and renamed it to 'SRW_MODS XML'. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'B200' WHERE format_name = 'Word XML' AND format_type = 'export'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Word XML' export format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Add new export formats in table 'formats'

$values = "(NULL, 'ADS', 'export', 'true', 'bibutils/export_xml2ads.php', 'B005', 2)";

$resultArray["Table 'formats': inserted 'ADS' export format"] = insertIfNotExists(array("format_name" => "ADS", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'ISI', 'export', 'true', 'bibutils/export_xml2isi.php', 'B050', 2)";

$resultArray["Table 'formats': inserted 'ISI' export format"] = insertIfNotExists(array("format_name" => "ISI", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'Atom XML', 'export', 'true', 'export_atomxml.php', 'B140', 1)";

$resultArray["Table 'formats': inserted 'Atom XML' export format"] = insertIfNotExists(array("format_name" => "Atom XML", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'OAI_DC XML', 'export', 'true', 'export_oaidcxml.php', 'B170', 1)";

$resultArray["Table 'formats': inserted 'OAI_DC XML' export format"] = insertIfNotExists(array("format_name" => "OAI_DC XML", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'ODF XML', 'export', 'true', 'export_odfxml.php', 'B180', 1)";

$resultArray["Table 'formats': inserted 'ODF XML' export format"] = insertIfNotExists(array("format_name" => "ODF XML", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'SRW_DC XML', 'export', 'true', 'export_srwxml.php', 'B190', 1)";

$resultArray["Table 'formats': inserted 'SRW_DC XML' export format"] = insertIfNotExists(array("format_name" => "SRW_DC XML", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'SRW_MODS XML', 'export', 'true', 'export_srwxml.php', 'B195', 1)";

$resultArray["Table 'formats': inserted 'SRW_MODS XML' export format"] = insertIfNotExists(array("format_name" => "SRW_MODS XML", "format_type" => "export"), $tableFormats, $values);

$values = "(NULL, 'Word XML', 'export', 'true', 'bibutils/export_xml2word.php', 'B200', 2)";

$resultArray["Table 'formats': inserted 'Word XML' export format"] = insertIfNotExists(array("format_name" => "Word XML", "format_type" => "export"), $tableFormats, $values);

// Update existing citation formats in table 'formats'

$query = "UPDATE " . $tableFormats . " SET order_by = 'C010' WHERE format_name = 'html' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'html' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C020' WHERE format_name = 'RTF' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'RTF' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C030' WHERE format_name = 'PDF' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'PDF' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C040' WHERE format_name = 'LaTeX' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'LaTeX' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C045' WHERE format_name = 'LaTeX .bbl' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'LaTeX .bbl' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C050' WHERE format_name = 'Markdown' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'Markdown' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

$query = "UPDATE " . $tableFormats . " SET order_by = 'C060' WHERE format_name = 'ASCII' AND format_type = 'cite'";

$result = queryMySQLDatabase($query);

$resultArray["Table 'formats': updated 'ASCII' citation format. Affected rows"] = ($result ? mysql_affected_rows($connection) : 0);

// Add new citation formats in table 'formats'

$values = "(NULL, 'html', 'cite', 'true', 'formats/cite_html.php', 'C010', 1)";

$resultArray["Table 'formats': inserted 'html' citation format"] = insertIfNotExists(array("format_name" => "html", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'RTF', 'cite', 'true', 'formats/cite_rtf.php', 'C020', 1)";

$resultArray["Table 'formats': inserted 'RTF' citation format"] = insertIfNotExists(array("format_name" => "RTF", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'PDF', 'cite', 'true', 'formats/cite_pdf.php', 'C030', 1)";

$resultArray["Table 'formats': inserted 'PDF' citation format"] = insertIfNotExists(array("format_name" => "PDF", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'LaTeX', 'cite', 'true', 'formats/cite_latex.php', 'C040', 1)";

$resultArray["Table 'formats': inserted 'LaTeX' citation format"] = insertIfNotExists(array("format_name" => "LaTeX", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'LaTeX .bbl', 'cite', 'true', 'formats/cite_latex_bbl.php', 'C045', 1)";

$resultArray["Table 'formats': inserted 'LaTeX .bbl' citation format"] = insertIfNotExists(array("format_name" => "LaTeX .bbl", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'Markdown', 'cite', 'true', 'formats/cite_markdown.php', 'C050', 1)";

$resultArray["Table 'formats': inserted 'Markdown' citation format"] = insertIfNotExists(array("format_name" => "Markdown", "format_type" => "cite"), $tableFormats, $values);

$values = "(NULL, 'ASCII', 'cite', 'true', 'formats/cite_ascii.php', 'C060', 1)";

$resultArray["Table 'formats': inserted 'ASCII' citation format"] = insertIfNotExists(array("format_name" => "ASCII", "format_type" => "cite"), $tableFormats, $values);

