From waveflux at gmail.com  Wed Dec  2 13:34:26 2015
From: waveflux at gmail.com (Tom Beaudry)
Date: Wed, 2 Dec 2015 13:34:26 -0500
Subject: [Loris-dev] 502 bad gateway
Message-ID: <CALzz+FOWXsk9wyrPS2gbFBmdtzMk64EqP0xoYn_S-RrdbLCAYQ@mail.gmail.com>

Hi Everyone,

I did a fresh install of the latest release recently, and now when i try to
access the main login page:  https://tnl.loris.ca/

I get a 502 Bad Gateway page.

Has anyone encountered this / has some suggestions as to how I can fix it.

Thanks!
Tom
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From relbadrawi at indocresearch.org  Thu Dec  3 15:13:12 2015
From: relbadrawi at indocresearch.org (Rachad El-Badrawi)
Date: Thu, 3 Dec 2015 15:13:12 -0500
Subject: [Loris-dev] LORIS data model/schema
Message-ID: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>

Hi All,

1) I was wondering if there is a comprehensive freely available project/study that uses LORIS, that can be used to show how the different tables/fields in the LORIS schema are used. I am basically looking for a MySQL dump that represents that study which I can upload into a MySQL instance that I have.

2) Anyone had 'complete' success in installing LORIS on a Linux - Debian (VM). If so, please share any tips.

Thanks for the feedback.

Regards,
Rashad Badrawi

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From christine.rogers at mcgill.ca  Thu Dec  3 15:37:47 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Thu, 3 Dec 2015 15:37:47 -0500
Subject: [Loris-dev] 502 bad gateway
In-Reply-To: <CALzz+FOWXsk9wyrPS2gbFBmdtzMk64EqP0xoYn_S-RrdbLCAYQ@mail.gmail.com>
References: <CALzz+FOWXsk9wyrPS2gbFBmdtzMk64EqP0xoYn_S-RrdbLCAYQ@mail.gmail.com>
Message-ID: <CALbt7NBrPY5qj2ueV3KAEBX7Duwx-kQgcB_2naM4+CQLMNreXw@mail.gmail.com>

Hi Tom,
This 502 message is likely to result from your Apache/DNS setup.
Let me know if you need any help troubleshooting our instructions for the
Apache configuration setup, e.g. from the 15.10 CentOS readme (
https://github.com/aces/Loris/blob/15.10-dev/README.CentOS6.md )

Best,
Christine

On Wed, Dec 2, 2015 at 1:34 PM, Tom Beaudry <waveflux at gmail.com> wrote:

> Hi Everyone,
>
> I did a fresh install of the latest release recently, and now when i try
> to access the main login page:  https://tnl.loris.ca/
>
> I get a 502 Bad Gateway page.
>
> Has anyone encountered this / has some suggestions as to how I can fix it.
>
> Thanks!
> Tom
>
> _______________________________________________
> 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
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From waveflux at gmail.com  Fri Dec  4 12:35:10 2015
From: waveflux at gmail.com (Tom Beaudry)
Date: Fri, 4 Dec 2015 12:35:10 -0500
Subject: [Loris-dev] graphics not appearing on Login
Message-ID: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>

Hi Everyone,

When i login to my LORIS instance, none of the graphics (menu bar, tables,
dashboard) load. I only have text (see the attached screen shots).  Does
anyone know how to fix this?

Thanks,
Tom
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From waveflux at gmail.com  Fri Dec  4 12:47:50 2015
From: waveflux at gmail.com (Tom Beaudry)
Date: Fri, 4 Dec 2015 12:47:50 -0500
Subject: [Loris-dev] graphics not appearing on Login
In-Reply-To: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>
References: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>
Message-ID: <CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>

Hi again,

I took a look at my chrome console and I have errors such as:

[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
ran insecure content from 'http://localhost//main.css': this content should
also be loaded over HTTPS. tnl.loris.ca/:4 <https://tnl.loris.ca/>
[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
ran insecure content from 'http://localhost//js/jquery/jquery-1.11.0.min.js':
this content should also be loaded over HTTPS. tnl.loris.ca/:1
<https://tnl.loris.ca/>
[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
ran insecure content from 'http://localhost//js/modernizr.min.js': this
content should also be loaded over HTTPS.
?

so I am thinking it might be because it trying to load stuff from
http://locahost  although I am not sure how to fix this yet...

Thanks,
Tom
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From christine.rogers at mcgill.ca  Fri Dec  4 12:56:32 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 4 Dec 2015 12:56:32 -0500
Subject: [Loris-dev] graphics not appearing on Login
In-Reply-To: <CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>
References: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>
	<CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>
Message-ID: <CALbt7NBDpirpRSCp_Ca_DNssvWXbF86L1S1Ab3v8VHmYjxbN=w@mail.gmail.com>

Hi Tom,

It looks like your Config setting(s) should be updated so that Loris will
source the CSS from the correct place.

As you will have difficulty accessing these settings through the front-end
Configuration module, here is a MySQL query you can run in the backend that
will prettily display all your configuration settings:
select c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description from Config
c, ConfigSettings cs where cs.ID=c.ConfigID;
Append the following to view the paths configuration variables which will
be of interest to you:
 AND c.ConfigID > '20' AND c.ConfigID < '40' ;

Best,
Christine

On Fri, Dec 4, 2015 at 12:47 PM, Tom Beaudry <waveflux at gmail.com> wrote:

> Hi again,
>
> I took a look at my chrome console and I have errors such as:
>
> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
> ran insecure content from 'http://localhost//main.css': this content
> should also be loaded over HTTPS. tnl.loris.ca/:4 <https://tnl.loris.ca/>
> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
> ran insecure content from '
> http://localhost//js/jquery/jquery-1.11.0.min.js': this content should
> also be loaded over HTTPS. tnl.loris.ca/:1 <https://tnl.loris.ca/>
> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
> ran insecure content from 'http://localhost//js/modernizr.min.js': this
> content should also be loaded over HTTPS.
> ?
>
> so I am thinking it might be because it trying to load stuff from
> http://locahost  although I am not sure how to fix this yet...
>
> Thanks,
> Tom
>
> _______________________________________________
> 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
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From waveflux at gmail.com  Fri Dec  4 13:09:44 2015
From: waveflux at gmail.com (Tom Beaudry)
Date: Fri, 4 Dec 2015 13:09:44 -0500
Subject: [Loris-dev] graphics not appearing on Login
In-Reply-To: <CALbt7NBDpirpRSCp_Ca_DNssvWXbF86L1S1Ab3v8VHmYjxbN=w@mail.gmail.com>
References: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>
	<CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>
	<CALbt7NBDpirpRSCp_Ca_DNssvWXbF86L1S1Ab3v8VHmYjxbN=w@mail.gmail.com>
Message-ID: <CALzz+FPVwrK=HEyvM7LbFmiHw9=LG4QPyT2Gd41L4rRQYiQE9Q@mail.gmail.com>

Awesome thanks Christine you're the best!  I had to change values 40 and 41.

Have a nice weekend,
Tom

On Fri, Dec 4, 2015 at 12:56 PM, Christine Rogers <
christine.rogers at mcgill.ca> wrote:

> Hi Tom,
>
> It looks like your Config setting(s) should be updated so that Loris will
> source the CSS from the correct place.
>
> As you will have difficulty accessing these settings through the front-end
> Configuration module, here is a MySQL query you can run in the backend that
> will prettily display all your configuration settings:
> select c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description from Config
> c, ConfigSettings cs where cs.ID=c.ConfigID;
> Append the following to view the paths configuration variables which will
> be of interest to you:
>  AND c.ConfigID > '20' AND c.ConfigID < '40' ;
>
> Best,
> Christine
>
> On Fri, Dec 4, 2015 at 12:47 PM, Tom Beaudry <waveflux at gmail.com> wrote:
>
>> Hi again,
>>
>> I took a look at my chrome console and I have errors such as:
>>
>> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
>> ran insecure content from 'http://localhost//main.css': this content
>> should also be loaded over HTTPS. tnl.loris.ca/:4 <https://tnl.loris.ca/>
>> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
>> ran insecure content from '
>> http://localhost//js/jquery/jquery-1.11.0.min.js': this content should
>> also be loaded over HTTPS. tnl.loris.ca/:1 <https://tnl.loris.ca/>
>> [blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but
>> ran insecure content from 'http://localhost//js/modernizr.min.js': this
>> content should also be loaded over HTTPS.
>> ?
>>
>> so I am thinking it might be because it trying to load stuff from
>> http://locahost  although I am not sure how to fix this yet...
>>
>> Thanks,
>> Tom
>>
>> _______________________________________________
>> 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
> LORIS data systems | loris.ca
> McGill Centre for Integrative Neuroscience| MCIN.ca
> McConnell Brain Imaging Centre
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
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From ramanandan.prabhakaran at gmail.com  Fri Dec  4 13:11:10 2015
From: ramanandan.prabhakaran at gmail.com (Ramanandan Prabhakaran)
Date: Fri, 4 Dec 2015 13:11:10 -0500
Subject: [Loris-dev] Regarding Loris installation
Message-ID: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>

Dear
?Loris developers
,

I tried installing the LORIS from Github in ubuntu.

