[Loris-dev] Import mri - scripts

Tue Sep 3 15:02:05 EDT 2019

Actually the current config.xml is the one from the output of the browser.

On Tue, 3 Sep 2019, 21:57 Shen Wang, <wangshen.mcin at gmail.com> wrote:

> Hi,
> you need to make a config.xml manually.
> Step 1: go to project folder. cd /var/www/loris/project;
> Step 2: touch config.xml;
> Step 3: paste all the xml content to config.xml file.
> then reload the localhost page.
> It should work.
>
> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>于2019年9月3日 周二下午2:39写道：
>
>> 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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