$gene_aa = "{$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}..."; } } print "{$n} ({$n_marked_pharma} existing variants changed to pharmacogenetic)\n"; print "Updating variant_external...";
include "lib/openid.php"; evidence_create_tables(); openid_create_tables(); if ($_REQUEST["test-insert"]) { if (!getCurrentUser("is_admin")) { die("yours is not an admin account."); } header("Content-type: text/plain"); $variant_id = evidence_get_variant_id("NPHP4", 848, "Arg", "Trp", true); $e = evidence_edit_id_generate(null, $variant_id); evidence_save_draft($e, array("variant_impact" => "unknown", "variant_dominance" => "unknown", "summary_short" => "This variant has been found together with R682X as a compound heterozygote in three nephronophthisis and retinitis pigmentosa, (Senior-Loken syndrome) patients from one family.")); print "after evidence_save_draft\n"; print_r(theDb()->getRow("SELECT * FROM edits WHERE edit_id=?", array($e))); evidence_submit($e); print "after evidence_submit\n"; print_r(evidence_get_report("latest", $variant_id)); evidence_signoff($e); $a = evidence_edit_id_generate(null, $variant_id); evidence_save_draft($a, array("article_pmid" => 12205563, "summary_short" => "Otto, E. et al. A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution. Am J Hum Genet 71, 1161-1167, doi:S0002-9297(07)60408-X [pii]")); evidence_submit($a); evidence_signoff($a); $a = evidence_edit_id_generate(null, $variant_id); evidence_save_draft($a, array("article_pmid" => 9734597, "summary_short" => "Lemmink, H. H. et al. Novel mutations in the thiazide-sensitive NaCl cotransporter gene in patients with Gitelman syndrome with predominant localization to the C-terminal domain. Kidney Int 54, 720-730, doi:10.1046/j.1523-1755.1998.00070.x (1998).")); evidence_submit($a); print "release:\n"; print_r(evidence_get_report("release", $variant_id)); print "latest:\n"; print_r(evidence_get_report("latest", $variant_id)); } else { header("Location: /"); }