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fetch_pmc.php
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fetch_pmc.php
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<?php
include_once 'data.php';
$proxy_name = '';
$proxy_port = '';
$proxy_username = '';
$proxy_password = '';
if (isset($_SESSION['connection']) && ($_SESSION['connection'] == "autodetect" || $_SESSION['connection'] == "url")) {
if (!empty($_GET['proxystr'])) {
$proxy_arr = explode(';', $_GET['proxystr']);
foreach ($proxy_arr as $proxy_str) {
if (stripos(trim($proxy_str), 'PROXY') === 0) {
$proxy_str = trim(substr($proxy_str, 6));
$proxy_name = parse_url($proxy_str, PHP_URL_HOST);
$proxy_port = parse_url($proxy_str, PHP_URL_PORT);
$proxy_username = parse_url($proxy_str, PHP_URL_USER);
$proxy_password = parse_url($proxy_str, PHP_URL_PASS);
break;
}
}
}
} else {
if (isset($_SESSION['proxy_name']))
$proxy_name = $_SESSION['proxy_name'];
if (isset($_SESSION['proxy_port']))
$proxy_port = $_SESSION['proxy_port'];
if (isset($_SESSION['proxy_username']))
$proxy_username = $_SESSION['proxy_username'];
if (isset($_SESSION['proxy_password']))
$proxy_password = $_SESSION['proxy_password'];
}
include_once 'functions.php';
########## reference fetching from PubMed ##########
if (isset($_GET['id'])) {
########## open efetch, read xml ##########
if (!empty($_GET['id'])) {
$request_url = 'http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Pubmed&rettype=abstract&retmode=XML&id=' . urlencode($_GET['id']) . '&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.');
foreach ($xml->PubmedArticle->PubmedData->ArticleIdList->ArticleId as $articleid) {
foreach ($articleid->attributes() as $a => $b) {
if ($a == 'IdType' && $b == 'doi')
$doi = $articleid[0];
}
}
$pmid = $xml->PubmedArticle->MedlineCitation->PMID;
$pmcid = $_GET['pmcid'];
$reference_type = 'article';
$title = $xml->PubmedArticle->MedlineCitation->Article->ArticleTitle;
$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";
}
$abstract = implode(' ', $abstract_array);
}
$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];
}
$date = '';
if (!empty($year)) {
if (empty($day))
$day = '01';
if (empty($month))
$month = '01';
$date = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
}
$volume = $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume;
$issue = $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue;
$pages = $xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn;
$journal_abbr = $xml->PubmedArticle->MedlineCitation->MedlineJournalInfo->MedlineTA;
$affiliation = $xml->PubmedArticle->MedlineCitation->Article->Affiliation;
$authors = $xml->PubmedArticle->MedlineCitation->Article->AuthorList->Author;
if (!empty($authors)) {
foreach ($authors as $author) {
$name_array[] = $author->LastName . ', ' . $author->ForeName;
}
}
$keywords = $xml->PubmedArticle->MedlineCitation->MeshHeadingList->MeshHeading;
if (!empty($keywords)) {
foreach ($keywords as $keywordsheading) {
$keywords_array[] = $keywordsheading->DescriptorName;
}
}
if (isset($name_array))
$names = join("; ", $name_array);
if (isset($keywords_array))
$keywords = join(" / ", $keywords_array);
}
if (empty($_GET['id']) && !empty($_GET['pmcid'])) {
$request_url = 'http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=abstract&retmode=XML&id=' . urlencode($_GET['pmcid']) . '&tool=I,Librarian&email=i.librarian.software@gmail.com';
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
foreach ($xml->article->front->{'article-meta'}->{'article-id'} as $articleid) {
foreach ($articleid->attributes() as $a => $b) {
if ($a == 'pub-id-type' && $b == 'doi')
$doi = $articleid[0];
if ($a == 'pub-id-type' && $b == 'pmid')
$pmid = $articleid[0];
}
}
$pmcid = $_GET['pmcid'];
$reference_type = 'article';
$title = strip_tags($xml->article->front->{'article-meta'}->{'title-group'}->{'article-title'}->asXML());
$xml_abstract = $xml->article->front->{'article-meta'}->abstract;
if (!empty($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";
}
$abstract = implode(' ', $abstract_array);
$abstract = trim($abstract);
}
if (empty($abstract))
$abstract = trim(strip_tags((string) $xml->article->front->{'article-meta'}->abstract->asXML()));
foreach ($xml->article->front->{'journal-meta'}->{'journal-id'} as $journalid) {
foreach ($journalid->attributes() as $a => $b) {
if ($a == 'journal-id-type' && $b == 'nlm-ta')
$journal_abbr = $journalid[0];
}
}
$secondary_title = $xml->article->front->{'journal-meta'}->{'journal-title-group'}->{'journal-title'};
$year = (string) $xml->article->front->{'article-meta'}->{'pub-date'}->year;
$month = (string) $xml->article->front->{'article-meta'}->{'pub-date'}->month;
$day = (string) $xml->article->front->{'article-meta'}->{'pub-date'}->day;
if (empty($day))
$day = '01';
if (empty($month))
$month = '01';
if (empty($year))
$year = '1969';
$date = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
$volume = $xml->article->front->{'article-meta'}->volume;
$issue = $xml->article->front->{'article-meta'}->issue;
$fpage = $xml->article->front->{'article-meta'}->fpage;
$lpage = $xml->article->front->{'article-meta'}->lpage;
$elocation = $xml->article->front->{'article-meta'}->{'elocation-id'};