As per the installation section, I performed following things
1) C
?reated
 LINUX user (emruser) and created EMR base directory.
2) Downloaded the LORIS file from rel
?e?
ase section and extracted it to "/var/www/emr"
3) Then I installed following dependencies (Smarty3 and Composer)
    3.1) Installing smarty3
           $ sudo apt-get install smarty3
    3.2) Installing composer
           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
https://getcomposer.org/installer | php;
           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
/usr/local/bin/composer
           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
           *Composer could not find a composer.json file in /home/emradmin*
*           To initialize a project, please create a composer.json file as
described in the https://getcomposer.org/ <https://getcomposer.org/>
"Getting Started" section*
4) Then moved to following directory path
     4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools

     4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
            LORIS installation Script starting at 2015-12-04 (Attached the
installation log file)
            Project name  : emr
            Database name : emrdb
            Database host : localhost
            MySQL user  (recommended lorisuser): emruser
            Where Loris' apache is hosted: localhost
            *But Benchmarj-1.2.9.tgz file could not be downloaded.*
            Finally I got "Installation complete" message.
5) Then executed following command
     5.1) $ sudo service apache2 reload
6) Then I tried in firefox, http://localhost. The page was blank.

Can you please guide me in resolving this issue.

Cheers,
Ram
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From christine.rogers at mcgill.ca  Fri Dec  4 13:14:03 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 4 Dec 2015 13:14:03 -0500
Subject: [Loris-dev] Loris 15.10 Release and Pear update
Message-ID: <CALbt7NDd1S5584EpNJMtk7gTCv-dZCkiY4VUe33_-67fruSbhg@mail.gmail.com>

Hi Everyone,

The new release 15.10 is now available on GitHub
<https://github.com/aces/Loris/releases>.

Pear is currently experiencing downtime which they are hoping to resolve
over the weekend.   ( http://pear.php.net/ | https://twitter.com/pear )
In the meantime, new Loris installations may find that Composer encounters
difficulties installing this dependency.

For existing projects upgrading to 15.10, please be sure to consult the
Release Notes on GitHub for important instructions and caveats, both in the
main Loris repo <https://github.com/aces/Loris/releases> -- and for imaging
projects, the Loris-MRI repo <https://github.com/aces/Loris-MRI/releases> as
well.

Regards,
the Loris team
-- 
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
Ludmer Centre for Neuroinformatics and Mental Health
Montreal Neurological Institute
McGill University | Montreal | Canada
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From david.macfarlane2 at mcgill.ca  Fri Dec  4 15:20:59 2015
From: david.macfarlane2 at mcgill.ca (Dave MacFarlane)
Date: Fri, 4 Dec 2015 15:20:59 -0500
Subject: [Loris-dev] graphics not appearing on Login
In-Reply-To: <CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>
References: <CALzz+FPLoPyxc6fyqpyZhVaRi3=CgTiKLzpSjtYoG+99M2yYgg@mail.gmail.com>,
	<CALzz+FNZvGbOK6tDDY1nUykHp1B3NtsOr7=6n_VtDHAFP+X21g@mail.gmail.com>
Message-ID: <BAY182-W78DDAF6D1AC40175B74BAEF80C0@phx.gbl>

It looks like your BaseURL config variable is set wrong (it should be https://tnl.loris.ca/, but it's set to http://localhost/)
-- Dave

Date: Fri, 4 Dec 2015 12:47:50 -0500
From: waveflux at gmail.com
To: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] graphics not appearing on Login

Hi again,
I took a look at my chrome console and I have errors such as:
[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but ran insecure content from 'http://localhost//main.css': this content should also be loaded over HTTPS.
 tnl.loris.ca/:4[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but ran insecure content from 'http://localhost//js/jquery/jquery-1.11.0.min.js': this content should also be loaded over HTTPS.
 tnl.loris.ca/:1[blocked] The page at 'https://tnl.loris.ca/' was loaded over HTTPS, but ran insecure content from 'http://localhost//js/modernizr.min.js': this content should also be loaded over HTTPS.?
so I am thinking it might be because it trying to load stuff from http://locahost  although I am not sure how to fix this yet...

Thanks,Tom

_______________________________________________
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 christine.rogers at mcgill.ca  Fri Dec  4 15:20:30 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 4 Dec 2015 15:20:30 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
Message-ID: <CALbt7NA2iJF=JCbt1a4GbSNBiD3CZDsMf3RjY+eBD5nBvo=4Xg@mail.gmail.com>

Hi Ramanandan,
Thanks for writing us with your feedback.

We've just now updated the wiki page to clarify these steps previously
mentioned in section 3.  The Install script should install composer and
smarty3 for Ubuntu installs (current Pear issues notwithstanding).

The Benchmark package issue you encountered (4.2) is a symptom of the
current Pear downtime.  ( http://pear.php.net/ | https://twitter.com/pear )
At the present time we are awaiting news regarding when this dependency's
installation packages will be next available - expected to be up and
running again this weekend.
Once Pear has resolved this issue, composer will be able to complete its
installation and verification of dependencies.

Once Pear is back up (see links above), try re-running the composer install
steps manually -- see:
https://github.com/aces/Loris/wiki/Install-Script#troubleshooting

Then it may be helpful verify your Configuration settings - see:
https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings

Usually if Loris is loading a blank page, the "base" path configuration
setting needs updating.  This setting should store the path to your main
Loris code - e.g. /var/www/loris

Regards,
Christine


On Fri, Dec 4, 2015 at 1:11 PM, Ramanandan Prabhakaran <
ramanandan.prabhakaran at gmail.com> wrote:

> Dear
> ?Loris developers
> ,
>
> I tried installing the LORIS from Github in ubuntu.
>
> As per the installation section, I performed following things
> 1) C
> ?reated
>  LINUX user (emruser) and created EMR base directory.
> 2) Downloaded the LORIS file from rel
> ?e?
> ase section and extracted it to "/var/www/emr"
> 3) Then I installed following dependencies (Smarty3 and Composer)
>     3.1) Installing smarty3
>            $ sudo apt-get install smarty3
>     3.2) Installing composer
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
> https://getcomposer.org/installer | php;
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
> /usr/local/bin/composer
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>            *Composer could not find a composer.json file in
> /home/emradmin*
> *           To initialize a project, please create a composer.json file as
> described in the https://getcomposer.org/ <https://getcomposer.org/>
> "Getting Started" section*
> 4) Then moved to following directory path
>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>
>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>             LORIS installation Script starting at 2015-12-04 (Attached
> the installation log file)
>             Project name  : emr
>             Database name : emrdb
>             Database host : localhost
>             MySQL user  (recommended lorisuser): emruser
>             Where Loris' apache is hosted: localhost
>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>             Finally I got "Installation complete" message.
> 5) Then executed following command
>      5.1) $ sudo service apache2 reload
> 6) Then I tried in firefox, http://localhost. The page was blank.
>
> Can you please guide me in resolving this issue.
>
> Cheers,
> Ram
>
>
>
>
> _______________________________________________
> 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
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From david.macfarlane2 at mcgill.ca  Fri Dec  4 15:27:38 2015
From: david.macfarlane2 at mcgill.ca (Dave MacFarlane)
Date: Fri, 4 Dec 2015 15:27:38 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
Message-ID: <BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>

Hi Ramanandan,
1. Smarty is installed from composer, you don't need to apt-get install it anymore as of Release 15.102. You need to run "composer install --no-dev" from the LORIS directory, not your home directory, which    is why it can't find composer.json3. The PHP/PEAR package repository (pear.php.net) had some downtime and the install script couldn't   retrieve dependencies (such as the Benchmark library). Can you try running "composer install --no-dev"  (from the LORIS directory) and see if it works now? They seem to be partially back up, but I'm not sure if all  their packages are restored yet..

-- Dave

Date: Fri, 4 Dec 2015 13:11:10 -0500
From: ramanandan.prabhakaran at gmail.com
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Regarding Loris installation

Dear ?Loris developers,

I tried installing the LORIS from Github in ubuntu.
As per the installation section, I performed following things1) C?reated LINUX user (emruser) and created EMR base directory.2) Downloaded the LORIS file from rel?e?ase section and extracted it to "/var/www/emr"3) Then I installed following dependencies (Smarty3 and Composer)    3.1) Installing smarty3           $ sudo apt-get install smarty3    3.2) Installing composer           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS https://getcomposer.org/installer | php;           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar /usr/local/bin/composer           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install           Composer could not find a composer.json file in /home/emradmin           To initialize a project, please create a composer.json file as described in the https://getcomposer.org/ "Getting Started" section4) Then moved to following directory path     4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools               4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh            LORIS installation Script starting at 2015-12-04 (Attached the installation log file)            Project name  : emr            Database name : emrdb            Database host : localhost            MySQL user  (recommended lorisuser): emruser            Where Loris' apache is hosted: localhost            But Benchmarj-1.2.9.tgz file could not be downloaded.            Finally I got "Installation complete" message.5) Then executed following command     5.1) $ sudo service apache2 reload6) Then I tried in firefox, http://localhost. The page was blank.
Can you please guide me in resolving this issue.
Cheers,Ram        




_______________________________________________
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 ramanandan.prabhakaran at gmail.com  Fri Dec  4 15:54:49 2015
From: ramanandan.prabhakaran at gmail.com (Ramanandan Prabhakaran)
Date: Fri, 4 Dec 2015 15:54:49 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CALbt7NA2iJF=JCbt1a4GbSNBiD3CZDsMf3RjY+eBD5nBvo=4Xg@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
	<CALbt7NA2iJF=JCbt1a4GbSNBiD3CZDsMf3RjY+eBD5nBvo=4Xg@mail.gmail.com>
Message-ID: <CA+5uKGFeyPU_vfPR75Jcq730Gx3JWhCgORvLCFU43Hay81aNqw@mail.gmail.com>

Thanks Christine Rogers for getting back to me. Sure I will try in the
weekend.

