}
$variant_id = evidence_get_variant_id($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}...";
}
}
print "{$n} ({$n_marked_pharma} existing variants changed to pharmacogenetic)\n";
print "Updating variant_external...";
theDb()->query("LOCK TABLES variant_external WRITE");
theDb()->query("DELETE FROM variant_external WHERE tag='PharmGKB'");
$q = theDb()->query("INSERT INTO variant_external\n (variant_id, tag, content, url, updated)\n SELECT variant_id, 'PharmGKB', annotation, url, NOW()\n FROM pharmgkb\n WHERE variant_id > 0");
if (theDb()->isError($q)) {
print "[" . $q->getMessage() . "]";
$taf = NULL;
}
if ($gene && $aa_change) {
$variant_name = "{$gene} {$aa_change}";
} else {
if ($rsid) {
$variant_name = $rsid;
} else {
continue;
}
}
$variant_id = evidence_get_variant_id($variant_name);
if (!$variant_id) {
// create the variant, and an "initial edit/add" row in edits table
$variant_id = evidence_get_variant_id($variant_name, false, false, false, true);
$edit_id = evidence_get_latest_edit($variant_id, 0, 0, 0, true);
}
if (ereg("^(rs?)([0-9]+)\$", $rsid, $regs)) {
$rsid = $regs[2];
} else {
$rsid = null;
}
if (isset($job2genome[$job_id])) {
$genome_id = $job2genome[$job_id];
} else {
$genome_id = evidence_get_genome_id($global_human_id);
}
theDb()->query("INSERT INTO import_genomes_tmp SET variant_id=?, genome_id=?, chr=?, chr_pos=?, trait_allele=?, taf=?, rsid=?, dataset_id=?, zygosity='{$zygosity[$hom_or_het]}'", array($variant_id, $genome_id, $chr, $chr_pos, $trait_allele, $taf, $rsid, "T/snp/{$job_id}"));
if (!isset($job2genome[$job_id])) {
theDb()->query("UPDATE genomes SET name=? WHERE genome_id=?", array($human_name, $genome_id));
theDb()->query("REPLACE INTO datasets SET dataset_id=?, genome_id=?, sex=?, dataset_url=?", array("T/snp/{$job_id}", $genome_id, $sex, "http://snp.med.harvard.edu/results/job/{$job_id}"));
if (aa_sane($_POST["variant_aa_change"])) {
if (ereg("^([^0-9]+)([0-9]+)([^0-9]+)\$", aa_long_form($_POST["variant_aa_change"]), $regs)) {
$aa_from = $regs[1];
$aa_pos = $regs[2];
$aa_to = $regs[3];
}
$gene = strtoupper($_POST["variant_gene"]);
$variant_id = evidence_get_variant_id($gene, $aa_pos, $aa_from, $aa_to, true);
$edit_id = evidence_get_latest_edit($variant_id, 0, 0, 0, true);
$response["latest_edit_v{$variant_id}a0g0"] = $edit_id;
$response["latest_edit_id"] = $edit_id;
$response["variant_id"] = $variant_id;
$response["please_reload"] = true;
$response["variant_key"] = "{$gene} " . aa_short_form("{$aa_from}{$aa_pos}{$aa_to}");
} else {
die("Invalid variant specified");
}
}
if ($article_pmid || $genome_id || $disease_id) {
$latest_edit_id = evidence_get_latest_edit($variant_id, $article_pmid, $genome_id, $disease_id, true);
$response["latest_edit_v{$variant_id}a{$article_pmid}g{$genome_id}"] = $latest_edit_id;
$response["latest_edit_id"] = $latest_edit_id;
$renderer = new evidence_row_renderer();
$renderer->render_row(theDb()->getRow("SELECT * FROM edits WHERE edit_id=?", array($latest_edit_id)));
$response["html"] = $renderer->html();
ereg("id=\"([^\"]+)", $response["html"], $regs);
$response["e_id"] = $regs[1];
}
header("Content-type: application/json");
print json_encode($response);
}
print theDb()->affectedRows();
print "\n";
print "Adding variants...";
$q = theDb()->query("\nSELECT gene_aa, snps, gwas_id\nFROM gwas\nWHERE variant_id IS NULL");
$n = 0;
$did = array();
while ($row =& $q->fetchRow()) {
$variant_name = $row["gene_aa"] ? $row["gene_aa"] : $row["snps"];
if (isset($did[$variant_name])) {
$variant_id = $did[$variant_name];
theDb()->query("UPDATE gwas SET variant_id=? WHERE gwas_id=?", array($variant_id, $row["gwas_id"]));
continue;
}
// create the variant, and an "initial edit/add" row in edits table
$variant_id = evidence_get_variant_id($variant_name, false, false, false, true);
$edit_id = evidence_get_latest_edit($variant_id, 0, 0, 0, true, array("variant_impact" => "pathogenic"));
$did[$variant_name] = $variant_id;
theDb()->query("UPDATE gwas SET variant_id=? WHERE gwas_id=?", array($variant_id, $row["gwas_id"]));
if ($row["gene_aa"]) {
theDb()->query("UPDATE variant_locations SET variant_id=? WHERE gene_aa=?", array($variant_id, $row["gene_aa"]));
}
++$n;
if ($n % 100 == 0) {
print "{$n}...";
}
}
print "{$n}\n";
print "Adding diseases...";
theDb()->query("INSERT IGNORE INTO diseases (disease_name) SELECT disease_trait FROM gwas");
print theDb()->affectedRows();
print "\n";
<?php
include "lib/setup.php";
$response = array();
if (!getCurrentUser()) {
$response["errors"][] = "Not logged in";
} else {
if ($item_id = evidence_get_latest_edit($_POST[v], $_POST[a], $_POST[g], $_POST[d])) {
$q = theDb()->query("INSERT INTO edits SET\n\t\t\tedit_oid=?, edit_timestamp=NOW(),\n\t\t\tis_draft=1, is_delete=1,\n\t\t\tprevious_edit_id=?,\n\t\t\tvariant_id=?,\n\t\t\tarticle_pmid=?, genome_id=?, disease_id=?", array(getCurrentUser("oid"), $item_id, $_POST[v], $_POST[a], $_POST[g], $_POST[d]));
if (theDb()->isError($q)) {
$response["errors"][] = $q->getMessage();
} else {
if ($delete_id = theDb()->getOne("SELECT LAST_INSERT_ID()")) {
evidence_submit($delete_id);
$response["deleted"] = true;
if ($_POST[v] && ($_POST[a] || $_POST[g]) && !$_POST[d]) {
// Delete per-disease entries for an article/genome entry
// TODO: evidence_submit() should take care of this
// TODO: snap_release will need special handling for this case too
theDb()->query("DELETE FROM snap_latest WHERE variant_id=? AND article_pmid=? AND genome_id=?", array($_POST[v], $_POST[a], $_POST[g]));
}
}
}
} else {
$response["errors"][] = "Nothing to delete";
}
}
header("Content-type: application/json");
print json_encode($response);
?>
