function handleFileUploads($uploadFile, $formVars)
{
global $filesBaseDir;
// these variables are defined in 'ini.inc.php'
global $moveFilesIntoSubDirectories;
global $dirNamingScheme;
global $renameUploadedFiles;
global $fileNamingScheme;
global $handleNonASCIIChars;
global $allowedFileNameCharacters;
global $allowedDirNameCharacters;
global $changeCaseInFileNames;
global $changeCaseInDirNames;
$tmpFilePath = $uploadFile["tmp_name"];
// Generate file name:
if ($renameUploadedFiles == "yes") {
if (preg_match("/.+\\.[^.]+\$/i", $uploadFile["name"])) {
// preserve any existing file name extension
$fileNameExtension = preg_replace("/.+(\\.[^.]+)\$/i", "\\1", $uploadFile["name"]);
} else {
$fileNameExtension = "";
}
// auto-generate a file name according to the naming scheme given in '$fileNamingScheme':
$newFileName = parsePlaceholderString($formVars, $fileNamingScheme, "<:serial:>");
// function 'parsePlaceholderString()' is defined in 'include.inc.php'
// handle non-ASCII and unwanted characters:
$newFileName = handleNonASCIIAndUnwantedCharacters($newFileName, $allowedFileNameCharacters, $handleNonASCIIChars);
// function 'handleNonASCIIAndUnwantedCharacters()' is defined in 'include.inc.php'
// add original file name extension:
$newFileName .= $fileNameExtension;
} else {
// take the file name as given by the user:
$newFileName = $uploadFile["name"];
}
// Generate directory structure:
if ($moveFilesIntoSubDirectories != "never") {
// remove any slashes (i.e., directory delimiter(s)) from the beginning or end of '$dirNamingScheme':
$dirNamingScheme = trimTextPattern($dirNamingScheme, "[\\/\\\\]+", true, true);
// function 'trimTextPattern()' is defined in 'include.inc.php'
$dirNamingSchemePartsArray = preg_split("#[/\\\\]+#", $dirNamingScheme);
// split on slashes to separate between multiple sub-directories
$subDirNamesArray = array();
// initialize array variable which will hold the generated sub-directory names
// auto-generate a directory name according to the naming scheme given in '$dirNamingScheme'
// and handle non-ASCII chars plus unwanted characters:
foreach ($dirNamingSchemePartsArray as $dirNamingSchemePart) {
// parse given placeholder string:
$subDirName = parsePlaceholderString($formVars, $dirNamingSchemePart, "");
// function 'parsePlaceholderString()' is defined in 'include.inc.php'
// handle non-ASCII and unwanted characters:
$subDirName = handleNonASCIIAndUnwantedCharacters($subDirName, $allowedDirNameCharacters, $handleNonASCIIChars);
// function 'handleNonASCIIAndUnwantedCharacters()' is defined in 'include.inc.php'
if (!empty($subDirName)) {
$subDirNamesArray[] = $subDirName;
}
}
if (!empty($subDirNamesArray)) {
$subDirName = implode("/", $subDirNamesArray) . "/";
} else {
$subDirName = "";
}
} else {
$subDirName = "";
}
// Perform any case transformations:
// change case of file name:
if (preg_match("/^(lower|upper)\$/i", $changeCaseInFileNames)) {
$newFileName = changeCase($changeCaseInFileNames, $newFileName);
}
// function 'changeCase()' is defined in 'include.inc.php'
// change case of DIR name:
if (preg_match("/^(lower|upper)\$/i", $changeCaseInDirNames) && !empty($subDirName)) {
$subDirName = changeCase($changeCaseInDirNames, $subDirName);
}
// Generate full destination path:
// - if '$moveFilesIntoSubDirectories = "existing"' and there's an existing sub-directory (within the default files directory '$filesBaseDir')
// whose name equals '$subDirName' we'll copy the new file into that sub-directory
// - if '$moveFilesIntoSubDirectories = "always"' and '$subDirName' isn't empty, we'll generate an appropriately named sub-directory if it
// doesn't exist yet
// - otherwise we just copy the file to the root-level of '$filesBaseDir':
if (!empty($subDirName) && ($moveFilesIntoSubDirectories == "existing" and is_dir($filesBaseDir . $subDirName) or $moveFilesIntoSubDirectories == "always")) {
$destFilePath = $filesBaseDir . $subDirName . $newFileName;
// new file will be copied into sub-directory within '$filesBaseDir'...
