From patrik.andersson at ling.su.se  Wed Aug  9 07:59:55 2017
From: patrik.andersson at ling.su.se (Patrik Andersson)
Date: Wed, 9 Aug 2017 11:59:55 +0000
Subject: [Loris-dev] database problem - local installation of LORIS
Message-ID: <1502279995215.5341@ling.su.se>

?Hi all,


I am trying to install LORIS on my desktop to test things out. I have installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For this LORIS test I would like to have all parts on the same computer.

I have managed to get as far as trying to install the database, but here I have run into problem. I should point out that I'm normally working with neuroscience and in other words, I am far outside my comfort zone...

I'm trying to follow the instructions at https://github.com/aces/Loris/wiki/Hosting-the-Database-Myself, but

when submitting the information on http://localhost/installdb.php I get a message

"Could not connect to MySQL server and create database with credentials provided.".

I used the following details:

Server Hostname: localhost
Admin Username: root
Admin Password: *************
Database name: LORIS

I have enabled the root user, in case that matters.
Any ideas or suggestions of where I have screwed things up? With my lack of knowledge on these things I realize it can be something really trivial or obvious.

Thanks!
Patrik
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From waveflux at gmail.com  Thu Aug 10 11:39:25 2017
From: waveflux at gmail.com (Tom Beaudry)
Date: Thu, 10 Aug 2017 11:39:25 -0400
Subject: [Loris-dev] header redirect
Message-ID: <CALzz+FPce-7Q6SZ4wRzYQuaZvOOkgKTfY2wdiskt7omGH9E97g@mail.gmail.com>

Hi Guys,

I am trying to do a redirect on my instrument (after the save button has
been clicked), and it doesn't work.  I am guessing there are some redirect
rules somewhere else that are affecting what I'm trying to do.

My code is the follows:

        $actual_link = "https://loris.loris.ca/main.php?test_name=E4_Data"
. $endOfURL;
        header("Location: '$actual_link'");

I then get redirected to this instead:

http://loris.concordia.ca/E4_Data/'https:/loris.loris.ca/main.php/?test_name=E4_Data&candID=936829&sessionID=53&commentID=936829PER0002531241502311230%27


Any help would be greatly appreciated,
Tom
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From david.macfarlane2 at mcgill.ca  Thu Aug 10 11:43:28 2017
From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr)
Date: Thu, 10 Aug 2017 15:43:28 +0000
Subject: [Loris-dev] header redirect
In-Reply-To: <CALzz+FPce-7Q6SZ4wRzYQuaZvOOkgKTfY2wdiskt7omGH9E97g@mail.gmail.com>
References: <CALzz+FPce-7Q6SZ4wRzYQuaZvOOkgKTfY2wdiskt7omGH9E97g@mail.gmail.com>
Message-ID: <DM5PR03MB3307871F119D76CAF91AFE1BA8880@DM5PR03MB3307.namprd03.prod.outlook.com>

The location HTTP header doesn't take quotation marks. The single quote at the start is likely causing the browser to treat it as a relative link.


Try:

        header("Location: $actual_link");


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Tom Beaudry <waveflux at gmail.com>
Sent: August 10, 2017 11:39:25 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] header redirect

Hi Guys,

I am trying to do a redirect on my instrument (after the save button has been clicked), and it doesn't work.  I am guessing there are some redirect rules somewhere else that are affecting what I'm trying to do.

My code is the follows:

        $actual_link = "https://loris.loris.ca/main.php?test_name=E4_Data" . $endOfURL;
        header("Location: '$actual_link'");

I then get redirected to this instead:

http://loris.concordia.ca/E4_Data/'https:/loris.loris.ca/main.php/?test_name=E4_Data&candID=936829&sessionID=53&commentID=936829PER0002531241502311230%27


Any help would be greatly appreciated,
Tom
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From waveflux at gmail.com  Thu Aug 10 12:06:50 2017
From: waveflux at gmail.com (Tom Beaudry)
Date: Thu, 10 Aug 2017 12:06:50 -0400
Subject: [Loris-dev] header redirect
In-Reply-To: <DM5PR03MB3307871F119D76CAF91AFE1BA8880@DM5PR03MB3307.namprd03.prod.outlook.com>
References: <CALzz+FPce-7Q6SZ4wRzYQuaZvOOkgKTfY2wdiskt7omGH9E97g@mail.gmail.com>
	<DM5PR03MB3307871F119D76CAF91AFE1BA8880@DM5PR03MB3307.namprd03.prod.outlook.com>
Message-ID: <CALzz+FNXee=H=-A8EL58fwKPsP09rNJWdM65FGtR_P3GJetvqA@mail.gmail.com>

Hi,

Sorry i added the single quote while i was fiddling with it to see why it
wasn't working.

In the end my problem is that $endOfURL was wrong.  It used to start with
candID, but it was switched to commentID sometime between LORIS version 15
and 17, and I never realized that until now.

Have a nice day,
Tom

On Thu, Aug 10, 2017 at 11:43 AM, David MacFarlane, Mr <
david.macfarlane2 at mcgill.ca> wrote:

> The location HTTP header doesn't take quotation marks. The single quote at
> the start is likely causing the browser to treat it as a relative link.
>
>
> Try:
>
>         header("Location: $actual_link");
>
> ------------------------------
> *From:* loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.
> mcgill.ca> on behalf of Tom Beaudry <waveflux at gmail.com>
> *Sent:* August 10, 2017 11:39:25 AM
> *To:* loris-dev at bic.mni.mcgill.ca
> *Subject:* [Loris-dev] header redirect
>
> Hi Guys,
>
> I am trying to do a redirect on my instrument (after the save button has
> been clicked), and it doesn't work.  I am guessing there are some redirect
> rules somewhere else that are affecting what I'm trying to do.
>
> My code is the follows:
>
>         $actual_link = "https://loris.loris.ca/main.php?test_name=E4_Data"
> . $endOfURL;
>         header("Location: '$actual_link'");
>
> I then get redirected to this instead:
>
> http://loris.concordia.ca/E4_Data/'https:/loris.loris.ca/
> main.php/?test_name=E4_Data&candID=936829&sessionID=53&commentID=
> 936829PER0002531241502311230%27
>
>
> Any help would be greatly appreciated,
> Tom
>
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From christine.rogers at mcgill.ca  Thu Aug 10 17:02:51 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Thu, 10 Aug 2017 17:02:51 -0400
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <1502279995215.5341@ling.su.se>
References: <1502279995215.5341@ling.su.se>
Message-ID: <CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>

Hi Patrik,
Thanks for your question.
Could you clarify for context --
Which version of MySQL do you have installed?  Is it locally installed on
the Ubuntu partition?
Does your root/*password* credential you provided successfully log you into
MySQL (trying from the commandline)?
Best,
Christine
on behalf of the Loris team


On Wed, Aug 9, 2017 at 7:59 AM, Patrik Andersson <
patrik.andersson at ling.su.se> wrote:

