From AMORALESPINZON at bwh.harvard.edu  Fri Nov  3 11:36:53 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Fri, 3 Nov 2017 15:36:53 +0000
Subject: [Loris-dev] Installation MySQL in different sever
Message-ID: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>

Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to require a more advanced configuration of MySql that default installation your provide in the Loris GitHub. As I think you might have done this type of setups, I was wondering if you have some documentation that can help me with this configuration process.

Regards,
Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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From christine.rogers at mcgill.ca  Fri Nov  3 11:56:26 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 3 Nov 2017 11:56:26 -0400
Subject: [Loris-dev] Installation MySQL in different sever
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>
Message-ID: <CALbt7NCuFtH1mGmODQmHpkS_y2CU9n+TjEjyyC21WngAToMiHQ@mail.gmail.com>

Hi Alfredo,

Which operating system and packages are you working with?  Perhaps someone
in this dev community has experience with a similar configuration.
In general we don't have ready documentation on how to configure MySQL
specially for a given setup.

Are there any special error messages you're encountering upon installation?
  (I'm not sure if you had attached a screenshot in your message.)

Best,
Christine

---------- Forwarded message ----------
From: Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Date: Fri, Nov 3, 2017 at 11:36 AM
Subject: [Loris-dev] Installation MySQL in different sever
To: "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>


Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to
require a more advanced configuration of MySql that default installation
your provide in the Loris GitHub. As I think you might have done this type
of setups, I was wondering if you have some documentation that can help me
with this configuration process.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is

addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

_______________________________________________
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  Fri Nov  3 12:30:49 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Fri, 3 Nov 2017 16:30:49 +0000
Subject: [Loris-dev] Installation MySQL in different sever
In-Reply-To: <CALbt7NCuFtH1mGmODQmHpkS_y2CU9n+TjEjyyC21WngAToMiHQ@mail.gmail.com>
References: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>,
	<CALbt7NCuFtH1mGmODQmHpkS_y2CU9n+TjEjyyC21WngAToMiHQ@mail.gmail.com>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349EB082@PHSX10MB8.partners.org>

Hi Christine,

I am using Ubuntu 16.04 in both machines, LORIS and MySQL servers.

Currently I am in the step where I have to setup the MySql connection (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#running-the-install-script) . Before doing it I want to be sure that I can access MySql from the LORIS machine. I am starting to read about how to do it, but maybe someone has done it already and can point me to a post or has some insights.

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca]
Sent: Friday, November 03, 2017 11:56 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Installation MySQL in different sever

Hi Alfredo,

Which operating system and packages are you working with?  Perhaps someone in this dev community has experience with a similar configuration.
In general we don't have ready documentation on how to configure MySQL specially for a given setup.

Are there any special error messages you're encountering upon installation?   (I'm not sure if you had attached a screenshot in your message.)

Best,
Christine

---------- Forwarded message ----------
From: Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Date: Fri, Nov 3, 2017 at 11:36 AM
Subject: [Loris-dev] Installation MySQL in different sever
To: "loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>" <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>


Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to require a more advanced configuration of MySql that default installation your provide in the Loris GitHub. As I think you might have done this type of setups, I was wondering if you have some documentation that can help me with this configuration process.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is

addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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
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From david.macfarlane2 at mcgill.ca  Fri Nov  3 15:22:48 2017
From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr)
Date: Fri, 3 Nov 2017 19:22:48 +0000
Subject: [Loris-dev] Installation MySQL in different sever
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>
Message-ID: <YQXPR0101MB16722D4D032B9D9F0EA22CBDA85D0@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>

Hi Alfredo,


There should be nothing special from the LORIS side about configuring MySQL whether it's on the same server or not. LORIS doesn't do anything special with the host that it connects to and uses the standard PHP PDO objects.


Things to keep in mind are that:

  1.  MySQL accounts are tied to the domain that the account is connecting from, so just because you can connect locally doesn't mean your same credentials will work remotely
  2.  There may be firewalls between your servers blocking the MySQL port.
  3.  There may be some kind of security settings (ie SELinux or apparmor) set up by your sysadmin which further restrict connections (particularly from web servers.) that need to be relaxed.


The first thing to do is work with your sysadmin to make sure you can connect to MySQL from the command line on the same server/with the same credentials as your LORIS instance. If you can get that working, LORIS itself should work fine (unless the problem is 3, in which case you can test by temporarily disabling it and seeing if that fixes it..)


- Dave

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: November 3, 2017 11:36:53 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Installation MySQL in different sever

Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to require a more advanced configuration of MySql that default installation your provide in the Loris GitHub. As I think you might have done this type of setups, I was wondering if you have some documentation that can help me with this configuration process.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From AMORALESPINZON at bwh.harvard.edu  Fri Nov  3 16:13:09 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Fri, 3 Nov 2017 20:13:09 +0000
Subject: [Loris-dev] Installation MySQL in different sever
In-Reply-To: <YQXPR0101MB16722D4D032B9D9F0EA22CBDA85D0@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>
References: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>,
	<YQXPR0101MB16722D4D032B9D9F0EA22CBDA85D0@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349EB368@PHSX10MB8.partners.org>

Hi David,

Thank you for your answer. Indeed I am dealing with point 3, as I am not a sysadmin guy I was looking for some light! We are figuring it out with the BIC Admins. I will share what I will learn :)

Best,
Alfredo.
________________________________
From: David MacFarlane, Mr [david.macfarlane2 at mcgill.ca]
Sent: Friday, November 03, 2017 3:22 PM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Subject: Re: Installation MySQL in different sever


Hi Alfredo,


There should be nothing special from the LORIS side about configuring MySQL whether it's on the same server or not. LORIS doesn't do anything special with the host that it connects to and uses the standard PHP PDO objects.


Things to keep in mind are that:

  1.  MySQL accounts are tied to the domain that the account is connecting from, so just because you can connect locally doesn't mean your same credentials will work remotely
  2.  There may be firewalls between your servers blocking the MySQL port.
  3.  There may be some kind of security settings (ie SELinux or apparmor) set up by your sysadmin which further restrict connections (particularly from web servers.) that need to be relaxed.


The first thing to do is work with your sysadmin to make sure you can connect to MySQL from the command line on the same server/with the same credentials as your LORIS instance. If you can get that working, LORIS itself should work fine (unless the problem is 3, in which case you can test by temporarily disabling it and seeing if that fixes it..)


- Dave

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: November 3, 2017 11:36:53 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Installation MySQL in different sever

Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to require a more advanced configuration of MySql that default installation your provide in the Loris GitHub. As I think you might have done this type of setups, I was wondering if you have some documentation that can help me with this configuration process.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 09:50:07 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 14:50:07 +0000
Subject: [Loris-dev] Blank white page
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>

Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From christine.rogers at mcgill.ca  Mon Nov  6 10:01:04 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Mon, 6 Nov 2017 10:01:04 -0500
Subject: [Loris-dev] Blank white page
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
Message-ID: <CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/*
> /var/www/loris)?


Yes, it's recommended to just move the code one directory up, to
/var/www/loris/

The clone command you executed should have used a period as the last
argument -- to clone to the current directory.  (I'll see if we can clarify
that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris
> /wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation)
> it is specified to check the 'base' path, but this path has not been
> declare before. Maybe it is a well known path in apache, but I don't know
> where to find and modify it.


