[Loris-dev] Update LORIS to v21.0.0

Ling Ma lingyun.ma at mcin.ca
Fri Feb 21 10:09:28 EST 2020 

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.
>>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>>
>>
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