> ?Hi all,
>
>
> I am trying to install LORIS on my desktop to test things out. I have
> installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For
> this LORIS test I would like to have all parts on the same computer.
>
> I have managed to get as far as trying to install the database, but here I
> have run into problem. I should point out that I'm normally working with
> neuroscience and in other words, I am far outside my comfort zone...
>
> I'm trying to follow the instructions at https://github.com/aces/
> Loris/wiki/Hosting-the-Database-Myself, but
>
> when submitting the information on http://localhost/installdb.php I get a
> message
>
> "Could not connect to MySQL server and create database with credentials
> provided.".
>
> I used the following details:
> Server Hostname: localhost
> Admin Username: root
> Admin Password: ?????????????
> Database name: LORIS
>
> I have enabled the root user, in case that matters.
> Any ideas or suggestions of where I have screwed things up? With my lack
> of knowledge on these things I realize it can be something really trivial
> or obvious.
>
> Thanks!
> Patrik
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.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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From wangshen.mcin at gmail.com  Mon Aug 14 10:21:16 2017
From: wangshen.mcin at gmail.com (Shen Wang)
Date: Mon, 14 Aug 2017 10:21:16 -0400
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>
References: <1502279995215.5341@ling.su.se>
	<CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>
Message-ID: <CADM4SCymVU_F7yo9Vc5Y0D+CnyLsU75o_p789HFY4ZDK0vjXpw@mail.gmail.com>

Hi Patrik,
I tested the installation guide last month, It works well.
Please try this https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief

or
reset your root password then try it again.
You can access my new Loris on http://132.206.37.22.
(https://github.com/aces/Loris/archive/v17.0.5.zip PHP 7.1 Mysql 5.7  Ubuntu
16.04.3 LTS)

Shen



On 10 August 2017 at 17:02, Christine Rogers <christine.rogers at mcgill.ca>
wrote:

> Hi Patrik,
> Thanks for your question.
> Could you clarify for context --
> Which version of MySQL do you have installed?  Is it locally installed on
> the Ubuntu partition?
> Does your root/*password* credential you provided successfully log you
> into MySQL (trying from the commandline)?
> Best,
> Christine
> on behalf of the Loris team
>
>
> On Wed, Aug 9, 2017 at 7:59 AM, Patrik Andersson <
> patrik.andersson at ling.su.se> wrote:
>
>> ?Hi all,
>>
>>
>> I am trying to install LORIS on my desktop to test things out. I have
>> installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For
>> this LORIS test I would like to have all parts on the same computer.
>>
>> I have managed to get as far as trying to install the database, but
>> here I have run into problem. I should point out that I'm normally working
>> with neuroscience and in other words, I am far outside my comfort zone...
>>
>> I'm trying to follow the instructions at https://github.com/aces/Lor
>> is/wiki/Hosting-the-Database-Myself, but
>>
>> when submitting the information on http://localhost/installdb.php I get
>> a message
>>
>> "Could not connect to MySQL server and create database with credentials
>> provided.".
>>
>> I used the following details:
>> Server Hostname: localhost
>> Admin Username: root
>> Admin Password: ?????????????
>> Database name: LORIS
>>
>> I have enabled the root user, in case that matters.
>> Any ideas or suggestions of where I have screwed things up? With my lack
>> of knowledge on these things I realize it can be something really trivial
>> or obvious.
>>
>> Thanks!
>> Patrik
>>
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> http://www.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
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From patrik.andersson at ling.su.se  Wed Aug 16 07:05:59 2017
From: patrik.andersson at ling.su.se (Patrik Andersson)
Date: Wed, 16 Aug 2017 11:05:59 +0000
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <1502802491572.5777@ling.su.se>
References: <1502279995215.5341@ling.su.se>
	<CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>,
	<CADM4SCymVU_F7yo9Vc5Y0D+CnyLsU75o_p789HFY4ZDK0vjXpw@mail.gmail.com>,
	<1502802491572.5777@ling.su.se>
Message-ID: <1502881559523.62408@ling.su.se>


Thank you for the help!

I am not sure what was wrong, but after a thorough reinstallation of mysql it seems to work. I had already tried to reinstall it, but it seems I needed to manually delete some files that kept some settings.


However, after creating the mysql accounts I get stuck again...


I can not access localhost. I get:

"localhost is currently unable to handle this request.
HTTP ERROR 500"

I have tried to restart Apache which did not help.

Looking at the PHP log, it says:

[16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): /var/www/TestProject/php/libraries/../../project/config.xml:1: parser error : Document is empty in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
[16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file():  in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
[16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): ^ in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
[16-Aug-2017 11:47:11 Europe/Berlin] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/TestProject/php/libraries/../../project/config.xml in /var/www/TestProject/php/libraries/NDB_Config.class.inc:111
Stack trace:
#0 /var/www/TestProject/php/libraries/NDB_Config.class.inc(92): NDB_Config->load('/var/www/TestPr...')
#1 /var/www/TestProject/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/TestPr...')
#2 /var/www/TestProject/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)
#3 /var/www/TestProject/htdocs/main.php(29): NDB_Client->initialize()
#4 {main}
  thrown in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 111

The config.xml file is indeed empty. Should it be?
Any suggestions for what to do?
Thanks again for your time!!


Best,

Patrik




________________________________
From: Shen Wang <wangshen.mcin at gmail.com>
Sent: 14 August 2017 16:21
Cc: Patrik Andersson; loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] database problem - local installation of LORIS

Hi Patrik,
I tested the installation guide last month, It works well.
Please try this https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
or
reset your root password then try it again.
You can access my new Loris on http://132.206.37.22.
(https://github.com/aces/Loris/archive/v17.0.5.zip PHP 7.1 Mysql 5.7  Ubuntu 16.04.3 LTS)

Shen



On 10 August 2017 at 17:02, Christine Rogers <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
Hi Patrik,
Thanks for your question.
Could you clarify for context --
Which version of MySQL do you have installed?  Is it locally installed on the Ubuntu partition?
Does your root/password credential you provided successfully log you into MySQL (trying from the commandline)?
Best,
Christine
on behalf of the Loris team


On Wed, Aug 9, 2017 at 7:59 AM, Patrik Andersson <patrik.andersson at ling.su.se<mailto:patrik.andersson at ling.su.se>> wrote:

?Hi all,


I am trying to install LORIS on my desktop to test things out. I have installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For this LORIS test I would like to have all parts on the same computer.

I have managed to get as far as trying to install the database, but here I have run into problem. I should point out that I'm normally working with neuroscience and in other words, I am far outside my comfort zone...

I'm trying to follow the instructions at https://github.com/aces/Loris/wiki/Hosting-the-Database-Myself, but

when submitting the information on http://localhost/installdb.php I get a message

"Could not connect to MySQL server and create database with credentials provided.".

I used the following details:

Server Hostname: localhost
Admin Username: root
Admin Password: ?????????????
Database name: LORIS

I have enabled the root user, in case that matters.
Any ideas or suggestions of where I have screwed things up? With my lack of knowledge on these things I realize it can be something really trivial or obvious.

