function pubmed_efetch($pmid)
{
// Setup the URL for efetch
$params = array('db' => 'pubmed', 'retmode' => 'xml', 'retmax' => 25, 'id' => (string) $pmid);
$efetch = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?';
$q = array();
foreach ($params as $key => $value) {
$q[] = $key . '=' . $value;
}
$httpquery = implode('&', $q);
$url = $efetch . $httpquery;
$XML = proxy_simplexml_load_file($url);
return $XML;
}
cache_start($db_change);
########## register the time of search ##############
if (!empty($_SESSION['session_download_arxiv_searchname']) && $from == 1) {
database_connect(IL_DATABASE_PATH, 'library');
$stmt = $dbHandle->prepare("UPDATE searches SET searchvalue=:searchvalue WHERE userID=:user AND searchname=:searchname AND searchfield='arxiv_last_search'");
$stmt->bindParam(':user', $user, PDO::PARAM_STR);
$stmt->bindParam(':searchname', $searchname, PDO::PARAM_STR);
$stmt->bindParam(':searchvalue', $searchvalue, PDO::PARAM_STR);
$user = $_SESSION['user_id'];
$searchname = "arxiv#" . $_SESSION['session_download_arxiv_searchname'];
$searchvalue = time();
$stmt->execute();
}
########## search arXiv ##############
$request_url = "http://export.arxiv.org/api/query?" . $query_string . $category_string . $edat_string . $year_string . "&start=" . ($from - 1) . "&max_results=10&sortBy=lastUpdatedDate&sortOrder=descending";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
if (empty($xml)) {
die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
}
}
########## display search result summaries ##############
if (!empty($xml)) {
print '<div style="padding:2px;font-weight:bold">arXiv search';
if (!empty($_SESSION['session_download_arxiv_searchname'])) {
print ': ' . htmlspecialchars($_SESSION['session_download_arxiv_searchname']);
}
print '</div>';
$count = 0;
$xmlxml = $xml->asXML();
preg_match('/<opensearch:totalResults.*opensearch:totalResults>/', $xmlxml, $xmlxml_match);
function fetch_from_pubmed($doi, $pmid)
{
global $proxy_name, $proxy_port, $proxy_username, $proxy_password, $response;
if (empty($pmid) && !empty($doi)) {
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=Pubmed&term=" . $doi . "[AID]&usehistory=y&retstart=&retmax=1&sort=&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
if (empty($xml)) {
die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
}
$count = $xml->Count;
if ($count == 1) {
$pmid = $xml->IdList->Id;
}
}
if (!empty($pmid)) {
########## open efetch, read xml ##########
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Pubmed&rettype=abstract&retmode=XML&id=" . urlencode($pmid) . "&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
if (empty($xml)) {
die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
}
$xml_type = '';
if (!empty($xml->PubmedBookArticle)) {
$xml_type = 'book';
}
if (!empty($xml->PubmedArticle)) {
$xml_type = 'article';
}
if ($xml_type == 'article') {
foreach ($xml->PubmedArticle->PubmedData->ArticleIdList->ArticleId as $articleid) {
foreach ($articleid->attributes() as $a => $b) {
if ($a == 'IdType' && $b == 'doi') {
$doi = $articleid[0];
}
if ($a == 'IdType' && $b == 'pmc') {
$response['pmcid'] = substr($articleid[0], 3);
$response['uid'][] = 'PMCID:' . $response['pmcid'];
}
}
}
if (!empty($doi)) {
$response['doi'] = $doi;
}
$response['uid'][] = 'PMID:' . $pmid;
$response['url'][] = "http://www.pubmed.org/{$pmid}";
$response['reference_type'] = 'article';
$response['title'] = $xml->PubmedArticle->MedlineCitation->Article->ArticleTitle;
$abstract_array = array();
$xml_abstract = $xml->PubmedArticle->MedlineCitation->Article->Abstract->AbstractText;
if (!empty($xml_abstract)) {
foreach ($xml_abstract as $mini_ab) {
foreach ($mini_ab->attributes() as $a => $b) {
if ($a == 'Label') {
$mini_ab = $b . ": " . $mini_ab;
}
}
$abstract_array[] = "{$mini_ab}";
}
$response['abstract'] = implode(' ', $abstract_array);
}
