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importmetadata.php
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<?php
ignore_user_abort(true);
include_once 'data.php';
session_write_close();
$url = '';
if (isset($_SESSION['auth']) && ($_SESSION['permissions'] == 'A' || $_SESSION['permissions'] == 'U')) {
include_once 'functions.php';
if (isset($_POST['form_sent']) && !isset($_FILES['form_import_file']) && empty($_POST['form_import_textarea']))
die();
if (isset($_POST['form_sent']) && isset($_POST['file_type']) && (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name']) || !empty($_POST['form_import_textarea']))) {
function trim_value(&$value) {
$value = trim($value);
}
$user_id = $_SESSION['user_id'];
$hashes = array();
$record_count = 0;
$duplicate_count = 0;
$pdf_count = 0;
$ids = array();
$dbname = uniqid() . '-temp.sq3';
$fdbname = uniqid() . '-ftemp.sq3';
$dbHandle = new PDO('sqlite:' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
$fdbHandle = new PDO('sqlite:' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
$dbHandle->beginTransaction();
$create = $dbHandle->exec("CREATE TABLE library (
id integer PRIMARY KEY,
file text NOT NULL DEFAULT '',
authors text NOT NULL DEFAULT '',
affiliation text NOT NULL DEFAULT '',
title text NOT NULL DEFAULT '',
journal text NOT NULL DEFAULT '',
secondary_title text NOT NULL DEFAULT '',
tertiary_title text NOT NULL DEFAULT '',
year text NOT NULL DEFAULT '',
volume text NOT NULL DEFAULT '',
issue text NOT NULL DEFAULT '',
pages text NOT NULL DEFAULT '',
abstract text NOT NULL DEFAULT '',
keywords text NOT NULL DEFAULT '',
editor text NOT NULL DEFAULT '',
publisher text NOT NULL DEFAULT '',
place_published text NOT NULL DEFAULT '',
reference_type text NOT NULL DEFAULT '',
uid text NOT NULL DEFAULT '',
doi text NOT NULL DEFAULT '',
url text NOT NULL DEFAULT '',
addition_date text NOT NULL DEFAULT '',
rating integer NOT NULL DEFAULT '',
authors_ascii text NOT NULL DEFAULT '',
title_ascii text NOT NULL DEFAULT '',
abstract_ascii text NOT NULL DEFAULT '',
added_by integer NOT NULL DEFAULT '',
modified_by integer NOT NULL DEFAULT '',
modified_date text NOT NULL DEFAULT '',
custom1 text NOT NULL DEFAULT '',
custom2 text NOT NULL DEFAULT '',
custom3 text NOT NULL DEFAULT '',
custom4 text NOT NULL DEFAULT '',
bibtex text NOT NULL DEFAULT '',
filehash text NOT NULL DEFAULT '',
bibtex_type text NOT NULL DEFAULT ''
)");
$create = null;
$create = $dbHandle->exec("CREATE TABLE notes (
notesID integer PRIMARY KEY,
userID integer NOT NULL,
fileID integer NOT NULL,
notes text NOT NULL DEFAULT ''
)");
$create = null;
$dbHandle->commit();
$create = $fdbHandle->exec("CREATE TABLE full_text (
id integer PRIMARY KEY,
fileID text NOT NULL DEFAULT '',
full_text text NOT NULL DEFAULT ''
)");
$create = null;
$query = "INSERT INTO library (file, authors, affiliation, title, journal, year, addition_date, abstract, rating, uid, volume, issue, pages, secondary_title, tertiary_title, editor,
url, reference_type, publisher, place_published, keywords, doi, authors_ascii, title_ascii, abstract_ascii, added_by, bibtex, bibtex_type)
VALUES (lower(hex(randomblob(4))) || '.pdf', :authors, :affiliation, :title, :journal,
:year, :addition_date, :abstract, :rating, :uid, :volume, :issue, :pages, :secondary_title, :tertiary_title, :editor,