Thanks!
Patrik

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev




--

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

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


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From chohenfeld at ukaachen.de  Wed Aug 16 07:38:38 2017
From: chohenfeld at ukaachen.de (Hohenfeld, Christian)
Date: Wed, 16 Aug 2017 11:38:38 +0000
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <1502881559523.62408@ling.su.se>
References: <1502279995215.5341@ling.su.se>
	<CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>
	<CADM4SCymVU_F7yo9Vc5Y0D+CnyLsU75o_p789HFY4ZDK0vjXpw@mail.gmail.com>
	<1502802491572.5777@ling.su.se> <1502881559523.62408@ling.su.se>
Message-ID: <F97BF43C-75D4-49BA-8E87-62491EA05FB2@ukaachen.de>

Hi Patrik, 

I am not one of the Loris devs, but my best guess would be that the permissions are not set correctly. Did you make sure that the /var/www/TestProject/project/ directory is accessible and writeable for your loris user *and* the apache2 group (www-data)? The same should be true for the config.xml file. 

Best regards
Christian  



> Am 16.08.2017 um 13:05 schrieb Patrik Andersson <patrik.andersson at ling.su.se>:
> 
> 
> Thank you for the help! 
> I am not sure what was wrong, but after a thorough reinstallation of mysql it seems to work. I had already tried to reinstall it, but it seems I needed to manually delete some files that kept some settings.
> 
> However, after creating the mysql accounts I get stuck again...
> 
> I can not access localhost. I get:
>  
> "localhost is currently unable to handle this request.
> HTTP ERROR 500"
> 
> I have tried to restart Apache which did not help.
> 
> Looking at the PHP log, it says:
> 
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): /var/www/TestProject/php/libraries/../../project/config.xml:1: parser error : Document is empty in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file():  in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): ^ in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/TestProject/php/libraries/../../project/config.xml in /var/www/TestProject/php/libraries/NDB_Config.class.inc:111
> Stack trace:
> #0 /var/www/TestProject/php/libraries/NDB_Config.class.inc(92): NDB_Config->load('/var/www/TestPr...')
> #1 /var/www/TestProject/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/TestPr...')
> #2 /var/www/TestProject/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)
> #3 /var/www/TestProject/htdocs/main.php(29): NDB_Client->initialize()
> #4 {main}
>   thrown in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 111
> 
> The config.xml file is indeed empty. Should it be?
> Any suggestions for what to do?
> Thanks again for your time!!
> 
> Best,
> Patrik
> 
> 
> 
> From: Shen Wang <wangshen.mcin at gmail.com>
> Sent: 14 August 2017 16:21
> Cc: Patrik Andersson; loris-dev at bic.mni.mcgill.ca
> Subject: Re: [Loris-dev] database problem - local installation of LORIS
>  
> Hi Patrik,
> I tested the installation guide last month, It works well.
> Please try this https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief 
> or 
> reset your root password then try it again.
> You can access my new Loris on http://132.206.37.22.
> (https://github.com/aces/Loris/archive/v17.0.5.zip PHP 7.1 Mysql 5.7  Ubuntu 16.04.3 LTS)
> 
> Shen
> 
> 
> 
> On 10 August 2017 at 17:02, Christine Rogers <christine.rogers at mcgill.ca> wrote:
> Hi Patrik,
> Thanks for your question. 
> Could you clarify for context -- 
> Which version of MySQL do you have installed?  Is it locally installed on the Ubuntu partition?  
> Does your root/password credential you provided successfully log you into MySQL (trying from the commandline)?   
> Best, 
> Christine 
> on behalf of the Loris team
> 
> 
> On Wed, Aug 9, 2017 at 7:59 AM, Patrik Andersson <patrik.andersson at ling.su.se> wrote:
> ?Hi all,
> 
> I am trying to install LORIS on my desktop to test things out. I have installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For this LORIS test I would like to have all parts on the same computer. 
> I have managed to get as far as trying to install the database, but here I have run into problem. I should point out that I'm normally working with neuroscience and in other words, I am far outside my comfort zone...
> I'm trying to follow the instructions at https://github.com/aces/Loris/wiki/Hosting-the-Database-Myself, but
> when submitting the information on http://localhost/installdb.php I get a message 
> "Could not connect to MySQL server and create database with credentials provided.".
> I used the following details:
> Server Hostname: localhost
> Admin Username: root
> Admin Password: ?????????????
> Database name: LORIS
> 
> I have enabled the root user, in case that matters.
> Any ideas or suggestions of where I have screwed things up? With my lack of knowledge on these things I realize it can be something really trivial or obvious. 
> 
> Thanks!
> Patrik
> 
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.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
> 
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> 
> 
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


From patrik.andersson at ling.su.se  Wed Aug 16 08:16:07 2017
From: patrik.andersson at ling.su.se (Patrik Andersson)
Date: Wed, 16 Aug 2017 12:16:07 +0000
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <F97BF43C-75D4-49BA-8E87-62491EA05FB2@ukaachen.de>
References: <1502279995215.5341@ling.su.se>
	<CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>
	<CADM4SCymVU_F7yo9Vc5Y0D+CnyLsU75o_p789HFY4ZDK0vjXpw@mail.gmail.com>
	<1502802491572.5777@ling.su.se> <1502881559523.62408@ling.su.se>,
	<F97BF43C-75D4-49BA-8E87-62491EA05FB2@ukaachen.de>
Message-ID: <1502885767262.65654@ling.su.se>

Thanks a lot Christian!
The permissions are as follows:

$ sudo ls -la /var/www/TestProject/project/
total 32
drwxrwx---  8 root       www-data   4096 aug 15 15:16 .
drwxr-xr-x 13 lorisadmin lorisadmin 4096 aug  8 14:51 ..
-rw-r--r--  1 www-data   www-data      0 aug 15 15:16 config.xml
drwxr-xr-x  2 root       root       4096 aug  8 12:13 data
drwxr-xr-x  2 root       root       4096 aug  8 12:13 instruments
drwxr-xr-x  2 root       root       4096 aug  8 12:13 libraries
drwxr-xr-x  2 root       root       4096 aug  8 12:13 modules
drwxr-xr-x  2 root       root       4096 aug  8 12:13 tables_sql
drwxr-xr-x  2 root       root       4096 aug  8 12:13 templates

lorisadmin is, as you might guess, the unix user.
Is there a problem here as you see it?

Thanks for taking the time to help a beginner!

Best,
Patrik
________________________________________
From: Hohenfeld, Christian <chohenfeld at ukaachen.de>
Sent: 16 August 2017 13:38
To: Patrik Andersson
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] database problem - local installation of LORIS

Hi Patrik,

I am not one of the Loris devs, but my best guess would be that the permissions are not set correctly. Did you make sure that the /var/www/TestProject/project/ directory is accessible and writeable for your loris user *and* the apache2 group (www-data)? The same should be true for the config.xml file.

