[Loris-dev] Import mri - scripts

Tue Sep 3 14:49:23 EDT 2019

Thanks Sotirios, those details help.
Try the following and let us know what happens:

cd /var/www/loris
make
sudo vi  /var/www/loris/project/config.xml
--> copy-paste the content shown in your  installdb.php screen. make sure the file saves
sudo chown -R lorisadmin:lorisadmin ./
sudo service apache2 restart

let us know --
Christine

On Tue, Sep 3, 2019 at 2:39 PM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
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/loris

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<http://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.png]

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

[image.png]

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

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--

christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
_______________________________________________
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--

christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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