:url, :reference_type, :publisher, :place_published, :keywords, :doi, :authors_ascii, :title_ascii, :abstract_ascii, :added_by, :bibtex, :bibtex_type)";
$stmt = $dbHandle->prepare($query);
$stmt->bindParam(':authors', $authors, PDO::PARAM_STR);
$stmt->bindParam(':affiliation', $affiliation, PDO::PARAM_STR);
$stmt->bindParam(':title', $title, PDO::PARAM_STR);
$stmt->bindParam(':journal', $journal, PDO::PARAM_STR);
$stmt->bindParam(':year', $year, PDO::PARAM_STR);
$stmt->bindParam(':addition_date', $addition_date, PDO::PARAM_STR);
$stmt->bindParam(':abstract', $abstract, PDO::PARAM_STR);
$stmt->bindParam(':rating', $rating, PDO::PARAM_INT);
$stmt->bindParam(':uid', $uid, PDO::PARAM_STR);
$stmt->bindParam(':volume', $volume, PDO::PARAM_STR);
$stmt->bindParam(':issue', $issue, PDO::PARAM_STR);
$stmt->bindParam(':pages', $pages, PDO::PARAM_STR);
$stmt->bindParam(':secondary_title', $secondary_title, PDO::PARAM_STR);
$stmt->bindParam(':tertiary_title', $tertiary_title, PDO::PARAM_STR);
$stmt->bindParam(':editor', $editor, PDO::PARAM_STR);
$stmt->bindParam(':url', $url, PDO::PARAM_STR);
$stmt->bindParam(':reference_type', $reference_type, PDO::PARAM_STR);
$stmt->bindParam(':publisher', $publisher, PDO::PARAM_STR);
$stmt->bindParam(':place_published', $place_published, PDO::PARAM_STR);
$stmt->bindParam(':keywords', $keywords, PDO::PARAM_STR);
$stmt->bindParam(':doi', $doi, PDO::PARAM_STR);
$stmt->bindParam(':authors_ascii', $authors_ascii, PDO::PARAM_STR);
$stmt->bindParam(':title_ascii', $title_ascii, PDO::PARAM_STR);
$stmt->bindParam(':abstract_ascii', $abstract_ascii, PDO::PARAM_STR);
$stmt->bindParam(':added_by', $added_by, PDO::PARAM_INT);
$stmt->bindParam(':bibtex', $bibtex, PDO::PARAM_STR);
$stmt->bindParam(':bibtex_type', $bibtex_type, PDO::PARAM_STR);
$query = "INSERT INTO notes (userID, fileID, notes) VALUES (:userID, :fileID, :notes)";
$stmt2 = $dbHandle->prepare($query);
$stmt2->bindParam(':userID', $user_id, PDO::PARAM_INT);
$stmt2->bindParam(':fileID', $last_id, PDO::PARAM_INT);
$stmt2->bindParam(':notes', $notes, PDO::PARAM_STR);
if ($_POST['file_type'] == "endnote") {
// XXE prevention.
libxml_disable_entity_loader(true);
if (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
try {
if (!$xml = @simplexml_load_file($_FILES['form_import_file']['tmp_name'])) {
throw new Exception('Not a valid XML file.');
}
} catch (Exception $e) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
print "Error! " . $e->getMessage();
die();
}
} elseif (!empty($_POST['form_import_textarea'])) {
try {
if (!$xml = @simplexml_load_string($_POST['form_import_textarea'])) {
throw new Exception('Not a valid XML.');
}
} catch (Exception $e) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
print "Error! " . $e->getMessage();
die();
}
}
$records = $xml->records->record;
$record_count = count($records);
$dbHandle->beginTransaction();
foreach ($records as $record) {
set_time_limit(60);
$authors = '';
$authors_ascii = '';
$authors = $record->contributors->authors->author;
if (!empty($authors)) {
$authors2 = array();
foreach ($authors as $author) {
$author = strip_tags($author->asXML());
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$authors2[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $authors2);
$authors_ascii = utf8_deaccent($authors);
}
$affiliation = '';
$affiliation = strip_tags($record->{'auth-address'}->asXML());
$title = '';
