Code end up on one line after Filezilla upload.

Issue description:

End of line are removed from file after uploading a file to your server through filezilla or any other FTP software.

One of the answer on the bug report above describe the issue clearly:

For the benefit of anyone like me who finds this after having experienced exactly the same issue, I believe I have a more rigorous explanation for exactly what’s going on. Codesquid posted a link on #5486 that provides all of the relevant information, which I shall re-post here for convenience:


The bug appears to lie in the standard itself, rather than Filezilla specifically. That is, the actions defined to ensure that \r\n line endings are always transmitted and then converted by the receiver to whatever is appropriate for that platform may fail if the source file itself has the wrong line endings for the client platform. For example (assuming one transfers the file using the ASCII data type):

IF: a file with CR-only line endings is uploaded
FROM: a windows client
TO: a linux server
THEN: the transmitted file will only feature CRs, which will be deleted
RESULTING: in a file with no newlines

Which is very bad news if your file contains line comments, since this will effectively change its meaning. Similarly,

IF: a file with Windows line endings (CR+LF) is downloaded
FROM: a Linux/Mac server
TO: a Windows or Mac/Linux client
THEN: additional unwanted CR/LFs will be inserted
RESULTING: in a file with mixed or double newlines

Other scenarios of this type can clearly be concocted, but I would have thought these two would be the most common. As codesquid pointed out, the data type can be specified for transfers. In the absense of a parser in Filezilla to handle malformed newlines, the only safe answer appears to be to use the binary type for all transfers.

More infor about Data type available here:

To check the type of carriage return used in your file, you can turn that on in notepad ++ in View->Show Symbol->Show End of Line.

In my case, once downloaded via ftp from the linux server to my windows machine, the file showed CR for mark the end of the line. Other files not causing issue are making use of both CR and LF.

When reuploading the file using only CR on the linux server. All CR are removed and the file open in a single line when I open it for edit through FTP. As it is an executable file including comment, some code are commented out and the script don’t execute properly anymore.

Solution: To solve the issue, you can open use find and replace extended mode in Notepad++ and, in my case, replace \r by \r\n and save.

CRON job http execution failed in hosting

Description: http execution of CRON job fails. Error:


The file is executed normally when run by accessing it directly by the browser without marked difference in execution time when the script is executed on a local server.

The site is running WordPress.

Solution: In that case change the https execution for a system execution in your webserver settings.

Apache access log structure

Recommended reading:

A typical access log structure looks as follow

LogFormat "%h %l %u %t \"%r\" %>s %b" common
CustomLog logs/access_log common

%h: IP of the visitor (it might be a VPN IP for instance).

%l RFC 1413 identity of the client (not check unless IdentityCheck set to On). Highly unreliable.

%u user id. If the document is not password protected, the value will be set to – as above.

%t The time the request was received

\”%r\” Request that the server received, between double quote. It starts with the method, then the requested resource, then the protocol (e.g. HTTP/2.0)

%>s The status code that the server sends back to the client

%b size of the object returned byt the server to the client.


213.18X.X.XXX – – [11/Oct/2019:11:52:08 +0300] “GET /index.phpXXXXXXX HTTP/2.0” 303 314 “” “Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/77.0.3865.90 Safari/537.36” (38FF183F-0.107)

You can see the two dash represented the fact that, for the first dash, the RFC 1413 identity is not used, and for the second, that the resource is public and no identification is requested.

Here you can see there are extra info after the size of the object returned. This indicates the server is using combined log format which goes as follow:

 "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-agent}i\"" 

\”%{Referer}i\” being the referer (e.g. a link to your site on another web site or a form with a POST action to your server)

\”%{User-agent}i\” the user agent (e.g. the browser specification used to navigate your site)

In a more readable way, you will often see your access log as follow:


Understanding joomla .htaccess

IndexIgnore *

## No directory listings
<IfModule autoindex>
IndexIgnore *

The indexIgnore directive prevent files in a directory with index on from being displayed in the directory listings. The star match all files which will prevent any file in the public directory to be displayed in a directory listings even if it directory listings is on ( apache.conf with the indexes option).

Options +FollowSymlinks

# The line 'Options +FollowSymLinks' may cause problems with some server configurations.
# It is required for the use of mod_rewrite, but it may have already been set by your
# server administrator in a way that disallows changing it in this .htaccess file.
# If using it causes your site to produce an error, comment it out (add # to the
# beginning of the line), reload your site in your browser and test your sef urls. If
# they work, then it has been set by your server administrator and you do not need to
# set it here.
#Can be commented out if causes errors, see notes above.
Options +FollowSymlinks
Options -Indexes

The options directive allow to set the directory behavior. Here FollowSymLinks indicate to follow the symbolic links in the directory (in that case this is the public directory as there is no directory specified).