Best regards
Christian



> Am 16.08.2017 um 13:05 schrieb Patrik Andersson <patrik.andersson at ling.su.se>:
>
>
> Thank you for the help!
> I am not sure what was wrong, but after a thorough reinstallation of mysql it seems to work. I had already tried to reinstall it, but it seems I needed to manually delete some files that kept some settings.
>
> However, after creating the mysql accounts I get stuck again...
>
> I can not access localhost. I get:
>
> "localhost is currently unable to handle this request.
> HTTP ERROR 500"
>
> I have tried to restart Apache which did not help.
>
> Looking at the PHP log, it says:
>
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): /var/www/TestProject/php/libraries/../../project/config.xml:1: parser error : Document is empty in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file():  in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Warning:  simplexml_load_file(): ^ in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 108
> [16-Aug-2017 11:47:11 Europe/Berlin] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/TestProject/php/libraries/../../project/config.xml in /var/www/TestProject/php/libraries/NDB_Config.class.inc:111
> Stack trace:
> #0 /var/www/TestProject/php/libraries/NDB_Config.class.inc(92): NDB_Config->load('/var/www/TestPr...')
> #1 /var/www/TestProject/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/TestPr...')
> #2 /var/www/TestProject/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)
> #3 /var/www/TestProject/htdocs/main.php(29): NDB_Client->initialize()
> #4 {main}
>   thrown in /var/www/TestProject/php/libraries/NDB_Config.class.inc on line 111
>
> The config.xml file is indeed empty. Should it be?
> Any suggestions for what to do?
> Thanks again for your time!!
>
> Best,
> Patrik
>
>
>
> From: Shen Wang <wangshen.mcin at gmail.com>
> Sent: 14 August 2017 16:21
> Cc: Patrik Andersson; loris-dev at bic.mni.mcgill.ca
> Subject: Re: [Loris-dev] database problem - local installation of LORIS
>
> Hi Patrik,
> I tested the installation guide last month, It works well.
> Please try this https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> or
> reset your root password then try it again.
> You can access my new Loris on http://132.206.37.22.
> (https://github.com/aces/Loris/archive/v17.0.5.zip PHP 7.1 Mysql 5.7  Ubuntu 16.04.3 LTS)
>
> Shen
>
>
>
> On 10 August 2017 at 17:02, Christine Rogers <christine.rogers at mcgill.ca> wrote:
> Hi Patrik,
> Thanks for your question.
> Could you clarify for context --
> Which version of MySQL do you have installed?  Is it locally installed on the Ubuntu partition?
> Does your root/password credential you provided successfully log you into MySQL (trying from the commandline)?
> Best,
> Christine
> on behalf of the Loris team
>
>
> On Wed, Aug 9, 2017 at 7:59 AM, Patrik Andersson <patrik.andersson at ling.su.se> wrote:
> ?Hi all,
>
> I am trying to install LORIS on my desktop to test things out. I have installed Ubuntu 16.04 (dual boot with Windows 10) for this purpose. For this LORIS test I would like to have all parts on the same computer.
> I have managed to get as far as trying to install the database, but here I have run into problem. I should point out that I'm normally working with neuroscience and in other words, I am far outside my comfort zone...
> I'm trying to follow the instructions at https://github.com/aces/Loris/wiki/Hosting-the-Database-Myself, but
> when submitting the information on http://localhost/installdb.php I get a message
> "Could not connect to MySQL server and create database with credentials provided.".
> I used the following details:
> Server Hostname: localhost
> Admin Username: root
> Admin Password: ?????????????
> Database name: LORIS
>
> I have enabled the root user, in case that matters.
> Any ideas or suggestions of where I have screwed things up? With my lack of knowledge on these things I realize it can be something really trivial or obvious.
>
> Thanks!
> Patrik
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.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
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


From chohenfeld at ukaachen.de  Wed Aug 16 08:54:51 2017
From: chohenfeld at ukaachen.de (Hohenfeld, Christian)
Date: Wed, 16 Aug 2017 12:54:51 +0000
Subject: [Loris-dev] database problem - local installation of LORIS
In-Reply-To: <1502885767262.65654@ling.su.se>
References: <1502279995215.5341@ling.su.se>
	<CALbt7NBg-4DDoeidPQ-c4x9Jas0uPCxe870YVxqTKkwJc2Y+eA@mail.gmail.com>
	<CADM4SCymVU_F7yo9Vc5Y0D+CnyLsU75o_p789HFY4ZDK0vjXpw@mail.gmail.com>
	<1502802491572.5777@ling.su.se> <1502881559523.62408@ling.su.se>
	<F97BF43C-75D4-49BA-8E87-62491EA05FB2@ukaachen.de>
	<1502885767262.65654@ling.su.se>
Message-ID: <A63CC194-EECB-47C1-B4B1-FB24F287E680@ukaachen.de>

Hi Patrik, 

it looks like the permissions you have there are off, independent of your configuration file, which might lead to issues. At the moment it seems like most things are owned by root and only writable to root, which is likely to cause issues further down the road. Did you do the installation as root? 
 
Have a look at https://en.wikipedia.org/wiki/File_system_permissions#Notation_of_traditional_Unix_permissions for a short explanation of unix permissions. 

You may want to look at what the chmod, chown and chgrp commands do if you are not familiar with them already (try the manages or googling for the commands). 

So you might want to try changing permissions of your loris installation to your lorisadmin user and the apache2 group:

sudo chown -R lorisadmin:www-data /var/www/TestProject

(be careful when doing this, as "sudo chown -R? on the wrong directory can mess up quite a lot of stuff ? I did my best to put the command here correctly but make sure you understand what it does before executing this)

Then you will need to fix a few permissions again, set the ownership of /var/www/TestProject/modules/document_repository/user_uploads and /var/www/TestProject/smarty/templates_c to www-data:www-data (should all work without sudo if you are logged in as lorisadmin). 

Finally, you should set the mode to 770 for the following directories: /var/www/TestProject/smarty/templates_c, /var/www/TestProject/tools/logs and /var/www/TestProject/project (some might require sudo).

Then try again. If this still fails you could try temporarily setting the mode of the config.xml file to 664, which might be required if you do the configuration through the webpage (on the system I manage it has 644 for lorisadmin:www-data, but if I remember correctly I added the database config manually to it). 

Best regards
Christian  








From iris.rodriguez at cneuro.edu.cu  Mon Aug 21 12:47:01 2017
From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=)
Date: Mon, 21 Aug 2017 11:47:01 -0500
Subject: [Loris-dev] HELP
Message-ID: <C3A14E086354C04B8DB16023948F98BA81D90234F6@exchange.cneuro.edu.cu>

Hello everyone,

I am having authentication problems on my Loris site after I migrate my Loris server to the VMWARE ESXI 5.0 platform.
When I try to access the site I block access for any user, I'm using Loris version 17.02, any suggestions will be appreciated.