The Base path is a Loris Config table setting -- usually accessible from
the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config
troubleshooting instructions in the wiki
<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
to
modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear LORIS Dev Team,
>
> I just finished the installation of LORIS but when I go to <loris-url> I
> get a blank white page! I think this is related to the way I got the code
> from git. In the instructions (https://github.com/aces/Loris
> /wiki/Setting-Up-Git) it is written to run:
>
> ------------------------------------------------------------
> -------------------
> Run cd /var/www (Or where your apache2 is serving files from)
> Run cd <loris-directory>
> Run git clone <git-clone-url>
> Wait while it clones
> Clone complete
> ------------------------------------------------------------
> -------------------
>
> This leaves the LORIS code in the folder:
>
> /var/www/loris/LORIS
>
> However, later in the installation process (https://github.com/aces/Loris
> /wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions
> make reference to the folder
>
> var/www/<project-name>
>
> All that to say that I think Apache is trying to access /var/www/loris but
> the real path is /var/www/loris/LORIS.
>
> When reading the troubleshooting section (https://github.com/aces/Loris
> /wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation)
> it is specified to check the 'base' path, but this path has not been
> declare before. Maybe it is a well known path in apache, but I don't know
> where to find and modify it.
>
> Could you help me this issue?
> Can I just move everything one folder up (mv /var/www/loris/LORIS/*
> /var/www/loris)?
>
> Thank you for any help.
>
> Regards,
> Alfredo.
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
> _______________________________________________
> 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  Mon Nov  6 10:13:47 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 15:13:47 +0000
Subject: [Loris-dev] Installation MySQL in different sever
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349EB368@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349EAF85@PHSX10MB8.partners.org>, 
	<YQXPR0101MB16722D4D032B9D9F0EA22CBDA85D0@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>,
	<6943CC45EE5DEC4089174E22E5478369349EB368@PHSX10MB8.partners.org>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ECB7F@PHSX10MB8.partners.org>

Dear LORIS Dev Team,

Here are the configuration steps that the BIC Admins and I did in order to get MySql running in an external machine and allowing connections from Loris server:

1. iptables rules for port 3306 in the mysql machine

iptables -I INPUT -p tcp -s <ip-loris-machine> --dport 3306 -j ACCEPT

2. File /etc/hosts.allow must contain the line

mysqld: <ip-loris-machine>

This second instruction was necessary as all the connections were block in the MySql sever, this is because the file "/etc/hosts.deny" contains "ALL: ALL".

3. Configure MySql to accept connections from outside. ( I mostly used this post: http://devdocs.magento.com/guides/v2.0/install-gde/prereq/mysql_remote.html)

3.1 Modify bind-adress. Modify this file (/etc/mysql/mysql.conf.d/mysqld.cnf) like this:
- bind-address          = 127.0.0.1
+ bind-address          = <ip-mysql-machine>

3.2 Grant access from the LORIS ip machine in the MySql database
// Login into mysql
GRANT ALL ON *.* TO root@<ip-loris-machine> IDENTIFIED BY '<root password>'
// Refresh grants using flush
FLUSH PRIVILEGES;
// Logout from MySql and restart the service
service mysql restart

That's it! Hope you can add this information to your github-wiki, that will ease/help the installation for future users.

Regards,
Alfredo.
________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni.mcgill.ca] on behalf of Morales Pinzon, Alfredo [AMORALESPINZON at bwh.harvard.edu]
Sent: Friday, November 03, 2017 4:13 PM
To: David MacFarlane, Mr; loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Installation MySQL in different sever

Hi David,

Thank you for your answer. Indeed I am dealing with point 3, as I am not a sysadmin guy I was looking for some light! We are figuring it out with the BIC Admins. I will share what I will learn :)

Best,
Alfredo.
________________________________
From: David MacFarlane, Mr [david.macfarlane2 at mcgill.ca]
Sent: Friday, November 03, 2017 3:22 PM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Subject: Re: Installation MySQL in different sever


Hi Alfredo,


There should be nothing special from the LORIS side about configuring MySQL whether it's on the same server or not. LORIS doesn't do anything special with the host that it connects to and uses the standard PHP PDO objects.


Things to keep in mind are that:

  1.  MySQL accounts are tied to the domain that the account is connecting from, so just because you can connect locally doesn't mean your same credentials will work remotely
  2.  There may be firewalls between your servers blocking the MySQL port.
  3.  There may be some kind of security settings (ie SELinux or apparmor) set up by your sysadmin which further restrict connections (particularly from web servers.) that need to be relaxed.


The first thing to do is work with your sysadmin to make sure you can connect to MySQL from the command line on the same server/with the same credentials as your LORIS instance. If you can get that working, LORIS itself should work fine (unless the problem is 3, in which case you can test by temporarily disabling it and seeing if that fixes it..)


- Dave

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: November 3, 2017 11:36:53 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Installation MySQL in different sever

Dear LorsiDev team,

My LORIS setup has the MySql server in a different machine and it seems to require a more advanced configuration of MySql that default installation your provide in the Loris GitHub. As I think you might have done this type of setups, I was wondering if you have some documentation that can help me with this configuration process.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
-------------- next part --------------
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 12:14:41 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 17:14:41 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>,
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>

Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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
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From christine.rogers at mcgill.ca  Mon Nov  6 13:51:26 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Mon, 6 Nov 2017 13:51:26 -0500
Subject: [Loris-dev] Blank white page
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>
Message-ID: <CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file
from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps
<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>,
does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Christine,
>
> I moved the code to /var/www/loris and changed the 'Base' and
> 'DownloadPath' in the database. After doing this I had to go again though
> the db installation (installdb.php). At the end of this step I got a
> webpage saying:
>
> ----------------------------------------------------
> Almost done! The LORIS username was configured, but the web server wasn't
> able to write to the file /var/www/loris//project/config.xml. Please copy
> and paste the following into that file on the server in which this web
> server is running or contact your system administer for help: <?xml
> version="1.0" encoding="ISO-8859-1" ?>
> ... </config>
>
> After that you should be able to access LORIS by visiting
> http://132.206.178.78 and logging in with the front end admin username
> and password you configured on the previous page.
> ----------------------------------------------------
>
> After that modification in the config.xml file I am still not able to
> access http://132.206.178.78 , I get a blank page (the variables Base has
> the right path in the new database that I had to create). Moreover if I go
> to http://132.206.178.78/installdb.php I can still start the database
> configuration process, before it was saying that an instance of LORIS was
> already configured.
>
> Here is what I have in the apache log (/var/log/apache2/loris-error.log)
>
> [Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client
> 170.223.207.30:23171] PHP Fatal error:  Uncaught ConfigurationException:
> Config file config.xml does not exist in the defined locations. in
> /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0
> /var/www/loris/php/libraries/NDB_Config.class.inc(73):
> NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
> NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
> NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29):
> NDB_Client->initialize()\n#4 {main}\n  thrown in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 146
>
> Any ideas?
>
> Best,
> Alfredo.
> ------------------------------
> *From:* Christine Rogers [christine.rogers at mcgill.ca]
> *Sent:* Monday, November 06, 2017 10:01 AM
> *To:* Morales Pinzon, Alfredo
> *Cc:* loris-dev at bic.mni.mcgill.ca
> *Subject:* Re: [Loris-dev] Blank white page
>
> Hi Alfredo,
>
> Can I just move everything one folder up (mv /var/www/loris/LORIS/*
>> /var/www/loris)?
>
>
> Yes, it's recommended to just move the code one directory up, to
> /var/www/loris/
>
> The clone command you executed should have used a period as the last
> argument -- to clone to the current directory.  (I'll see if we can clarify
> that in the wiki.)
>
> When reading the troubleshooting section (https://github.com/aces/Loris
>> /wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation)
>> it is specified to check the 'base' path, but this path has not been
>> declare before. Maybe it is a well known path in apache, but I don't know
>> where to find and modify it.
>
>
> The Base path is a Loris Config table setting -- usually accessible from
> the front-end Configuration module, under the "Paths" section.
> Given that your front-end is not loading, follow the detailed config
> troubleshooting instructions in the wiki
> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to
> modify this setting from the MySQL back-end.
>
> Best,
> Christine
> on behalf of the LORIS team
>
> On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Dear LORIS Dev Team,
>>
>> I just finished the installation of LORIS but when I go to <loris-url> I
>> get a blank white page! I think this is related to the way I got the code
>> from git. In the instructions (https://github.com/aces/Loris
>> /wiki/Setting-Up-Git) it is written to run:
>>
>> ------------------------------------------------------------
>> -------------------
>> Run cd /var/www (Or where your apache2 is serving files from)
>> Run cd <loris-directory>
>> Run git clone <git-clone-url>
>> Wait while it clones
>> Clone complete
>> ------------------------------------------------------------
>> -------------------
>>
>> This leaves the LORIS code in the folder:
>>
>> /var/www/loris/LORIS
>>
>> However, later in the installation process (https://github.com/aces/Loris
>> /wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions
>> make reference to the folder
>>
>> var/www/<project-name>
>>
>> All that to say that I think Apache is trying to access /var/www/loris
>> but the real path is /var/www/loris/LORIS.
>>
>> When reading the troubleshooting section (https://github.com/aces/Loris
>> /wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation)
>> it is specified to check the 'base' path, but this path has not been
>> declare before. Maybe it is a well known path in apache, but I don't know
>> where to find and modify it.
>>
>> Could you help me this issue?
>> Can I just move everything one folder up (mv /var/www/loris/LORIS/*
>> /var/www/loris)?
>>
>> Thank you for any help.
>>
>> Regards,
>> Alfredo.
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>> _______________________________________________
>> 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
>
>