Indexes indicates that if a directory path is entered and there is no index file in this directory, then a directory listing will be displayes. The minus sign preceding the Indexes option indicate that we remove this behavior, (meaning that it will return a 404?)

This settings might have been set by the host on your server so they might cause issue, in that case you can comment those lines, as stated in the note.

## Mod_rewrite in use.
RewriteEngine On

Turn the rewrite engine on so you can perform redirection from .htaccess according to the conditions you set.

Rewrite rules to block out some common exploits.

## Begin - Rewrite rules to block out some common exploits.
# If you experience problems on your site then comment out the operations listed
# below by adding a # to the beginning of the line.
# This attempts to block the most common type of exploit `attempts` on Joomla!
# Block any script trying to base64_encode data within the URL.
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
# Block any script trying to set a PHP GLOBALS variable via URL.
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block any script trying to modify a _REQUEST variable via URL.
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Return 403 Forbidden header and show the content of the root home page
RewriteRule .* index.php [F]

As a platform concerned with security, joomla try to deflect some common attack straight from the start.

Let’s have a look at the rewriteCond directives that they use.

Rewrite condition syntax:
RewriteCond TestString CondPattern [flags]

The Teststring is set to match the query string %{QUERY_STRING}

The condition pattern CondPattern is a regular expression.


base64_encode is a php function that will encode a string in base 64

Now let’s have a look at the regular expression that follows:

[^(] in the square brakets is the expression to evaluate. The circumflex accent indicates that it is a negative match (match everything NOT in the list), followed by the list of character to NOT match, here a single opening bracket. The star after the bracket indicates to do that any number of time. We have then an escape string followed by an opening bracket to match an opening bracket (otherwise we would just start a marked sub expression). Then [^)]* will match any character that is not a closing bracket any number of time. And we finish with an escaped closing bracket. So our condition tell us to catch any string ” base64_encode ” followed by any suit of characters containing any string between brackets.

Let’s say this evaluate to true, the rewrite rule will then apply and the whole URL including the query strng will be substituted by index.php and it will be displayed instead.

Rewrite rule syntax:

. match any character and * indicates to do that any number of time.

RewriteRule Pattern Substitution [flags]

The [F] flag indicate to return a 403 response (forbidden)

The flag is [OR] which indicates to evaluate the next condition instead (instead of skipping it?) (or next condition)

GLOBALS and _Request

Here it will match the string GLOBALS. The opening bracket indicate that we will match a group. This group will start with an equal sign OR ( or being the pipe symbol ‘|’) an (escaped) square bracket OR a percent signed folowed by any number or upper case alphabetical characters. The numbers within the curly brackets indicates that the preceding rule shall at least 0 but nor more than 2 times. Check the figure below to have an illustrated example.

The following condition does the same but with the string _REQUEST instead of GLOBALS

Catching script injection

And there is one more condition to catch the query string containing a script tag: (<|%3C)([^s]s)+cript.(>|%3E)

%3C is the unicode for less than. So the first group will catch “less than” character. the second group will catch any character preceding a s and the s character one or more time (that is the plus, the star * catch zero or more time). Then it will catch “cript”. The dot “.” match any character and the last group match the closing “greater than” character .

That was a big part! Now the rest should be easy peasy.

So we have a rewrite base that indicates with what string the URL should be prefixed. In our case it is just a slash

RewriteBase /

SEF Section

RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]

Pattern: .* any URL (any suit of any character)

Substitution: – (dash) indicates that no substitution should be performed.


E= Causes an environment variable VAR to be set (to the value VAL if provided). The form !VAR causes the environment variable VAR to be unset.

HTTP_AUTHORIZATION: is an environment variable sent in the header of the http request.

%{HTTP:Authorization} obtains the actual value from the header.

Read more about authentication.

RewriteCond %{REQUEST_URI} !^/index\.php

%{REQUEST_URI}  match against the full URL-path in a per-directory RewriteRule

 The NOT character (‘!‘) as a pattern prefix inverse the condition, so it returns true if it does not match the following pattern. Here, the condition returns true if the full URL path is NOT index.php

%{REQUEST_FILENAME} !-f if the requested file is not a file (so if does not exist).

RewriteCond %{REQUEST_FILENAME} !-d or not a directory (so if such directory does not exist)

RewriteRule .* index.php [L]

then rewrite the full path to index.php

[L] is the Last flag which stops the rewriting process.