Best Regards,
Iris


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From christine.rogers at mcgill.ca  Tue Aug 22 09:41:48 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Tue, 22 Aug 2017 09:41:48 -0400
Subject: [Loris-dev] HELP
In-Reply-To: <C3A14E086354C04B8DB16023948F98BA81D90234F6@exchange.cneuro.edu.cu>
References: <C3A14E086354C04B8DB16023948F98BA81D90234F6@exchange.cneuro.edu.cu>
Message-ID: <CALbt7NDJYXLUhU1n+iwYmaRNtUOjknRkiW3op9izhdOjdVEKKQ@mail.gmail.com>

Hi Iris,

It looks like your user accounts exist, but may have expired or been
deactivated.

(See Troubleshooting notes for user logins in the wiki
<https://github.com/aces/Loris/wiki/Project-Customization/_edit#troubleshooting-user-login>,
summarized below.)

To fix this, update your *users
<https://github.com/aces/Loris/blob/17.0-dev/SQL/0000-00-00-schema.sql#L1295>*
table records
via the MySQL database back-end:
- Ensure the *Password_expiry*
<https://github.com/aces/Loris/blob/17.0-dev/SQL/0000-00-00-schema.sql#L1320>
column stores a value later than today
- Verify *Active* column = 'Y'
- Verify *Pending_approval* = 'N'

Best,
Christine


On Mon, Aug 21, 2017 at 12:47 PM, Iris Rodr?guez Gil <
iris.rodriguez at cneuro.edu.cu> wrote:

> Hello everyone,
>
>
>
> I am having authentication problems on my Loris site after I migrate my
> Loris server to the VMWARE ESXI 5.0 platform.
>
> When I try to access the site I block access for any user, I'm using Loris
> version 17.02, any suggestions will be appreciated.
>
>
>
> Best Regards,
>
> Iris
>
>
>
>
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.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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From AMORALESPINZON at bwh.harvard.edu  Tue Aug 22 14:32:47 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Tue, 22 Aug 2017 18:32:47 +0000
Subject: [Loris-dev] Help: MaxCenters = 255
Message-ID: <6943CC45EE5DEC4089174E22E5478369348ACD3A@PHSX10MB8.partners.org>

Dear LORIS team and users,

I was testing the insertion of Centers and I got an error referring to the CenterID of table psc. This CenterID is defined as a tinyint(2) and has a maximum value of 255 (see https://dev.mysql.com/doc/refman/5.7/en/integer-types.html). In my project, we will handle hundreds of Centers. Is it possible to easily migrate the database to change this CenterID as SMALL INT or MEDIUM INT?

Here is the error:

mysql> insert into psc(Name,Alias,MRI_Alias) values ('test_1238-UCD','CAB','CAB');
ERROR 1062 (23000): Duplicate entry '255' for key 'PRIMARY'

mysql> describe psc;
+------------+---------------------+------+-----+---------+----------------+
| Field      | Type                | Null | Key | Default | Extra          |
+------------+---------------------+------+-----+---------+----------------+
| CenterID   | tinyint(2) unsigned | NO   | PRI | NULL    | auto_increment |
| Name       | varchar(150)        | NO   | UNI |         |                |
| PSCArea    | varchar(150)        | YES  |     | NULL    |                |
| Address    | varchar(150)        | YES  |     | NULL    |                |
| City       | varchar(150)        | YES  |     | NULL    |                |
| StateID    | tinyint(2) unsigned | YES  |     | NULL    |                |
| ZIP        | varchar(12)         | YES  |     | NULL    |                |
| Phone1     | varchar(12)         | YES  |     | NULL    |                |
| Phone2     | varchar(12)         | YES  |     | NULL    |                |
| Contact1   | varchar(150)        | YES  |     | NULL    |                |
| Contact2   | varchar(150)        | YES  |     | NULL    |                |
| Alias      | char(3)             | NO   |     |         |                |
| MRI_alias  | varchar(4)          | NO   |     |         |                |
| Account    | varchar(8)          | YES  |     | NULL    |                |
| Study_site | enum('N','Y')       | YES  |     | Y       |                |
+------------+---------------------+------+-----+---------+----------------+
15 rows in set (0.01 sec)

Regards,
Alfredo Morales Pinzon


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
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dispose of the e-mail.
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From iris.rodriguez at cneuro.edu.cu  Tue Aug 22 16:34:32 2017
From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=)
Date: Tue, 22 Aug 2017 15:34:32 -0500
Subject: [Loris-dev] HELP
Message-ID: <C3A14E086354C04B8DB16023948F98BA81D9023802@exchange.cneuro.edu.cu>

Hello everyone,

I am having authentication problems on my Loris site after I migrate my Loris server to the VMWARE ESXI 5.0 platform.
When I try to access the site I block access for any user, I'm using Loris version 17.0.4.
Any suggestions will be appreciated.

Best Regards,
Iris

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From ganeshchauhan at iisc.ac.in  Wed Aug 23 05:32:35 2017
From: ganeshchauhan at iisc.ac.in (Ganesh Chauhan)
Date: Wed, 23 Aug 2017 09:32:35 +0000
Subject: [Loris-dev] Any solutions for offline situations when we have no
 internet connectivity
Message-ID: <PN1PR01MB102324F31CC30E00CFA2E57981850@PN1PR01MB1023.INDPRD01.PROD.OUTLOOK.COM>

Hi,


I was wondering if there are any solutions to offline situations. This is because we want to use the LORIS framework in remote place to collect some data and we are likely to have no internet connectivity.


Any suggestions are greatly appreciated.


Many thanks.


With best regards,

Ganesh


Ganesh Chauhan (PhD)
Scientist
Centre for Brain Research (CBR)
Indian Institute of Science (IISc)
Bengaluru, INDIA
+91 80 2293 3009
https://www.cbr.iisc.ac.in
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From waveflux at gmail.com  Wed Aug 23 10:35:15 2017
From: waveflux at gmail.com (Tom Beaudry)
Date: Wed, 23 Aug 2017 10:35:15 -0400
Subject: [Loris-dev] Any solutions for offline situations when we have
 no internet connectivity
In-Reply-To: <PN1PR01MB102324F31CC30E00CFA2E57981850@PN1PR01MB1023.INDPRD01.PROD.OUTLOOK.COM>
References: <PN1PR01MB102324F31CC30E00CFA2E57981850@PN1PR01MB1023.INDPRD01.PROD.OUTLOOK.COM>
Message-ID: <CALzz+FN+9DjmLZobirN945HfmPNh+uCAWNJeX9Rr=S7=SyaBog@mail.gmail.com>

Hi Ganesh,

If you have LORIS installed locally on a laptop, you can run it from there
without an internet connection.