// copy the new subdir name & file name to the 'file' field variable:
// Note: if a user uploads a file and there was already a file specified within the 'file' field, the old file will NOT get removed
// from the files directory! Automatic file removal is omitted on purpose since it's way more difficult to recover an
// inadvertently deleted file than to delete it manually. However, future versions should introduce a smarter way of handling
// orphaned files...
$fileName = $subDirName . $newFileName;
if ($moveFilesIntoSubDirectories == "always" and !is_dir($filesBaseDir . $subDirName)) {
// make sure the directory we're moving the file to exists before proceeding:
recursiveMkdir($filesBaseDir . $subDirName);
}
} else {
$destFilePath = $filesBaseDir . $newFileName;
// new file will be copied to root-level of '$filesBaseDir'...
$fileName = $newFileName;
// copy the new file name to the 'file' field variable (see note above!)
}
// Copy uploaded file from temporary location to the default file directory specified in '$filesBaseDir':
// (for more on PHP file uploads see <http://www.php.net/manual/en/features.file-upload.php>)
move_uploaded_file($tmpFilePath, $destFilePath);
return $fileName;
}
function findDuplicates($sqlQuery, $originalDisplayType)
{
global $tableRefs, $tableUserData;
// defined in 'db.inc.php'
global $alnum, $alpha, $cntrl, $dash, $digit, $graph, $lower, $print, $punct, $space, $upper, $word, $patternModifiers;
// defined in 'transtab_unicode_charset.inc.php' and 'transtab_latin1_charset.inc.php'
// re-assign the correct display type (i.e. the view that was active when the user clicked the 'dups' link in the header):
if (!empty($originalDisplayType)) {
$displayType = $originalDisplayType;
}
// Extract form variables provided by the 'duplicateSearch' form in 'duplicate_search.php':
if (isset($_REQUEST['matchFieldsSelector'])) {
if (is_string($_REQUEST['matchFieldsSelector'])) {
// we accept a string containing a (e.g. comma delimited) list of field names
$selectedFieldsArray = preg_split("/[^a-z_]+/", $_REQUEST['matchFieldsSelector'], -1, PREG_SPLIT_NO_EMPTY);
} else {
// the field list is already provided as array:
$selectedFieldsArray = $_REQUEST['matchFieldsSelector'];
}
} else {
$selectedFieldsArray = array();
}
if (isset($_REQUEST['ignoreWhitespace']) and $_REQUEST['ignoreWhitespace'] == "1") {
$ignoreWhitespace = "1";
} else {
$ignoreWhitespace = "0";
}
if (isset($_REQUEST['ignorePunctuation']) and $_REQUEST['ignorePunctuation'] == "1") {
$ignorePunctuation = "1";
} else {
$ignorePunctuation = "0";
}
if (isset($_REQUEST['ignoreCharacterCase']) and $_REQUEST['ignoreCharacterCase'] == "1") {
$ignoreCharacterCase = "1";
} else {
$ignoreCharacterCase = "0";
}
if (isset($_REQUEST['ignoreAuthorInitials']) and $_REQUEST['ignoreAuthorInitials'] == "1") {
$ignoreAuthorInitials = "1";
} else {
$ignoreAuthorInitials = "0";
}
if (isset($_REQUEST['nonASCIIChars'])) {
$nonASCIIChars = $_REQUEST['nonASCIIChars'];
} else {
$nonASCIIChars = "keep";
}
// VALIDATE FORM DATA:
$errors = array();
// Validate the field selector:
if (empty($selectedFieldsArray)) {
$errors["matchFieldsSelector"] = "You must select at least one field:";
}
// Validate the 'SQL Query' field:
if (empty($sqlQuery)) {
$errors["sqlQuery"] = "You must specify a query string:";
} elseif (!preg_match("/^SELECT/i", $sqlQuery)) {
$errors["sqlQuery"] = "You can only execute SELECT queries:";
}
// Check if there were any errors:
if (count($errors) > 0) {
// In case of an error, we write all form variables back to the '$formVars' array
// (which 'duplicate_search.php' requires to reload form values):
foreach ($_REQUEST as $varname => $value) {
$formVars[$varname] = $value;
}
// Since checkbox form fields do only get included in the '$_REQUEST' array if they were marked,
// we have to add appropriate array elements for all checkboxes that weren't set:
if (!isset($formVars["ignoreWhitespace"])) {
$formVars["ignoreWhitespace"] = "0";
}
if (!isset($formVars["ignorePunctuation"])) {
$formVars["ignorePunctuation"] = "0";
}
if (!isset($formVars["ignoreCharacterCase"])) {
$formVars["ignoreCharacterCase"] = "0";
}
if (!isset($formVars["ignoreAuthorInitials"])) {
$formVars["ignoreAuthorInitials"] = "0";
}
if (!isset($formVars["showLinks"])) {
$formVars["showLinks"] = "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 'duplicate_search.php':