$title = strip_tags($record->titles->title->asXML());
if (empty($title))
$title = 'No title.';
$title_ascii = utf8_deaccent($title);
$journal = '';
$journal = strip_tags($record->titles->{'secondary-title'}->asXML());
$journal = str_replace(".", "", strip_tags($journal));
$year = '';
$year = strip_tags($record->dates->year->asXML());
$addition_date = date('Y-m-d');
$abstract = '';
$abstract = strip_tags($record->abstract->asXML());
$abstract_ascii = utf8_deaccent($abstract);
$rating = 2;
$uid = '';
$doi = '';
$uid = strip_tags($record->{'accession-num'}->asXML());
if (preg_match('/10\.\d{4}\/\S+/ui', $uid) == 1) {
$doi = $uid;
$uid = '';
}
$volume = '';
$volume = strip_tags($record->volume->asXML());
$issue = '';
$issue = strip_tags($record->number->asXML());
$pages = '';
$pages = strip_tags($record->pages->asXML());
$secondary_title = '';
$tertiary_title = '';
$editor = '';
$reference_type = 'article';
foreach ($record->{'ref-type'}->attributes() as $a => $b) {
if ($a == 'name') {
$reference_type = convert_type($b, 'endnote', 'ilib');
break;
}
}
$publisher = '';
$place_published = '';
$keywords = '';
$keywords2 = array();
$keywords = $record->keywords;
if (!empty($keywords)) {
foreach ($keywords->keyword as $keyword) {
if (!empty($keyword)) {
$keyword = strip_tags($keyword->asXML());
$keywords2[] = preg_replace('/\[|\]|\||\"|\/|\*/', ' ', $keyword);
}
}
$keywords = join(" / ", $keywords2);
}
$bibtex = '';
$bibtex_type = '';
$url = '';
$urls = '';
$urls2 = array();
$urls = $record->urls->{'related-urls'}->url;
if (!empty($urls)) {
foreach ($urls as $url) {
if (!empty($url)) {
$url = strip_tags($url->asXML());
$urls2[] = $url;
} else {
$urls2[] = '';
}
}
$url = join("|", $urls2);
}
$added_by = $user_id;
foreach ($record->database->attributes() as $a => $b) {
if ($a == 'path') {
$pdf_path1 = dirname($b) . DIRECTORY_SEPARATOR . basename($record->database, ".enl") . ".Data" . DIRECTORY_SEPARATOR;
break;
}
}
$pdf_path2 = $record->urls->{'pdf-urls'}->url;
$file_to_copy = '';
if (!empty($pdf_path2)) {
if (strstr($pdf_path2, "internal-pdf"))
$pdf_path = $pdf_path1 . 'PDF' . DIRECTORY_SEPARATOR . substr($pdf_path2, 15);
if (strstr($pdf_path2, "file:"))
$pdf_path = substr($pdf_path2, 7);
$file_to_copy = strtr($pdf_path, "/", DIRECTORY_SEPARATOR);
}
if (!empty($title))
$insert = $stmt->execute();
$last_id = $dbHandle->lastInsertId();
$ids[] = $last_id;
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('No records found.');
}
if ($hosted === false && is_file($file_to_copy) && is_readable($file_to_copy)) {
$result = $dbHandle->query("SELECT file FROM library WHERE id=" . $last_id);
$pdf_filename = $result->fetchColumn();
$result = null;
copy($file_to_copy, IL_PDF_PATH . DIRECTORY_SEPARATOR . $pdf_filename);
system(select_pdftotext() . ' -enc UTF-8 ' . escapeshellarg($file_to_copy) . ' ' . escapeshellarg(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . '.txt'));
if (is_file(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt")) {
$string = file_get_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
// Replace line breaks with spaces.
$order = array("\r\n", "\n", "\r");
$string = str_replace($order, ' ', $string);
// Strip invalid UTF-8 characters.
$string = preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $string);
$string = preg_replace('/\s{2,}/ui', ' ', $string);
// Strip non-printing characters.
