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Data entry utility - Do Not Merge. #252

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362 changes: 362 additions & 0 deletions www/addpairs.php
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Original file line number Diff line number Diff line change
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<?php

chdir(__DIR__);
require_once("../predict/protutils.php");
require_once("../predict/odorutils.php");
$odors = json_decode(file_get_contents("../data/odorant.json"), true);

$page_title = "Add Empirical Pairs";
include("header.php");

if (!file_exists("../www/security.json"))
{
if (isset($_POST['apw']))
{
$salt = substr(md5(random_bytes(53)), 13, 2);
$security = ['apw' => crypt($_POST['apw'], $salt), 'salt' => $salt];
$fp = fopen("../www/security.json", "wb");
if (!$fp) die("Unable to write security file; please check permissions.");
else
{
fwrite($fp, json_encode($security));
fclose($fp);
}
}
else
{
?>
<form action="" method="POST">
Please set an administrator password:
<br>
<input type="password" name="apw">
<br>
<input type="submit">
</form>
<?php
exit;
}
}
else
{
$security = json_decode(file_get_contents("../www/security.json"), true);
}

if (!isset($security)) exit;

if (!isset($_REQUEST["token"]))
{
if (isset($_POST["pw"]))
{
if (hash_equals($security["apw"], crypt($_POST["pw"], $security["salt"])))
{
$token = bin2hex(random_bytes(128));
$security['token'] = $token;
$security['ip'] = $_SERVER["REMOTE_ADDR"];
$fp = fopen("../www/security.json", "wb");
if (!$fp) die("Unable to update security file; please check permissions.");
else
{
fwrite($fp, json_encode($security));
fclose($fp);
}
}
else die("Password incorrect.");
}
else
{
_relogin:
?>
<form action="" method="POST">
Please enter the administrator password:
<br>
<input type="password" name="pw">
<br>
<?php
foreach ($_POST as $k => $v)
{
if ($k != "token") echo "<input type=\"hidden\" name=\"$k\" value=\"$v\">\n";
}
?>
<input type="submit">
</form>
<?php
exit;
}
}
else $token = $_REQUEST["token"];

if ($security['token'] != $token || $security['ip'] != $_SERVER["REMOTE_ADDR"]) goto _relogin;

if (isset($_POST["refurl"]))
{
$new_ref = [ "short_name" => $_POST["sname"], "citation" => $_POST["cite"] ];
if (!isset($refs[$_POST["refurl"]]))
{
if (!$_POST["sname"] || !$_POST["cite"]) die("Short name and citation are required.");
else $refs[$_POST["refurl"]] = $new_ref;
}

$tallest = 0.0;
for ($i=1; isset($_POST["prot$i"]); $i++)
{
$f = floatval(@$_POST["top$i"]);
if (abs($f) > $tallest) $tallest = $f;
}
$scale = $tallest ? (10.0 / $tallest) : 1;

for ($i=1; isset($_POST["prot$i"]); $i++)
{
if ($_POST["prot$i"] && $_POST["odor$i"])
{
$new_odor =
[
"full_name" => $_POST["odorfn$i"],
"smiles" => $_POST["smiles$i"],
];

if (@$_POST["olept$i"])
{
$olept = explode(" ", $_POST["olept$i"]);
$new_odor["aroma"]["http://www.thegoodscentscompany.com"] = $olept;
}

if (@$_POST["top$i"]) $new_odor["activity"][$_POST["refurl"]][$_POST["prot$i"]]["adjusted_curve_top"]
= floatval($_POST["top$i"]) * $scale;

else if (@$_POST["top$i"] === "0") $new_odor["activity"][$_POST["refurl"]][$_POST["prot$i"]]["adjusted_curve_top"] = "0";

if (@$_POST["ec$i"])
{
$ec50 = floatval($_POST["ec$i"]);

// TODO: type of ec50, e.g. log10, mM, μM, etc.
$ec50 = pow(10.0, $ec50); // log10.

if ($ec50 > 0 && $ec50 <= 1) $new_odor["activity"][$_POST["refurl"]][$_POST["prot$i"]]["ec50"] = $ec50;
}

if (@$_POST["ant$i"]) $new_odor["activity"][$_POST["refurl"]][$_POST["prot$i"]]["antagonist"] = 1;

if ($_POST["odor$i"] == "new")
{
$oid = md5($new_odor["smiles"]);
}
else
{
$oid = $_POST["odor$i"];
}

if (isset($odors[$oid]))
{
$odors[$oid]["activity"][$_POST["refurl"]] = $new_odor["activity"][$_POST["refurl"]];
}
else
{
$odors[$oid] = $new_odor;
}