// Enable some of the existing export formats (which were previously disabled by default) for anyone who's not logged in ('$userID = 0'):

// Fetch IDs for all formats that shall be enabled:

$formatIDArray = array();

$query = "SELECT format_id, format_name FROM " . $tableFormats . " WHERE (format_name RLIKE '^(BibTeX|Endnote|RIS)$' AND format_type = 'export')";

$result = queryMySQLDatabase($query);

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0)

{

while ($row = @ mysql_fetch_array($result))

$formatIDArray[$row['format_id']] = $row['format_name'];

}

foreach ($formatIDArray as $formatID => $formatName)

{

$values = "(NULL, " . $formatID . ", 0, 'true')";

$resultArray["Table 'user_formats': enabled format '" . $formatName . "' for anyone who's not logged in"] = insertIfNotExists(array("format_id" => $formatID), $tableUserFormats, $values, "0");

}

// Enable some of the newly created export/citation formats, citation styles & resource types for all users:

// Fetch IDs for all formats that shall be enabled:

$formatIDArray = array();

$query = "SELECT format_id, format_name FROM " . $tableFormats . " WHERE (format_name RLIKE '^(ISI|ODF XML|Word XML)$' AND format_type = 'export') OR (format_name RLIKE '^(html|RTF|PDF|LaTeX)$' AND format_type = 'cite')";

$result = queryMySQLDatabase($query);

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0)

{

while ($row = @ mysql_fetch_array($result))

$formatIDArray[$row['format_id']] = $row['format_name'];

}

// Fetch IDs for all styles that shall be enabled:

$styleIDArray = array();

$query = "SELECT style_id, style_name FROM " . $tableStyles . " WHERE style_name RLIKE '^(AMA|APA|Chicago|Harvard( [0-9]+)?|J Glaciol|MLA|Vancouver)$'";

$result = queryMySQLDatabase($query);

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0)

{

while ($row = @ mysql_fetch_array($result))

$styleIDArray[$row['style_id']] = $row['style_name'];

}

// Fetch IDs for all types that shall be enabled:

$typeIDArray = array();

$query = "SELECT type_id, type_name FROM " . $tableTypes . " WHERE type_name RLIKE '^(Abstract|Conference Article|Conference Volume|Magazine Article|Manual|Miscellaneous|Newspaper Article|Patent|Report|Software)$'";

$result = queryMySQLDatabase($query);

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0)

{

while ($row = @ mysql_fetch_array($result))

$typeIDArray[$row['type_id']] = $row['type_name'];

}

// Enable formats, styles & types for anyone who's not logged in ('$userID = 0'):

foreach ($formatIDArray as $formatID => $formatName)

{

$values = "(NULL, " . $formatID . ", 0, 'true')";

$resultArray["Table 'user_formats': enabled format '" . $formatName . "' for anyone who's not logged in"] = insertIfNotExists(array("format_id" => $formatID), $tableUserFormats, $values, "0");

}

foreach ($styleIDArray as $styleID => $styleName)

{

$values = "(NULL, " . $styleID . ", 0, 'true')";

$resultArray["Table 'user_styles': enabled style '" . $styleName . "' for anyone who's not logged in"] = insertIfNotExists(array("style_id" => $styleID), $tableUserStyles, $values, "0");

}

foreach ($typeIDArray as $typeID => $typeName)

{

$values = "(NULL, " . $typeID . ", 0, 'true')";

$resultArray["Table 'user_types': enabled type '" . $typeName . "' for anyone who's not logged in"] = insertIfNotExists(array("type_id" => $typeID), $tableUserTypes, $values, "0");

}

// Enable formats, styles & types for all users:

// First, check how many users are contained in table 'users':

$query = "SELECT user_id, first_name, last_name FROM " . $tableUsers;

$result = queryMySQLDatabase($query);

$rowsFound = @ mysql_num_rows($result);

if ($rowsFound > 0) // If there were rows (= user IDs) found ...

{

while ($row = @ mysql_fetch_array($result))

{

foreach ($formatIDArray as $formatID => $formatName)

{

$values = "(NULL, " . $formatID . ", " . $row['user_id'] . ", 'true')";

$resultArray["Table 'user_formats': enabled format '" . $formatName . "' for user " . $row['user_id'] . " (" . $row['first_name'] . " " . $row['last_name'] . ")"] = insertIfNotExists(array("format_id" => $formatID), $tableUserFormats, $values, $row['user_id']);

}

foreach ($styleIDArray as $styleID => $styleName)

{

$values = "(NULL, " . $styleID . ", " . $row['user_id'] . ", 'true')";