-- 

christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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From david.macfarlane2 at mcgill.ca  Mon Nov  6 13:53:58 2017
From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr)
Date: Mon, 6 Nov 2017 18:53:58 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>,
	<CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>
Message-ID: <YQXPR0101MB1672CFA60BCA495E2FADBDB7A8500@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>

You should also ensure that the directory (and any parent directories) have the executable bit set.


(The executable bit means that you can "enter" the directory, which the web server requires in order to read

the file..)

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Christine Rogers <christine.rogers at mcgill.ca>
Sent: November 6, 2017 1:51:26 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>, does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171<http://170.223.207.30:23171>] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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




--

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
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 14:10:56 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 19:10:56 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>,
	<CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ED279@PHSX10MB8.partners.org>

Hi Christine,

The modified the permission and run the configuration steps for apache, but still have the same error. I am sending the output "ls -l /var/www/loris/project/"


lorisadmin at ipmsa-loris:/var/www/loris$ ls -l /var/www/loris/project/

total 40

-rwxrwxr-x 1 lorisadmin lorisadmin 7360 Nov  6 11:44 config.xml

-rw-r--r-- 1 lorisadmin lorisadmin 7344 Nov  6 11:43 config.xml_bk_20171106

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 data

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 instruments

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 libraries

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 modules

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 tables_sql

drwxrwxr-x 2 lorisadmin lorisadmin 4096 Nov  6 10:21 templates

where is the path to the project.xml stored?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca]
Sent: Monday, November 06, 2017 1:51 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>, does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171<http://170.223.207.30:23171>] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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




--

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
-------------- next part --------------
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 14:36:45 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 19:36:45 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <YQXPR0101MB1672CFA60BCA495E2FADBDB7A8500@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>,
	<CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>,
	<YQXPR0101MB1672CFA60BCA495E2FADBDB7A8500@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ED300@PHSX10MB8.partners.org>

Hi David,

That was it! The folder project didn't have the executable bit set.

Thank you!

Cheers,
Alfredo.
________________________________
From: David MacFarlane, Mr [david.macfarlane2 at mcgill.ca]
Sent: Monday, November 06, 2017 1:53 PM
To: Christine Rogers, Ms.; Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page


You should also ensure that the directory (and any parent directories) have the executable bit set.


(The executable bit means that you can "enter" the directory, which the web server requires in order to read

the file..)

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Christine Rogers <christine.rogers at mcgill.ca>
Sent: November 6, 2017 1:51:26 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>, does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171<http://170.223.207.30:23171>] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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




--

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
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 14:54:26 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 19:54:26 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349ED300@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>,
	<CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>,
	<YQXPR0101MB1672CFA60BCA495E2FADBDB7A8500@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>,
	<6943CC45EE5DEC4089174E22E5478369349ED300@PHSX10MB8.partners.org>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ED35A@PHSX10MB8.partners.org>

Still not working ...

Now I have this error:


[Mon Nov 06 14:42:28.532380 2017] [:error] [pid 16121] [client 170.223.207.30:24735] PHP Fatal error:  Uncaught PDOException: SQLSTATE[HY000] [1044] Access denied for user 'ipmsalorisuser'@'132.206.178.78' to database 'IPMSA_LORIS' in /var/www/loris/php/libraries/Database.class.inc:171\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(171): PDO->__construct('mysql:host=132....', 'ipmsalorisuser', '**pwd**')\n#1 /var/www/loris/php/libraries/Database.class.inc(118): Database->connect('IPMSA_LORIS', 'ipmsalorisuser', '**pwd**', '132.206.178.80', true)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('IPMSA_LORIS', 'ipmsalorisuser', '<**pwd**>', '132.206.178.80', true)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/Database.class.inc on line 171



I can access the database from the command line using the user "ipmsalorisuser" but it seems it cannot access in the code.


moralf at ipmsa-loris:/var/www$ mysql -u ipmsalorisuser -h 132.206.178.80  -p

Enter password:

Welcome to the MySQL monitor.  Commands end with ; or \g.

Your MySQL connection id is 72

Server version: 5.7.20-0ubuntu0.16.04.1 (Ubuntu)


Copyright (c) 2000, 2017, Oracle and/or its affiliates. All rights reserved.


Oracle is a registered trademark of Oracle Corporation and/or its

affiliates. Other names may be trademarks of their respective

owners.


Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.


mysql>

Any ideas?

Best,
Alfredo.
________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni.mcgill.ca] on behalf of Morales Pinzon, Alfredo [AMORALESPINZON at bwh.harvard.edu]
Sent: Monday, November 06, 2017 2:36 PM
To: David MacFarlane, Mr; Christine Rogers, Ms.
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi David,

That was it! The folder project didn't have the executable bit set.

Thank you!

Cheers,
Alfredo.
________________________________
From: David MacFarlane, Mr [david.macfarlane2 at mcgill.ca]
Sent: Monday, November 06, 2017 1:53 PM
To: Christine Rogers, Ms.; Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page


You should also ensure that the directory (and any parent directories) have the executable bit set.


(The executable bit means that you can "enter" the directory, which the web server requires in order to read

the file..)

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Christine Rogers <christine.rogers at mcgill.ca>
Sent: November 6, 2017 1:51:26 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>, does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171<http://170.223.207.30:23171>] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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--

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

_______________________________________________
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--

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
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From AMORALESPINZON at bwh.harvard.edu  Mon Nov  6 15:24:18 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 6 Nov 2017 20:24:18 +0000
Subject: [Loris-dev] Blank white page
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349ED35A@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349ECABE@PHSX10MB8.partners.org>
	<CALbt7NDTrKzS=0+O3RT6SHW8htwesB-aQT-E-RCiKSZmtC+G9Q@mail.gmail.com>
	<6943CC45EE5DEC4089174E22E5478369349ECD0A@PHSX10MB8.partners.org>,
	<CALbt7NAhZ5T+FfkdBJue1R-CtfkDhWsRJJUogU09WYJBNvjR5Q@mail.gmail.com>,
	<YQXPR0101MB1672CFA60BCA495E2FADBDB7A8500@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>,
	<6943CC45EE5DEC4089174E22E5478369349ED300@PHSX10MB8.partners.org>,
	<6943CC45EE5DEC4089174E22E5478369349ED35A@PHSX10MB8.partners.org>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349ED3C3@PHSX10MB8.partners.org>

Got it!