$string = trim(filter_var($string, FILTER_SANITIZE_STRING, FILTER_FLAG_STRIP_LOW));
if (!empty($string)) {
$fulltext_query = $fdbHandle->quote($string);
$fdbHandle->exec("INSERT INTO full_text (fileID,full_text) VALUES (" . $last_id . ",$fulltext_query)");
}
}
}
}
$dbHandle->commit();
$insert = null;
$stmt = null;
}
if ($_POST['file_type'] == "RIS") {
if (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode('ER -', $file_contents);
$file_records = array_filter($file_records);
$record_count = count($file_records) - 1;
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$bibtex = '';
$bibtex_type = '';
$affiliation = '';
$added_by = $user_id;
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
set_time_limit(60);
$record_array = array();
$record_array = explode("\n", $record);
$title_match = array();
$type_match = array();
$journal_match = array();
$secondary_title_match = array();
$tertiary_title_match = array();
$volume_match = array();
$issue_match = array();
$year_match = array();
$start_page_match = array();
$end_page_match = array();
$publisher_match = array();
$place_published_match = array();
$url_match = array();
$keywords_match = array();
$editors_match = array();
$authors_match = array();
$file_to_copy_match = array();
$doi_match = array();
$notes_match = array();
$affiliation_match = array();
$abstract_match = array();
preg_match("/(?<=AB - \n|AB - |AB - \r\n|N2 - \n|N2 - |N2 - \r\n).+/u", $record, $abstract_match);
$abstract = '';
$abstract_ascii = '';
if (!empty($abstract_match[0])) {
$abstract = trim($abstract_match[0]);
$abstract_ascii = utf8_deaccent($abstract);
}
preg_match("/(?<=N1 - doi:|M3 - doi: DOI:).+|(10\.\d{4}\/\S+)/u", $record, $doi_match);
$doi = '';
if (!empty($doi_match[0]))
$doi = trim($doi_match[0]);
foreach ($record_array as $line) {
if (strpos($line, "T1") === 0 || strpos($line, "TI") === 0) {
$title_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "TY") === 0) {
$type_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "JA") === 0 || strpos($line, "J2") === 0) {
$journal_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "JF") === 0 || strpos($line, "JO") === 0 || strpos($line, "BT") === 0 || strpos($line, "T2") === 0) {
$secondary_title_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "T3") === 0) {
$tertiary_title_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "VL") === 0) {
$volume_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "IS") === 0) {
$issue_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "PY") === 0 || strpos($line, "Y1") === 0 || strpos($line, "DA") === 0) {
$year_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "SP") === 0) {
$start_page_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "EP") === 0) {
$end_page_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "PB") === 0) {
$publisher_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "CY") === 0) {
$place_published_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "UR") === 0) {
$url_match[0][] = trim(substr($line, 6));
} elseif (strpos($line, "KW") === 0) {
$keywords_match[0][] = trim(substr($line, 6));
} elseif (strpos($line, "ED") === 0 || strpos($line, "A2") === 0) {
$editors_match[0][] = trim(substr($line, 6));
} elseif (strpos($line, "AU") === 0 || strpos($line, "A1") === 0) {
$authors_match[0][] = trim(substr($line, 6));
} elseif (strpos($line, "L1") === 0) {
$file_to_copy_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "DO") === 0) {
$doi_match[0] = trim(substr($line, 6));
} elseif (strpos($line, "N1") === 0) {
$notes_match[0][] = trim(substr($line, 6));
} elseif (strpos($line, "AD") === 0) {
$affiliation_match[0] = trim(substr($line, 6));
}
}
$authors = '';
$authors_ascii = '';
if (!empty($authors_match[0])) {
$name_array = array();
foreach ($authors_match[0] as $author) {
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$name_array[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $name_array);
$authors_ascii = utf8_deaccent($authors);
}
$editor = '';
if (!empty($editors_match[0])) {
$name_array = array();
foreach ($editors_match[0] as $editor) {
$editor_array = explode(",", $editor);
$first_name = '';