if (!empty($fpage)) {
if ($fpage > $lpage) {
$pages = "$fpage-$lpage";
} else {
$pages = $fpage;
}
} elseif (!empty($elocation)) {
$pages = $elocation;
}
$affiliation = strip_tags($xml->article->front->{'article-meta'}->aff->asXML());
$authors = $xml->article->front->{'article-meta'}->{'contrib-group'};
if (!empty($authors)) {
foreach ($authors->contrib as $author) {
foreach ($author->attributes() as $a => $b) {
if ($a == 'contrib-type' && $b == 'author')
$name_array[] = $author->name->surname . ", " . $author->name->{'given-names'};
}
}
}
$keywords = $xml->article->front->{'article-meta'}->{'kwd-group'}->kwd;
if (!empty($keywords)) {
foreach ($keywords as $keyword) {
$keywords_array[] = $keyword;
}
}
if (isset($name_array))
$names = join("; ", $name_array);
if (isset($keywords_array))
$keywords = join(" / ", $keywords_array);
}
########## print results into table ##########
print '<form enctype="application/x-www-form-urlencoded" action="upload.php" method="POST" class="fetch-form">';
print '<table cellspacing="0" width="100%"><tr><td class="items">';
print '<div>';
if (!empty($journal_abbr))
print htmlspecialchars($journal_abbr);
if (!empty($year))
print " (" . htmlspecialchars($date) . ")";
if (!empty($volume))
print " " . htmlspecialchars($volume);
if (!empty($issue))
print " ($issue)";
if (!empty($pages))
print ": " . htmlspecialchars($pages);
print '</div>';
if (!empty($names)) {
print '<div class="authors"><span class="author_expander ui-icon ui-icon-plus" style="float:left"></span><div>' . htmlspecialchars($names) . '</div></div>';
$array = explode(';', $names);
$array = array_filter($array);
if (!empty($array)) {
foreach ($array as $author) {
$array2 = explode(',', $author);
$last = trim($array2[0]);
$first = trim($array2[1]);
$new_authors[] = 'L:"' . $last . '",F:"' . $first . '"';
}
$names = join(';', $new_authors);
}
}
if (!empty($affiliation))
print '<div class="authors"><span class="author_expander ui-icon ui-icon-plus" style="float:left"></span><div>' . htmlspecialchars($affiliation) . '</div></div>';
print '</td></tr>';
print '<tr><td><div class="abstract" style="padding:0 10px">';
!empty($abstract) ? print htmlspecialchars($abstract) : print 'No abstract available.';
print '</div></td></tr><tr><td class="items">';
$uid_array[] = 'PMCID:' . $pmcid;
if (!empty($pmid))
$uid_array[] = 'PMID:' . $pmid;
foreach ($uid_array as $uid) {
print '<input type="hidden" name="uid[]" value="' . htmlspecialchars($uid) . '">';
}
$url_array[] = 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC' . $pmcid . '/';
if (!empty($pmid))
$url_array[] = 'http://www.pubmed.org/' . $pmid;
foreach ($url_array as $url) {
print '<input type="hidden" name="url[]" value="' . htmlspecialchars($url) . '">';
}
?>
<input type="hidden" name="doi" value="<?php if (!empty($doi)) print htmlspecialchars($doi); ?>">
<input type="hidden" name="reference_type" value="<?php if (!empty($reference_type)) print htmlspecialchars($reference_type); ?>">
<input type="hidden" name="authors" value="<?php if (!empty($names)) print htmlspecialchars($names); ?>">
<input type="hidden" name="affiliation" value="<?php if (!empty($affiliation)) print htmlspecialchars($affiliation); ?>">
<input type="hidden" name="title" value="<?php if (!empty($title)) print htmlspecialchars($title); ?>">
<input type="hidden" name="secondary_title" value="<?php if (!empty($secondary_title)) print htmlspecialchars($secondary_title); ?>">
<input type="hidden" name="journal_abbr" value="<?php if (!empty($journal_abbr)) print htmlspecialchars($journal_abbr); ?>">
<input type="hidden" name="year" value="<?php if (!empty($date)) print htmlspecialchars($date); ?>">
<input type="hidden" name="volume" value="<?php if (!empty($volume)) print htmlspecialchars($volume); ?>">
<input type="hidden" name="issue" value="<?php if (!empty($issue)) print htmlspecialchars($issue); ?>">
<input type="hidden" name="pages" value="<?php if (!empty($pages)) print htmlspecialchars($pages); ?>">
<input type="hidden" name="keywords" value="<?php if (!empty($keywords)) print htmlspecialchars($keywords); ?>">
<input type="hidden" name="abstract" value="<?php print !empty($abstract) ? htmlspecialchars($abstract) : "No abstract available."; ?>">
<input type="hidden" name="form_new_file_link" value="<?php print !empty($pmcid) ? htmlspecialchars("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC" . $pmcid . "/pdf") : ""; ?>">
<?php
########## print full text links ##########
print '<b>Full text options:</b><br>';
print '<a href="' . htmlspecialchars('http://www.ncbi.nlm.nih.gov/pmc/articles/PMC' . $pmcid . '/') . '" target="_blank">
PubMed Central</a>';
print ' <b>·</b> <a href="' . htmlspecialchars('http://www.ncbi.nlm.nih.gov/pmc/articles/PMC' . $pmcid . '/pdf/') . '" target="_blank">
Full Text PDF</a>';
if (!empty($doi))
print ' <b>·</b> <a href="' . htmlspecialchars('http://dx.doi.org/' . urlencode($doi)) . '" target="_blank">Publishers Website</a>';
print '<br><button class="save-item">Save</button> <button class="quick-save-item">Quick Save</button>';
print '</td></tr></table>';
?>
</form>
<?php
} ########## reference fetching from PubMed ##########
?>
</body>
</html>