Cheers,
Ram


On Fri, Dec 4, 2015 at 3:20 PM, Christine Rogers <christine.rogers at mcgill.ca
> wrote:

> Hi Ramanandan,
> Thanks for writing us with your feedback.
>
> We've just now updated the wiki page to clarify these steps previously
> mentioned in section 3.  The Install script should install composer and
> smarty3 for Ubuntu installs (current Pear issues notwithstanding).
>
> The Benchmark package issue you encountered (4.2) is a symptom of the
> current Pear downtime.  ( http://pear.php.net/ | https://twitter.com/pear
>  )
> At the present time we are awaiting news regarding when this dependency's
> installation packages will be next available - expected to be up and
> running again this weekend.
> Once Pear has resolved this issue, composer will be able to complete its
> installation and verification of dependencies.
>
> Once Pear is back up (see links above), try re-running the composer
> install steps manually -- see:
> https://github.com/aces/Loris/wiki/Install-Script#troubleshooting
>
> Then it may be helpful verify your Configuration settings - see:
>
> https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
>
> Usually if Loris is loading a blank page, the "base" path configuration
> setting needs updating.  This setting should store the path to your main
> Loris code - e.g. /var/www/loris
>
> Regards,
> Christine
>
>
> On Fri, Dec 4, 2015 at 1:11 PM, Ramanandan Prabhakaran <
> ramanandan.prabhakaran at gmail.com> wrote:
>
>> Dear
>> ?Loris developers
>> ,
>>
>> I tried installing the LORIS from Github in ubuntu.
>>
>> As per the installation section, I performed following things
>> 1) C
>> ?reated
>>  LINUX user (emruser) and created EMR base directory.
>> 2) Downloaded the LORIS file from rel
>> ?e?
>> ase section and extracted it to "/var/www/emr"
>> 3) Then I installed following dependencies (Smarty3 and Composer)
>>     3.1) Installing smarty3
>>            $ sudo apt-get install smarty3
>>     3.2) Installing composer
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
>> https://getcomposer.org/installer | php;
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
>> /usr/local/bin/composer
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>>            *Composer could not find a composer.json file in
>> /home/emradmin*
>> *           To initialize a project, please create a composer.json file
>> as described in the https://getcomposer.org/ <https://getcomposer.org/>
>> "Getting Started" section*
>> 4) Then moved to following directory path
>>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>>
>>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>>             LORIS installation Script starting at 2015-12-04 (Attached
>> the installation log file)
>>             Project name  : emr
>>             Database name : emrdb
>>             Database host : localhost
>>             MySQL user  (recommended lorisuser): emruser
>>             Where Loris' apache is hosted: localhost
>>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>>             Finally I got "Installation complete" message.
>> 5) Then executed following command
>>      5.1) $ sudo service apache2 reload
>> 6) Then I tried in firefox, http://localhost. The page was blank.
>>
>> Can you please guide me in resolving this issue.
>>
>> Cheers,
>> Ram
>>
>>
>>
>>
>> _______________________________________________
>> 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
> LORIS data systems | loris.ca
> McGill Centre for Integrative Neuroscience| MCIN.ca
> McConnell Brain Imaging Centre
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
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From ramanandan.prabhakaran at gmail.com  Fri Dec  4 15:58:21 2015
From: ramanandan.prabhakaran at gmail.com (Ramanandan Prabhakaran)
Date: Fri, 4 Dec 2015 15:58:21 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
	<BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>
Message-ID: <CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>

Dear Dave,

Thanks for getting me back to me on my query. Yeah now, it recongized the
.json file.

emradmin at jsn-HP-Pavilion-g6-1c33ca:*/var/www/emr*$ composer install --no-dev
Loading composer repositories with package information
Installing dependencies from lock file
  - Installing pear-pear.php.net/benchmark (1.2.9)
    Downloading: 100%


  [Composer\Downloader\TransportException]

  The "https://pear.php.net/get/Benchmark-1.2.9.tgz" file could not be
downloaded (HTTP/1.1 404 Not Found)


install [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev]
[--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts]
[--no-progress] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader]
[-a|--classmap-authoritative] [--ignore-platform-reqs] [--] [<packages>]...

emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$

Cheers,
Ram

On Fri, Dec 4, 2015 at 3:27 PM, Dave MacFarlane <david.macfarlane2 at mcgill.ca
> wrote:

> Hi Ramanandan,
>
> 1. Smarty is installed from composer, you don't need to apt-get install it
> anymore as of Release 15.10
> 2. You need to run "composer install --no-dev" from the LORIS directory,
> not your home directory, which
>     is why it can't find composer.json
> 3. The PHP/PEAR package repository (pear.php.net) had some downtime and the
> install script couldn't
>   retrieve dependencies (such as the Benchmark library). Can you try
> running "composer install --no-dev"
>  (from the LORIS directory) and see if it works now? They seem to be
> partially back up, but I'm not sure if all
>  their packages are restored yet..
>
>
> -- Dave
>
>
> ------------------------------
> Date: Fri, 4 Dec 2015 13:11:10 -0500
> From: ramanandan.prabhakaran at gmail.com
> To: loris-dev at bic.mni.mcgill.ca
> Subject: [Loris-dev] Regarding Loris installation
>
>
> Dear
> ?Loris developers
> ,
>
> I tried installing the LORIS from Github in ubuntu.
>
> As per the installation section, I performed following things
> 1) C
> ?reated
>  LINUX user (emruser) and created EMR base directory.
> 2) Downloaded the LORIS file from rel
> ?e?
> ase section and extracted it to "/var/www/emr"
> 3) Then I installed following dependencies (Smarty3 and Composer)
>     3.1) Installing smarty3
>            $ sudo apt-get install smarty3
>     3.2) Installing composer
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
> https://getcomposer.org/installer | php;
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
> /usr/local/bin/composer
>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>            *Composer could not find a composer.json file in
> /home/emradmin*
> *           To initialize a project, please create a composer.json file as
> described in the https://getcomposer.org/ <https://getcomposer.org/>
> "Getting Started" section*
> 4) Then moved to following directory path
>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>
>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>             LORIS installation Script starting at 2015-12-04 (Attached
> the installation log file)
>             Project name  : emr
>             Database name : emrdb
>             Database host : localhost
>             MySQL user  (recommended lorisuser): emruser
>             Where Loris' apache is hosted: localhost
>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>             Finally I got "Installation complete" message.
> 5) Then executed following command
>      5.1) $ sudo service apache2 reload
> 6) Then I tried in firefox, http://localhost. The page was blank.
>
> Can you please guide me in resolving this issue.
>
> Cheers,
> Ram
>
>
>
>
> _______________________________________________ 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 christine.rogers at mcgill.ca  Fri Dec  4 17:37:45 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 4 Dec 2015 17:37:45 -0500
Subject: [Loris-dev] LORIS data model/schema
In-Reply-To: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
References: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
Message-ID: <CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>

Hello,
Thank you for your questions.
1) We don't presently have a freely available example dataset that can be
loaded to simulate a complete LORIS project.  We may be interested in
providing this in future, and will keep this suggestion in mind.

2) The similarities between Debian and Ubuntu should indicate success for a
Debian installation, but we don't at present have any specific
implementation that can provide detailed guidance.  Perhaps someone in the
user community has some input?

Best,
Christine

On Thu, Dec 3, 2015 at 3:13 PM, Rachad El-Badrawi <
relbadrawi at indocresearch.org> wrote:

> Hi All,
>
>
>
> 1) I was wondering if there is a comprehensive freely available
> project/study that uses LORIS, that can be used to show how the different
> tables/fields in the LORIS schema are used. I am basically looking for a
> MySQL dump that represents that study which I can upload into a MySQL
> instance that I have.
>
>
>
> 2) Anyone had 'complete' success in installing LORIS on a Linux - Debian
> (VM). If so, please share any tips.
>
>
>
> Thanks for the feedback.
>
>
>
> Regards,
>
> Rashad Badrawi
>
>
>
> _______________________________________________
> 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
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From samirdas99 at gmail.com  Sun Dec  6 12:51:26 2015
From: samirdas99 at gmail.com (Samir Das)
Date: Sun, 6 Dec 2015 12:51:26 -0500
Subject: [Loris-dev] LORIS data model/schema
In-Reply-To: <CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>
References: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
	<CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>
Message-ID: <CAF6xo=MkH=XDScnQGcLXG2QOwLf8i2RQKsdNqtkJCYC_cX6Ddg@mail.gmail.com>

Hi Rachad,

We used to install LORIS on Debian, but it should work the same as the
Ubuntu install. Let me know if you have some specific issues when
installing.

