mailRe: Uploading and setting up new extensions for the relax wiki.


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Posted by Troels Emtekær Linnet on September 08, 2014 - 10:59:
You can have a look here:

http://www.pymolwiki.org/index.php/Special:MostLinkedTemplates
http://www.pymolwiki.org/index.php/Template:Infobox_script-repo

Example from:
http://www.pymolwiki.org/index.php/Propka

Wiki code

{{Infobox script-repo
|type      = script
|filename  = propka.py
|author    = [[User:Tlinnet|Troels E. Linnet]]
|license   = BSD
}}

Best
Troels

2014-09-08 10:55 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
It takes bacup of mysql and all data.

Then it takes, to run a php update script.

This script is not available without command line.

Then one can replace the whole installation.

But it can take time, and I am truly afraid of destroying the installation.

Best
Troels

2014-09-08 10:41 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
It sounds risky, but might be the only way.  Scribunto is relatively
new, being introduced with Mediawiki 1.20, so they were probably still
sorting out bugs with the 1.21 version.  But maybe I'll put the
infobox data for the relax release notes into some other element for
now.  What does it take to upgrade to 1.23.3?  It seems like Scirbunto
is being used more and more for templates and extensions in Wikipedia.

Cheers,

Edward


On 8 September 2014 10:26, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
wrote:
We can upgrade the wiki ?

http://wiki.nmr-relax.com/Special:Version
It is versions 1.21.1, and 1.23.3 is out.
http://www.mediawiki.org/wiki/Manual:Upgrading

Backup up both sql and files, should be done before.
I have screwed this up before.

And then are are some extensions to make maintenance.
http://www.mediawiki.org/wiki/Extension:Maintenance

Best
Troels

2014-09-08 10:04 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,

Oh well, I'll have to keep playing with this to try to work out what
is happening.  It's looking like a version issue (Mediawiki or PHP),
but I can't be sure.  I'll have to set up a VM with Apache, Mediawiki
and PHP to test this :S

Cheers,

Edward



On 8 September 2014 09:48, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
wrote:
Hi Edward.

There is no SSH access to the server.
There one needs a dedicated server from Gigahost.

Normal: 4 euro per month, unlimited domains, 34 GB.

while:

Virtual server, 100 GB, 1 TB trafic per month, dedicated IPv4-adresse,
full root access to Debian GNU/Linux system, is 20 euro per month.

Best
Troels

2014-09-05 21:17 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,

The php problems seem to be fixed, and the current error, as can be
seen at http://wiki.nmr-relax.com/Relax_3.2.2, is the message "The
interpreter exited with status 139".  This indicates that Lua was
launched by gave up with some error, probably a segfault.  This will
be a difficult one to solve :S  Is there some type of telnet/SSH
access that can be used to run the lua binary on the server directly?

Cheers,

Edward


On 5 September 2014 21:05, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
There is a range of stuff I can change

Her kan du ændre indstillingerne for PHP for dit domæne 
wiki.nmr-relax.com.

allow_url_fopen
 Slået til
 Slået fra
allow_url_include
 Slået til
 Slået fra
apc.rfc1867
 Slået til
 Slået fra
asp_tags
 Slået til
 Slået fra
date.timezone

default_mimetype

6 - 63 tegn
display_errors
 Slået til
 Slået fra
engine
 Slået til
 Slået fra
expose_php
 Slået til
 Slået fra
file_uploads
 Slået til
 Slået fra
html_errors
 Slået til
 Slået fra
max_execution_time

10 til 300.
max_input_time

10 til 300.
max_input_vars

100 til 15000.
mbstring.func_overload

0 til 4.
mbstring.internal_encoding

0 - 16 tegn
memory_limit
 MB
8 - 512 MB
mysql.allow_persistent
 Slået til
 Slået fra
mysql.default_host

0 - 63 tegn
mysql.default_port

1024 til 65534.
mysql.default_user

0 - 16 tegn
mysql.trace_mode
 Slået til
 Slået fra
output_buffering
 Slået til
 Slået fra
post_max_size
 MB
0 - 256 MB
register_globals
Denne PHP-indstilling er ikke længere tilgængelig fra PHP version 5.4.
Du benytter PHP version 5.4.
safe_mode
Denne PHP-indstilling er ikke længere tilgængelig fra PHP version 5.4.
Du benytter PHP version 5.4.
session.auto_start
 Slået til
 Slået fra
session.bug_compat_42
Denne PHP-indstilling er ikke længere tilgængelig fra PHP version 5.4.
Du benytter PHP version 5.4.
session.bug_compat_warn
Denne PHP-indstilling er ikke længere tilgængelig fra PHP version 5.4.
Du benytter PHP version 5.4.
session.cookie_domain

