我提交了这两个文件：
由于sample_synteny.txt 304420020185300000016_synteny``仅包含列名mgsv，function syn($filename)数据库似乎未在SELECT * FROM数据库的帮助下加载org1, org1_start, org1_end, org2, org2_start, org2_end, length, SYNcolor没有任何数据。在处理此文件期间，我得到以下输出：
insert into 304530020182800000020_synteny (org1, org1_start, org1_end, org2, org2_start, org2_end, length, SYNcolor) VALUES('Organism_A','25787','22159','Organism_B','18060','25102','20','3.0E-3','3629','#8953BA')
...
另一方面，sample_annotation.txt已在mgsv的帮助下加载function annotation($annfilename)，因为SELECT * FROM 304420020185300000016_annotation``为我提供了一系列值（{{1} }}）。在处理此文件期间，我得到以下输出：
org_id, start, end, strand, feature_name, feature_value, track_name, track_shape, track_color insert into 304500120185700000019_annotation (org_id, start, end, strand, feature_name, feature_value, track_name, track_shape, track_color) VALUES('Organism_C','42','3972','+','XG001','','gene','arrow','brown')
...
如下所示，导致上述错误：
mgsv/index.php我创建了一个doker-compose.yml，可以通过以下方式运行：
<?php
$link = mysql_connect($database_host, $database_user, $database_pass);
if($link == FALSE){
echo 'Cannot connect to database';
}
@mysql_select_db($database_name) or die("Unable to connect to database");
function execute_sql($sql){
$result = mysql_query($sql);
return $result;
}
function synteny_table($newsession_id, $synfilename) {
## initialize bool
$bool = 'true';
## Get the first line of the file
$header_line = exec("head -n 1 tmp/" . $newsession_id . $synfilename);
## split the line into items
$header_pieces = explode("\t",$header_line);
## the file header line is good
if( $bool == 'true'){
## Initialize a string to create fields for additional columns
$userdef = "";
## Iterate from the 7th column till the end
for( $i = 6; $i < count( $header_pieces); $i++){
$userdef .= "`".$header_pieces[$i]."`"."varchar(100) DEFAULT NULL,";
}
## Check if there is a length function
$check_length = array_search('length', $header_pieces);
## if not create a column
if($check_length == '') {
$userdef .= "`length` varchar(100) DEFAULT NULL,";
}
## get the create statement
$createTable = "CREATE TABLE `{$newsession_id}_synteny` (
`id` int(10) NOT NULL AUTO_INCREMENT,
`org1` varchar(250) NOT NULL,
`org1_start` int(10) unsigned NOT NULL,
`org1_end` bigint(20) unsigned NOT NULL,
`org2` varchar(250) NOT NULL,
`org2_start` int(10) unsigned NOT NULL,
`org2_end` bigint(20) unsigned NOT NULL,
$userdef
`SYNcolor` varchar(8) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `org1_start` (`org1_start`),
KEY `org1_end` (`org1_end`),
KEY `org2_start` (`org2_start`),
KEY `org2_end` (`org2_end`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 AUTO_INCREMENT=1 ;";
## execute the
$result = mysql_query($createTable);
if(! $result){
$bool = "Unable to create the synteny table.<br>" . mysql_error();
}
}
## return the boolean information
return $bool;
}
function desc_synteny_table($newsession_id) {
$cnames = array();
$sql = "DESCRIBE `{$newsession_id}_synteny`";
$result = mysql_query($sql);
if( ! $result){
return mysql_error();
}
while( $row = mysql_fetch_assoc( $result)){
array_push($cnames, $row['Field']);
}
return $cnames;
}
function getRandomColorHex($max_r = 255, $max_g = 255, $max_b = 255) {
return sprintf( '#%02X%02X%02X', rand(0,$max_r), rand(0,$max_g), rand(0,$max_b) );
}
function syn($filename) {
$bool_page = 'true';
#echo "($filename[0])<br>";
## Get the global values
global $upload_dir, $newsession_id, $email;
#echo "($upload_dir)<br>";
## Get the first line
$header_line = exec( "head -n 1 mgsv/tmp/".$newsession_id . $filename);
if($header_line == ''){
$bool_page = 'Synteny file: Unable to store in /tmp folder.';
return $bool_page;
}
## convert into array
$header_pieces = explode( "\t", $header_line);
## check if the first item starts with #
if( ! preg_match("/^#/i", $header_pieces[0])) {
$bool_page = 'Synteny file: The # symbol at line 1 is not present.';
return $bool_page;
}
## Replace the # for further analysis
$header_pieces[0] = str_replace('#', '', $header_pieces[0]);
## Get the fixed column names
$fixed_org = array('org1', 'org1_start', 'org1_end', 'org2', 'org2_start', 'org2_end');
## Check if the header matches our column names
## for each fixed name
for($i = 0; $i < sizeof($fixed_org); $i++){