Cheers,

Samir Das

On Fri, Dec 4, 2015 at 5:37 PM, Christine Rogers <christine.rogers at mcgill.ca
> wrote:

> Hello,
> Thank you for your questions.
> 1) We don't presently have a freely available example dataset that can be
> loaded to simulate a complete LORIS project.  We may be interested in
> providing this in future, and will keep this suggestion in mind.
>
> 2) The similarities between Debian and Ubuntu should indicate success for
> a Debian installation, but we don't at present have any specific
> implementation that can provide detailed guidance.  Perhaps someone in the
> user community has some input?
>
> Best,
> Christine
>
> On Thu, Dec 3, 2015 at 3:13 PM, Rachad El-Badrawi <
> relbadrawi at indocresearch.org> wrote:
>
>> Hi All,
>>
>>
>>
>> 1) I was wondering if there is a comprehensive freely available
>> project/study that uses LORIS, that can be used to show how the different
>> tables/fields in the LORIS schema are used. I am basically looking for a
>> MySQL dump that represents that study which I can upload into a MySQL
>> instance that I have.
>>
>>
>>
>> 2) Anyone had 'complete' success in installing LORIS on a Linux - Debian
>> (VM). If so, please share any tips.
>>
>>
>>
>> Thanks for the feedback.
>>
>>
>>
>> Regards,
>>
>> Rashad Badrawi
>>
>>
>>
>> _______________________________________________
>> 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
> LORIS data systems | loris.ca
> McGill Centre for Integrative Neuroscience| MCIN.ca
> McConnell Brain Imaging Centre
> 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 relbadrawi at indocresearch.org  Mon Dec  7 13:00:46 2015
From: relbadrawi at indocresearch.org (Rachad El-Badrawi)
Date: Mon, 7 Dec 2015 13:00:46 -0500
Subject: [Loris-dev] LORIS data model/schema
In-Reply-To: <CAF6xo=MkH=XDScnQGcLXG2QOwLf8i2RQKsdNqtkJCYC_cX6Ddg@mail.gmail.com>
References: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
	<CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>
	<CAF6xo=MkH=XDScnQGcLXG2QOwLf8i2RQKsdNqtkJCYC_cX6Ddg@mail.gmail.com>
Message-ID: <33818018D901F648AE76005E1CC317340E80E8513C@exsrv01.oit.loc>

Hi Samir and Christine,

Thanks for your responses.

The Debian (Release 7.7, Wheezy) installation does go to completion, at least as far as the backend table creation, but it does choke at some points. Here are a couple of snapshots from the installation output, when running the install.sh script. :

....
Debian Linux distribution detected. We currently do not support this. Please manually set the permissions for user_uploads directory in
../modules/document_repository
....
./install.sh: line 446: composer: command not found
Debian Linux distribution detected. We currently do not support this. Please configure Apache manually.

So, obviously, the front end of the system was not automatically set. I did not have the chance, yet, to do this manually or to investigate the reason behind this.

Regards,
Rachad


From: Samir Das [mailto:samirdas99 at gmail.com]
Sent: December 6, 2015 12:51 PM
To: Christine Rogers
Cc: Rachad El-Badrawi; loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] LORIS data model/schema

Hi Rachad,

We used to install LORIS on Debian, but it should work the same as the Ubuntu install. Let me know if you have some specific issues when installing.

Cheers,

Samir Das

On Fri, Dec 4, 2015 at 5:37 PM, Christine Rogers <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
Hello,
Thank you for your questions.
1) We don't presently have a freely available example dataset that can be loaded to simulate a complete LORIS project.  We may be interested in providing this in future, and will keep this suggestion in mind.

2) The similarities between Debian and Ubuntu should indicate success for a Debian installation, but we don't at present have any specific implementation that can provide detailed guidance.  Perhaps someone in the user community has some input?

Best,
Christine

On Thu, Dec 3, 2015 at 3:13 PM, Rachad El-Badrawi <relbadrawi at indocresearch.org<mailto:relbadrawi at indocresearch.org>> wrote:
Hi All,

1) I was wondering if there is a comprehensive freely available project/study that uses LORIS, that can be used to show how the different tables/fields in the LORIS schema are used. I am basically looking for a MySQL dump that represents that study which I can upload into a MySQL instance that I have.

2) Anyone had 'complete' success in installing LORIS on a Linux - Debian (VM). If so, please share any tips.

Thanks for the feedback.

Regards,
Rashad Badrawi


_______________________________________________
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>
LORIS data systems | loris.ca<http://loris.ca>
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
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 ramanandan.prabhakaran at gmail.com  Mon Dec  7 15:37:36 2015
From: ramanandan.prabhakaran at gmail.com (Ramanandan Prabhakaran)
Date: Mon, 7 Dec 2015 15:37:36 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
	<BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>
	<CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>
Message-ID: <CA+5uKGGQvvCtxwoSNztedTi4Jcs+2ty6hMB122Gba9FRTqH-ow@mail.gmail.com>

Dear Dave,

I tried executing the .install.sh script again. This time from the first. I
received a message " Installation Complete".

But I noticed following message as well "ln: failed to create symbolic link
?/etc/apache2/sites-enabled/emr.conf?: File exists".

Then I executed this command " sudo service apache2 reload". I received a
message "* Reloading web server apache2".

Finally, I tried accessing the http://localhost. The webpage is blank, I
couldn't see any LORIS core database.

Kindly, let me know where I am missing. I have attached the installation
log file for your reference.

Settings for database:
Enter project name: *emr*
What is the database name? *emrdb*
Database host?* localhost*
What MySQL user will LORIS connect as? (Recommended: lorisuser*)emruser*
What is the host from which MySQL user 'emruser' will connect? (Where
Loris' Apache is hosted)*localhost*
Choose a password for MySQL user 'emruser'?
Re-enter the password to check for accuracy:
Choose a different password for the front-end LORIS 'admin' user account:
Re-enter the password to check for accuracy:
Existing root or admin-level MySQL username:* root*
MySQL password for user 'root':
Re-enter the password to check for accuracy:



Cheers,
Ram

On Fri, Dec 4, 2015 at 3:58 PM, Ramanandan Prabhakaran <
ramanandan.prabhakaran at gmail.com> wrote:

> Dear Dave,
>
> Thanks for getting me back to me on my query. Yeah now, it recongized the
> .json file.
>
> emradmin at jsn-HP-Pavilion-g6-1c33ca:*/var/www/emr*$ composer install
> --no-dev
> Loading composer repositories with package information
> Installing dependencies from lock file
>   - Installing pear-pear.php.net/benchmark (1.2.9)
>     Downloading: 100%
>
>
>   [Composer\Downloader\TransportException]
>
>   The "https://pear.php.net/get/Benchmark-1.2.9.tgz" file could not be
> downloaded (HTTP/1.1 404 Not Found)
>
>
> install [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev]
> [--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts]
> [--no-progress] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader]
> [-a|--classmap-authoritative] [--ignore-platform-reqs] [--] [<packages>]...
>
> emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$
>
> Cheers,
> Ram
>
> On Fri, Dec 4, 2015 at 3:27 PM, Dave MacFarlane <
> david.macfarlane2 at mcgill.ca> wrote:
>
>> Hi Ramanandan,
>>
>> 1. Smarty is installed from composer, you don't need to apt-get install
>> it anymore as of Release 15.10
>> 2. You need to run "composer install --no-dev" from the LORIS directory,
>> not your home directory, which
>>     is why it can't find composer.json
>> 3. The PHP/PEAR package repository (pear.php.net) had some downtime and the
>> install script couldn't
>>   retrieve dependencies (such as the Benchmark library). Can you try
>> running "composer install --no-dev"
>>  (from the LORIS directory) and see if it works now? They seem to be
>> partially back up, but I'm not sure if all
>>  their packages are restored yet..
>>
>>
>> -- Dave
>>
>>
>> ------------------------------
>> Date: Fri, 4 Dec 2015 13:11:10 -0500
>> From: ramanandan.prabhakaran at gmail.com
>> To: loris-dev at bic.mni.mcgill.ca
>> Subject: [Loris-dev] Regarding Loris installation
>>
>>
>> Dear
>> ?Loris developers
>> ,
>>
>> I tried installing the LORIS from Github in ubuntu.
>>
>> As per the installation section, I performed following things
>> 1) C
>> ?reated
>>  LINUX user (emruser) and created EMR base directory.
>> 2) Downloaded the LORIS file from rel
>> ?e?
>> ase section and extracted it to "/var/www/emr"
>> 3) Then I installed following dependencies (Smarty3 and Composer)
>>     3.1) Installing smarty3
>>            $ sudo apt-get install smarty3
>>     3.2) Installing composer
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
>> https://getcomposer.org/installer | php;
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
>> /usr/local/bin/composer
>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>>            *Composer could not find a composer.json file in
>> /home/emradmin*
>> *           To initialize a project, please create a composer.json file
>> as described in the https://getcomposer.org/ <https://getcomposer.org/>
>> "Getting Started" section*
>> 4) Then moved to following directory path
>>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>>
>>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>>             LORIS installation Script starting at 2015-12-04 (Attached
>> the installation log file)
>>             Project name  : emr
>>             Database name : emrdb
>>             Database host : localhost
>>             MySQL user  (recommended lorisuser): emruser
>>             Where Loris' apache is hosted: localhost
>>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>>             Finally I got "Installation complete" message.
>> 5) Then executed following command
>>      5.1) $ sudo service apache2 reload
>> 6) Then I tried in firefox, http://localhost. The page was blank.
>>
>> Can you please guide me in resolving this issue.
>>
>> Cheers,
>> Ram
>>
>>
>>
>>
>> _______________________________________________ Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
>
>
>
>


-- 

*Cheers,*
*Ram*
*613-400-8890*
*ramanandan.prabhakaran at gmail.com* <ramanandan.prabhakaran at gmail.com>
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From samirdas99 at gmail.com  Wed Dec  9 12:57:03 2015
From: samirdas99 at gmail.com (Samir Das)
Date: Wed, 9 Dec 2015 12:57:03 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CA+5uKGGQvvCtxwoSNztedTi4Jcs+2ty6hMB122Gba9FRTqH-ow@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
	<BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>
	<CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>
	<CA+5uKGGQvvCtxwoSNztedTi4Jcs+2ty6hMB122Gba9FRTqH-ow@mail.gmail.com>
Message-ID: <CAF6xo=PXtdTL=jR19k0DAexStJ1spBbF-2NmEg1amTfihTMAbw@mail.gmail.com>

Hi Ram,

Can you send your Apache log? I wonder if this is a permission issue, or
some other kind of Apache error. You are installing this with sudo
permissions?