Tom

On Wed, Aug 23, 2017 at 5:32 AM, Ganesh Chauhan <ganeshchauhan at iisc.ac.in>
wrote:

> Hi,
>
>
> I was wondering if there are any solutions to offline situations. This is
> because we want to use the LORIS framework in remote place to collect some
> data and we are likely to have no internet connectivity.
>
>
> Any suggestions are greatly appreciated.
>
>
> Many thanks.
>
>
> With best regards,
>
> Ganesh
>
>
> Ganesh Chauhan (PhD)
> Scientist
> Centre for Brain Research (CBR)
> Indian Institute of Science (IISc)
> Bengaluru, INDIA
> +91 80 2293 3009 <+91%2080%202293%203009>
> https://www.cbr.iisc.ac.in
>
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From wangshen.mcin at gmail.com  Wed Aug 23 10:43:13 2017
From: wangshen.mcin at gmail.com (Shen Wang)
Date: Wed, 23 Aug 2017 10:43:13 -0400
Subject: [Loris-dev] HELP
In-Reply-To: <C3A14E086354C04B8DB16023948F98BA81D9023802@exchange.cneuro.edu.cu>
References: <C3A14E086354C04B8DB16023948F98BA81D9023802@exchange.cneuro.edu.cu>
Message-ID: <CADM4SCz8V8P-vthJ98rr-22u2nt6MiZd1nSqWoK5rAZm3002ZQ@mail.gmail.com>

Hi Iris,
Please try to insert a new admin user in your database, log in with this
admin user.
Then check whether the permissions of other users are correct or activated.

[ user name :admin password: testpassword ]
INSERT INTO `users`
(ID,UserID,Real_name,First_name,Last_name,Email,Privilege,PSCPI,DBAccess,Active,Pending_approval,Password_hash,Password_expiry)
VALUES (99,'admin','Admin account','Admin','account','admin at example.com
',0,'N','','Y','N','$2y$10$qmPDbENCsUvClwPDbVG.SOsTMtI7War1ggkjA60ElJkYM4LpSUbrC','2016-03-30');
UPDATE users SET
Password_hash='$2y$10$DYvowoM2WGZ00IVljItljeSjnUaZx5az4/Bfb3PxZSofnEGHb0KJC',
Pending_approval='N', Password_expiry='2100-01-01' WHERE ID=1;

Best Regards,
Shen


On 22 August 2017 at 16:34, Iris Rodr?guez Gil <iris.rodriguez at cneuro.edu.cu
> wrote:

> Hello everyone,
>
>
>
> I am having authentication problems on my Loris site after I migrate my
> Loris server to the VMWARE ESXI 5.0 platform.
>
> When I try to access the site I block access for any user, I'm using Loris
> version 17.0.4.
>
> Any suggestions will be appreciated.
>
>
>
> Best Regards,
>
> Iris
>
>
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From ganeshchauhan at iisc.ac.in  Wed Aug 23 10:43:26 2017
From: ganeshchauhan at iisc.ac.in (Ganesh Chauhan)
Date: Wed, 23 Aug 2017 14:43:26 +0000
Subject: [Loris-dev] Any solutions for offline situations when we have
 no internet connectivity
In-Reply-To: <CALzz+FN+9DjmLZobirN945HfmPNh+uCAWNJeX9Rr=S7=SyaBog@mail.gmail.com>
References: <PN1PR01MB102324F31CC30E00CFA2E57981850@PN1PR01MB1023.INDPRD01.PROD.OUTLOOK.COM>,
	<CALzz+FN+9DjmLZobirN945HfmPNh+uCAWNJeX9Rr=S7=SyaBog@mail.gmail.com>
Message-ID: <PN1PR01MB1023DE51A91CE5BAFC678AD281850@PN1PR01MB1023.INDPRD01.PROD.OUTLOOK.COM>

Hi,

But I have multiple sites with multiple people recording data and everything needs to go into one database which is located in one central place.

Thanks for any suggestions.

With best regards,
Ganesh

Get Outlook for Android<https://aka.ms/ghei36>

________________________________
From: Tom Beaudry <waveflux at gmail.com>
Sent: Wednesday, August 23, 2017 8:05:15 PM
To: Ganesh Chauhan
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Any solutions for offline situations when we have no internet connectivity

Hi Ganesh,

If you have LORIS installed locally on a laptop, you can run it from there without an internet connection.

Tom

On Wed, Aug 23, 2017 at 5:32 AM, Ganesh Chauhan <ganeshchauhan at iisc.ac.in<mailto:ganeshchauhan at iisc.ac.in>> wrote:

Hi,


I was wondering if there are any solutions to offline situations. This is because we want to use the LORIS framework in remote place to collect some data and we are likely to have no internet connectivity.


Any suggestions are greatly appreciated.


Many thanks.


With best regards,

Ganesh


Ganesh Chauhan (PhD)
Scientist
Centre for Brain Research (CBR)
Indian Institute of Science (IISc)
Bengaluru, INDIA
+91 80 2293 3009<tel:+91%2080%202293%203009>
https://www.cbr.iisc.ac.in

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


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From Bonhwang.Koo at childmind.org  Thu Aug 24 11:44:09 2017
From: Bonhwang.Koo at childmind.org (Bonhwang Koo)
Date: Thu, 24 Aug 2017 15:44:09 +0000
Subject: [Loris-dev] Data Query Tool Download Log
Message-ID: <BB2FE157-E2C0-456C-B556-FB670B1B4EDE@childmind.org>

Hi all,

My group is interested in finding out how many times users have downloaded data from our data query tool. Is there a log file that tracks this information?

Best,
--
Bonhwang Koo
Research Assistant, CDB
Child Mind Institute
childmind.org<http://childmind.org/>
445 Park Avenue (entrance on 56th Street)
New York, NY 10022
E: Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>
p: 646.625.4398
f: 646.625.4348

Facebook: facebook.com/ChildMindInstitute<http://facebook.com/ChildMindInstitute> | Follow us on Twitter: twitter.com/ChildMindDotOrg<http://twitter.com/ChildMindDotOrg>

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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From jordan.stirling at mail.mcgill.ca  Thu Aug 24 16:36:13 2017
From: jordan.stirling at mail.mcgill.ca (Jordan Stirling, Mr)
Date: Thu, 24 Aug 2017 20:36:13 +0000
Subject: [Loris-dev] Data Query Tool Download Log
In-Reply-To: <BB2FE157-E2C0-456C-B556-FB670B1B4EDE@childmind.org>
References: <BB2FE157-E2C0-456C-B556-FB670B1B4EDE@childmind.org>
Message-ID: <2730E56A-F1E6-4167-A5F5-9863792BB8F3@mail.mcgill.ca>

Hi Bonhwang,

At this point we do not keep logs of when users download data from the DQT. Are you looking to get logs when users download the data as a CSV or when they run the query?

Cheers,

Jordan Stirling

Sent from my iPhone

On Aug 24, 2017, at 11:44 AM, Bonhwang Koo <Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>> wrote:

Hi all,

My group is interested in finding out how many times users have downloaded data from our data query tool. Is there a log file that tracks this information?

