php problems with union select distinct - php

Question

I submitted these two files:
sample_annotation.txt
sample_synteny.txt
I got on the next page the following error:
304501820180500000018.304501820180500000018<br><br>select distinct org1,org2 from '.304501820180500000018.'_synteny union select distinct org1,org2 from '.304501820180500000018.'_synteny<br><br>
Invalid query: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ''.304501820180500000018.'_synteny union select distinct org1,org2 from '.3045018' at line 1
Whole query: select distinct org1,org2 from '.304501820180500000018.'_synteny union select distinct org1,org2 from '.304501820180500000018.'_synteny[]
The mGSV/lib/data.php looks like below and caused the above error:
<?php
include('database.php');
## Get parameters
$org = $_GET['org'];
$data = $_GET['data'];
$session_id = $_GET['session_id'];
$array = array();
if($data == 'annotation') {
$query = "SELECT track_name FROM ".$session_id."_annotation WHERE org_id like '$org' GROUP BY track_name ";
$result = mysql_query($query);
if($result != ''){
while($row = mysql_fetch_assoc($result)){
array_push($array, $row['track_name']);
}
}
//array_push($syn_array, "10_50_20_70");
}
else if ($data == 'synteny') {
$query = "DESC ".$session_id."_synteny";
$result = mysql_query($query);
while($row = mysql_fetch_assoc($result)){
if($row['Field'] == 'id'){ continue; }
if($row['Field'] == 'blocks'){ continue; }
if($row['Field'] == 'SYNcolor'){ continue; }
if(! preg_match("/^org[12]+[_]?[start|end]?/", $row['Field'])){
array_push($array, $row['Field']);
}
}
}
else if ($data == 'size'){
echo "$session_id.", $session_id, "<br>";
echo "$org", $org, "<br>";
$query = "select distinct org1,org2 from '.$session_id.'_synteny union select distinct org1,org2 from '.$session_id.'_synteny";
echo $query,"<br>";
$result = mysql_query($query);
echo $results,"<br>";
if ($results) {
while($row = mysql_fetch_assoc($result)){
echo $row['org1'], "<br>";
$q = "select max(output) as max from (select max(greatest(org1_start, org1_end)) as output from ".$session_id."_synteny where org1 like '" . $row['org1'] . "' union select max(greatest(org2_start, org2_end)) as output from ".$session_id."_synteny where org2 like '" . $row['org1'] . "') as t1";
echo $q, "<br>";
$res = mysql_query($q);
if (!$res) {
die('Could not query:' . mysql_error());
}
echo $row['org1'],"<br>";
echo $row['org2'],"<br>";
if (! isset($array[$row['org1']])){
//echo "add<br>";
$array[$row['org1']] = mysql_result($res,0);
}
$q = "select max(output) as max from (select max(greatest(org1_start, org1_end)) as output from ".$session_id."_synteny where org1 like '" . $row['org2'] . "' union select max(greatest(org2_start, org2_end)) as output from ".$session_id."_synteny where org2 like '" . $row['org2'] . "') as t1";
#echo $q, "<br>";
$res = mysql_query($q);
if (!$res) {
die('Could not query:' . mysql_error());
}
if (! isset($array[$row['org2']])){
//echo "add<br>";
$array[$row['org2']] = mysql_result($res,0);
}
}
}
else {
echo 'Invalid query: ' . mysql_error() . "\n";
echo 'Whole query: ' . $query;
}
}
else if ($data == 'order'){
$query = "select distinct org1 from ".$session_id."_synteny union select distinct org2 from ".$session_id."_synteny ";
//echo $query,"<br>";
$result = mysql_query($query);
$default = array();
while($row = mysql_fetch_assoc($result)){
array_push($default, $row['org1']);
}
$array = join('__ORDER__', $default);
}
else if ($data == 'sorder'){
$query = "select distinct org1,org2 from ".$session_id."_synteny union select distinct org1,org2 from ".$session_id."_synteny ";
//echo $query,"<br>";
$result = mysql_query($query);
$default = array();
$assarr = array();
while($row = mysql_fetch_assoc($result)){
if( ! in_array($row['org1'], $default)){
array_push($default, $row['org1']);
$assarr[sizeof($assarr)] = array();
}
if( ! in_array($row['org2'], $default)){
array_push($default, $row['org2']);
$assarr[sizeof($assarr)] = array();
}