// echo "<pre>".json_encode_pretty($new_odor)."</pre>";
}
}

$fp = fopen("../data/refs.json", "wb");
if (!$fp) die("Unable to open data/refs.json; check permissions.");
else
{
fwrite($fp, json_encode_pretty($refs));
fclose($fp);
}

$fp = fopen("../data/odorant.json", "wb");
if (!$fp) die("Unable to open data/odorant.json; check permissions.");
else
{
fwrite($fp, json_encode_pretty($odors));
fclose($fp);
}

echo "<h2>Success!</h2><p>You may optionally add more pairs if desired.</p>";
}

?>
<style>
body
{
overflow: auto!important;
}

textarea
{
border-radius: 4px;
background-color: #aabbb7;
color: #08101b;
border: 1px solid #214577;
margin: 2px;
}

div.pair
{
margin: 15px;
border: 1px solid #069;
background-color: #235;
padding: 15px;
}

div.pair label
{
width: 7%;
display: inline-block;
}
</style>

<script language="Javascript">
var lastselor = false;
function new_pair()
{
var pairno = $("div.pair").length + 1;

var ctnr = $("#pairs")[0];
var div = document.createElement("div");
div.className = "pair";
div.id = "pair" + pairno;

var lbl = document.createElement("label");
lbl.innerText = "Prot:";
div.appendChild(lbl);

var ctl = document.createElement("select");
ctl.name = ctl.id = "prot" + pairno;
var opt = document.createElement("option");
opt.value = "";
opt.innerText = "-----";
ctl.appendChild(opt);
<?php
foreach (array_keys($prots) as $rcpid)
{
?>
opt = document.createElement("option");
opt.value = "<?php echo $rcpid; ?>";
opt.innerText = opt.value;
ctl.appendChild(opt);

<?php
}
?>
if (lastselor) ctl.value = lastselor;
ctl.setAttribute("onchange", "lastselor = this.value;");
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

var lbl = document.createElement("label");
lbl.innerText = "Odor:";
div.appendChild(lbl);

ctl = document.createElement("select");
ctl.name = ctl.id = "odor" + pairno;
opt = document.createElement("option");
opt.value = "";
opt.innerText = "-----";
ctl.appendChild(opt);
<?php
foreach ($odors as $oid => $odor)
{
?>
opt = document.createElement("option");
opt.value = "<?php echo $oid; ?>";
opt.innerText = "<?php echo $odor["full_name"]; ?>";
ctl.appendChild(opt);

<?php
}
?>
opt = document.createElement("option");
opt.value = "new";
opt.innerText = "(add new)";
ctl.appendChild(opt);

ctl.setAttribute("onchange", "(this.value == 'new') ? new_odorant(this.parentElement) : new_pair();");
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

lbl = document.createElement("label");
lbl.innerText = "Top:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.name = ctl.id = "top" + pairno;
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

lbl = document.createElement("label");
lbl.innerHTML = "EC<sub>50</sub>:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.name = ctl.id = "ec" + pairno;
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

lbl = document.createElement("label");
lbl.innerHTML = "Antagonist:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.type = "checkbox";
ctl.name = ctl.id = "ant" + pairno;
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

ctnr.appendChild(div);
}

function new_odorant(div)
{
var pairno = parseInt(div.id.substr(4));

lbl = document.createElement("label");
lbl.innerHTML = "Odor:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.name = ctl.id = "odorfn" + pairno;
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

lbl = document.createElement("label");
lbl.innerHTML = "SMILES:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.name = ctl.id = "smiles" + pairno;
ctl.setAttribute("onchange", "new_pair();");
div.appendChild(ctl);
div.appendChild(document.createElement("br"));

lbl = document.createElement("label");
lbl.innerHTML = "Aroma:";
div.appendChild(lbl);
ctl = document.createElement("input");
ctl.name = ctl.id = "olept" + pairno;
ctl.setAttribute("onchange", "new_pair();");
div.appendChild(ctl);
div.appendChild(document.createElement("br"));
}
</script>
<h2>Add Empirical Receptor-Ligand Pairs</h2>

<form action="" method="POST">
<input type="hidden" name="token" value="<?php echo $token; ?>">
<label for="refurl">Reference URL:</label>
<input type="text" name="refurl" style="width: 81%;">
<br>
<label for="sname">Short Name:</label>
<input type="text" name="sname" style="width: 31%;">
<br>
<label for="cite">Citation:</label>
<textarea name="cite" style="width: 100%; height: 111px;"></textarea>
<br>

<div id="pairs">
</div>
<br>

<input type="submit" value="Save">

<script>
new_pair();
</script>