[Loris-dev] Update LORIS to v21.0.0

Ling Ma lingyun.ma at mcin.ca
Fri Feb 21 17:12:51 EST 2020 

Evidently the RAM is not enough, I am outside, I don't have the recommended
value for you. You can check document for how much. I would recommend to
increase the PHP memory allowance. Try to check PHP document for that,
otherwise I can check later. Or maybe any other people knows better on this
subject could help you.

Good weekend.

Ling

On Fri., Feb. 21, 2020, 5:06 p.m. Morales Pinzon, Alfredo, <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Ling Ma,
>
> All set regarding php 7.2, is now enable and working. Going back to the
> error in the website: when I select Imaging -> Imaging Browser I got a 500
> error in the front-end and the following error in the server:
>
> ===
> [Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client
> 170.223.207.1:46078] PHP Fatal error:  Allowed memory size of 134217728
> bytes exhausted (tried to allocate 20480 bytes) in
> /var/www/loris/php/libraries/Database.class.inc on line 714, referer:
> https://ipmsa-loris.bic.mni.mcgill.ca/
> ===
>
> Any ideas?
>
> Thank you in advance.
>
> Best,
> Alfredo.
>
> On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> If you go to "/etc/apache2/mods-enabled", you can easily find which PHP
> version is enabled if after restart Apache2 you still have problem. Please
> don't modify source code to remove "?", there should be a lot of them, not
> possible to remove all.
>
> On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> Hi Alfredo,
>>
>> You installed PHP7.2, but you might not use the new version, you might
>> need to restart the Apache2, or enable Apache2 to use PHP7.2. Because
>> currently your server is still running PHP7.0 or PHP5.6. Because "?" is
>> part of PHP7.1
>>
>> Please check.
>>
>> Good luck.
>>
>> Ling Ma
>>
>> On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Dear Ling Ma and Cécile,
>>>
>>> Thank you for the help and tips. After installing php7.2-xml and
>>> php7.2-mysql I was able to finish all the steps listed in the upgrade
>>> process. I followed this post to upgrade to PHP 7.2:
>>> https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642
>>>
>>> Now we come back to the first error. Actually, the server is not running
>>> right now. I have the following error:
>>>
>>> ===
>>> [Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client
>>> 216.15.126.108:52419] PHP Parse error:  syntax error, unexpected '?',
>>> expecting variable (T_VARIABLE) in
>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>>> ===
>>>
>>> After modifying the line 49 in NDB_Client.class.inc from
>>>
>>> ===
>>> function initialize(?string $configFile = null)
>>> ===
>>>
>>> to (removing the ?)
>>>
>>> ===
>>> function initialize(string $configFile = null)
>>> ===
>>>
>>> but I got the following error:
>>>
>>> ===
>>> [Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client
>>> 216.15.126.108:52603] PHP Parse error:  syntax error, unexpected '?',
>>> expecting variable (T_VARIABLE) in
>>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
>>> ===
>>>
>>> Is this an error in the code or I am missing something?
>>>
>>> Thank you for help.
>>>
>>> Best,
>>> Alfredo.
>>>
>>> On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> Since simplexml_load_file is part of php-xml package, I feel that you
>>> need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install
>>> this package with apt-get install php7.2-xml, and make sure that this
>>> module is enabled in Apache2 if you are using Apache2. You can check which
>>> module is enabled via phpinfo() call from a PHP enabled web page, or just
>>> check your Apache2 PHP modules, the later is easier.
>>>
>>> Good luck.
>>>
>>> Ling Ma
>>>
>>> On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Hi Ling Ma,
>>>>
>>>> Thank you for the information. I would suggest to add this link to each
>>>> release, where the upgrading instructions are listed, and also mention
>>>> upgrading system requirements if needed.
>>>>
>>>> Continuing with the upgrade to v21.0.0. I checked that all the system
>>>> requirements are met. Now, in having this error when executing
>>>> data_dictionary_cleaner.php:
>>>>
>>>> ===
>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris/tools/single_use*$ php
>>>> data_dictionary_cleaner.php
>>>> PHP Fatal error:  Uncaught Error: Call to undefined function
>>>> simplexml_load_file() in
>>>> /var/www/loris/php/libraries/NDB_Config.class.inc:96
>>>> Stack trace:
>>>> #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
>>>> NDB_Config->load('/var/www/loris/...')
>>>> #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
>>>> NDB_Config::singleton('/var/www/loris/...')
>>>> #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
>>>> NDB_Factory->config('/var/www/loris/...')
>>>> #3 /var/www/loris/tools/generic_includes.php(25):
>>>> NDB_Client->initialize('/var/www/loris/...')
>>>> #4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24):
>>>> require_once('/var/www/loris/...')
>>>> #5 {main}
>>>>   thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
>>>> ===
>>>>