Thanks,

Samir Das

On Mon, Dec 7, 2015 at 3:37 PM, Ramanandan Prabhakaran <
ramanandan.prabhakaran at gmail.com> wrote:

> Dear Dave,
>
> I tried executing the .install.sh script again. This time from the first.
> I received a message " Installation Complete".
>
> But I noticed following message as well "ln: failed to create symbolic
> link ?/etc/apache2/sites-enabled/emr.conf?: File exists".
>
> Then I executed this command " sudo service apache2 reload". I received a
> message "* Reloading web server apache2".
>
> Finally, I tried accessing the http://localhost. The webpage is blank, I
> couldn't see any LORIS core database.
>
> Kindly, let me know where I am missing. I have attached the installation
> log file for your reference.
>
> Settings for database:
> Enter project name: *emr*
> What is the database name? *emrdb*
> Database host?* localhost*
> What MySQL user will LORIS connect as? (Recommended: lorisuser*)emruser*
> What is the host from which MySQL user 'emruser' will connect? (Where
> Loris' Apache is hosted)*localhost*
> Choose a password for MySQL user 'emruser'?
> Re-enter the password to check for accuracy:
> Choose a different password for the front-end LORIS 'admin' user account:
> Re-enter the password to check for accuracy:
> Existing root or admin-level MySQL username:* root*
> MySQL password for user 'root':
> Re-enter the password to check for accuracy:
>
>
>
> Cheers,
> Ram
>
> On Fri, Dec 4, 2015 at 3:58 PM, Ramanandan Prabhakaran <
> ramanandan.prabhakaran at gmail.com> wrote:
>
>> Dear Dave,
>>
>> Thanks for getting me back to me on my query. Yeah now, it recongized the
>> .json file.
>>
>> emradmin at jsn-HP-Pavilion-g6-1c33ca:*/var/www/emr*$ composer install
>> --no-dev
>> Loading composer repositories with package information
>> Installing dependencies from lock file
>>   - Installing pear-pear.php.net/benchmark (1.2.9)
>>     Downloading: 100%
>>
>>
>>   [Composer\Downloader\TransportException]
>>
>>   The "https://pear.php.net/get/Benchmark-1.2.9.tgz" file could not be
>> downloaded (HTTP/1.1 404 Not Found)
>>
>>
>> install [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev]
>> [--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts]
>> [--no-progress] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader]
>> [-a|--classmap-authoritative] [--ignore-platform-reqs] [--] [<packages>]...
>>
>> emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$
>>
>> Cheers,
>> Ram
>>
>> On Fri, Dec 4, 2015 at 3:27 PM, Dave MacFarlane <
>> david.macfarlane2 at mcgill.ca> wrote:
>>
>>> Hi Ramanandan,
>>>
>>> 1. Smarty is installed from composer, you don't need to apt-get install
>>> it anymore as of Release 15.10
>>> 2. You need to run "composer install --no-dev" from the LORIS directory,
>>> not your home directory, which
>>>     is why it can't find composer.json
>>> 3. The PHP/PEAR package repository (pear.php.net) had some downtime and the
>>> install script couldn't
>>>   retrieve dependencies (such as the Benchmark library). Can you try
>>> running "composer install --no-dev"
>>>  (from the LORIS directory) and see if it works now? They seem to be
>>> partially back up, but I'm not sure if all
>>>  their packages are restored yet..
>>>
>>>
>>> -- Dave
>>>
>>>
>>> ------------------------------
>>> Date: Fri, 4 Dec 2015 13:11:10 -0500
>>> From: ramanandan.prabhakaran at gmail.com
>>> To: loris-dev at bic.mni.mcgill.ca
>>> Subject: [Loris-dev] Regarding Loris installation
>>>
>>>
>>> Dear
>>> ?Loris developers
>>> ,
>>>
>>> I tried installing the LORIS from Github in ubuntu.
>>>
>>> As per the installation section, I performed following things
>>> 1) C
>>> ?reated
>>>  LINUX user (emruser) and created EMR base directory.
>>> 2) Downloaded the LORIS file from rel
>>> ?e?
>>> ase section and extracted it to "/var/www/emr"
>>> 3) Then I installed following dependencies (Smarty3 and Composer)
>>>     3.1) Installing smarty3
>>>            $ sudo apt-get install smarty3
>>>     3.2) Installing composer
>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
>>> https://getcomposer.org/installer | php;
>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
>>> /usr/local/bin/composer
>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>>>            *Composer could not find a composer.json file in
>>> /home/emradmin*
>>> *           To initialize a project, please create a composer.json file
>>> as described in the https://getcomposer.org/ <https://getcomposer.org/>
>>> "Getting Started" section*
>>> 4) Then moved to following directory path
>>>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>>>
>>>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>>>             LORIS installation Script starting at 2015-12-04 (Attached
>>> the installation log file)
>>>             Project name  : emr
>>>             Database name : emrdb
>>>             Database host : localhost
>>>             MySQL user  (recommended lorisuser): emruser
>>>             Where Loris' apache is hosted: localhost
>>>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>>>             Finally I got "Installation complete" message.
>>> 5) Then executed following command
>>>      5.1) $ sudo service apache2 reload
>>> 6) Then I tried in firefox, http://localhost. The page was blank.
>>>
>>> Can you please guide me in resolving this issue.
>>>
>>> Cheers,
>>> Ram
>>>
>>>
>>>
>>>
>>> _______________________________________________ Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>
>>
>>
>>
>>
>
>
> --
>
> *Cheers,*
> *Ram*
> *613-400-8890*
> *ramanandan.prabhakaran at gmail.com* <ramanandan.prabhakaran at gmail.com>
>
> _______________________________________________
> 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 ramanandan.prabhakaran at gmail.com  Wed Dec  9 14:06:44 2015
From: ramanandan.prabhakaran at gmail.com (Ramanandan Prabhakaran)
Date: Wed, 9 Dec 2015 14:06:44 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CAF6xo=PXtdTL=jR19k0DAexStJ1spBbF-2NmEg1amTfihTMAbw@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>
	<BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>
	<CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>
	<CA+5uKGGQvvCtxwoSNztedTi4Jcs+2ty6hMB122Gba9FRTqH-ow@mail.gmail.com>
	<CAF6xo=PXtdTL=jR19k0DAexStJ1spBbF-2NmEg1amTfihTMAbw@mail.gmail.com>
Message-ID: <CA+5uKGHCrY5OC4VYuoETgwfPR2-SqigG3FzXeYGE8mpMEACfLw@mail.gmail.com>

Dear Samir,

Please find attached the apache log files.

As per the following GitHub installation procedure ",Set up LINUX user
lorisadmin and create LORIS base directory"

sudo useradd -U -m -G sudo -s /bin/bash *emradmin*
sudo passwd *emradmin*
su - *emradmin*

sudo mkdir -m 775 -p /var/www/emr
sudo chown emradmin.emradmin /var/www/emr

Using this emradmin user, I have carried out the LORIS installation.

Cheers,
Ram
?
 access.log
<https://drive.google.com/file/d/0BwZhtRmLZFgIVDZjTGNHT1JHNEk/view?usp=drive_web>
??
 emr-access.log
<https://drive.google.com/file/d/0BwZhtRmLZFgIMFVNaF8tZEdNVEU/view?usp=drive_web>
??
 emr-error.log
<https://drive.google.com/file/d/0BwZhtRmLZFgIaDBPbVdtRFNlZWs/view?usp=drive_web>
??
 error.log
<https://drive.google.com/file/d/0BwZhtRmLZFgISk5iWDlzNmV4ck0/view?usp=drive_web>
??
 other_vhosts_access.log
<https://drive.google.com/file/d/0BwZhtRmLZFgIdzdQUTJCa3FnMVE/view?usp=drive_web>
?

