print "Updating variant_external for existing searches...";
$q = theDb()->query("SELECT DISTINCT variant_id FROM yahoo_boss_cache");
if ($q && !theDb()->isError($q)) {
$n = 0;
while ($row =& $q->fetchRow()) {
yahoo_boss_update_external($row["variant_id"]);
++$n;
if ($n % 10 == 0) {
print ".";
}
}
print "{$n}";
} else {
print "(none)";
}
print "\n";
}
print "Building queue...";
$q = theDb()->query("CREATE TEMPORARY TABLE yahoo_boss_queue (\n variant_id BIGINT UNSIGNED NOT NULL\n) AS\n SELECT v.variant_id\n FROM variants v\n LEFT JOIN gene_disease\n ON gene=v.variant_gene\n LEFT JOIN flat_summary\n ON v.variant_id=flat_summary.variant_id AND n_genomes=1\n LEFT JOIN yahoo_boss_cache c\n ON c.variant_id=v.variant_id\n WHERE (gene IS NOT NULL OR flat_summary.variant_id IS NOT NULL)\n AND c.xml IS NULL\n GROUP BY v.variant_id");
if (theDb()->isError($q)) {
die($q->getMessage());
}
print theDb()->affectedRows();
print "\n";
$q = theDb()->query("SELECT q.variant_id variant_id, v.*\n FROM yahoo_boss_queue q\n LEFT JOIN variants v\n ON v.variant_id=q.variant_id");
while ($row =& $q->fetchRow()) {
$r = yahoo_boss_lookup($row["variant_id"]);
yahoo_boss_update_external($row["variant_id"]);
printf("%8d %s %s%d%s (%d)\n", $r["hitcount"], $row["variant_gene"], $row["variant_aa_from"], $row["variant_aa_pos"], $row["variant_aa_to"], $row["variant_id"]);
sleep(1);
}
function yahoo_boss_update_external($variant_id)
{
$cache = yahoo_boss_lookup($variant_id);
if (!$cache) {
print "No search results\n";
return;
}
$variant = theDb()->getRow("SELECT v.*, vo.rsid rsid FROM variants v\n\t\t\t\t LEFT JOIN variant_occurs vo\n\t\t\t\t ON v.variant_id=vo.variant_id\n\t\t\t\t AND vo.rsid IS NOT NULL\n\t\t\t\t WHERE v.variant_id=?\n\t\t\t\t GROUP BY v.variant_id", array($variant_id));
if (!$variant || theDb()->isError($variant)) {
print "No such variant\n";
return FALSE;
}
if ($variant["variant_gene"]) {
$gene_aa_long = $variant["variant_gene"] . " " . $variant["variant_aa_from"] . $variant["variant_aa_pos"] . $variant["variant_aa_to"];
$gene_aa_short = $variant["variant_gene"] . " " . aa_short_form($variant["variant_aa_from"]) . $variant["variant_aa_pos"] . aa_short_form($variant["variant_aa_to"]);
$search_string = "{$gene_aa_long} OR {$gene_aa_short}";
if (($rsid = $variant["variant_rsid"]) || ($rsid = $variant["rsid"])) {
$search_string .= " OR rs{$rsid}";
}
} else {
$search_string = "rs" . $variant["variant_rsid"];
}
$user_url = "http://search.yahoo.com/search?p=" . urlencode($search_string);
$content = "";
$skipped_hits = 0;
if ($cache["hitcount"] > 0) {
preg_match_all('{<result>.*?</result>}is', $cache["xml"], $matches, PREG_PATTERN_ORDER);
foreach ($matches[0] as $result) {
$resulttag = array();
foreach (array("url", "dispurl", "abstract", "title") as $t) {
if (preg_match("{<{$t}>(.*?)</{$t}>}i", $result, $regs)) {
$resulttag[$t] = preg_replace('{<\\!\\[CDATA\\[(.*?)\\]\\]>}s', '$1', $regs[1]);
} else {
$resulttag = FALSE;
continue;
}
}
if (ereg("snp\\.med\\.harvard\\.edu|evidence\\.personalgenomes\\.org", $resulttag["url"])) {
$skipped_hits++;
continue;
}
if ($resulttag) {
$content .= "<LI><A href=\"" . $resulttag["url"] . "\">" . $resulttag["title"] . "</A><BR />" . $resulttag["abstract"] . "<BR /><DIV class=\"searchurl\">" . $resulttag["dispurl"] . "</DIV></LI>\n";
}
}
}
// If we skipped some hits (because they point to this page or
// Trait-o-matic), subtract them from the cached hitcount so "no
// web results except this page" gets counted as 0 for
// statistics/display.
if ($skipped_hits > 0 && preg_match('/<resultset_web\\b[^<]*\\sdeephits="?(\\d+)"?/s', $cache["xml"], $regs) && $regs[1] >= $skipped_hits) {
$hitcount = $regs[1] - $skipped_hits;
if ($hitcount != $cache["hitcount"]) {
$cache["hitcount"] = $hitcount;
theDb()->query("UPDATE yahoo_boss_cache SET hitcount=? WHERE variant_id=?", array($hitcount, $variant_id));
}
}
// Build html display for variant page
$content = "<UL><STRONG>Web search results (" . $cache["hitcount"] . " hit" . ($cache["hitcount"] == 1 ? "" : "s") . " -- <A href=\"" . $user_url . "\">see all</A>)</STRONG>" . $content . "</UL>";
theDb()->query("DELETE FROM variant_external WHERE variant_id=? AND tag=?", array($variant_id, "Yahoo!"));
$q = theDb()->query("INSERT INTO variant_external SET variant_id=?, tag=?, content=?, url=NULL, updated=NOW()", array($variant_id, "Yahoo!", $content));
}