if (isset($editor_array[1]))
$first_name = $editor_array[1];
$name_array[] = 'L:"' . trim($editor_array[0]) . '",F:"' . trim($first_name) . '"';
}
$editor = join(";", $name_array);
}
$title = '';
$title_ascii = '';
if (!empty($title_match[0])) {
$title = trim($title_match[0]);
$title_ascii = utf8_deaccent($title);
}
$journal = '';
if (!empty($journal_match[0]))
$journal = trim(str_replace(".", "", $journal_match[0]));
$year = '';
if (!empty($year_match[0])) {
$date_array = array();
$month = '01';
$day = '01';
$date_array = explode('/', $year_match[0]);
if (!empty($date_array[0]))
$year = $date_array[0];
if (!empty($date_array[1]))
$month = $date_array[1];
if (!empty($date_array[2]))
$day = $date_array[2];
if (!is_numeric($year)) {
$year = '';
}
if (!empty($year) && is_numeric($year)) {
$year = $year . '-' . $month . '-' . $day;
}
if (empty($year)) {
preg_match('/\d{4}/u', $year_match[0], $year_match2);
if (!empty($year_match2[0]) && is_numeric($year_match2[0]))
$year = $year_match2[0] . '-01-01';
}
}
$volume = '';
if (!empty($volume_match[0]))
$volume = trim($volume_match[0]);
$issue = '';
if (!empty($issue_match[0]))
$issue = trim($issue_match[0]);
$pages = '';
if (!empty($start_page_match[0]))
$pages = trim($start_page_match[0]);
if (!empty($end_page_match[0]))
$pages .= '-' . trim($end_page_match[0]);
$secondary_title = '';
if (!empty($secondary_title_match[0]))
$secondary_title = trim($secondary_title_match[0]);
$tertiary_title = '';
if (!empty($tertiary_title_match[0]))
$tertiary_title = trim($tertiary_title_match[0]);
$url = '';
if (!empty($url_match[0])) {
array_walk($url_match[0], 'trim_value');
$url = join('|', $url_match[0]);
}
$publisher = '';
if (!empty($publisher_match[0]))
$publisher = trim($publisher_match[0]);
$affiliation = '';
if (!empty($affiliation_match[0]))
$affiliation = trim($affiliation_match[0]);
$place_published = '';
if (!empty($place_published_match[0]))
$place_published = trim($place_published_match[0]);
$reference_type = 'article';
if (!empty($type_match[0]))
$reference_type = convert_type(trim($type_match[0]), 'ris', 'ilib');
$keywords = '';
if (!empty($keywords_match[0])) {
$order = array("\r\n", "\n", "\r");
$keywords_match[0] = str_replace($order, ' ', $keywords_match[0]);
$patterns = array('[', ']', '|', '"', '/', '*');
$keywords_match[0] = str_replace($patterns, ' ', $keywords_match[0]);
array_walk($keywords_match[0], 'trim_value');
$keywords_match[0] = join("#", $keywords_match[0]);
$keywords = str_replace("#", " / ", $keywords_match[0]);
}
$notes = '';
if (!empty($notes_match[0])) {
$notes = join(' ', $notes_match[0]);
}
$file_to_copy = '';
if (isset($file_to_copy_match[0])) {
$file_to_copy = $file_to_copy_match[0];
$file_to_copy = str_replace("\\", "/", $file_to_copy);
}
if (strpos($file_to_copy, "file://") === 0)
$file_to_copy = preg_replace('/(file:\/\/.*\/)(.*)/Ui', "$2", $file_to_copy);
if (substr(strtoupper(PHP_OS), 0, 3) != 'WIN')
$file_to_copy = '/' . $file_to_copy;
if (!empty($title)) {
$insert = $stmt->execute();
$last_id = $dbHandle->lastInsertId();
$ids[] = $last_id;
}
$insert = null;
if (!empty($title) && !empty($notes)) {
$user_id = $_SESSION['user_id'];
$insert = $stmt2->execute();
$insert = null;
}
if ($hosted === false && !empty($title) && is_file($file_to_copy) && is_readable($file_to_copy)) {
$result = $dbHandle->query("SELECT file FROM library WHERE id=" . $last_id);
$pdf_filename = $result->fetchColumn();
$result = null;
copy($file_to_copy, IL_PDF_PATH . DIRECTORY_SEPARATOR . $pdf_filename);
system(select_pdftotext() . ' -enc UTF-8 ' . escapeshellarg($file_to_copy) . ' ' . escapeshellarg(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . '.txt'));
if (is_file(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt")) {
$string = file_get_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
// Replace line breaks with spaces.
$order = array("\r\n", "\n", "\r");
$string = str_replace($order, ' ', $string);
// Strip invalid UTF-8 characters.
$string = preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $string);
$string = preg_replace('/\s{2,}/ui', ' ', $string);
// Strip non-printing characters.