For some reason the user ipmsalorisuser didn't have the appropiate GRANT rules in MySql:


mysql> SHOW GRANTS FOR 'ipmsalorisuser'@'132.206.178.78';

+---------------------------------------------------------+

| Grants for ipmsalorisuser at 132.206.178.78                |

+---------------------------------------------------------+

| GRANT USAGE ON *.* TO 'ipmsalorisuser'@'132.206.178.78' |

+---------------------------------------------------------+

1 row in set (0.00 sec)

After modification the user has:


mysql> SHOW GRANTS FOR 'ipmsalorisuser'@'132.206.178.78';

+------------------------------------------------------------------------------+

| Grants for ipmsalorisuser at 132.206.178.78                                     |

+------------------------------------------------------------------------------+

| GRANT USAGE ON *.* TO 'ipmsalorisuser'@'132.206.178.78'                      |

| GRANT ALL PRIVILEGES ON `IPMSA_LORIS`.* TO 'ipmsalorisuser'@'132.206.178.78' |

+------------------------------------------------------------------------------+

2 rows in set (0.00 sec)

... and now I can access the Front-End of LORIS :)

Thank you all for the help, each tip was helpful.

Cheers,
Alfredo.

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni.mcgill.ca] on behalf of Morales Pinzon, Alfredo [AMORALESPINZON at bwh.harvard.edu]
Sent: Monday, November 06, 2017 2:54 PM
To: David MacFarlane, Mr; Christine Rogers, Ms.
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Still not working ...

Now I have this error:


[Mon Nov 06 14:42:28.532380 2017] [:error] [pid 16121] [client 170.223.207.30:24735] PHP Fatal error:  Uncaught PDOException: SQLSTATE[HY000] [1044] Access denied for user 'ipmsalorisuser'@'132.206.178.78' to database 'IPMSA_LORIS' in /var/www/loris/php/libraries/Database.class.inc:171\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(171): PDO->__construct('mysql:host=132....', 'ipmsalorisuser', '**pwd**')\n#1 /var/www/loris/php/libraries/Database.class.inc(118): Database->connect('IPMSA_LORIS', 'ipmsalorisuser', '**pwd**', '132.206.178.80', true)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('IPMSA_LORIS', 'ipmsalorisuser', '<**pwd**>', '132.206.178.80', true)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/Database.class.inc on line 171



I can access the database from the command line using the user "ipmsalorisuser" but it seems it cannot access in the code.


moralf at ipmsa-loris:/var/www$ mysql -u ipmsalorisuser -h 132.206.178.80  -p

Enter password:

Welcome to the MySQL monitor.  Commands end with ; or \g.

Your MySQL connection id is 72

Server version: 5.7.20-0ubuntu0.16.04.1 (Ubuntu)


Copyright (c) 2000, 2017, Oracle and/or its affiliates. All rights reserved.


Oracle is a registered trademark of Oracle Corporation and/or its

affiliates. Other names may be trademarks of their respective

owners.


Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.


mysql>

Any ideas?

Best,
Alfredo.
________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni.mcgill.ca] on behalf of Morales Pinzon, Alfredo [AMORALESPINZON at bwh.harvard.edu]
Sent: Monday, November 06, 2017 2:36 PM
To: David MacFarlane, Mr; Christine Rogers, Ms.
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi David,

That was it! The folder project didn't have the executable bit set.

Thank you!

Cheers,
Alfredo.
________________________________
From: David MacFarlane, Mr [david.macfarlane2 at mcgill.ca]
Sent: Monday, November 06, 2017 1:53 PM
To: Christine Rogers, Ms.; Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page


You should also ensure that the directory (and any parent directories) have the executable bit set.


(The executable bit means that you can "enter" the directory, which the web server requires in order to read

the file..)

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Christine Rogers <christine.rogers at mcgill.ca>
Sent: November 6, 2017 1:51:26 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

It sounds like your file system permissions are preventing config.xml file from being read, as they prevented writing to it during installation.

If you reset the ownership on your (new) loris root path:
 sudo chown -R lorisadmin.lorisadmin /var/www/loris

and then verify and restart your apache configuration steps<https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2>, does that help?

If not, can you run and send the output of this command:
> ls -l /var/www/loris/project/

Best,
Christine

On Mon, Nov 6, 2017 at 12:14 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Christine,

I moved the code to /var/www/loris and changed the 'Base' and 'DownloadPath' in the database. After doing this I had to go again though the db installation (installdb.php). At the end of this step I got a webpage saying:

----------------------------------------------------
Almost done! The LORIS username was configured, but the web server wasn't able to write to the file /var/www/loris//project/config.xml. Please copy and paste the following into that file on the server in which this web server is running or contact your system administer for help: <?xml version="1.0" encoding="ISO-8859-1" ?>
... </config>

After that you should be able to access LORIS by visiting http://132.206.178.78<http://132.206.178.78/> and logging in with the front end admin username and password you configured on the previous page.
----------------------------------------------------

After that modification in the config.xml file I am still not able to access http://132.206.178.78 , I get a blank page (the variables Base has the right path in the new database that I had to create). Moreover if I go to http://132.206.178.78<http://132.206.178.78/>/installdb.php I can still start the database configuration process, before it was saying that an instance of LORIS was already configured.

Here is what I have in the apache log (/var/log/apache2/loris-error.log)


[Mon Nov 06 12:05:39.773502 2017] [:error] [pid 16522] [client 170.223.207.30:23171<http://170.223.207.30:23171>] PHP Fatal error:  Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:146\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(73): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/main.php(29): NDB_Client->initialize()\n#4 {main}\n  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 146

Any ideas?

Best,
Alfredo.
________________________________
From: Christine Rogers [christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>]
Sent: Monday, November 06, 2017 10:01 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Blank white page

Hi Alfredo,

Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Yes, it's recommended to just move the code one directory up, to /var/www/loris/

The clone command you executed should have used a period as the last argument -- to clone to the current directory.  (I'll see if we can clarify that in the wiki.)

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

The Base path is a Loris Config table setting -- usually accessible from the front-end Configuration module, under the "Paths" section.
Given that your front-end is not loading, follow the detailed config troubleshooting instructions in the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to modify this setting from the MySQL back-end.

Best,
Christine
on behalf of the LORIS team

On Mon, Nov 6, 2017 at 9:50 AM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS Dev Team,

I just finished the installation of LORIS but when I go to <loris-url> I get a blank white page! I think this is related to the way I got the code from git. In the instructions (https://github.com/aces/Loris/wiki/Setting-Up-Git) it is written to run:

-------------------------------------------------------------------------------
Run cd /var/www (Or where your apache2 is serving files from)
Run cd <loris-directory>
Run git clone <git-clone-url>
Wait while it clones
Clone complete
-------------------------------------------------------------------------------

This leaves the LORIS code in the folder:

/var/www/loris/LORIS

However, later in the installation process (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#configuring-apache2) the instructions make reference to the folder

var/www/<project-name>

All that to say that I think Apache is trying to access /var/www/loris but the real path is /var/www/loris/LORIS.

When reading the troubleshooting section (https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#troubleshooting-the-basic-installation) it is specified to check the 'base' path, but this path has not been declare before. Maybe it is a well known path in apache, but I don't know where to find and modify it.

Could you help me this issue?
Can I just move everything one folder up (mv /var/www/loris/LORIS/* /var/www/loris)?

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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




--

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
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From AMORALESPINZON at bwh.harvard.edu  Wed Nov  8 08:59:18 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Wed, 8 Nov 2017 13:59:18 +0000
Subject: [Loris-dev] [IPMSA] Loris-MRI installation path /data
Message-ID: <6943CC45EE5DEC4089174E22E5478369349F23A2@PHSX10MB8.partners.org>

Dear LORIS Dev Team,

I have a problem with the installation of Loris-MRI in the BIC infrastructure regarding the installation path. In the BIC infrastructure the folder /data is reserved! I have seen that the default path /data is everywhere in the installation script (bin/mri/imaging_install.sh), and therefore I have to manually change it. Not a big deal but I suggest to make this path configurable in the future. That said, I would like to ask you if this change in the installation script won't impact the function of the Loris-MRI? Maybe in some place in the code there are pointers to /data.

Thank you for any help.