0 - 63 tegn
session.cookie_lifetime

0 til 31622400.
session.cookie_path

1 - 63 tegn
session.gc_maxlifetime

0 til 86400.
session.name

2 - 16 tegn
session.use_cookies
 Slået til
 Slået fra
session.use_trans_sid
 Slået til
 Slået fra
short_open_tag
 Slået til
 Slået fra
suhosin.post.max_value_length

0 til 10000000.
suhosin.post.max_vars

0 til 10000.
suhosin.request.max_value_length

0 til 10000000.
suhosin.request.max_vars

0 til 10000.
suhosin.session.cryptua
 Slået til
 Slået fra
suhosin.session.encrypt
 Slået til
 Slået fra
upload_max_filesize
 MB
0 - 256 MB
upload_tmp_dir

4 - 64 tegn
zlib.output_compression
 Slået til
 Slået fra

2014-09-05 21:03 GMT+02:00 Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx>:
I have changed php from 5.3 to 5.4.

There is also 5.5 and 5.6 available.
But 5.5 made a mess of the frontpage.

Best
T

2014-09-05 20:51 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
From my testing, it's in the folder.  It comes with it, just in case
it is not on the server.  But I'm not sure why it's segfaulting (or 
it
has some other problem).  I'll continue trying to debug this another
day.

Cheers,

Edward



On 5 September 2014 20:45, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
Maybe there is an easy answer?

The gigahost support wrote this to me:

"""
Jeg er ikke sikker på at 'lua' binarien er på serverne men I kan i 
hvert fald
slå proc_open til."""

""" I am not sure the "lua" binary is on the servers, but you
definitely make proc_open on"""

So, does scribuntu use a Lua binary on the servers or from the 
folder?

Best
Troesl


2014-09-05 19:45 GMT+02:00 Edward d'Auvergne 
<edward@xxxxxxxxxxxxx>:
Hi,

Still no luck with the test page
http://wiki.nmr-relax.com/Relax_3.2.2.  I have enabled verbose
exception information in the LocalSettings.php file, and now see:

Lua error: Internal error: The interpreter exited with status 139.

Backtrace:

#0 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php(454):
ScribuntoEngineBase->newException('scribunto-luast...', Array)
#1 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php(324):
Scribunto_LuaStandaloneInterpreter->checkStatus()
#2 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php(287):
Scribunto_LuaStandaloneInterpreter->receiveMessage()
#3 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php(213):
Scribunto_LuaStandaloneInterpreter->dispatch(Array)
#4 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(114):
Scribunto_LuaStandaloneInterpreter->registerLibrary('mw_interface',
Array)
#5 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(89):
Scribunto_LuaEngine->registerInterface('mw.lua', Array, Array)
#6 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php(8):
Scribunto_LuaEngine->load()
#7 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(158):
Scribunto_LuaStandaloneEngine->load()
#8 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(549):
Scribunto_LuaEngine->getInterpreter()
#9 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(533):
Scribunto_LuaModule->getInitChunk()
#10 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaCommon/LuaCommon.php(561):
Scribunto_LuaModule->execute()
#11 
/home/www/wiki.nmr-relax.com/extensions/Scribunto/common/Hooks.php(96):
Scribunto_LuaModule->invoke('infobox', 
Object(PPTemplateFrame_DOM))
#12 [internal function]: 
ScribuntoHooks::invokeHook(Object(Parser),
Object(PPTemplateFrame_DOM), Array)
#13 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(3532):
call_user_func_array('ScribuntoHooks:...', Array)
#14 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(3251):
Parser->callParserFunction(Object(PPTemplateFrame_DOM), '#invoke',
Array)
#15 
/home/www/wiki.nmr-relax.com/includes/parser/Preprocessor_DOM.php(1077):
Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
#16 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(3404):
PPFrame_DOM->expand(Object(PPNode_DOM))
#17 
/home/www/wiki.nmr-relax.com/includes/parser/Preprocessor_DOM.php(1077):
Parser->braceSubstitution(Array, Object(PPFrame_DOM))
#18 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(3073):
PPFrame_DOM->expand(Object(PPNode_DOM), 0)
#19 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(1153):
Parser->replaceVariables('{{lowercase tit...')
#20 /home/www/wiki.nmr-relax.com/includes/parser/Parser.php(383):
Parser->internalParse('{{lowercase tit...')
#21 
/home/www/wiki.nmr-relax.com/includes/content/WikitextContent.php(299):
Parser->parse('{{lowercase tit...', Object(Title),
Object(ParserOptions), true, true, 2897)
#22 /home/www/wiki.nmr-relax.com/includes/WikiPage.php(3402):
WikitextContent->getParserOutput(Object(Title), 2897,
Object(ParserOptions))
#23 /home/www/wiki.nmr-relax.com/includes/PoolCounter.php(209):
PoolWorkArticleView->doWork()
#24 /home/www/wiki.nmr-relax.com/includes/Article.php(707):
PoolCounterWork->execute()
#25 
/home/www/wiki.nmr-relax.com/includes/actions/ViewAction.php(44):
Article->view()
#26 /home/www/wiki.nmr-relax.com/includes/Wiki.php(439): 
ViewAction->show()
#27 /home/www/wiki.nmr-relax.com/includes/Wiki.php(305):
MediaWiki->performAction(Object(Article), Object(Title))
#28 /home/www/wiki.nmr-relax.com/includes/Wiki.php(565):
MediaWiki->performRequest()
#29 /home/www/wiki.nmr-relax.com/includes/Wiki.php(458): 
MediaWiki->main()
#30 /home/www/wiki.nmr-relax.com/index.php(59): MediaWiki->run()
#31 {main}