On Wed, Dec 9, 2015 at 12:57 PM, Samir Das <samirdas99 at gmail.com> wrote:

> Hi Ram,
>
> Can you send your Apache log? I wonder if this is a permission issue, or
> some other kind of Apache error. You are installing this with sudo
> permissions?
>
> Thanks,
>
> Samir Das
>
> On Mon, Dec 7, 2015 at 3:37 PM, Ramanandan Prabhakaran <
> ramanandan.prabhakaran at gmail.com> wrote:
>
>> Dear Dave,
>>
>> I tried executing the .install.sh script again. This time from the first.
>> I received a message " Installation Complete".
>>
>> But I noticed following message as well "ln: failed to create symbolic
>> link ?/etc/apache2/sites-enabled/emr.conf?: File exists".
>>
>> Then I executed this command " sudo service apache2 reload". I received a
>> message "* Reloading web server apache2".
>>
>> Finally, I tried accessing the http://localhost. The webpage is blank, I
>> couldn't see any LORIS core database.
>>
>> Kindly, let me know where I am missing. I have attached the installation
>> log file for your reference.
>>
>> Settings for database:
>> Enter project name: *emr*
>> What is the database name? *emrdb*
>> Database host?* localhost*
>> What MySQL user will LORIS connect as? (Recommended: lorisuser*)emruser*
>> What is the host from which MySQL user 'emruser' will connect? (Where
>> Loris' Apache is hosted)*localhost*
>> Choose a password for MySQL user 'emruser'?
>> Re-enter the password to check for accuracy:
>> Choose a different password for the front-end LORIS 'admin' user account:
>> Re-enter the password to check for accuracy:
>> Existing root or admin-level MySQL username:* root*
>> MySQL password for user 'root':
>> Re-enter the password to check for accuracy:
>>
>>
>>
>> Cheers,
>> Ram
>>
>> On Fri, Dec 4, 2015 at 3:58 PM, Ramanandan Prabhakaran <
>> ramanandan.prabhakaran at gmail.com> wrote:
>>
>>> Dear Dave,
>>>
>>> Thanks for getting me back to me on my query. Yeah now, it recongized
>>> the .json file.
>>>
>>> emradmin at jsn-HP-Pavilion-g6-1c33ca:*/var/www/emr*$ composer install
>>> --no-dev
>>> Loading composer repositories with package information
>>> Installing dependencies from lock file
>>>   - Installing pear-pear.php.net/benchmark (1.2.9)
>>>     Downloading: 100%
>>>
>>>
>>>   [Composer\Downloader\TransportException]
>>>
>>>   The "https://pear.php.net/get/Benchmark-1.2.9.tgz" file could not be
>>> downloaded (HTTP/1.1 404 Not Found)
>>>
>>>
>>> install [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev]
>>> [--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts]
>>> [--no-progress] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader]
>>> [-a|--classmap-authoritative] [--ignore-platform-reqs] [--] [<packages>]...
>>>
>>> emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$
>>>
>>> Cheers,
>>> Ram
>>>
>>> On Fri, Dec 4, 2015 at 3:27 PM, Dave MacFarlane <
>>> david.macfarlane2 at mcgill.ca> wrote:
>>>
>>>> Hi Ramanandan,
>>>>
>>>> 1. Smarty is installed from composer, you don't need to apt-get install
>>>> it anymore as of Release 15.10
>>>> 2. You need to run "composer install --no-dev" from the LORIS
>>>> directory, not your home directory, which
>>>>     is why it can't find composer.json
>>>> 3. The PHP/PEAR package repository (pear.php.net) had some downtime
>>>> and the install script couldn't
>>>>   retrieve dependencies (such as the Benchmark library). Can you try
>>>> running "composer install --no-dev"
>>>>  (from the LORIS directory) and see if it works now? They seem to be
>>>> partially back up, but I'm not sure if all
>>>>  their packages are restored yet..
>>>>
>>>>
>>>> -- Dave
>>>>
>>>>
>>>> ------------------------------
>>>> Date: Fri, 4 Dec 2015 13:11:10 -0500
>>>> From: ramanandan.prabhakaran at gmail.com
>>>> To: loris-dev at bic.mni.mcgill.ca
>>>> Subject: [Loris-dev] Regarding Loris installation
>>>>
>>>>
>>>> Dear
>>>> ?Loris developers
>>>> ,
>>>>
>>>> I tried installing the LORIS from Github in ubuntu.
>>>>
>>>> As per the installation section, I performed following things
>>>> 1) C
>>>> ?reated
>>>>  LINUX user (emruser) and created EMR base directory.
>>>> 2) Downloaded the LORIS file from rel
>>>> ?e?
>>>> ase section and extracted it to "/var/www/emr"
>>>> 3) Then I installed following dependencies (Smarty3 and Composer)
>>>>     3.1) Installing smarty3
>>>>            $ sudo apt-get install smarty3
>>>>     3.2) Installing composer
>>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS
>>>> https://getcomposer.org/installer | php;
>>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar
>>>> /usr/local/bin/composer
>>>>            emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install
>>>>            *Composer could not find a composer.json file in
>>>> /home/emradmin*
>>>> *           To initialize a project, please create a composer.json file
>>>> as described in the https://getcomposer.org/ <https://getcomposer.org/>
>>>> "Getting Started" section*
>>>> 4) Then moved to following directory path
>>>>      4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools
>>>>
>>>>      4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh
>>>>             LORIS installation Script starting at 2015-12-04 (Attached
>>>> the installation log file)
>>>>             Project name  : emr
>>>>             Database name : emrdb
>>>>             Database host : localhost
>>>>             MySQL user  (recommended lorisuser): emruser
>>>>             Where Loris' apache is hosted: localhost
>>>>             *But Benchmarj-1.2.9.tgz file could not be downloaded.*
>>>>             Finally I got "Installation complete" message.
>>>> 5) Then executed following command
>>>>      5.1) $ sudo service apache2 reload
>>>> 6) Then I tried in firefox, http://localhost. The page was blank.
>>>>
>>>> Can you please guide me in resolving this issue.
>>>>
>>>> Cheers,
>>>> Ram
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________ 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
>>
>>
>
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From david.macfarlane2 at mcgill.ca  Wed Dec  9 14:56:13 2015
From: david.macfarlane2 at mcgill.ca (Dave MacFarlane)
Date: Wed, 9 Dec 2015 14:56:13 -0500
Subject: [Loris-dev] Regarding Loris installation
In-Reply-To: <CA+5uKGHCrY5OC4VYuoETgwfPR2-SqigG3FzXeYGE8mpMEACfLw@mail.gmail.com>
References: <CA+5uKGHDh_PcDgCuUy95RPuP+=OPVwKf7aO2tEQxc7fZv_HLRw@mail.gmail.com>,
	<BAY182-W8594FFE35806B5C4147C81F80C0@phx.gbl>,
	<CA+5uKGFEH0Tbb5eN4+HT7LGiLLrFLERrk7mQLNBSGQ2s=uQAEQ@mail.gmail.com>,
	<CA+5uKGGQvvCtxwoSNztedTi4Jcs+2ty6hMB122Gba9FRTqH-ow@mail.gmail.com>,
	<CAF6xo=PXtdTL=jR19k0DAexStJ1spBbF-2NmEg1amTfihTMAbw@mail.gmail.com>,
	<CA+5uKGHCrY5OC4VYuoETgwfPR2-SqigG3FzXeYGE8mpMEACfLw@mail.gmail.com>
Message-ID: <BAY182-W490D917B9DE09194C1F4C4F8E80@phx.gbl>

Hi Ramanandan,
It looks like you don't have PEAR installed, which is a prerequisite for LORIS. Please makesure you have all the prerequisites at the start of the LORIS README installed. (The bracketsgive the package name that needs to be installed on Ubuntu. In this case, you should run"sudo apt-get install php-pear".. but all the other prerequisites need to also be present beforeLORIS will run.)
- Dave
Date: Wed, 9 Dec 2015 14:06:44 -0500
From: ramanandan.prabhakaran at gmail.com
To: samirdas99 at gmail.com
CC: loris-dev at bic.mni.mcgill.ca; david.macfarlane2 at mcgill.ca
Subject: Re: [Loris-dev] Regarding Loris installation

Dear Samir,

Please find attached the apache log files.

As per the following GitHub installation procedure ",Set up LINUX user lorisadmin and create LORIS base directory"
sudo useradd -U -m -G sudo -s /bin/bash emradminsudo passwd emradminsu - emradmin
sudo mkdir -m 775 -p /var/www/emrsudo chown emradmin.emradmin /var/www/emr
Using this emradmin user, I have carried out the LORIS installation.
Cheers,Ram?
 access.log??
 emr-access.log??
 emr-error.log??
 error.log??
 other_vhosts_access.log?

On Wed, Dec 9, 2015 at 12:57 PM, Samir Das <samirdas99 at gmail.com> wrote:
Hi Ram,
Can you send your Apache log? I wonder if this is a permission issue, or some other kind of Apache error. You are installing this with sudo permissions?
Thanks,
Samir Das
On Mon, Dec 7, 2015 at 3:37 PM, Ramanandan Prabhakaran <ramanandan.prabhakaran at gmail.com> wrote:
Dear Dave,

I tried executing the .install.sh script again. This time from the first. I received a message " Installation Complete".

But I noticed following message as well "ln: failed to create symbolic link ?/etc/apache2/sites-enabled/emr.conf?: File exists".

Then I executed this command " sudo service apache2 reload". I received a message "* Reloading web server apache2".

Finally, I tried accessing the http://localhost. The webpage is blank, I couldn't see any LORIS core database.

Kindly, let me know where I am missing. I have attached the installation log file for your reference. 