Regards,
Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From mouna.safi-harb at mail.mcgill.ca  Wed Nov  8 09:27:59 2017
From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab)
Date: Wed, 8 Nov 2017 14:27:59 +0000
Subject: [Loris-dev] [IPMSA] Loris-MRI installation path /data
In-Reply-To: <6943CC45EE5DEC4089174E22E5478369349F23A2@PHSX10MB8.partners.org>
References: <6943CC45EE5DEC4089174E22E5478369349F23A2@PHSX10MB8.partners.org>
Message-ID: <YTXPR0101MB217558D0EA8A4AA3DF1107BC8E560@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>

Hi Alfredo,


The path /data/$PROJECT/bin/mri/

and

/data/$PROJECT/data/

are hardcoded at install time, but they become variables in either your 'prod' file (before release 18.0.0), or in the in the Config table in the database (accessible also through the Configuration menu under Imaging Pipeline and Paths sub-menus, after release 18.0.0). As long as you configure them properly in either of these 2 places (depending on which version of Loris and Loris-MRI you are running), I do not think this should cause any future issues in the expected functionality of Loris-MRI. Let me know otherwise!


- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Wednesday, November 8, 2017 8:59:18 AM
To: loris-dev at bic.mni.mcgill.ca
Cc: Guttmann, Charles,M.D.
Subject: [Loris-dev] [IPMSA] Loris-MRI installation path /data

Dear LORIS Dev Team,

I have a problem with the installation of Loris-MRI in the BIC infrastructure regarding the installation path. In the BIC infrastructure the folder /data is reserved! I have seen that the default path /data is everywhere in the installation script (bin/mri/imaging_install.sh), and therefore I have to manually change it. Not a big deal but I suggest to make this path configurable in the future. That said, I would like to ask you if this change in the installation script won't impact the function of the Loris-MRI? Maybe in some place in the code there are pointers to /data.

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From AMORALESPINZON at bwh.harvard.edu  Wed Nov  8 09:49:48 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Wed, 8 Nov 2017 14:49:48 +0000
Subject: [Loris-dev] [IPMSA] Loris-MRI installation path /data
In-Reply-To: <YTXPR0101MB217558D0EA8A4AA3DF1107BC8E560@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>
References: <6943CC45EE5DEC4089174E22E5478369349F23A2@PHSX10MB8.partners.org>,
	<YTXPR0101MB217558D0EA8A4AA3DF1107BC8E560@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <6943CC45EE5DEC4089174E22E5478369349F7458@PHSX10MB8.partners.org>

Hi Mouna,

I am installing the sweet 18.0.0 last version of LORIS. I will then modify the hard coded paths in the installation script and then check the Config table after installation.

Thank you for the fast reply :)

Best,
Alfredo.
________________________________
From: Mouna Safi-Harab [mouna.safi-harb at mail.mcgill.ca]
Sent: Wednesday, November 08, 2017 9:27 AM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Cc: Guttmann, Charles,M.D.
Subject: Re: [IPMSA] Loris-MRI installation path /data


Hi Alfredo,


The path /data/$PROJECT/bin/mri/

and

/data/$PROJECT/data/

are hardcoded at install time, but they become variables in either your 'prod' file (before release 18.0.0), or in the in the Config table in the database (accessible also through the Configuration menu under Imaging Pipeline and Paths sub-menus, after release 18.0.0). As long as you configure them properly in either of these 2 places (depending on which version of Loris and Loris-MRI you are running), I do not think this should cause any future issues in the expected functionality of Loris-MRI. Let me know otherwise!


- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Wednesday, November 8, 2017 8:59:18 AM
To: loris-dev at bic.mni.mcgill.ca
Cc: Guttmann, Charles,M.D.
Subject: [Loris-dev] [IPMSA] Loris-MRI installation path /data

Dear LORIS Dev Team,

I have a problem with the installation of Loris-MRI in the BIC infrastructure regarding the installation path. In the BIC infrastructure the folder /data is reserved! I have seen that the default path /data is everywhere in the installation script (bin/mri/imaging_install.sh), and therefore I have to manually change it. Not a big deal but I suggest to make this path configurable in the future. That said, I would like to ask you if this change in the installation script won't impact the function of the Loris-MRI? Maybe in some place in the code there are pointers to /data.

Thank you for any help.

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From AMORALESPINZON at bwh.harvard.edu  Thu Nov  9 15:37:56 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Thu, 9 Nov 2017 20:37:56 +0000
Subject: [Loris-dev] [IPMSA] User insertion Loris 18.0.0
Message-ID: <DM5PR04MB11978BB2205E381164BC5DD58F570@DM5PR04MB1197.namprd04.prod.outlook.com>

Dear Loris Dev Team,


In the past version of Loris (17.1) I was creating users for each center inside the database using a mysql script, I need to create hundreds of centers and consequently hundreds of users. In the previous version a given User had an associated CenterID but in the new one it does not. How are you handling this?


This is an example of one line of my script:


insert into users(UserID,Email,CenterID,Password_hash,Pending_approval,Password_expiry) values ('UserID','user at ipmsa.com',99,'**************','N','2055-01-01');


I remember Mouna told me that now one user can be associated to multiple centers, if that is the case,


(1) could you give me a light on how the database is structured so that I can modify my scripts, and


(2) tell me if the API is able to handle the creation of candidates and visits for a given Candidate by login with a user that is affiliated to multiple sites (right now, if I want to add a new Candidate and Visits, for that candidate, in a given Center, I have to login with the associated User to that Center)


Thank you.


Best,

Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From mouna.safi-harb at mail.mcgill.ca  Thu Nov  9 16:04:40 2017
From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab)
Date: Thu, 9 Nov 2017 21:04:40 +0000
Subject: [Loris-dev] [IPMSA] User insertion Loris 18.0.0
In-Reply-To: <DM5PR04MB11978BB2205E381164BC5DD58F570@DM5PR04MB1197.namprd04.prod.outlook.com>
References: <DM5PR04MB11978BB2205E381164BC5DD58F570@DM5PR04MB1197.namprd04.prod.outlook.com>
Message-ID: <YTXPR0101MB21751BB2E7A8BF56711A2CF48E570@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>

Hi Alfredo,


My answers to your questions:


1) The CenterID column is no longer in the users table. It is now in a table called user_psc_rel which would be the relation between a user (ID column from the users table) and the center (CenterID column from the psc table).

This would allow one user to have as many rows as needed (i.e. as many center affiliations as needed).

So in your case, you would probably have a line to create the user in the users table, and another one to add that user to the user_psc_rel table with the centerID/affiliation.


2) The API in v18.0.0 allows the candidate/visit creation if the API user is at one site only. So for now, you can have an API user per site. But we will extend the API capabilities to allow users at multiple sites to create candidates/visits (changes are done and can be consulted in this pull request which is yet to be approved/tested: https://github.com/aces/Loris/pull/3014).


Let me know if this does not address all your concerns.


- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Thursday, November 9, 2017 3:37:56 PM
To: loris-dev at bic.mni.mcgill.ca
Cc: Sridar Narayanan, Dr.; Guttmann, Charles, M.D.
Subject: [Loris-dev] [IPMSA] User insertion Loris 18.0.0


Dear Loris Dev Team,


In the past version of Loris (17.1) I was creating users for each center inside the database using a mysql script, I need to create hundreds of centers and consequently hundreds of users. In the previous version a given User had an associated CenterID but in the new one it does not. How are you handling this?


This is an example of one line of my script:


insert into users(UserID,Email,CenterID,Password_hash,Pending_approval,Password_expiry) values ('UserID','user at ipmsa.com',99,'**************','N','2055-01-01');


I remember Mouna told me that now one user can be associated to multiple centers, if that is the case,


(1) could you give me a light on how the database is structured so that I can modify my scripts, and


(2) tell me if the API is able to handle the creation of candidates and visits for a given Candidate by login with a user that is affiliated to multiple sites (right now, if I want to add a new Candidate and Visits, for that candidate, in a given Center, I have to login with the associated User to that Center)


Thank you.