$response['secondary_title'] = $xml->PubmedArticle->MedlineCitation->Article->Journal->Title;
$day = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Day;
$month = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Month;
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year;
if (empty($year)) {
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->MedlineDate;
preg_match('/\\d{4}/', $year, $year_match);
$year = $year_match[0];
}
$response['year'] = '';
if (!empty($year)) {
if (empty($day)) {
$day = '01';
}
if (empty($month)) {
$month = '01';
}
$response['year'] = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
}
$response['volume'] = $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume;
$response['issue'] = $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue;
$response['pages'] = $xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn;
$response['journal_abbr'] = $xml->PubmedArticle->MedlineCitation->MedlineJournalInfo->MedlineTA;
$authors = $xml->PubmedArticle->MedlineCitation->Article->AuthorList->Author;
$name_array = array();
$response['affiliation'] = '';
if (!empty($authors)) {
foreach ($authors as $author) {
$name_array[] = 'L:"' . $author->LastName . '",F:"' . $author->ForeName . '"';
if (empty($response['affiliation'])) {
$response['affiliation'] = $author->Affiliation;
}
}
}
$mesh = $xml->PubmedArticle->MedlineCitation->MeshHeadingList->MeshHeading;
if (!empty($mesh)) {
foreach ($mesh as $meshheading) {
$mesh_array[] = $meshheading->DescriptorName;
}
}
if (isset($name_array)) {
$response['authors'] = join(";", $name_array);
}
if (isset($mesh_array)) {
$response['keywords'] = join(" / ", $mesh_array);
}
}
if ($xml_type == 'book') {
$pmid = $xml->PubmedBookArticle->BookDocument->PMID;
$response['uid'][] = "PMID:{$pmid}";
$response['url'][] = "http://www.pubmed.org/{$pmid}";
$response['title'] = $xml->PubmedBookArticle->BookDocument->ArticleTitle;
if (empty($response['title'])) {
$response['reference_type'] = 'book';
$response['title'] = $xml->PubmedBookArticle->BookDocument->Book->BookTitle;
$response['secondary_title'] = $xml->PubmedBookArticle->BookDocument->Book->CollectionTitle;
} else {
$response['reference_type'] = 'chapter';
$response['secondary_title'] = $xml->PubmedBookArticle->BookDocument->Book->BookTitle;
$response['tertiary_title'] = $xml->PubmedBookArticle->BookDocument->Book->CollectionTitle;
}
$response['publisher'] = $xml->PubmedBookArticle->BookDocument->Book->Publisher->PublisherName;
$response['place_published'] = $xml->PubmedBookArticle->BookDocument->Book->Publisher->PublisherLocation;
$abstract_array = array();
foreach ($xml->PubmedBookArticle->BookDocument->Abstract->AbstractText as $mini_ab) {
foreach ($mini_ab->attributes() as $a => $b) {
if ($a == 'Label') {
$mini_ab = $b . ": " . $mini_ab;
}
}
$abstract_array[] = "{$mini_ab}";
}
$response['abstract'] = implode(' ', $abstract_array);
$day = $xml->PubmedBookArticle->BookDocument->Book->PubDate->Day;
$month = $xml->PubmedBookArticle->BookDocument->Book->PubDate->Month;
$year = $xml->PubmedBookArticle->BookDocument->Book->PubDate->Year;
$response['year'] = '';
if (!empty($year)) {
if (empty($day)) {
$day = '01';
}
if (empty($month)) {
$month = '01';
}
$response['year'] = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
}
$authors = $xml->PubmedBookArticle->BookDocument->AuthorList->Author;
$name_array = array();
if (!empty($authors)) {
foreach ($authors as $author) {
$name_array[] = 'L:"' . $author->LastName . '",F:"' . $author->ForeName . '"';
}
}
if (isset($name_array)) {
$response['authors'] = join(";", $name_array);
}
$editors = $xml->PubmedBookArticle->BookDocument->Book->AuthorList->Author;
$name_array = array();
if (!empty($editors)) {
foreach ($editors as $editor) {
$name_array[] = 'L:"' . $editor->LastName . '",F:"' . $editor->ForeName . '"';
}
}
if (isset($name_array)) {
$response['editors'] = join(";", $name_array);
}
}
}
}
