function add_article($query)
{
global $dbname;
global $connection;
$cmd = $query['command'];
switch ($cmd) {
case "new":
$result = mysqli_query($connection, "SELECT * FROM Articles WHERE PMID = '" . $query['PMID'] . "'");
if (mysqli_num_rows($result) >= 1) {
echo "ERROR: Article is already in the database";
} else {
$q = "INSERT INTO Articles (Title, Authors, Abstract, Reference, PMID, DOI, Experiments, Metadata) VALUES(";
$q .= "'" . mysqli_real_escape_string($connection, $query['Title']) . "'";
// CDATA removed, escape_string added
$q .= ",'" . mysqli_real_escape_string($connection, $query['Authors']) . "'";
//mysql_real_escape_string($article['Authors']);
$q .= ",'" . mysqli_real_escape_string($connection, $query['Abstract']) . "'";
//mysql_real_escape_string($article['Abstract']);
$q .= ",'" . mysqli_real_escape_string($connection, $query['Reference']) . "'";
//mysql_real_escape_string($article['Reference']);
$q .= ",'" . $query['PMID'] . "'";
//mysql_real_escape_string($article['PMID']);
$q .= ",'" . $query['DOI'] . "'";
//mysql_real_escape_string($article['PMID']);
$q .= ",'" . mysqli_real_escape_string($connection, $query['Experiments']) . "'";
//mysql_real_escape_string($article['Experiments']); // CDATA removed, escape_string added
$q .= ",'" . $query['Metadata'] . "')";
//mysql_real_escape_string($article['Metadata'])."')";
$result2 = mysqli_query($connection, $q);
if ($result2) {
echo "SUCCESS. Query: " . $q;
} else {
echo "ERROR: Unable to process query: " . $q;
}
index_lucene($article, 0);
}
mysqli_free_result($result);
break;
case "experiments":
$result = mysqli_query($connection, "SELECT * FROM Articles WHERE PMID = '" . $query['PMID'] . "'");
if (mysqli_num_rows($result) >= 1) {
$q = "UPDATE Articles SET Experiments=";
$q .= "'" . mysqli_real_escape_string($connection, $query['Experiments']) . "'";
// CDATA removed, escape_string added
$q .= " WHERE PMID='" . $query['PMID'] . "'";
$result2 = mysqli_query($connection, $q);
if ($result2) {
echo "SUCCESS ";
} else {
echo "ERROR: Unable to process query: " . $q;
}
index_lucene($article, 0);
}
mysqli_free_result($result);
break;
case "metadata":
$result = mysqli_query($connection, "SELECT * FROM Articles WHERE PMID = '" . $query['PMID'] . "'");
if (mysqli_num_rows($result) >= 1) {
$q = "UPDATE Articles SET Metadata=";
$q .= "'" . mysqli_real_escape_string($connection, $query['Metadata']) . "'";
// CDATA removed, escape_string added
$q .= " WHERE PMID='" . $query['PMID'] . "'";
$result2 = mysqli_query($connection, $q);
if ($result2) {
echo "SUCCESS ";
} else {
echo "ERROR: Unable to process query: " . $q;
}
index_lucene($article, 0);
}
mysqli_free_result($result);
break;
}
}
$success++;
} else {
echo "ERROR: Unable to process query: " . $q;
}
echo ".\n";
}
mysqli_free_result($result);
}
/*------------------------------/
/ Upload to Lucene /
/------------------------------*/
if ($addToLucene) {
$article["Title"] = $title;
$article["Authors"] = $authors;
$article["Abstract"] = $abstract;
$article["Year"] = $year;
$article["Journal"] = $journal;
$article["PMID"] = $pmid;
$article["Reference"] = $reference;
$article["MeshHeadings"] = $mesh;
if ($k == count($papers) - 1) {
$optimise = 1;
} else {
$optimise = 0;
}
index_lucene($article, $optimise);
}
}
echo "Total articles processes: " . count($papers) . "\n";
echo "Total uploaded: " . $uploaded . "\n";
echo "Total successfully added: " . $success . "\n";
user_logout();
break;
case "article":
article($_GET["PMID"]);
break;
case "article_json_pmid":
article_json_pmid($_GET["PMID"]);
break;
case "article_json_doi":
article_json_doi($_GET["PMID"]);
break;
case "search_lucene":
search_lucene($_GET["query"]);
break;
case "index_lucene":
index_lucene($_GET);
break;
case "add_article":
add_article($_GET);
break;
case "get_article":
get_article($_GET);
break;
case "get_concept":
get_concept($_GET);
break;
case "add_log":
add_log($_GET);
break;
case "get_log":
get_log($_GET);