Best,

Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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From AMORALESPINZON at bwh.harvard.edu  Thu Nov  9 16:15:16 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Thu, 9 Nov 2017 21:15:16 +0000
Subject: [Loris-dev] [IPMSA] User insertion Loris 18.0.0
In-Reply-To: <YTXPR0101MB21751BB2E7A8BF56711A2CF48E570@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>
References: <DM5PR04MB11978BB2205E381164BC5DD58F570@DM5PR04MB1197.namprd04.prod.outlook.com>,
	<YTXPR0101MB21751BB2E7A8BF56711A2CF48E570@YTXPR0101MB2175.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <DM5PR04MB11976897C4D81589AD07E4C98F570@DM5PR04MB1197.namprd04.prod.outlook.com>

Hi Mouna,


Thank you for the answer, that's all I needed (y). I created a user linked to all the centers that I have, but as you say I am not able to create Candidate/Visits for all the Center.s I'll make some changes in my scripts to reflect the relationship user_psc_rel and move forward.


The new API sounds wonderful, hope you guys can test it and make it available soon.


Thank you one more time.


Best,

Alfredo.

________________________________
From: Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca>
Sent: Thursday, November 9, 2017 4:04:40 PM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Cc: Sridar Narayanan, Dr.; Guttmann, Charles,M.D.
Subject: Re: [IPMSA] User insertion Loris 18.0.0


Hi Alfredo,


My answers to your questions:


1) The CenterID column is no longer in the users table. It is now in a table called user_psc_rel which would be the relation between a user (ID column from the users table) and the center (CenterID column from the psc table).

This would allow one user to have as many rows as needed (i.e. as many center affiliations as needed).

So in your case, you would probably have a line to create the user in the users table, and another one to add that user to the user_psc_rel table with the centerID/affiliation.


2) The API in v18.0.0 allows the candidate/visit creation if the API user is at one site only. So for now, you can have an API user per site. But we will extend the API capabilities to allow users at multiple sites to create candidates/visits (changes are done and can be consulted in this pull request which is yet to be approved/tested: https://github.com/aces/Loris/pull/3014).


Let me know if this does not address all your concerns.


- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Thursday, November 9, 2017 3:37:56 PM
To: loris-dev at bic.mni.mcgill.ca
Cc: Sridar Narayanan, Dr.; Guttmann, Charles, M.D.
Subject: [Loris-dev] [IPMSA] User insertion Loris 18.0.0


Dear Loris Dev Team,


In the past version of Loris (17.1) I was creating users for each center inside the database using a mysql script, I need to create hundreds of centers and consequently hundreds of users. In the previous version a given User had an associated CenterID but in the new one it does not. How are you handling this?


This is an example of one line of my script:


insert into users(UserID,Email,CenterID,Password_hash,Pending_approval,Password_expiry) values ('UserID','user at ipmsa.com',99,'**************','N','2055-01-01');


I remember Mouna told me that now one user can be associated to multiple centers, if that is the case,


(1) could you give me a light on how the database is structured so that I can modify my scripts, and


(2) tell me if the API is able to handle the creation of candidates and visits for a given Candidate by login with a user that is affiliated to multiple sites (right now, if I want to add a new Candidate and Visits, for that candidate, in a given Center, I have to login with the associated User to that Center)


Thank you.


Best,

Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From dave.macfarlane at mcin.ca  Wed Nov 15 15:50:08 2017
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Wed, 15 Nov 2017 15:50:08 -0500
Subject: [Loris-dev] LORIS Survey
Message-ID: <CAN9cDwH=DLikcFUp7D1OfrGbd+n1o-oOx3zUUX+gM-Oxb2OBww@mail.gmail.com>

Hi LORISers,

I've put together a survey to try and gather some data about how people are
using LORIS (in particular, mostly about all the modules in LORIS.)

I'd appreciate it if any LORIS users or developers (or people generally
familiar with LORIS) could fill it out in order to help make us make better
data driven decisions about how to improve LORIS in the future.

After a couple weeks for responses, I'll try and put together a summary
presentation for anyone interested.

The survey is anonymous and available at:

https://docs.google.com/forms/d/e/1FAIpQLSdEiUzh5okFRNMnRh1Y17gLCmolbkgV2x-iDQ31WsWhvqtQ-A/viewform?usp=sf_link

It should take about 5-10 minutes to fill out.

Thanks in advance!
Dave
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From AMORALESPINZON at bwh.harvard.edu  Tue Nov 28 11:47:44 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Tue, 28 Nov 2017 16:47:44 +0000
Subject: [Loris-dev] Error: Acquisition protocol is unknown
Message-ID: <DM5PR04MB1197E7ECAE8857E6AC480ED68F3A0@DM5PR04MB1197.namprd04.prod.outlook.com>

Dear LORIS team,

I am in the final phase of image batch-uploading using the script "batch_uploads_imageuploader" and need some help. It seems that everything goes well before the 'acquisition protocol" checking step, where the type of image cannot be determined and it's left as "unknown". It is strange that this happens because the parameters of the images are inside the ranges specified in the table "mri_protocol", and even stranger when I have an entry, for type NA, with everything NULL:

-------------------------------------------------------------------------------
mysql> select * from mri_protocol where ID=1008 \G;
*************************** 1. row ***************************
                      ID: 1008
             Center_name: ZZZZ
               ScannerID: 0
               Scan_type: 1000
                TR_range: NULL
                TE_range: NULL
                TI_range: NULL
   slice_thickness_range: NULL
             FoV_x_range: NULL
             FoV_y_range: NULL
             FoV_z_range: NULL
            xspace_range: NULL
            yspace_range: NULL
            zspace_range: NULL
             xstep_range: NULL
             ystep_range: NULL
             zstep_range: NULL
              time_range: NULL
series_description_regex: NULL
1 row in set (0.00 sec)
-------------------------------------------------------------------------------

I was trying to see where the error can comes from and it seems to come from the file "Loris-MRI/uploadNeuroDB/NeuroDB/MRI.pm" (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm). I actually activate the printing part of the code (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L435 and https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L485) to see the parameter values of the images.

Here are the instruction that I am using and the logs that I get (I removed information related to my project by PPP):

Instruction
-------------------------------------------------------------------------------
PPP/bin/mri//batch_uploads_imageuploader -profile prod < PPP.txt > PPP_log_batch_uploads_imageuploader.txt 2>&
-------------------------------------------------------------------------------

File: log from batch_uploads_imageuploader script (PPP_log_batch_uploads_imageuploader.txt)
-------------------------------------------------------------------------------
Running now the following command: PPP/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 5 PPP.tar.gz -verbose

PPP/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-11-6-0NOcLo PPP/data/tarchive -clobber -database -profile prod -verbose
 Source: /tmp/ImagingUpload-11-6-0NOcLo
Target: PPP/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir                : ImagingUpload-11-6-0NOcLo

You are creating a tar with the following command:
tar -cf PPP/data/tarchive/ImagingUpload-11-6-0NOcLo.tar ImagingUpload-11-6-0NOcLo


getting md5sums and gzipping!!