## if the fixed name doesnt match the file column name
if( $header_pieces[$i] != $fixed_org[$i]) {
## raise error
$bool_page = "Synteny file: Column No." . ($i + 1) . " header should be '" . $fixed_org[$i] . "'.";
return $bool_page;
}
}
## Check if the number of columns is the same as column headers
$second_line = exec( "head -n 2 mgsv/tmp/" . $newsession_id . $filename . "| tail -n 1");
$second_pieces = explode( "\t", $second_line);
if( sizeof($header_pieces) != sizeof($second_pieces)){
$bool_page = "Synteny file: There are " . sizeof($header_pieces) . " column names but " . sizeof($second_pieces) . " columns.";
return $bool_page;
}
## For the non-fixed column names
for($i = 6; $i < sizeof($header_pieces); $i++){
## make sure they are not empty
if( preg_match("/^\s*$/i", $header_pieces[$i])) {
$bool_page = "Synteny file: Column No." . ($i + 1) . " header is blank.";
return $bool_page;
}
}
## Check if the column names are unique
if( count( array_unique( $header_pieces)) < count( $header_pieces)) {
$bool_page = 'Synteny file: There are more than one column with the same name';
return $bool_page;
}
## create the table in the database
$bool_page = synteny_table( $newsession_id, $filename);
if($bool_page != 'true'){
return $bool_page;
}
## Get the field names
$cnames = desc_synteny_table($newsession_id);
if(is_string($cnames)){
return $cnames;
}
## Remove the id field name
array_shift($cnames);
## get a string from the array
$insert_into = implode(', ', $cnames);
## look for column name 'length'
$check_length = array_search('length', $header_pieces);
## define pattern
$pattern = '/^.*\t[0-9]+\t[0-9]+\t.*\t[0-9]+\t[0-9]+';
## Get the starting index of the new items
$newitems = count($header_pieces) - 7;
## If no addition items are provided
for ($i = 0; $i <= $newitems; $i++) {
## generate the regex for each additional column
$pattern .= '\t[0-9\.Ee\-\+]*';
}
## close the $pattern here.
$pattern .= '$/';
## create a read file handle to the uplaoded file
$fh = fopen($upload_dir . $newsession_id . $filename, "r");
## Remove the first line
fgets($fh);
## initialize a line_number to know
$line_number = 1;
while( ! feof( $fh)){
## increment it
$line_number++;
## get each line
$line = fgets($fh);
## continue if it is an empty line
if($line == ''){ continue; }
## trim for end of line characters
$line = trim($line);
## compare with the pattern
$correct_format = preg_match($pattern, $line);
if($correct_format == false){
$bool_page = "Synteny File: line number $line_number, is not in the correct format";
break;
}
#echo "($line)<br>";
$values = "VALUES(";
$num_of_items = explode("\t", $line);
for ($jj = 0; $jj < count($num_of_items); $jj++) {
$values .= "'" . $num_of_items[$jj] . "',";
}
## check for the first 250 characters of org1 and org2
if(substr($num_of_items[0], 0, 250) == substr($num_of_items[3], 0, 250)){
## If they are similar they throw an error and quit
$bool_page = "Synteny File: Org1 and Org2 are similar at line $line_number.";
break;
}
## If there is no column called length in the input synteny file
if($check_length == false){
## get the difference between start and end of org2
$org2 = abs($num_of_items[4] - $num_of_items[5]) + 1;
## get the difference between start and end of org1
$org1 = abs($num_of_items[1] - $num_of_items[2]) + 1;
## get the minimum of the above two lengths
$minlength = min($org1, $org2);
## concatenate this minimum value to the input command
$values .= "'" . $minlength . "',";
}
## generate a random color to store each synteny
$values .= "'" . getRandomColorHex() . "')";
## If everything is good
if( $bool_page == 'true'){
## Insert the values into the table
$sql = "insert into {$newsession_id}_synteny ($insert_into) $values";
## show the statement
#echo "insert command: $sql<br>";
## execute the statement
$result = execute_sql($sql);
}
}
## Delete the files from server
if(file_exists($upload_dir . $newsession_id . $filename)){
unlink($upload_dir . $newsession_id . $filename);
}
## return the boolean parameter
return $bool_page;
}
可以通过git clone https://github.com/mictadlo/mGSV-docker.git
docker-compose up --build
访问该服务，可以通过localhost访问PhpMyAdmin
我错过了什么？
提前谢谢