$string = trim(filter_var($string, FILTER_SANITIZE_STRING, FILTER_FLAG_STRIP_LOW));
if (!empty($string)) {
$fulltext_query = $fdbHandle->quote($string);
$fdbHandle->exec("INSERT INTO full_text (fileID,full_text) VALUES (" . $last_id . ",$fulltext_query)");
}
}
}
}
$dbHandle->commit();
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('No records found.');
}
$insert = null;
$stmt = null;
$stmt2 = null;
$last_id = null;
}
}
if ($_POST['file_type'] == "isi") {
if (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode("ER\r\n", $file_contents);
$record_count = count($file_records) - 1;
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
set_time_limit(60);
$record = str_replace("\n ", "{#}", $record);
if (!empty($record) && !ctype_cntrl($record) && strstr($record, "TI ")) {
preg_match("/(?<=TI ).+/u", $record, $title_match);
preg_match("/(?<=SO ).+/u", $record, $secondary_title_match);
preg_match("/(?<=VL ).+/u", $record, $volume_match);
preg_match("/(?<=IS ).+/u", $record, $issue_match);
preg_match("/(?<=PY ).+/u", $record, $year_match);
preg_match("/(?<=BP ).+/u", $record, $start_page_match);
preg_match("/(?<=EP ).+/u", $record, $end_page_match);
preg_match("/(?<=AB ).+/u", $record, $abstract_match);
preg_match("/(?<=AU ).+/u", $record, $authors_match);
preg_match("/(?<=DI ).+/u", $record, $doi_match);
preg_match("/(?<=ID ).+/u", $record, $keywords_match);
preg_match("/(?<=JI ).+/u", $record, $journal_match);
$authors = '';
$authors_ascii = '';
$name_array = array();
if (!empty($authors_match[0])) {
$name_array = array();
$authors_match[0] = explode("{#}", $authors_match[0]);
foreach ($authors_match[0] as $author) {
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$name_array[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $name_array);
$authors_ascii = utf8_deaccent($authors);
}
$affiliation = '';
$title = '';
$title_ascii = '';
if (!empty($title_match[0])) {
$title = trim($title_match[0]);
$title = str_replace("{#}", " ", $title);
$title_ascii = utf8_deaccent($title);
}
$journal = '';
if (!empty($journal_match[0]))
$journal = trim(str_replace(".", "", $journal_match[0]));
$year = '';
if (!empty($year_match[0]))
$year = intval(substr($year_match[0], 0, 4));
$addition_date = date('Y-m-d');
$abstract = '';
$abstract_ascii = '';
if (!empty($abstract_match[0])) {
$abstract = trim($abstract_match[0]);
$abstract = str_replace("{#}", " ", $abstract);
$abstract_ascii = utf8_deaccent($abstract);
}
$rating = 2;
$uid = '';
$bibtex = '';
$bibtex_type = '';
$volume = '';
if (!empty($volume_match[0]))
$volume = trim($volume_match[0]);
$issue = '';
if (!empty($issue_match[0]))
$issue = trim($issue_match[0]);
$pages = '';
if (!empty($start_page_match[0]))
$pages = trim($start_page_match[0]);
if (!empty($end_page_match[0]))
$pages .= '-' . trim($end_page_match[0]);
$secondary_title = '';
if (!empty($secondary_title_match[0])) {
$secondary_title = str_replace("{#}", " ", $secondary_title_match[0]);
$secondary_title = ucfirst(strtolower(trim($secondary_title)));
}
$editor = '';
$reference_type = 'article';
$publisher = '';
$place_published = '';
$url = '';
$keywords = '';
if (!empty($keywords_match[0])) {
$keywords = str_replace("{#}", " ", $keywords_match[0]);
$keywords = preg_replace('/\[|\]|\||\"|\/|\*/u', ' ', $keywords);
$keywords = str_replace("; ", " / ", $keywords);
$keywords = ucwords(strtolower($keywords));
}
$doi = '';
if (!empty($doi_match[0]))
$doi = trim($doi_match[0]);
$added_by = $user_id;
if (!empty($title))
$insert = $stmt->execute();
$last_id = $dbHandle->query("SELECT last_insert_rowid() FROM library");
$ids[] = $last_id->fetchColumn();
$last_id = null;
}
}
$dbHandle->commit();
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('No records found.');
}
$insert = null;
$stmt = null;
}
}
if ($_POST['file_type'] == "bibtex") {
if (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $dbname);
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode('@', $file_contents);
$file_records = array_filter($file_records);
$record_count = count($file_records);
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
set_time_limit(60);
$record = trim($record);
$record = str_replace('={', ' = {', $record);
$record = preg_replace('/ {2,}/um', ' ', $record);
$record = preg_replace('/\},\s*\r?\n/um', "},\n", $record);
$title = preg_match("/(?<=title \=).+/iu", $record, $title_match);
if ($title == 1) {
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$affiliation = '';
$added_by = $user_id;
$type_match = array();
$journal_match = array();
$secondary_title_match = array();
$volume_match = array();
$issue_match = array();
$year_match = array();
$start_page_match = array();
$end_page_match = array();
$publisher_match = array();
$place_published_match = array();
$url_match = array();
$keywords_match = array();
$editors_match = array();
$authors_match = array();
$bibtex_match = array();
$abstract_match = array();
$doi_match = array();
$file_to_copy_match = array();
$notes_match = array();
$type_match[0] = strtolower(trim(strstr($record, "{", true)));
$record = trim(substr($record, strpos($record, "{") + 1, strrpos($record, "}") - strlen($record)));
$record = str_replace("\r", "", $record);