Best,
--
Bonhwang Koo
Research Assistant, CDB
Child Mind Institute
childmind.org<http://childmind.org/>
445 Park Avenue (entrance on 56th Street)
New York, NY 10022
E: Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>
p: 646.625.4398
f: 646.625.4348

Facebook: facebook.com/ChildMindInstitute<http://facebook.com/ChildMindInstitute> | Follow us on Twitter: twitter.com/ChildMindDotOrg<http://twitter.com/ChildMindDotOrg>

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
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From Bonhwang.Koo at childmind.org  Thu Aug 24 16:58:02 2017
From: Bonhwang.Koo at childmind.org (Bonhwang Koo)
Date: Thu, 24 Aug 2017 20:58:02 +0000
Subject: [Loris-dev] Data Query Tool Download Log
In-Reply-To: <2730E56A-F1E6-4167-A5F5-9863792BB8F3@mail.mcgill.ca>
References: <BB2FE157-E2C0-456C-B556-FB670B1B4EDE@childmind.org>
	<2730E56A-F1E6-4167-A5F5-9863792BB8F3@mail.mcgill.ca>
Message-ID: <89420CDD-92EE-42ED-87D1-75567F65C199@childmind.org>

Jordan,

I think we could use both, but if we only had one choice, then when users download the data as a CSV.

Thanks!
--
Bonhwang Koo
Research Assistant, CDB
Child Mind Institute
childmind.org<http://childmind.org/>
445 Park Avenue (entrance on 56th Street)
New York, NY 10022
E: Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>
p: 646.625.4398
f: 646.625.4348

Facebook: facebook.com/ChildMindInstitute<http://facebook.com/ChildMindInstitute> | Follow us on Twitter: twitter.com/ChildMindDotOrg<http://twitter.com/ChildMindDotOrg>

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.

From: "Jordan Stirling, Mr" <jordan.stirling at mail.mcgill.ca>
Date: Thursday, August 24, 2017 at 4:36 PM
To: Bonhwang Koo <Bonhwang.Koo at childmind.org>
Cc: "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Data Query Tool Download Log

Hi Bonhwang,

At this point we do not keep logs of when users download data from the DQT. Are you looking to get logs when users download the data as a CSV or when they run the query?

Cheers,

Jordan Stirling

Sent from my iPhone

On Aug 24, 2017, at 11:44 AM, Bonhwang Koo <Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>> wrote:
Hi all,

My group is interested in finding out how many times users have downloaded data from our data query tool. Is there a log file that tracks this information?

Best,
--
Bonhwang Koo
Research Assistant, CDB
Child Mind Institute
childmind.org<http://childmind.org/>
445 Park Avenue (entrance on 56th Street)
New York, NY 10022
E: Bonhwang.Koo at childmind.org<mailto:Bonhwang.Koo at childmind.org>
p: 646.625.4398
f: 646.625.4348

Facebook: facebook.com/ChildMindInstitute<http://facebook.com/ChildMindInstitute> | Follow us on Twitter: twitter.com/ChildMindDotOrg<http://twitter.com/ChildMindDotOrg>

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
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From mukhan at ualberta.ca  Fri Aug 25 14:49:43 2017
From: mukhan at ualberta.ca (Muhammad Khan)
Date: Fri, 25 Aug 2017 12:49:43 -0600
Subject: [Loris-dev] Similar instruments for different cohorts
Message-ID: <CACYqeJ80Li+mpTqVvAzYeCnS2_iRPjNxhmdU7gdfomZkVnn58g@mail.gmail.com>

Hi guys!

In our project, patients and control, for the most part, are administered
the same set of instruments. However, the patients are usually asked a few
additional questions for a particular instrument, and so the 'control
version' of the instrument is just a subset of the 'patient version' of the
instrument.

In terms of creating the instrument on the Behavioral database, I have
thought of two ways to go about implementing this:

i. Create two versions of the same instrument ( one called "Instrument Name
(Control), the other "Instrument Name (Patient)), and assign the
appropriate Sub_group in the test_names table.

ii. Create one instrument, and only display the 'patient fields' if the
subject belongs to the patient Sub_group. This wouldn't be difficult, but
there would be a lot of NULL entries for the control Sub_group. When
querying the data using the Data Query Tool, this may cause some issues.

My question is, which would be the better way of doing it, creating one
instrument for both Sub_group, or have two separate instruments, one for
each Sub_group?

Thanks,
Muhammad
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From christine.rogers at mcgill.ca  Fri Aug 25 15:46:15 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 25 Aug 2017 15:46:15 -0400
Subject: [Loris-dev] Similar instruments for different cohorts
In-Reply-To: <CACYqeJ80Li+mpTqVvAzYeCnS2_iRPjNxhmdU7gdfomZkVnn58g@mail.gmail.com>
References: <CACYqeJ80Li+mpTqVvAzYeCnS2_iRPjNxhmdU7gdfomZkVnn58g@mail.gmail.com>
Message-ID: <CALbt7NAgE1Q9JDykJWhVZKxmQnsrEN8amezF5_=EwM9yuicEUw@mail.gmail.com>

Hi Muhammad,

In general, we'd recommend creating one instrument to administer to both
cohort/subproject populations, particularly given that one version is a
proper subset of the other.
As you mention, certain questions can be automatically marked NULL.

There are a few reasons for this best practice, but the key reasons all
boil down to clarity and compatibility of data, whether in the Data
Dictionary or when using the Data Querying Tool for dissemination, or
reproducing an analysis years later.

Christine
On behalf of the LORIS team


On Fri, Aug 25, 2017 at 2:49 PM, Muhammad Khan <mukhan at ualberta.ca> wrote:

> Hi guys!
>
> In our project, patients and control, for the most part, are administered
> the same set of instruments. However, the patients are usually asked a few
> additional questions for a particular instrument, and so the 'control
> version' of the instrument is just a subset of the 'patient version' of the
> instrument.
>
> In terms of creating the instrument on the Behavioral database, I have
> thought of two ways to go about implementing this:
>
> i. Create two versions of the same instrument ( one called "Instrument
> Name (Control), the other "Instrument Name (Patient)), and assign the
> appropriate Sub_group in the test_names table.
>
> ii. Create one instrument, and only display the 'patient fields' if the
> subject belongs to the patient Sub_group. This wouldn't be difficult, but
> there would be a lot of NULL entries for the control Sub_group. When
> querying the data using the Data Query Tool, this may cause some issues.
>
> My question is, which would be the better way of doing it, creating one
> instrument for both Sub_group, or have two separate instruments, one for
> each Sub_group?
>
> Thanks,
> Muhammad
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.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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From mukhan at ualberta.ca  Fri Aug 25 19:32:09 2017
From: mukhan at ualberta.ca (Muhammad Khan)
Date: Fri, 25 Aug 2017 17:32:09 -0600
Subject: [Loris-dev] Similar instruments for different cohorts
In-Reply-To: <CALbt7NAgE1Q9JDykJWhVZKxmQnsrEN8amezF5_=EwM9yuicEUw@mail.gmail.com>
References: <CACYqeJ80Li+mpTqVvAzYeCnS2_iRPjNxhmdU7gdfomZkVnn58g@mail.gmail.com>
	<CALbt7NAgE1Q9JDykJWhVZKxmQnsrEN8amezF5_=EwM9yuicEUw@mail.gmail.com>
Message-ID: <CACYqeJ9TFB7Y9pSBEcBHPg59hoL5Wg1NMCkerDS-32GfErz=1g@mail.gmail.com>

That makes sense.
Thanks!