header("Location: duplicate_search.php");
exit;
// >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !EXIT! <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
}
// CONSTRUCT SQL QUERY (1. DUPLICATE SEARCH):
// To identify any duplicates within the results of the original query, we build a new query based on the original SQL query:
$query = $sqlQuery;
// Replace SELECT list of columns with those from '$selectedFieldsArray' (plus the 'serial' column):
$selectedFieldsString = implode(", ", $selectedFieldsArray);
$query = newSELECTclause("SELECT " . $selectedFieldsString . ", serial", $query, false);
// function 'newSELECTclause()' is defined in 'include.inc.php'
// Replace any existing ORDER BY clause with the list of columns given in '$selectedFieldsArray':
$query = newORDERclause("ORDER BY " . $selectedFieldsString, $query, false);
// function 'newORDERclause()' is defined in 'include.inc.php'
// Fix escape sequences within the SQL query:
$query = stripSlashesIfMagicQuotes($query);
// RUN the query on the database through the connection:
$result = queryMySQLDatabase($query);
// function 'queryMySQLDatabase()' is defined in 'include.inc.php'
// PROCESS RESULTS:
$recordSerialsArray = array();
$duplicateRecordSerialsArray = array();
$rowsFound = @mysql_num_rows($result);
// Identify any records with matching field data:
if ($rowsFound > 0) {
// Count the number of fields:
$fieldsFound = mysql_num_fields($result);
// Loop over each row in the result set:
for ($rowCounter = 0; $row = @mysql_fetch_array($result); $rowCounter++) {
$recordIdentifier = "";
// make sure our buffer variable is empty
// For each row, loop over each field (except for the last one which is the 'serial' field):
for ($i = 0; $i < $fieldsFound - 1; $i++) {
// fetch the current attribute name:
$fieldName = getMySQLFieldInfo($result, $i, "name");
// function 'getMySQLFieldInfo()' is defined in 'include.inc.php'
// normalize author names:
if ($fieldName == "author" and $ignoreAuthorInitials == "1") {
// this is a stupid hack that maps the names of the '$row' array keys to those used
// by the '$formVars' array (which is required by function 'parsePlaceholderString()')
// (eventually, the '$formVars' array should use the MySQL field names as names for its array keys)
$formVars = buildFormVarsArray($row);
// function 'buildFormVarsArray()' is defined in 'include.inc.php'
// ignore initials in author names:
$row[$i] = parsePlaceholderString($formVars, "<:authors[0||]:>", "");
// function 'parsePlaceholderString()' is defined in 'include.inc.php'
}
$recordIdentifier .= $row[$i];
// merge all field values to form a unique record identifier string
}
// Normalize record identifier string:
if ($ignoreWhitespace == "1") {
// ignore whitespace
$recordIdentifier = preg_replace("/\\s+/", "", $recordIdentifier);
}
if ($ignorePunctuation == "1") {
// ignore punctuation
$recordIdentifier = preg_replace("/[{$punct}]+/{$patternModifiers}", "", $recordIdentifier);
}
if ($ignoreCharacterCase == "1") {
// ignore character case
$recordIdentifier = strtolower($recordIdentifier);
}
if ($nonASCIIChars == "strip") {
// strip non-ASCII characters
$recordIdentifier = handleNonASCIIAndUnwantedCharacters($recordIdentifier, "\\S\\s", "strip");
} elseif ($nonASCIIChars == "transliterate") {
// transliterate non-ASCII characters
$recordIdentifier = handleNonASCIIAndUnwantedCharacters($recordIdentifier, "\\S\\s", "transliterate");
}
// Check whether the record identifier string has occurred already:
if (isset($recordSerialsArray[$recordIdentifier])) {
// this record identifier string has already been seen
$recordSerialsArray[$recordIdentifier][] = $row["serial"];
} else {
// new record identifier string
$recordSerialsArray[$recordIdentifier] = array($row["serial"]);
}
// add a new array element for this record's identifier string (and store its serial number as value within a sub-array)
}
// Collect all array elements from '$recordSerialsArray' where their sub-array contains more than one serial number:
foreach ($recordSerialsArray as $recordSerials) {
if (count($recordSerials) > 1) {
foreach ($recordSerials as $recordSerial) {
$duplicateRecordSerialsArray[] = $recordSerial;
}
}
// add this record's serial number to the array of duplicate record serials
}
} else {
// TODO!