>>>> Any ideas on how to solve this?
>>>>
>>>> Regards,
>>>> Alfredo.
>>>>
>>>> On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hi Alfredo,
>>>>
>>>> If you check this link:
>>>>
>>>> https://github.com/aces/Loris/blob/21.0-release/README.md
>>>>
>>>> and
>>>>
>>>> https://github.com/aces/Loris/blob/22.0-release/README.md
>>>>
>>>> You will see that the system requires:
>>>>
>>>> *System Requirements*
>>>>
>>>>    - Apache *2.4* or higher
>>>>    - MySQL >= 5.7 (or MariaDB >= 10.3)
>>>>    - PHP *7.2* or higher
>>>>    - Composer <https://getcomposer.org/>
>>>>    - NodeJS *8.0* or higher
>>>>    - NPM
>>>>    - make
>>>>
>>>> Please make sure that you have all the latest or recent versions for
>>>> each of them, otherwise you will run into trouble later.
>>>>
>>>> Ling Ma
>>>>
>>>> On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>
>>>>> Hi Ling Ma,
>>>>>
>>>>> Thank you. I will upgrade to PHP 7.2.
>>>>>
>>>>> BTW, I cannot find the requirements for PHP for v21, I am looking at
>>>>> this link:
>>>>>
>>>>> https://github.com/aces/Loris/releases/tag/v21.0.0
>>>>>
>>>>> Regards,
>>>>> Alfredo.
>>>>>
>>>>>
>>>>> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> Hi Alfredo,
>>>>>
>>>>> The warning is OK to ignore. As to php, please check v21 version
>>>>> requirements, I believe a php minimum 7.1 even 7.2 is required.
>>>>>
>>>>> In fact, PHP 5.6 is no longer supported.
>>>>>
>>>>> Best regards,
>>>>> Ling Ma
>>>>>
>>>>> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
>>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>>
>>>>>> Dear Ling and Cécile,
>>>>>>
>>>>>> Thank for your responses.
>>>>>>
>>>>>> I had an issue with "git checkout”, somehow I had to remove some
>>>>>> files before being able to checkout the v21.0.0. That was the reason I
>>>>>> didn’t have the make file. Now that I have it, I have some errors:
>>>>>>
>>>>>> After running “make” I have the following error:
>>>>>>
>>>>>> ===
>>>>>>     *WARNING in configuration*
>>>>>> *    The 'mode' option has not been set, webpack will fallback to
>>>>>> 'production' for this value. Set 'mode' option to 'development' or
>>>>>> 'production' to enable defaults for each environment.*
>>>>>> *    You can also set it to 'none' to disable any default behavior.
>>>>>> Learn more: https://webpack.js.org/concepts/mode/
>>>>>> <https://webpack.js.org/concepts/mode/>*
>>>>>> composer install --no-dev
>>>>>> > mkdir -p project/libraries
>>>>>> Loading composer repositories with package information
>>>>>> Installing dependencies from lock file
>>>>>> Your requirements could not be resolved to an installable set of
>>>>>> packages.
>>>>>>
>>>>>>   Problem 1
>>>>>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>>>>>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>>>>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>>>>>> version (7.0.33) does not satisfy that requirement.
>>>>>> ===
>>>>>>
>>>>>> Do I have to upgrade PHP to 7.1?
>>>>>>
>>>>>> Thank you again for your help.
>>>>>>
>>>>>> Regards,
>>>>>> Alfredo.
>>>>>>
>>>>>>
>>>>>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>> wrote:
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hi Alfredo,
>>>>>>
>>>>>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0.
>>>>>> See below.
>>>>>>
>>>>>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>>>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>>>
>>>>>>> Hi Cécile,
>>>>>>>
>>>>>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and
>>>>>>> then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to
>>>>>>> v21.0.0, I have two issues:
>>>>>>>
>>>>>>> 1. I cannot access the link “Imaging->Imaging Browser” in the LORIS
>>>>>>> website. I get a 500 error. Any ideas on what should I check?
>>>>>>>
>>>>>>
>>>>>> Could you send us what you see in the Apache error file for that 500
>>>>>> error? Although, might be worth focusing on fixing your second issue before
>>>>>> we dive too much into that one.
>>>>>>
>>>>>>
>>>>>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>>>>>
>>>>>>> "Run make from the Loris root directory to update all dependencies.
>>>>>>> ”"
>>>>>>>
>>>>>>> However when I run “make” In the Loris root direction it does
>>>>>>> nothing. Here is the result:
>>>>>>>
>>>>>>> ===
>>>>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>>>>>> make: *** No targets specified and no makefile found.  Stop.
>>>>>>> ===
>>>>>>>
>>>>>> It that the right directory? Maybe I am missing some files?
>>>>>>>
>>>>>>
>>>>>> Are you sure you are on the 21.0.0 release of LORIS before you run
>>>>>> make? Do you see a Makefile in your /var/www/loris directory? In theory it
>>>>>> is supposed to be there on branch 21.0.0 (
>>>>>> https://github.com/aces/Loris/tree/v21.0.0)
>>>>>>
>>>>>> Hope this helps.
>>>>>>
>>>>>> Cécile
>>>>>>
>>>>>>
>>>>>>> Thank you for your help.
>>>>>>>
>>>>>>> Best,
>>>>>>> Alfredo.
>>>>>>>
>>>>>>
>>>>>>
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners Compliance
>>>>>> HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20200221/6573d819/attachment-0001.html>

More information about the Loris-dev mailing list