Muhammad
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From ncote at aviscuriosa.com  Tue Aug 29 22:02:48 2017
From: ncote at aviscuriosa.com (=?UTF-8?B?Tm9ybWFuZCBDw7R0w6k=?=)
Date: Tue, 29 Aug 2017 22:02:48 -0400
Subject: [Loris-dev] Date format
Message-ID: <CAFkTtf935nXi8oZE1PzQNaM3q9Zc0x=0tym0Q4mvNsingBLB3Q@mail.gmail.com>

Is there a mechanism for changing the date format throughout Loris?  We
need to accept (and display) dates in this format: DD-MMM-YYYY e.g.
01-Jun-2016.
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From david.macfarlane2 at mcgill.ca  Thu Aug 31 10:17:28 2017
From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr)
Date: Thu, 31 Aug 2017 14:17:28 +0000
Subject: [Loris-dev] Date format
In-Reply-To: <CAFkTtf935nXi8oZE1PzQNaM3q9Zc0x=0tym0Q4mvNsingBLB3Q@mail.gmail.com>
References: <CAFkTtf935nXi8oZE1PzQNaM3q9Zc0x=0tym0Q4mvNsingBLB3Q@mail.gmail.com>
Message-ID: <DM5PR03MB3307499549551B06B0BA1259A89D0@DM5PR03MB3307.namprd03.prod.outlook.com>

Hi Normand,


Where are you referring to exactly? For data entry, LORIS generally uses an HTML5 "date" input type. For internationalization reasons, the HTML date input type's visual display is dependent on the user's locale, so that users consistently see dates in the format that makes sense to them throughout the internet while having a defined way of sending the date to the server for processing. As a result, LORIS should consistently use the date format for the locale of the user's web browser/operating system for display.


I just tried changing my computer's settings from Canada to Iran, and the format of the date displayed changed as expected. (I assume, I'm not familiar enough with Iranian culture to know how they format dates over there, but it was different..)


So:

  1.  If the display of dates isn't being shown in accordance with your operating system preferences, it's probably a bug in your web browser* and you should file a bug with them.
  2.  If your operating system locale is correct, but you're not seeing dates in the format that's standard for that region of the world, that's probably a bug in your operating system or web browser. (Though it seems unlikely to me that a bug like this would be discovered by using LORIS.. OS/web browser companies have a lot of global users who would catch things like this pretty quickly.)
  3.  If there's somewhere in LORIS displaying dates in a way that's inconsistent with other places in LORIS, that's a bug to report to us that we should fix. (I verified on the "New Profile" page, so you can see how it's displayed there for the expected format for your locale.)
  4.  If you want to change how you see dates, you should probably change your operating system preferences. (As a bonus, this should affect how you see dates everywhere on the internet to be your preferred format.) If that doesn't affect how you see dates in LORIS after restarting your browser, it's probably a bug in your web browser*.


 * Unless your web browser is Firefox, which doesn't support HTML date elements and LORIS uses a jQuery shim. Unfortunately, it's not customizable. Hopefully one day Firefox will add support date for elements, we can remove the shim and this will be a moot point.

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Normand C?t? <ncote at aviscuriosa.com>
Sent: August 29, 2017 10:02:48 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Date format

Is there a mechanism for changing the date format throughout Loris?  We need to accept (and display) dates in this format: DD-MMM-YYYY e.g. 01-Jun-2016.
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From ncote at aviscuriosa.com  Thu Aug 31 10:39:36 2017
From: ncote at aviscuriosa.com (=?UTF-8?B?Tm9ybWFuZCBDw7R0w6k=?=)
Date: Thu, 31 Aug 2017 10:39:36 -0400
Subject: [Loris-dev] Date format
In-Reply-To: <DM5PR03MB3307499549551B06B0BA1259A89D0@DM5PR03MB3307.namprd03.prod.outlook.com>
References: <CAFkTtf935nXi8oZE1PzQNaM3q9Zc0x=0tym0Q4mvNsingBLB3Q@mail.gmail.com>
	<DM5PR03MB3307499549551B06B0BA1259A89D0@DM5PR03MB3307.namprd03.prod.outlook.com>
Message-ID: <CAFkTtf8q4qySg-QdGQiQvsY2KgQMHqSQ8xE9HmBLeW3HQK5aog@mail.gmail.com>

Thanks for the response.

The idea was to have the date format appear in a consistent manner for all
Loris users involved in a particular study, regardless of their OS or
browser settings, for both input and display.  It seems to be a standard of
sorts.



On Thu, Aug 31, 2017 at 10:17 AM, David MacFarlane, Mr <
david.macfarlane2 at mcgill.ca> wrote:

> Hi Normand,
>
>
> Where are you referring to exactly? For data entry, LORIS generally uses
> an HTML5 "date" input type. For internationalization reasons, the HTML date
> input type's visual display is dependent on the user's locale, so that
> users consistently see dates in the format that makes sense to them
> throughout the internet while having a defined way of sending the date to
> the server for processing. As a result, LORIS should consistently use the
> date format for the locale of the user's web browser/operating system for
> display.
>
>
> I just tried changing my computer's settings from Canada to Iran, and the
> format of the date displayed changed as expected. (I assume, I'm not
> familiar enough with Iranian culture to know how they format dates over
> there, but it was different..)
>
>
> So:
>
>
>    1. If the display of dates isn't being shown in accordance with your
>    operating system preferences, it's probably a bug in your web browser* and
>    you should file a bug with them.
>    2. If your operating system locale is correct, but you're not seeing
>    dates in the format that's standard for that region of the world, that's
>    probably a bug in your operating system or web browser. (Though it seems
>    unlikely to me that a bug like this would be discovered by using LORIS..
>    OS/web browser companies have a lot of global users who would catch things
>    like this pretty quickly.)
>    3. If there's somewhere in LORIS displaying dates in a way that's
>    inconsistent with other places in LORIS, that's a bug to report to us that
>    we should fix. (I verified on the "New Profile" page, so you can see how
>    it's displayed there for the expected format for your locale.)
>    4. If you want to change how you see dates, you should probably change
>    your operating system preferences. (As a bonus, this should affect how you
>    see dates everywhere on the internet to be your preferred format.) If that
>    doesn't affect how you see dates in LORIS after restarting your browser,
>    it's probably a bug in your web browser*.
>
>
>  * Unless your web browser is Firefox, which doesn't support HTML date
> elements and LORIS uses a jQuery shim. Unfortunately, it's not
> customizable. Hopefully one day Firefox will add support date for elements,
> we can remove the shim and this will be a moot point.
>
> ------------------------------
> *From:* loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.
> mcgill.ca> on behalf of Normand C?t? <ncote at aviscuriosa.com>
> *Sent:* August 29, 2017 10:02:48 PM
> *To:* loris-dev at bic.mni.mcgill.ca
> *Subject:* [Loris-dev] Date format
>
> Is there a mechanism for changing the date format throughout Loris?  We
> need to accept (and display) dates in this format: DD-MMM-YYYY e.g.
> 01-Jun-2016.
>
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