* Taken from dir                   :    /tmp/ImagingUpload-11-6-0NOcLo
* Archive target location          :    PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar
* Name of creating host            :    PPP
* Name of host OS                  :    PPP
* Created by user                  :    lorisadmin
* Archived on                      :    2017-11-28 11:06:33
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    12c2e901dbb88a7cbcb71ede54ff2fdf  ImagingUpload-11-6-0NOcLo.tar
* md5sum for DICOM tarball gzipped :    9fc33ff9fbd72a4c5aa14d4c6235c238  ImagingUpload-11-6-0NOcLo.tar.gz
* md5sum for complete archive      :    5afa4143e07d50a2e340ddf45b5338d9  PPP_ImagingUpload-11-6-0NOcLo.tar

Adding archive info into database

Removing temporary files from target location


Done adding archive info into database

PPP/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar -verbose
 md5sum PPP/data/tarchive/DPPP_ImagingUpload-11-6-0NOcLo.tar
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP

Number of MINC files that will be considered for inserting into the database: 5

log dir is PPP/data/logs and log file is PPP/data/logs/TarLoad-11-6-MewKHm.log
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP

tr:     2500
te:     12.1
ti:
st:     3
time;
xspace: 256
yspace: 256
zspace: 60
xstep:  -0.9765723348
ystep:  -0.9765625
zstep:  3.
        Checking flair (41) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking pdw (1001) (Axial PD =~ NULL)
        TR      TE      xspace  yspace  zspace  ST
        Checking t1 (44) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking t2w (1002) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking NA (1000) (Axial PD =~ NULL)

...
... // the other 4 images //
...

Cleaning up temp files: rm -rf /tmp/TarLoad-11-6-FYfBtg/ImagingUpload-11-6-0NOcLo*

 No Mincs inserted

The insertion scripts have failed
-------------------------------------------------------------------------------

File: $project/data/logs/TarLoad-11-6-MewKHm.log
-------------------------------------------------------------------------------
==> Loading file from disk /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

--> mapping DICOM parameter for /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

==> computing md5 hash for MINC body.

--> md5: 2278a2f9c6f586a16316d41390a0c045

==> verifying acquisition protocol

Acquisition protocol is unknown

  --> The minc file cannot be registered since the AcquisitionProtocol is unknown
-------------------------------------------------------------------------------


I can provide more information if needed.

Any help is welcomed :)

Regards,
Alfredo.


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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From mouna.safi-harb at mail.mcgill.ca  Tue Nov 28 13:48:35 2017
From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab)
Date: Tue, 28 Nov 2017 18:48:35 +0000
Subject: [Loris-dev] Error: Acquisition protocol is unknown
In-Reply-To: <DM5PR04MB1197E7ECAE8857E6AC480ED68F3A0@DM5PR04MB1197.namprd04.prod.outlook.com>
References: <DM5PR04MB1197E7ECAE8857E6AC480ED68F3A0@DM5PR04MB1197.namprd04.prod.outlook.com>
Message-ID: <YQXPR0101MB12864C71C1FF05DB00F94C0F8E3A0@YQXPR0101MB1286.CANPRD01.PROD.OUTLOOK.COM>

Hi Alfredo,


Which version of Loris-MRI are you on?

A couple of things that I can ask you to check:

1) instead of selecting from the mri_protocol at the mysql command, can you get a dump of the mri_protocol table into a text file. That row entry corresponding to ID=1008, does it have NULL or 'NULL' entries? i.e. when you inserted it, did you insert the NULL values with a single quotation? if so, this might be the issue

2) in your prod file, what is inside the routine: isFileToBeRegisteredGivenProtocol{}

3) in the mri_scan_types, I assume you have a scan_type entry for ID=1008?

4) the print statements you have enabled is a great start. I would add manually a few more a few lines later;

i.e. when the script does this:

   else {
            if ((!$rowref->{'TR_range'} || &in_range($tr, $rowref->{'TR_range'}))
                && (!$rowref->{'TE_range'} || &in_range($te, $rowref->{'TE_range'}))
...
}
I would add inside this if statement a few print. If the NULL comparison is working, the condition !$rowref->{'TR_range'} should be true, same thing for  !$rowref->{'TE_range'}, etc..., so try to see if this is indeed the case by printing it.

Let me know if this helps, otherwise, do not hesitate to ask more!

- Mouna





________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Tuesday, November 28, 2017 11:47:44 AM
To: loris-dev at bic.mni.mcgill.ca
Cc: Louis Collins, Dr.; Sridar Narayanan, Dr.; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: [Loris-dev] Error: Acquisition protocol is unknown


Dear LORIS team,

I am in the final phase of image batch-uploading using the script "batch_uploads_imageuploader" and need some help. It seems that everything goes well before the 'acquisition protocol" checking step, where the type of image cannot be determined and it's left as "unknown". It is strange that this happens because the parameters of the images are inside the ranges specified in the table "mri_protocol", and even stranger when I have an entry, for type NA, with everything NULL:

-------------------------------------------------------------------------------
mysql> select * from mri_protocol where ID=1008 \G;
*************************** 1. row ***************************
                      ID: 1008
             Center_name: ZZZZ
               ScannerID: 0
               Scan_type: 1000
                TR_range: NULL
                TE_range: NULL
                TI_range: NULL
   slice_thickness_range: NULL
             FoV_x_range: NULL
             FoV_y_range: NULL
             FoV_z_range: NULL
            xspace_range: NULL
            yspace_range: NULL
            zspace_range: NULL
             xstep_range: NULL
             ystep_range: NULL
             zstep_range: NULL
              time_range: NULL
series_description_regex: NULL
1 row in set (0.00 sec)
-------------------------------------------------------------------------------

I was trying to see where the error can comes from and it seems to come from the file "Loris-MRI/uploadNeuroDB/NeuroDB/MRI.pm" (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm). I actually activate the printing part of the code (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L435 and https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L485) to see the parameter values of the images.

Here are the instruction that I am using and the logs that I get (I removed information related to my project by PPP):

Instruction
-------------------------------------------------------------------------------
PPP/bin/mri//batch_uploads_imageuploader -profile prod < PPP.txt > PPP_log_batch_uploads_imageuploader.txt 2>&
-------------------------------------------------------------------------------

File: log from batch_uploads_imageuploader script (PPP_log_batch_uploads_imageuploader.txt)
-------------------------------------------------------------------------------
Running now the following command: PPP/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 5 PPP.tar.gz -verbose

PPP/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-11-6-0NOcLo PPP/data/tarchive -clobber -database -profile prod -verbose
 Source: /tmp/ImagingUpload-11-6-0NOcLo
Target: PPP/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir                : ImagingUpload-11-6-0NOcLo

You are creating a tar with the following command:
tar -cf PPP/data/tarchive/ImagingUpload-11-6-0NOcLo.tar ImagingUpload-11-6-0NOcLo


getting md5sums and gzipping!!

* Taken from dir                   :    /tmp/ImagingUpload-11-6-0NOcLo
* Archive target location          :    PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar
* Name of creating host            :    PPP
* Name of host OS                  :    PPP
* Created by user                  :    lorisadmin
* Archived on                      :    2017-11-28 11:06:33
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    12c2e901dbb88a7cbcb71ede54ff2fdf  ImagingUpload-11-6-0NOcLo.tar
* md5sum for DICOM tarball gzipped :    9fc33ff9fbd72a4c5aa14d4c6235c238  ImagingUpload-11-6-0NOcLo.tar.gz
* md5sum for complete archive      :    5afa4143e07d50a2e340ddf45b5338d9  PPP_ImagingUpload-11-6-0NOcLo.tar

Adding archive info into database

Removing temporary files from target location


Done adding archive info into database

PPP/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar -verbose
 md5sum PPP/data/tarchive/DPPP_ImagingUpload-11-6-0NOcLo.tar
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP

Number of MINC files that will be considered for inserting into the database: 5

log dir is PPP/data/logs and log file is PPP/data/logs/TarLoad-11-6-MewKHm.log
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP

tr:     2500
te:     12.1
ti:
st:     3
time;
xspace: 256
yspace: 256
zspace: 60
xstep:  -0.9765723348
ystep:  -0.9765625
zstep:  3.
        Checking flair (41) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking pdw (1001) (Axial PD =~ NULL)
        TR      TE      xspace  yspace  zspace  ST
        Checking t1 (44) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking t2w (1002) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking NA (1000) (Axial PD =~ NULL)

...
... // the other 4 images //
...