Settings for database:
Enter project name: emr
What is the database name? emrdb
Database host? localhost
What MySQL user will LORIS connect as? (Recommended: lorisuser)emruser
What is the host from which MySQL user 'emruser' will connect? (Where Loris' Apache is hosted)localhost
Choose a password for MySQL user 'emruser'? 
Re-enter the password to check for accuracy: 
Choose a different password for the front-end LORIS 'admin' user account: 
Re-enter the password to check for accuracy: 
Existing root or admin-level MySQL username: root
MySQL password for user 'root': 
Re-enter the password to check for accuracy: 



Cheers,
Ram

On Fri, Dec 4, 2015 at 3:58 PM, Ramanandan Prabhakaran <ramanandan.prabhakaran at gmail.com> wrote:
Dear Dave,
Thanks for getting me back to me on my query. Yeah now, it recongized the .json file.
emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$ composer install --no-devLoading composer repositories with package informationInstalling dependencies from lock file  - Installing pear-pear.php.net/benchmark (1.2.9)    Downloading: 100%                                                                                                                  
  [Composer\Downloader\TransportException]                                                                    The "https://pear.php.net/get/Benchmark-1.2.9.tgz" file could not be downloaded (HTTP/1.1 404 Not Found)                                                                                                              install [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev] [--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts] [--no-progress] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader] [-a|--classmap-authoritative] [--ignore-platform-reqs] [--] [<packages>]...
emradmin at jsn-HP-Pavilion-g6-1c33ca:/var/www/emr$
Cheers,Ram
On Fri, Dec 4, 2015 at 3:27 PM, Dave MacFarlane <david.macfarlane2 at mcgill.ca> wrote:



Hi Ramanandan,
1. Smarty is installed from composer, you don't need to apt-get install it anymore as of Release 15.102. You need to run "composer install --no-dev" from the LORIS directory, not your home directory, which    is why it can't find composer.json3. The PHP/PEAR package repository (pear.php.net) had some downtime and the install script couldn't   retrieve dependencies (such as the Benchmark library). Can you try running "composer install --no-dev"  (from the LORIS directory) and see if it works now? They seem to be partially back up, but I'm not sure if all  their packages are restored yet..

-- Dave

Date: Fri, 4 Dec 2015 13:11:10 -0500
From: ramanandan.prabhakaran at gmail.com
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Regarding Loris installation

Dear ?Loris developers,

I tried installing the LORIS from Github in ubuntu.
As per the installation section, I performed following things1) C?reated LINUX user (emruser) and created EMR base directory.2) Downloaded the LORIS file from rel?e?ase section and extracted it to "/var/www/emr"3) Then I installed following dependencies (Smarty3 and Composer)    3.1) Installing smarty3           $ sudo apt-get install smarty3    3.2) Installing composer           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ curl -sS https://getcomposer.org/installer | php;           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ sudo mv composer.phar /usr/local/bin/composer           emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ composer install           Composer could not find a composer.json file in /home/emradmin           To initialize a project, please create a composer.json file as described in the https://getcomposer.org/ "Getting Started" section4) Then moved to following directory path     4.1) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ cd /var/www/emr/tools               4.2) emradmin at jsn-HP-Pavilion-g6-1c33ca:~$ ./install.sh            LORIS installation Script starting at 2015-12-04 (Attached the installation log file)            Project name  : emr            Database name : emrdb            Database host : localhost            MySQL user  (recommended lorisuser): emruser            Where Loris' apache is hosted: localhost            But Benchmarj-1.2.9.tgz file could not be downloaded.            Finally I got "Installation complete" message.5) Then executed following command     5.1) $ sudo service apache2 reload6) Then I tried in firefox, http://localhost. The page was blank.
Can you please guide me in resolving this issue.
Cheers,Ram        




_______________________________________________
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









_______________________________________________
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 frank1987lee1987 at gmail.com  Wed Dec  9 16:31:34 2015
From: frank1987lee1987 at gmail.com (Frank Leman)
Date: Wed, 9 Dec 2015 16:31:34 -0500
Subject: [Loris-dev] how to upload data into LORIS
Message-ID: <CALb=YUwSEVYBB_TM-_+Cxq4vtjKA0QFuqXNh4GWkjmoowuR1Kg@mail.gmail.com>

Hello David,

I am currently using LORIS database architecture for my application. I
followed the instructions and installed LORIS in ubuntu as suggested.

Through localhost, I am able to access LORIS's main.php.

I am interested in using SNP under Genomic Browser. I have few doubts,

Where to create initial patients data?
Where to link the patient information with clinical data (variants)?
How to  upload the information into SNP for some patients?
Can I add or delete columns in existing tables?


Best,
Frank
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From waveflux at gmail.com  Thu Dec 10 11:52:22 2015
From: waveflux at gmail.com (Tom Beaudry)
Date: Thu, 10 Dec 2015 11:52:22 -0500
Subject: [Loris-dev] dyanmic instrument
Message-ID: <CALzz+FMFdE=WJ2-7OFiwjqvg+dSJhZTSbEVMVOvwiVyRqPgiuw@mail.gmail.com>

Hi everyone,

Just out of curiosity has anyone made a dynamic instrument before (i.e.
with a button that allows you to add more text fields).  I can imagine a
number of reasons why this wouldn't work with LORIS architecture, but maybe
someone has figured out a workaround (idk have a script that writes all of
the text fields to one variable when the user clicks save).

Anyways, I thought I would ask,
Tom
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From christine.rogers at mcgill.ca  Thu Dec 10 18:05:41 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Thu, 10 Dec 2015 18:05:41 -0500
Subject: [Loris-dev] how to upload data into LORIS
In-Reply-To: <CALb=YUwSEVYBB_TM-_+Cxq4vtjKA0QFuqXNh4GWkjmoowuR1Kg@mail.gmail.com>
References: <CALb=YUwSEVYBB_TM-_+Cxq4vtjKA0QFuqXNh4GWkjmoowuR1Kg@mail.gmail.com>
Message-ID: <CALbt7NBbDyejkXQDe_0uC5EdSan6n40+O8imy3on396ridS9NA@mail.gmail.com>

Hi Frank,
I'm responding to your email on behalf of the Loris team.

Patient profiles can be created in Loris by clicking on the Candidate menu,
and then clicking on "New Profile" to register a new patient (candidate)
profile.

Patient information (stored in the candidate database table) is linked to
the SNP database table through a common patient ID field called CandID,
which currently appears in both tables.

SNP data can be loaded directly into database tables;  we are working on
certain kinds of genomic uploader functionality for future releases.

In the front-end data table views, columns can be added or removed from
view through the php (and smarty template) code.  Columns can be added to
or deleted from database tables through the MySQL back-end.

Best,
Christine
-- 
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada

On Wed, Dec 9, 2015 at 4:31 PM, Frank Leman <frank1987lee1987 at gmail.com>
wrote:

> Hello David,
>
> I am currently using LORIS database architecture for my application. I
> followed the instructions and installed LORIS in ubuntu as suggested.
>
> Through localhost, I am able to access LORIS's main.php.
>
> I am interested in using SNP under Genomic Browser. I have few doubts,
>
> Where to create initial patients data?
> Where to link the patient information with clinical data (variants)?
> How to  upload the information into SNP for some patients?
> Can I add or delete columns in existing tables?
>
>
> Best,
> Frank
>
> _______________________________________________
> 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 christine.rogers at mcgill.ca  Thu Dec 10 18:19:08 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Thu, 10 Dec 2015 18:19:08 -0500
Subject: [Loris-dev] LORIS data model/schema
In-Reply-To: <33818018D901F648AE76005E1CC317340E80E8513C@exsrv01.oit.loc>
References: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
	<CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>
	<CAF6xo=MkH=XDScnQGcLXG2QOwLf8i2RQKsdNqtkJCYC_cX6Ddg@mail.gmail.com>
	<33818018D901F648AE76005E1CC317340E80E8513C@exsrv01.oit.loc>
Message-ID: <CALbt7NC95nA30KMD44_n__GUjC7scziykoB2o8OgMFJ+o3F4QA@mail.gmail.com>

Hi Rachad,

There are a few steps which the Install script did not complete for you
because it didn't explicitly detect an Ubuntu (or CentOS) OS running.
These steps will likely work for Debian when copied from the install script
(with appropriate values populated) and manually run, for the following
steps:

- Installing composer - line 82 in tools/install.sh :
cd /var/www/loris/tools
curl -sS https://getcomposer.org/installer | php
mv composer.phar ../composer
cd /var/www/loris/
./composer install --no-dev

- Setting directory permissions:
e.g. line 193: sudo chown www-data.www-data
../modules/document_repository/user_uploads
and 206: sudo chgrp www-data logs

- Configuring Apache: line 450+

Troubleshooting this by checking the messages you saw from your install
script log is a great place to start.
Best,
Christine

--
christine.rogers at mcgill.ca
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada


On Mon, Dec 7, 2015 at 1:00 PM, Rachad El-Badrawi <
relbadrawi at indocresearch.org> wrote:
>
> Hi Samir and Christine,
>
>
>
> Thanks for your responses.
>
>
>
> The Debian (Release 7.7, Wheezy) installation does go to completion, at
least as far as the backend table creation, but it does choke at some
points. Here are a couple of snapshots from the installation output, when
running the install.sh script. :
>
>
>
> ....
>
> Debian Linux distribution detected. We currently do not support this.
Please manually set the permissions for user_uploads directory in
>
> ../modules/document_repository
>
> ....
>
> ./install.sh: line 446: composer: command not found
>
> Debian Linux distribution detected. We currently do not support this.
Please configure Apache manually.
>
>
>
> So, obviously, the front end of the system was not automatically set. I
did not have the chance, yet, to do this manually or to investigate the
reason behind this.
>
>
>
> Regards,
>
> Rachad
>
>
>
>
>
> From: Samir Das [mailto:samirdas99 at gmail.com]
> Sent: December 6, 2015 12:51 PM
> To: Christine Rogers
> Cc: Rachad El-Badrawi; loris-dev at bic.mni.mcgill.ca
> Subject: Re: [Loris-dev] LORIS data model/schema
>
>
>
> Hi Rachad,
>
>
>
> We used to install LORIS on Debian, but it should work the same as the
Ubuntu install. Let me know if you have some specific issues when
installing.
>
>
>
> Cheers,
>
>
>
> Samir Das
>
>
>
> On Fri, Dec 4, 2015 at 5:37 PM, Christine Rogers <
christine.rogers at mcgill.ca> wrote:
>
> Hello,
>
> Thank you for your questions.
>
> 1) We don't presently have a freely available example dataset that can be
loaded to simulate a complete LORIS project.  We may be interested in
providing this in future, and will keep this suggestion in mind.
>
>
>
> 2) The similarities between Debian and Ubuntu should indicate success for
a Debian installation, but we don't at present have any specific
implementation that can provide detailed guidance.  Perhaps someone in the
user community has some input?
>
>
>
> Best,
>
> Christine
>
>
>
> On Thu, Dec 3, 2015 at 3:13 PM, Rachad El-Badrawi <
relbadrawi at indocresearch.org> wrote:
>
> Hi All,
>
>
>
> 1) I was wondering if there is a comprehensive freely available
project/study that uses LORIS, that can be used to show how the different
tables/fields in the LORIS schema are used. I am basically looking for a
MySQL dump that represents that study which I can upload into a MySQL
instance that I have.
>
>
>
> 2) Anyone had 'complete' success in installing LORIS on a Linux - Debian
(VM). If so, please share any tips.
>
>
>
> Thanks for the feedback.
>
>
>
> Regards,
>
> Rashad Badrawi
>
>
>
>
>
> _______________________________________________
> 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
> LORIS data systems | loris.ca
> McGill Centre for Integrative Neuroscience| MCIN.ca
>
> McConnell Brain Imaging Centre
> 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
>
>
>
>
> ______________________________________________________________________
> This email has been scanned by the Symantec Email Security.cloud service.
> For more information please visit http://www.symanteccloud.com
> ______________________________________________________________________
>
>
> _______________________________________________
> 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 christine.rogers at mcgill.ca  Thu Dec 10 18:24:36 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Thu, 10 Dec 2015 18:24:36 -0500
Subject: [Loris-dev] dyanmic instrument
In-Reply-To: <CALzz+FMFdE=WJ2-7OFiwjqvg+dSJhZTSbEVMVOvwiVyRqPgiuw@mail.gmail.com>
References: <CALzz+FMFdE=WJ2-7OFiwjqvg+dSJhZTSbEVMVOvwiVyRqPgiuw@mail.gmail.com>
Message-ID: <CALbt7NCZjYLFHm=iV1J7-t-4QrZAbauAfZ4gGXA8ceR-+LkcpQ@mail.gmail.com>

Hi Tom,
Thanks for your question - Loris's current structure doesn't feature
dynamically expandable forms.
When it comes to form design, we do recommend including extra comment
(textarea) fields, and overestimating the allowable number of responses
(e.g. on a form where "medications taken" might be asked).
Best,
Christine

On Thu, Dec 10, 2015 at 11:52 AM, Tom Beaudry <waveflux at gmail.com> wrote:

> Hi everyone,
>
> Just out of curiosity has anyone made a dynamic instrument before (i.e.
> with a button that allows you to add more text fields).  I can imagine a
> number of reasons why this wouldn't work with LORIS architecture, but maybe
> someone has figured out a workaround (idk have a script that writes all of
> the text fields to one variable when the user clicks save).
>
> Anyways, I thought I would ask,
> Tom
>
> _______________________________________________
> 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
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From relbadrawi at indocresearch.org  Thu Dec 10 19:03:25 2015
From: relbadrawi at indocresearch.org (Rachad El-Badrawi)
Date: Thu, 10 Dec 2015 19:03:25 -0500
Subject: [Loris-dev] LORIS data model/schema
In-Reply-To: <CALbt7NC95nA30KMD44_n__GUjC7scziykoB2o8OgMFJ+o3F4QA@mail.gmail.com>
References: <33818018D901F648AE76005E1CC317340E80E84F07@exsrv01.oit.loc>
	<CALbt7NDBmdwy+-75avVJuFw1D0w1zXx5Cy69OgGTEmtJKyoZjQ@mail.gmail.com>
	<CAF6xo=MkH=XDScnQGcLXG2QOwLf8i2RQKsdNqtkJCYC_cX6Ddg@mail.gmail.com>
	<33818018D901F648AE76005E1CC317340E80E8513C@exsrv01.oit.loc>,
	<CALbt7NC95nA30KMD44_n__GUjC7scziykoB2o8OgMFJ+o3F4QA@mail.gmail.com>
Message-ID: <33818018D901F648AE76005E1CC317340E80B421CD@exsrv01.oit.loc>

Hi Christine, 

Thanks for your informative feedback. I did look into this earlier today, installing composer separately, with minor tweaks in the script. The Apache part is still broken, as I mentioned earlier. Anyway, my focus was on the back-end and the data model, so I wanted to ensure that gets setup appropriately. 

Thanks, 
Rashad Badrawi


________________________________________
From: Christine Rogers [christine.rogers at mcgill.ca]
Sent: Thursday, December 10, 2015 6:19 PM
To: Rachad El-Badrawi
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] LORIS data model/schema

Hi Rachad,

There are a few steps which the Install script did not complete for you because it didn't explicitly detect an Ubuntu (or CentOS) OS running.
These steps will likely work for Debian when copied from the install script (with appropriate values populated) and manually run, for the following steps:

- Installing composer - line 82 in tools/install.sh :
cd /var/www/loris/tools
curl -sS https://getcomposer.org/installer | php
mv composer.phar ../composer
cd /var/www/loris/
./composer install --no-dev

- Setting directory permissions:
e.g. line 193: sudo chown www-data.www-data ../modules/document_repository/user_uploads
and 206: sudo chgrp www-data logs

- Configuring Apache: line 450+

Troubleshooting this by checking the messages you saw from your install script log is a great place to start.
Best,
Christine

--
christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
LORIS data systems | loris.ca<http://loris.ca>
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada


On Mon, Dec 7, 2015 at 1:00 PM, Rachad El-Badrawi <relbadrawi at indocresearch.org<mailto:relbadrawi at indocresearch.org>> wrote:
>
> Hi Samir and Christine,
>
>
>
> Thanks for your responses.
>
>
>
> The Debian (Release 7.7, Wheezy) installation does go to completion, at least as far as the backend table creation, but it does choke at some points. Here are a couple of snapshots from the installation output, when running the install.sh script. :
>
>
>
> ....
>
> Debian Linux distribution detected. We currently do not support this. Please manually set the permissions for user_uploads directory in
>
> ../modules/document_repository
>
> ....
>
> ./install.sh: line 446: composer: command not found
>
> Debian Linux distribution detected. We currently do not support this. Please configure Apache manually.
>
>
>
> So, obviously, the front end of the system was not automatically set. I did not have the chance, yet, to do this manually or to investigate the reason behind this.
>
>
>
> Regards,
>
> Rachad
>
>
>
>
>
> From: Samir Das [mailto:samirdas99 at gmail.com<mailto:samirdas99 at gmail.com>]
> Sent: December 6, 2015 12:51 PM
> To: Christine Rogers
> Cc: Rachad El-Badrawi; loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
> Subject: Re: [Loris-dev] LORIS data model/schema
>
>
>
> Hi Rachad,
>
>
>
> We used to install LORIS on Debian, but it should work the same as the Ubuntu install. Let me know if you have some specific issues when installing.
>
>
>
> Cheers,
>
>
>
> Samir Das
>
>
>
> On Fri, Dec 4, 2015 at 5:37 PM, Christine Rogers <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
>
> Hello,
>
> Thank you for your questions.
>
> 1) We don't presently have a freely available example dataset that can be loaded to simulate a complete LORIS project.  We may be interested in providing this in future, and will keep this suggestion in mind.
>
>
>
> 2) The similarities between Debian and Ubuntu should indicate success for a Debian installation, but we don't at present have any specific implementation that can provide detailed guidance.  Perhaps someone in the user community has some input?
>
>
>
> Best,
>
> Christine
>
>
>
> On Thu, Dec 3, 2015 at 3:13 PM, Rachad El-Badrawi <relbadrawi at indocresearch.org<mailto:relbadrawi at indocresearch.org>> wrote:
>
> Hi All,
>
>
>
> 1) I was wondering if there is a comprehensive freely available project/study that uses LORIS, that can be used to show how the different tables/fields in the LORIS schema are used. I am basically looking for a MySQL dump that represents that study which I can upload into a MySQL instance that I have.
>
>
>
> 2) Anyone had 'complete' success in installing LORIS on a Linux - Debian (VM). If so, please share any tips.
>
>
>
> Thanks for the feedback.
>
>
>
> Regards,
>
> Rashad Badrawi
>
>