$len_query = "select sum(org1_end) - sum(org1_start) + sum(org2_end) - sum(org1_start) as sum from ".$session_id."_synteny where (org1 like '".$row['org1']."' and org2 like '".$row['org2']."') OR (org1 like '".$row['org2']."' and org2 like '".$row['org1']."')";
$q_result = mysql_query($len_query);
$q_row = mysql_fetch_assoc($q_result);
#echo $len_query,"<br>";
#echo $q_row['sum'],"<br>";
$assarr[array_search($row['org1'], $default)][array_search($row['org2'], $default)] = $q_row['sum'];
#$assarr[array_search($row['org1'], $default)][array_search($row['org2'], $default)] = 1;
$assarr[array_search($row['org2'], $default)][array_search($row['org1'], $default)] = $q_row['sum'];
#$assarr[array_search($row['org2'], $default)][array_search($row['org1'], $default)] = 1;
#echo array_search($row['org1'], $default) . "][ ". array_search($row['org2'], $default) . '<br>';
$assarr[array_search($row['org1'], $default)][array_search($row['org1'], $default)] = 0;
#echo array_search($row['org1'], $default) . "][ ". array_search($row['org1'], $default) . '<br>';
$assarr[array_search($row['org2'], $default)][array_search($row['org2'], $default)] = 0;
#echo array_search($row['org2'], $default) . "][ ". array_search($row['org2'], $default) . '<br>';
}
$a = FindOrder($assarr);
$sugg = array();
//echo sizeof($a),'<br>';
foreach($a as $b){
//echo $default[$b],"<br>";
array_push($sugg, $default[$b]);
}
$array = join('__ORDER__', $sugg);
}
function FindOrder($graph){
$r = array();
$last = -1;
while(!isEmpty($graph)){
$start = leastEdges($graph);
$path = longestPath($graph, $start, 0);
$path = completeCycle($graph, $path);
if($path[0] != $last){
array_push($r, $path[0]);
}
for($x = 1; $x < sizeof($path); $x++){
array_push($r, $path[$x]);
}
$last = $path[sizeof($path)-1];
$graph = removePath($graph, $path);
}
return $r;
}
function longestPath($graph, $cur, $len){
$path = array();
array_push($path, $cur);
$longestSubpath = array();
for($x = 0; $x < sizeof($graph); $x++){
if($graph[$cur][$x] != 0){
$subpath = longestPath(removeVertex($graph, $cur), $x, $len + $graph[$cur][$x]);
if(sizeof($subpath) > sizeof($longestSubpath)){
$longestSubpath = $subpath;
}
}
}
foreach($longestSubpath as $x){
array_push($path, $x);
}
return $path;
}
function completeCycle($graph, $path){
$graph = removePath($graph, $path);
$last = $path[sizeof($path)-1];
for($x = 0; $x < sizeof($graph); $x++){
if($graph[$last][$x] != 0){
array_push($path, $x);
return $path;
}
}
return $path;
}
function removePath($graph, $path){
for($x = 0; $x < sizeof($path) - 1; $x++){
$arr = $path[$x]; //***forgot the $ in front of path***
$b = $path[$x+1]; //***forgot the $ in front of path***
$graph[$arr][$b] = 0;
$graph[$b][$arr] = 0;
}
return $graph;
}
function removeVertex($graph, $vtx){
if($vtx < 0 || $vtx >= sizeof($graph)){
return copy($graph);
}
for($x = 0; $x < sizeof($graph); $x++){
$graph[$x][$vtx] = 0;
$graph[$vtx][$x] = 0;
}
return $graph;
}
function numEdges($vtx){
$r = 0;
foreach($vtx as $x){
if($x != 0){
$r++;
}
}
return $r;
}
function leastEdges($graph){
$r = -1;
$min = 2147483647;
for($x = 0; $x < sizeof($graph); $x++){
$e = numEdges($graph[$x]);
if($e != 0 && $e < $min){
$r = $x;
$min = $e;
}
}
return $r;
}
function isEmpty($arr){
$r = true;
foreach($arr as $x){
$r = $r && numEdges($x) == 0;
}
return $r;
}
## Return the JSON object
echo json_encode($array);
?>
I created a docker-compose.yml and the can be run in the following way:
git clone https://github.com/mictadlo/mGSV-docker.git
docker-compose up --build
The service can be accessed via localhost and PhpMyAdmin can be accessed via localhost:8183
What did I miss?
Thank you in advance

Answer 1

Try to run independently both query in your Mysql phpmyadmin
select distinct org1,org2 from '.304342020180200000016.'_synteny
select distinct org1,org2 from '.304342020180200000016.'_synteny
As i see your query seems to be correct since union requires the same numbers of columns and same data type.
And why is your table name in the union query is both the same.