function evidence_generate_edit($previous_edit_id = null, $variant_id = null, $row = array())
{
if ($previous_edit_id) {
$row = evidence_get_edit($previous_edit_id);
$variant_id = $row["variant_id"];
} else {
if ($variant_id) {
$row["variant_id"] = $variant_id;
} else {
if (!$row["variant_id"]) {
die("evidence_edit_id_generate(): need either previous edit id or variant id");
}
}
}
$row["is_draft"] = 1;
$row["is_delete"] = 0;
$row["previous_edit_id"] = $previous_edit_id;
$row["edit_oid"] = $_SESSION["user"]["oid"];
unset($row["edit_id"]);
unset($row["edit_timestamp"]);
unset($row["signoff_oid"]);
unset($row["signoff_timestamp"]);
$sqlfields = "edit_timestamp=NOW()";
$sqlparams = array();
foreach ($row as $column => $value) {
$sqlfields .= ", {$column}=?";
$sqlparams[] = $value;
}
theDb()->query("INSERT INTO edits SET {$sqlfields}", $sqlparams);
$new_edit_id = theDb()->getOne("SELECT LAST_INSERT_ID()");
return theDb()->getRow("SELECT * FROM edits WHERE edit_id=?", array($new_edit_id));
}
while ($row =& $q->fetchRow()) {
// create the variant, and an "initial edit/add" row in edits table
$gene_aa = $row["gene_aa"];
if (eregi('([a-z0-9]+):([0-9]+) ?([a-z][a-z][a-z])>([a-z][a-z][a-z])', $gene_aa, $r)) {
$gene_aa = "{$r['1']} {$r['3']}{$r['2']}{$r['4']}";
} else {
if (eregi('([a-z0-9]+):([a-z]+)([0-9]+)([a-z]+)', $gene_aa, $r)) {
$gene_aa = "{$r['1']} {$r['2']}{$r['3']}{$r['4']}";
}
}
$variant_id = evidence_get_variant_id($gene_aa, false, false, false, true);
if (!$variant_id && $row["rsid"]) {
$variant_id = evidence_get_variant_id("rs" . $row["rsid"], false, false, false, true);
}
$edit_id = evidence_get_latest_edit($variant_id, 0, 0, 0, true, array("variant_impact" => "pharmacogenetic"));
$latestrow = evidence_get_edit($edit_id);
if (in_array($latestrow["variant_impact"], array("not reviewed", "none", "unknown"))) {
$newrow = evidence_generate_edit(null, null, $latestrow);
$newrow["variant_impact"] = "pharmacogenetic";
$new_edit_id = evidence_save_draft(null, $newrow);
evidence_submit($new_edit_id);
++$n_marked_pharma;
}
if (ereg('^[0-9]+$', $row["pmid"])) {
evidence_get_latest_edit($variant_id, $row["pmid"], 0, 0, true);
}
$did[$variant_name] = $variant_id;
theDb()->query("UPDATE pharmgkb SET variant_id=? WHERE pharmgkb_id=?", array($variant_id, $row["pharmgkb_id"]));
++$n;
if ($n % 100 == 0) {
print "{$n}...";
