$history_box .= "<LI>View the <A href=\"{$variant_name};{$next_version}\">next version</A>";
}
if ($next_version) {
$history_box .= "<LI>View the <A href=\"{$variant_name}\">latest version";
} else {
$history_box .= "<LI>View <A href=\"{$variant_name}\">this version without highlighted changes";
}
$history_box .= "</A>";
if (getCurrentUser()) {
$history_box .= " and enable editing features";
}
$history_box .= "</LI>\n";
$history_box .= "</UL></DIV>";
$gDisableEditing = TRUE;
}
$report =& evidence_get_report($history_box && $max_edit_id ? 0 + $max_edit_id : "latest", $variant_id);
$row0 =& $report[0];
$variant_name_long = evidence_get_variant_name($row0, " ", false);
$variant_name_short = evidence_get_variant_name($row0, " ", true);
$gOut["title"] = "{$variant_name_short} - GET-Evidence";
$gOut["content"] = "<h1>{$variant_name_short}</h1>\n<!-- {$variant_id} -->\n";
if ($variant_name_long != $variant_name_short) {
$gOut["content"] .= "<p>({$variant_name_long})</p>\n";
}
$gOut["content"] .= seealso_related($row0["variant_gene"], $row0["variant_aa_pos"], $variant_id);
$gOut["content"] .= $history_box;
$renderer = new evidence_row_renderer();
foreach ($report as $row) {
if ($row["article_pmid"] > 0 || $row["genome_id"] > 0) {
break;
}
function evidence_get_assoc($snap, $variant_id)
{
$rows =& evidence_get_report($snap, $variant_id);
global $gWantKeysForAssoc;
if (!is_array($gWantKeysForAssoc["variant"])) {
foreach ($gWantKeysForAssoc as $k => &$v) {
if ($k == "all") {
continue;
}
$v = explode(" ", $gWantKeysForAssoc["all"] . " " . $v);
}
}
$variant = array("genomes" => array(), "articles" => array(), "diseases" => array());
for ($i = 0; $i < sizeof($rows); $i++) {
$row =& $rows[$i];
$editor = user::lookup($row["edit_oid"]);
$row["editor_name"] = $editor->get("fullname");
if (strlen($row["summary_long"]) == 0) {
$row["summary_long"] = $row["summary_short"];
}
if ($row["article_pmid"] > 0) {
$section =& $variant["articles"]["" . $row["article_pmid"]];
$want_keys =& $gWantKeysForAssoc["article"];
} else {
if ($row["genome_id"] > 0) {
$section =& $variant["genomes"]["" . $row["genome_id"]];
$want_keys =& $gWantKeysForAssoc["genome"];
} else {
$section =& $variant;
$want_keys =& $gWantKeysForAssoc["variant"];
$row["aa_change"] = $row["variant_aa_from"] . $row["variant_aa_pos"] . $row["variant_aa_to"];
$row["aa_change_short"] = aa_short_form($row["aa_change"]);
// TODO: combine these into one array and add labels
$row["quality_scores"] = str_split(str_pad($row["variant_quality"], 6, "-"));
$row["quality_comments"] = $row["variant_quality_text"] ? json_decode($row["variant_quality_text"], true) : array();
$diseases = evidence_get_all_oddsratios($rows);
unset($max_or_id);
foreach ($diseases as $id => &$d) {
if (!isset($max_or_id) || $diseases[$max_or_id]["figs"]["or"] < $d["figs"]["or"]) {
$max_or_id = $id;
}
}
if (isset($max_or_id)) {
$row["disease_max_or"] = $diseases[$max_or_id];
}
}
}
if ($row["disease_id"] > 0) {
$section =& $section["diseases"]["" . $row["disease_id"]];
if (ereg('^\\[', $row["summary_short"])) {
$row = array_merge(json_decode($row["summary_short"], true), $row);
}
$want_keys =& $gWantKeysForAssoc["disease"];
}
foreach ($want_keys as $k) {
list($inkey, $outkey) = explode(":", $k);
if (!$outkey) {
$outkey = $inkey;
}
$section[$outkey] = $row[$inkey];
}
unset($section);
}
foreach (array("articles", "genomes") as $section) {
$variant[$section] = array_values($variant[$section]);
foreach ($variant[$section] as &$x) {
if (is_array($x["diseases"])) {
$x["diseases"] = array_values($x["diseases"]);
}
}
}
return $variant;
}
include "lib/openid.php";
evidence_create_tables();
openid_create_tables();
if ($_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: /");
}