Cleaning up temp files: rm -rf /tmp/TarLoad-11-6-FYfBtg/ImagingUpload-11-6-0NOcLo*

 No Mincs inserted

The insertion scripts have failed
-------------------------------------------------------------------------------

File: $project/data/logs/TarLoad-11-6-MewKHm.log
-------------------------------------------------------------------------------
==> Loading file from disk /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

--> mapping DICOM parameter for /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

==> computing md5 hash for MINC body.

--> md5: 2278a2f9c6f586a16316d41390a0c045

==> verifying acquisition protocol

Acquisition protocol is unknown

  --> The minc file cannot be registered since the AcquisitionProtocol is unknown
-------------------------------------------------------------------------------


I can provide more information if needed.

Any help is welcomed :)

Regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From AMORALESPINZON at bwh.harvard.edu  Tue Nov 28 16:20:01 2017
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Tue, 28 Nov 2017 21:20:01 +0000
Subject: [Loris-dev] Error: Acquisition protocol is unknown
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References: <DM5PR04MB1197E7ECAE8857E6AC480ED68F3A0@DM5PR04MB1197.namprd04.prod.outlook.com>,
	<YQXPR0101MB12864C71C1FF05DB00F94C0F8E3A0@YQXPR0101MB1286.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <DM5PR04MB1197BC01723A957E5011EE018F3A0@DM5PR04MB1197.namprd04.prod.outlook.com>

Hi Mouna.


The error was coming from the 'NULL' entries in the "mri_protocol", I have modified them and the insertion is working.


Thank you very much!


Best,

Alfredo.

________________________________
From: Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca>
Sent: Tuesday, November 28, 2017 1:48:35 PM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Cc: Louis Collins, Dr.; Sridar Narayanan, Dr.; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: Re: Error: Acquisition protocol is unknown


Hi Alfredo,


Which version of Loris-MRI are you on?

A couple of things that I can ask you to check:

1) instead of selecting from the mri_protocol at the mysql command, can you get a dump of the mri_protocol table into a text file. That row entry corresponding to ID=1008, does it have NULL or 'NULL' entries? i.e. when you inserted it, did you insert the NULL values with a single quotation? if so, this might be the issue

2) in your prod file, what is inside the routine: isFileToBeRegisteredGivenProtocol{}

3) in the mri_scan_types, I assume you have a scan_type entry for ID=1008?

4) the print statements you have enabled is a great start. I would add manually a few more a few lines later;

i.e. when the script does this:

   else {
            if ((!$rowref->{'TR_range'} || &in_range($tr, $rowref->{'TR_range'}))
                && (!$rowref->{'TE_range'} || &in_range($te, $rowref->{'TE_range'}))
...
}
I would add inside this if statement a few print. If the NULL comparison is working, the condition !$rowref->{'TR_range'} should be true, same thing for  !$rowref->{'TE_range'}, etc..., so try to see if this is indeed the case by printing it.

Let me know if this helps, otherwise, do not hesitate to ask more!

- Mouna





________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Tuesday, November 28, 2017 11:47:44 AM
To: loris-dev at bic.mni.mcgill.ca
Cc: Louis Collins, Dr.; Sridar Narayanan, Dr.; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: [Loris-dev] Error: Acquisition protocol is unknown


Dear LORIS team,

I am in the final phase of image batch-uploading using the script "batch_uploads_imageuploader" and need some help. It seems that everything goes well before the 'acquisition protocol" checking step, where the type of image cannot be determined and it's left as "unknown". It is strange that this happens because the parameters of the images are inside the ranges specified in the table "mri_protocol", and even stranger when I have an entry, for type NA, with everything NULL:

-------------------------------------------------------------------------------
mysql> select * from mri_protocol where ID=1008 \G;
*************************** 1. row ***************************
                      ID: 1008
             Center_name: ZZZZ
               ScannerID: 0
               Scan_type: 1000
                TR_range: NULL
                TE_range: NULL
                TI_range: NULL
   slice_thickness_range: NULL
             FoV_x_range: NULL
             FoV_y_range: NULL
             FoV_z_range: NULL
            xspace_range: NULL
            yspace_range: NULL
            zspace_range: NULL
             xstep_range: NULL
             ystep_range: NULL
             zstep_range: NULL
              time_range: NULL
series_description_regex: NULL
1 row in set (0.00 sec)
-------------------------------------------------------------------------------

I was trying to see where the error can comes from and it seems to come from the file "Loris-MRI/uploadNeuroDB/NeuroDB/MRI.pm" (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm). I actually activate the printing part of the code (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L435 and https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L485) to see the parameter values of the images.

Here are the instruction that I am using and the logs that I get (I removed information related to my project by PPP):

Instruction
-------------------------------------------------------------------------------
PPP/bin/mri//batch_uploads_imageuploader -profile prod < PPP.txt > PPP_log_batch_uploads_imageuploader.txt 2>&
-------------------------------------------------------------------------------

File: log from batch_uploads_imageuploader script (PPP_log_batch_uploads_imageuploader.txt)
-------------------------------------------------------------------------------
Running now the following command: PPP/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 5 PPP.tar.gz -verbose

PPP/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-11-6-0NOcLo PPP/data/tarchive -clobber -database -profile prod -verbose
 Source: /tmp/ImagingUpload-11-6-0NOcLo
Target: PPP/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir                : ImagingUpload-11-6-0NOcLo

You are creating a tar with the following command:
tar -cf PPP/data/tarchive/ImagingUpload-11-6-0NOcLo.tar ImagingUpload-11-6-0NOcLo


getting md5sums and gzipping!!

* Taken from dir                   :    /tmp/ImagingUpload-11-6-0NOcLo
* Archive target location          :    PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar
* Name of creating host            :    PPP
* Name of host OS                  :    PPP
* Created by user                  :    lorisadmin
* Archived on                      :    2017-11-28 11:06:33
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    12c2e901dbb88a7cbcb71ede54ff2fdf  ImagingUpload-11-6-0NOcLo.tar
* md5sum for DICOM tarball gzipped :    9fc33ff9fbd72a4c5aa14d4c6235c238  ImagingUpload-11-6-0NOcLo.tar.gz
* md5sum for complete archive      :    5afa4143e07d50a2e340ddf45b5338d9  PPP_ImagingUpload-11-6-0NOcLo.tar

Adding archive info into database

Removing temporary files from target location


Done adding archive info into database

PPP/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar -verbose
 md5sum PPP/data/tarchive/DPPP_ImagingUpload-11-6-0NOcLo.tar
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP

Number of MINC files that will be considered for inserting into the database: 5

log dir is PPP/data/logs and log file is PPP/data/logs/TarLoad-11-6-MewKHm.log
PSCID is: PPP
 CandID id: PPP
 visit_label is: PPP
candidate id PPP

tr:     2500
te:     12.1
ti:
st:     3
time;
xspace: 256
yspace: 256
zspace: 60
xstep:  -0.9765723348
ystep:  -0.9765625
zstep:  3.
        Checking flair (41) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking pdw (1001) (Axial PD =~ NULL)
        TR      TE      xspace  yspace  zspace  ST
        Checking t1 (44) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking t2w (1002) (Axial PD =~ NULL)
        xspace  yspace  zspace  ST
        Checking NA (1000) (Axial PD =~ NULL)

...
... // the other 4 images //
...

Cleaning up temp files: rm -rf /tmp/TarLoad-11-6-FYfBtg/ImagingUpload-11-6-0NOcLo*

 No Mincs inserted

The insertion scripts have failed
-------------------------------------------------------------------------------

File: $project/data/logs/TarLoad-11-6-MewKHm.log
-------------------------------------------------------------------------------
==> Loading file from disk /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

--> mapping DICOM parameter for /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc

==> computing md5 hash for MINC body.

--> md5: 2278a2f9c6f586a16316d41390a0c045

==> verifying acquisition protocol

Acquisition protocol is unknown

  --> The minc file cannot be registered since the AcquisitionProtocol is unknown
-------------------------------------------------------------------------------


I can provide more information if needed.

Any help is welcomed :)

Regards,
Alfredo.

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