The problem might require SSH access to work out why Lua is not
running, by just running the binary directly:

$ 
/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/binaries/lua5_1_5_linux_64_generic/lua


That should just work.  On my system I see:

$ 
./extensions/Scribunto/engines/LuaStandalone/binaries/lua5_1_5_linux_64_generic/lua
Lua 5.1.5  Copyright (C) 1994-2012 Lua.org, PUC-Rio


Troels, could you check this if there is SSH access?  There might 
be a
file permission problem somewhere.  Though from what I'm reading 
on
the internet, this 139 error could be a segfault :S

Cheers,

Edward



On 5 September 2014 18:33, Edward d'Auvergne 
<edward@xxxxxxxxxxxxx> wrote:
Thanks!  The page http://wiki.nmr-relax.com/Relax_3.2.2 now 
gives a
different error:

[d64d1913] 2014-09-05 16:25:18: Fatal exception of type 
ScribuntoException

I now need to work out why Lua is not working and giving such an 
error
:S  For that I'll need to log back into the server with the new
details.

Cheers,

Edward



On 5 September 2014 18:19, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
Hi Edward.

I have now removed "isolation" safety from the domain.
This means that scripts should be available.

That also means that the FTP user for the sub domain is now 
gone.

You would need another account to access the wiki domain again.
That will be a global account for all the domains at the domain 
hotel.

Be careful, I will email you the details.

Best
Troels



2014-09-05 17:13 GMT+02:00 Edward d'Auvergne 
<edward@xxxxxxxxxxxxx>:
Hi Troels,

I've also activated the Cite extension and installed the
HarvardReferences extension for the wiki.  I'm using this for 
paper
references.  You can see that at the new page
http://wiki.nmr-relax.com/Relax_3.2.0 where I have cited 
Andy's paper.

Regards,

Edward



On 5 September 2014 16:24, Edward d'Auvergne 
<edward@xxxxxxxxxxxxx> wrote:
Thank you!  As for the visitors to the
http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x 
page, there
is a 96% drop off rate, so they obviously stumbled across the 
page by
accident :)

Regards,

Edward


On 5 September 2014 16:22, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
I have written to the support, to ask for help.

They should respond within 24 hours.

Best
Troels

2014-09-05 16:20 GMT+02:00 Edward d'Auvergne 
<edward@xxxxxxxxxxxxx>:
Hi,

I think that that will be the only way to get this running. 
 The
php.ini file needs to be edited and proc_open removed from 
the
disable_functions list, as listed at
http://wiki.nmr-relax.com/phpinfo.php.  Without that, the 
Lua binary
cannot run.  I'm guessing that we don't have access to this 
ourselves.

Cheers!

Edward


On 5 September 2014 16:13, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
Hi Edward.

There is maybe a work-around for that.

I had another homepage, a problem with:
#
open_basedir

Warning: file_exists() [function.file-exists]: 
open_basedir restriction in
effect.

http://premium.wpmudev.org/forums/topic/open_basedir-restriction-in-effect
####

I got it to work, after contacting the domain hotel, which 
changed a setting.