}
if (empty($duplicateRecordSerialsArray)) {
$duplicateRecordSerialsArray[] = "0";
}
// if no duplicate records were found, the non-existing serial number '0' will result in a "nothing found" feedback
// CONSTRUCT SQL QUERY (2. DUPLICATES DISPLAY):
// To display any duplicates that were found within the results of the original query, we build again a new query based on the original SQL query:
$query = $sqlQuery;
// Replace WHERE clause:
// TODO: maybe make this into a generic function? (compare with function 'extractWHEREclause()' in 'include.inc.php')
$duplicateRecordSerialsString = implode("|", $duplicateRecordSerialsArray);
$query = preg_replace("/(?<=WHERE )(.+?)(?= ORDER BY| LIMIT| GROUP BY| HAVING| PROCEDURE| FOR UPDATE| LOCK IN|[ ;]+(SELECT|INSERT|UPDATE|DELETE|CREATE|ALTER|DROP|FILE)\\b|\$)/i", "serial RLIKE \"^(" . $duplicateRecordSerialsString . ")\$\"", $query);
// Replace any existing ORDER BY clause with the list of columns given in '$selectedFieldsArray':
$query = newORDERclause("ORDER BY " . $selectedFieldsString, $query, false);
return array($query, $displayType);
}
function generateCiteKey($formVars)
{
global $defaultCiteKeyFormat;
// defined in 'ini.inc.php'
global $handleNonASCIICharsInCiteKeysDefault;
global $userOptionsArray;
// '$userOptionsArray' is made globally available in file 'import_modify.php' as well as by functions 'generateExport()' and 'generateCitations()' in 'search.php'
// by default, we use any record-specific cite key that was entered manually by the user:
if (isset($formVars['citeKeyName'])) {
$citeKey = $formVars['citeKeyName'];
} else {
$citeKey = "";
}
// check if the user's options for auto-generation of cite keys command us to replace the manually entered cite key:
if (!empty($userOptionsArray)) {
if ($userOptionsArray['export_cite_keys'] == "yes") {
if ($userOptionsArray['autogenerate_cite_keys'] == "yes") {
if (empty($citeKey) or $userOptionsArray['prefer_autogenerated_cite_keys'] == "yes") {
if ($userOptionsArray['use_custom_cite_key_format'] == "yes") {
// if the user wants to use a custom cite key format
$citeKeyFormat = $userOptionsArray['cite_key_format'];
} else {
// use the default cite key format that was specified by the admin in 'ini.inc.php'
$citeKeyFormat = $defaultCiteKeyFormat;
}
// auto-generate a cite key according to the given naming scheme:
$citeKey = parsePlaceholderString($formVars, $citeKeyFormat, "<:authors:><:year:>");
}
}
} else {
$citeKey = "";
}
// by omitting a cite key Bibutils will take care of generation of cite keys for its export formats (BibTeX, Endnote, RIS)
}
// check how to handle non-ASCII characters:
if (!empty($userOptionsArray) and !empty($userOptionsArray['nonascii_chars_in_cite_keys'])) {
// use the user's own setting
$handleNonASCIIChars = $userOptionsArray['nonascii_chars_in_cite_keys'];
} else {
$handleNonASCIIChars = $handleNonASCIICharsInCiteKeysDefault;
}
// use the default setting that was specified by the admin in 'ini.inc.php'
// in addition to the handling of non-ASCII chars (given in '$handleNonASCIIChars') we'll
// strip additional characters from the generated cite keys: for cite keys, we only allow
// letters, digits, and the following characters: !$&*+-./:;<>?[]^_`|
// see e.g. the discussion of cite keys at: <http://search.cpan.org/~gward/btparse-0.34/doc/bt_language.pod>
if (!empty($citeKey)) {
$citeKey = handleNonASCIIAndUnwantedCharacters($citeKey, "[:alnum:]" . preg_quote("!\$&*+-./:;<>?[]^_`|", "/"), $handleNonASCIIChars);
}
// ensure that each cite key is unique:
if (!empty($citeKey) and !empty($userOptionsArray) and $userOptionsArray['export_cite_keys'] == "yes" and $userOptionsArray['uniquify_duplicate_cite_keys'] == "yes") {
// if the generated cite key already exists in the global array of found cite keys
// ('$citeKeysArray'), we'll uniquify it, otherwise we'll keep it as is:
$citeKey = ensureUniqueCiteKey($citeKey);
}
return $citeKey;
}
