PHP filteralpha Examples

Example #1

File: godm.php Project: mahogny/esexpress

<?php

include "common.php";
$query = json_decode(getdef($_GET, 'q', '{}'), TRUE);
$ds1 = filteralpha(getdef($query, 'dataset1', ''));
$ds2 = filteralpha(getdef($query, 'dataset2', ''));
if ($ds1 == "" && $ds2 == "") {
    $ps = pg_prepare($db, 'getgene', "SELECT DISTINCT * FROM godm NATURAL JOIN goinfo");
    $rs = pg_execute($db, 'getgene', array());
} else {
    $ps = pg_prepare($db, 'getgene', "SELECT DISTINCT * FROM godm NATURAL JOIN goinfo WHERE dataset1=\$1 AND dataset2=\$2 ORDER BY pvalue");
    $rs = pg_execute($db, 'getgene', array($ds1, $ds2));
}
echo '"dataset1","dataset2","goid","goname","pvalue","tscore"' . "\n";
while ($line = pg_fetch_array($rs, null, PGSQL_ASSOC)) {
    echo '"' . $line["dataset1"] . '","' . $line["dataset2"] . '","' . $line["goid"] . '","' . $line["goname"] . '","' . $line["pvalue"] . '","' . $line["tscore"] . "\"\n";
}
pg_free_result($rs);
### Return result
#header('Content-Type: application/json; ');
#header('filename="godm.json"; ');
include "end.php";

Example #2

File: genedm.php Project: mahogny/esexpress

<?php

include "common.php";
$query = json_decode(getdef($_GET, 'q', '{}'), TRUE);
$ds1 = filteralpha(getdef($query, 'dataset', ''));
if ($ds1 == "") {
    $ps = pg_prepare($db, 'getgene', "SELECT DISTINCT * FROM genedm");
    $rs = pg_execute($db, 'getgene', array());
} else {
    $ps = pg_prepare($db, 'getgene', "SELECT DISTINCT * FROM genedm WHERE dataset=\$1");
    $rs = pg_execute($db, 'getgene', array($ds1));
}
echo '"dataset","geneid","genedm"' . "\n";
while ($line = pg_fetch_array($rs, null, PGSQL_ASSOC)) {
    echo '"' . $line["dataset"] . '","' . $line["geneid"] . '","' . $line["genedm"] . "\"\n";
}
pg_free_result($rs);
### Return result
#header('Content-Type: application/json; ');
#header('filename="godm.json"; ');
include "end.php";

Example #3

File: corrgenegene.php Project: mahogny/esexpress

<?php

include "common.php";
$query = json_decode(getdef($_GET, 'q', '{}'), TRUE);
$geneid = getdef($query, 'geneset', array("ENSMUSG00000000126", "ENSMUSG00000000028"));
$graphw = filteralpha(getdef($query, 'graphw', 500));
$dataset = filteralpha(getdef($query, 'dataset', 'es_lif'));
$cmd = "echo 'genes <- c();";
foreach ($geneid as $s) {
    $cmd = $cmd . "genes <- c(genes,\"" . filteralpha($s) . "\");";
}
$cmd = $cmd . "graphw<-" . $graphw . ";";
$cmd = $cmd . "dataset<-\"" . $dataset . "\";";
$cmd = $cmd . "source(\"corrgenegene.R\")' | /usr/bin/R --vanilla --slave";
#echo $cmd;
$handle = popen($cmd, "r");
$ret = "";
do {
    $data = fread($handle, 8192);
    if (strlen($data) == 0) {
        break;
    }
    $ret .= $data;
} while (true);
pclose($handle);
header("Cache-Control: no-cache, must-revalidate");
if (strlen($ret) == 0) {
    echo "error running " . $cmd;
} else {
    header("Content-type:image/png");
    echo $ret;

Example #4

File: corrgenecell.php Project: mahogny/esexpress

<?php

include "common.php";
$query = json_decode(getdef($_GET, 'q', '{}'), TRUE);
$geneid = getdef($query, 'geneset', array("ENSMUSG00000000126", "ENSMUSG00000000028"));
$datasets = getdef($query, 'datasets', array("ola_a2i"));
$graphw = filteralpha(getdef($query, 'graphw', 500));
$cmd = "echo 'genes <- c();";
foreach ($geneid as $s) {
    $cmd = $cmd . "genes <- c(genes,\"" . filteralpha($s) . "\");";
}
$cmd = $cmd . "datasets <- c();";
foreach ($datasets as $s) {
    $cmd = $cmd . "datasets <- c(datasets,\"" . filteralpha($s) . "\");";
}
$cmd = $cmd . "graphw<-" . $graphw . ";";
$cmd = $cmd . "source(\"corrgenecell.R\")' | /usr/bin/R --vanilla --slave";
$handle = popen($cmd, "r");
$ret = "";
do {
    $data = fread($handle, 8192);
    if (strlen($data) == 0) {
        break;
    }
    $ret .= $data;
} while (true);
pclose($handle);
header("Cache-Control: no-cache, must-revalidate");
if (strlen($ret) < 100) {
    #for any errors?
    echo "error running " . $cmd;

Example #5

File: geneinfo.php Project: mahogny/esexpress

<?php

ini_set('memory_limit', '512M');
## http://localhost/geneinfo.php?q={%22gene%22:%22ENSMUSG00000000049%22}
include "common.php";
$query = json_decode(getdef($_GET, 'q', '{}'), TRUE);
$geneid = filteralpha(getdef($query, 'gene', ''));
### Query database for expression counts, for all datasets
$time_getgene = microtime();
$ps = pg_prepare($db, 'getgene', 'SELECT * FROM geneexp WHERE fromgene=$1');
$rs = pg_execute($db, 'getgene', array($geneid));
$resultsexp = array();
while ($line = pg_fetch_array($rs, null, PGSQL_ASSOC)) {
    $resultsexp[$line['dataset']] = array('fromcell' => splitcomma($line['fromcell']), 'exp' => splitcomma($line['exp']));
}
pg_free_result($rs);
$time_getgene = microtime() - $time_getgene;
$results = array();
$results['dataset'] = $resultsexp;
$results['geneid'] = $geneid;
### Query database for gene info --- this particular gene
$time_getgenei = microtime();
$ps = pg_prepare($db, 'getgenei', 'SELECT * FROM geneinfo WHERE geneid=$1 LIMIT 1');
$rs = pg_execute($db, 'getgenei', array($geneid));
while ($line = pg_fetch_array($rs, null, PGSQL_ASSOC)) {
    $results['genesym'] = $line['genesym'];
}
pg_free_result($rs);
$time_getgenei = microtime() - $time_getgenei;
### Query database for DM
$time_getgenedm = microtime();