Do you want me to pursue this?



2014-09-05 16:01 GMT+02:00 Edward d'Auvergne 
<edward@xxxxxxxxxxxxx>:
Doh!  This doesn't seem to work.  According to
https://www.mediawiki.org/wiki/Extension:Scribunto#Lua_binary,
 to run
the Lua binary, which is required for this extension, the 
proc_open()
PHP function is required.  But according to the new page
http://wiki.nmr-relax.com/phpinfo.php, it is in the 
disabled_functions
list.  I've just tried to create an infobox at
http://wiki.nmr-relax.com/Relax_3.2.2 and see:

"""
Warning: proc_open() has been disabled for security 
reasons in
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php
on line 134

Fatal error: Call to a member function getStatus() on a 
non-object in
/home/www/wiki.nmr-relax.com/extensions/Scribunto/engines/LuaStandalone/LuaStandaloneEngine.php
on line 10
"""

I didn't realise how painful installing MediaWiki 
extensions can be!!!

Regards,

Edward



On 5 September 2014 15:52, Edward d'Auvergne 
<edward@xxxxxxxxxxxxx> wrote:
Hi Troels,

This might be a duplication, but to obtain PHP 
information about the
server, I have created the page 
http://wiki.nmr-relax.com/phpinfo.php.
This required a text file of this name being uploaded to 
the base
directory of the wiki via FTP.

Regards,

Edward


On 5 September 2014 15:14, Edward d'Auvergne 
<edward@xxxxxxxxxxxxx> wrote:
Hi,

I just noticed that the devel_scripts/wiki_ftpdump.sh 
script, which
cron runs every day for me, does this:  '--exclude-glob
LocalSettings.php'.  That might be my problem.  For the 
upload
command, what do you use?  I don't want to accidentally 
wipe out
everything.  Thanks!

Cheers,

Edward


P. S.  I'll just use an FTP client to manually upload 
just the
extension and modified LocalSettings.php file.  That 
should be the
safest way.



On 5 September 2014 14:56, Troels Emtekær Linnet 
<tlinnet@xxxxxxxxxxxxx> wrote:
Hi Edward.

I can see: LocalSettings.php
in the folder.

And also the old one?

You could probably just add it after this list

require_once( 
"$IP/extensions/ConfirmEdit/ConfirmEdit.php" );
require_once( "$IP/extensions/Gadgets/Gadgets.php" );
require_once( "$IP/extensions/ImageMap/ImageMap.php" );
require_once( "$IP/extensions/InputBox/InputBox.php" );
require_once( "$IP/extensions/Interwiki/Interwiki.php" 
);
#require_once( 
"$IP/extensions/LocalisationUpdate/LocalisationUpdate.php"
 );
require_once( "$IP/extensions/Nuke/Nuke.php" );
require_once( 
"$IP/extensions/ParserFunctions/ParserFunctions.php" );
require_once( 
"$IP/extensions/PdfHandler/PdfHandler.php" );
require_once( "$IP/extensions/Poem/Poem.php" );
require_once( 
"$IP/extensions/Renameuser/Renameuser.php" );
require_once( 
"$IP/extensions/SpamBlacklist/SpamBlacklist.php" );
require_once( 
"$IP/extensions/SyntaxHighlight_GeSHi/SyntaxHighlight_GeSHi.php"
);
require_once( 
"$IP/extensions/TitleBlacklist/TitleBlacklist.php" );
require_once( "$IP/extensions/Vector/Vector.php" );
require_once( 
"$IP/extensions/WikiEditor/WikiEditor.php" );

I normally just download with cyberduck or filezilla.
Modify, and upload again.

Best
Troels



2014-09-05 14:27 GMT+02:00 Edward d'Auvergne 
<edward@xxxxxxxxxxxxx>:
Hi Troels,

I was wondering if you could help.  I'm looking at 
installing the
following Scribunto extension:

https://www.mediawiki.org/wiki/Extension:Scribunto

However I cannot find the LocalSettings.php file, only
LocalSettings_old.php.  Where should I add the 
'require_once' text to
get this extension to load?  And what FTP command do 
you use to upload
to the wiki FTP area?  I already have the user name 
and password, but
I'm not sure what the best way to upload this is.

Cheers,

Edward


P. S.  The aim for using this extension is to 
replicate the Wikipedia
Template:Infobox element.  This will be very useful 
for the relax
release notes pages (e.g. 
http://wiki.nmr-relax.com/Relax_3.3.0), as I
could include all the info for that release in a 
concise format.

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