$resultArray["Table 'user_styles': enabled style '" . $styleName . "' for user " . $row['user_id'] . " (" . $row['first_name'] . " " . $row['last_name'] . ")"] = insertIfNotExists(array("style_id" => $styleID), $tableUserStyles, $values, $row['user_id']);

}

foreach ($typeIDArray as $typeID => $typeName)

{

$values = "(NULL, " . $typeID . ", " . $row['user_id'] . ", 'true')";

$resultArray["Table 'user_types': enabled type '" . $typeName . "' for user " . $row['user_id'] . " (" . $row['first_name'] . " " . $row['last_name'] . ")"] = insertIfNotExists(array("type_id" => $typeID), $tableUserTypes, $values, $row['user_id']);

}

}

}

// (3) ERRORS

// Check whether any tables/rows were affected by the performed SQL queries:

unset($resultArray["Table 'deleted': altered table specification. Affected rows"]); // currently, we simply remove again the results of the 'ALTER TABLE' queries since they will always affect every row in that table

unset($resultArray["Table 'refs': altered table specification. Affected rows"]);

unset($resultArray["Table 'formats': altered table specification. Affected rows"]);

foreach($resultArray as $varname => $value)

if (($value == "0") OR ($value == "false"))

unset($resultArray[$varname]); // remove any action that didn't affect any table or rows

if (empty($resultArray))

{

$HeaderString = "<b><span class=\"ok\">Nothing was changed! Your refbase installation is up-to-date.</span></b>";

// Write back session variables:

saveSessionVariable("HeaderString", $HeaderString);

}

// (4) CLOSE ADMIN CONNECTION

disconnectFromMySQLDatabase();

// --------------------------------------------------------------------

// Provide a feedback page:

// If there's no stored message available:

if (!isset($_SESSION['HeaderString'])) // provide a default message:

{

$HeaderString = "<b><span class=\"ok\">Update of the Web Reference Database was successful!</span></b>";

}

else

{

$HeaderString = $_SESSION['HeaderString']; // extract 'HeaderString' session variable (only necessary if register globals is OFF!)

// Note: though we clear the session variable, the current message is still available to this script via '$HeaderString':

deleteSessionVariable("HeaderString");

}

// Extract the view type requested by the user (either 'Mobile', 'Print', 'Web' or ''):

// ('' will produce the default 'Web' output style)

if (isset($_REQUEST['viewType']))

$viewType = $_REQUEST['viewType'];

else

$viewType = "";

// Show the login status:

showLogin(); // (function 'showLogin()' is defined in 'include.inc.php')

// DISPLAY header:

// call the 'displayHTMLhead()' and 'showPageHeader()' functions (which are defined in 'header.inc.php'):

displayHTMLhead(encodeHTML($officialDatabaseName) . " -- Update Feedback", "index,follow", "Update feedback for the " . encodeHTML($officialDatabaseName), "", false, "", $viewType, array());

showPageHeader($HeaderString);

// Start a <table>:

?>

<table align="center" border="0" cellpadding="0" cellspacing="10" width="95%" summary="This table holds the update feedback info"><?php

if (!empty($resultArray)) // if something was changed, add a welcome title:

{

?>

<tr>

<td colspan="2"><h3>Welcome to refbase v0.9.6!</h3></td>

</tr><?php

}

// following note will be always displayed no matter if something was changed or not:

?>

<tr>

<td valign="top"><b>Important Note:</b></td>

<td>

The files <em>update.php</em> and <em>update.sql</em> (as well as <em>install.php</em> and <em>install.sql</em>) are only provided for update/installation purposes and are not needed anymore. Due to security considerations you should <span class="warning">remove these files</span> from your web directory NOW!!

</td>

</tr><?php

if (!empty($resultArray)) // if something was changed, add some configuration info:

{

?>

<tr>

<td valign="top"><b>Configure refbase:</b></td>

<td>

In order to re-establish your existing settings, please open file <em>initialize/ini.inc.php</em> in a text editor and restore all values from your old <em>ini.inc.php</em> file. The new include file contains new settings which you should check out and adopt to your needs if needed. Please see the comments within the file for further information.

</td>

</tr>

<tr>

<td valign="top"><b>Log:</b></td>

<td>

Following update actions were performed successfully:

</td>

</tr>

<tr>

<td valign="top">&nbsp;</td>

<td>

<pre><?php

foreach($resultArray as $varname => $value)

{

if ($value == "true")

echo $varname . ".\n";

else

echo $varname . ": " . $value . "\n";

}

?>

</pre>

</td>

</tr><?php

}

?>

</table><?php

// --------------------------------------------------------------------

// DISPLAY THE HTML FOOTER:

// call the 'showPageFooter()' and 'displayHTMLfoot()' functions (which are defined in 'footer.inc.php')

showPageFooter($HeaderString);

displayHTMLfoot();

// --------------------------------------------------------------------

}

?>