[Loris-dev] Import mri - scripts

Tue Sep 3 14:39:18 EDT 2019

I tried to change the permissions but afterwards i got the previous error
again that was reporting that could not find the the config.xml, although
now the config.xml exists ... I also execute
* sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris*

*to reverse what i did but it didn't work.*

[Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client
127.0.0.1:40460] PHP Fatal error:  Uncaught ConfigurationException: Config
file config.xml does not exist in the defined locations. in
/var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0
/var/www/loris/php/libraries/NDB_Config.class.inc(66):
NDB_Config->configFilePath()\n#1
/var/www/loris/php/libraries/NDB_Factory.class.inc(118):
NDB_Config::singleton(NULL)\n#2
/var/www/loris/php/libraries/NDB_Client.class.inc(54):
NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27):
NDB_Client->initialize()\n#4 {main}\n  thrown in
/var/www/loris/php/libraries/NDB_Config.class.inc on line 139

[image: image.png]

Lastly i tried to re-create the config.xml using the installdb.php but now
it couldn't write to the directory.

[image: image.png]

Στις Τρί, 3 Σεπ 2019 στις 4:20 μ.μ., ο/η Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> έγραψε:

> It seems that the links's point is correct. And yes i only runned composer
> not the makefile.
>
> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l
> total 116
> drwxr-xr-x  2 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 acknowledgements
> -rw-r--r--  1 lorisadmin lorisadmin  3217 Ιούλ 23 20:37 AjaxHelper.php
> drwxr-xr-x  4 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 api
> drwxr-xr-x  5 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 bootstrap
> drwxr-xr-x  4 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 css
> -rw-r--r--  1 lorisadmin lorisadmin  7730 Ιούλ 23 20:37 direct.css
> -rw-r--r--  1 lorisadmin lorisadmin  5361 Ιούλ 23 20:37
> feedback_mri_popup.php
> lrwxrwxrwx  1 lorisadmin lorisadmin    48 Αύγ  31 02:17 fontawesome ->
> ./../node_modules/@fortawesome/fontawesome-free/
> drwxr-xr-x  2 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 images
> -rw-r--r--  1 lorisadmin lorisadmin  2040 Ιούλ 23 20:37 index.php
> -rw-r--r--  1 lorisadmin lorisadmin  8311 Ιούλ 23 20:37 installdb.php
> drwxr-xr-x 11 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 js
> -rw-r--r--  1 lorisadmin lorisadmin 12640 Ιούλ 23 20:37 main.css
> -rw-r--r--  1 lorisadmin lorisadmin  9189 Ιούλ 23 20:37 main.php
> drwxr-xr-x  3 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 mri
> -rw-r--r--  1 lorisadmin lorisadmin  2532 Ιούλ 23 20:37 postdeploy.php
> -rw-r--r--  1 lorisadmin lorisadmin  2293 Ιούλ 23 20:37 router.php
> -rw-r--r--  1 lorisadmin lorisadmin 12131 Ιούλ 23 20:37 survey.php
> drwxr-xr-x  4 lorisadmin lorisadmin  4096 Ιούλ 23 20:37 vendor
>
> Στις Τρί, 3 Σεπ 2019 στις 3:48 μ.μ., ο/η Christine Rogers, Ms. <
> christine.rogers at mcgill.ca> έγραψε:
>
>> Hi Sotirios,
>> You've got your LORIS up and running, and are running into font library
>> issues?  great.
>>
>> The symlink under htdocs/ for fontawesome is supposed to point to:
>> ./../node_modules/@fortawesome/fontawesome-free/
>> (see:  https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome
>>  )
>> This sounds like it may be a permissions issue, or with your node
>> modules.
>> Can you give us more specifics on the permissions in your htdocs
>> directory and if any other links or packages look funny?
>>
>> You have run composer commands but not the makefile, is that correct?
>>
>> Note we have an even newer stable release out already:  21.0.1
>> <https://github.com/aces/Loris/releases>
>>
>> Best,
>> Christine
>>
>> On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> i didn't remember that config.xml was being created during the execution
>>> of installdb.php. Now am i getting white content on the pages only because
>>> fontawesome is missing? Was that part of the composer install? because i
>>> hadn't such error.
>>>
>>> Thanks
>>>
>>> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client
>>> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/
>>> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client
>>> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/imaging_browser/
>>> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/imaging_uploader/
>>> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/examiner/
>>> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/conflict_resolver/
>>> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/imaging_browser/
>>> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/dicom_archive/
>>> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client
>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not
>>> accessible: /var/www/loris/htdocs/fontawesome, referer:
>>> http://localhost/imaging_uploader/
>>>
>>> Στις Δευ, 2 Σεπ 2019 στις 10:16 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>>> Hi,
>>>>
>>>> it there a solution for this?
>>>> https://github.com/aces/Loris/issues/3313
>>>>
>>>> I need to meet a deadline about Loris by the end of September.
>>>>
>>>> Thanks
>>>>
>>>> Στις Κυρ, 1 Σεπ 2019 στις 10:19 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>>> Hi,
>>>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04
>>>>>
>>>>> i installed composer 1.9 with these following commands.
>>>>>
>>>>>
>>>>> curl -sS https://getcomposer.org/installer -o composer-setup.php
>>>>>
>>>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;"
>>>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer
>>>>>
>>>>> And afterwards composer install worked and the only warning i got at the end of the installation was
>>>>>
>>>>> <<phpunit/phpunit suggests installing phpunit/php-invoker (^1.1)
>>>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested.
>>>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>>
>>>>>
>>>>> And from the loris-error.log
>>>>>
>>>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139
>>>>>
>>>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>
>>
>> --
>>
>> christine.rogers at mcgill.ca
>> McGill Centre for Integrative Neuroscience | MCIN.ca
>> Montreal Neurological Institute
>> McGill University | Montreal | Canada
>>
>
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