[Loris-dev] loris server
Melanie Legault, Mrs
melanie.legault2 at mcgill.ca
Tue Nov 12 07:06:51 EST 2019
Hello,
Sorry, I didn't used the exact name of the parameter. It is <host>.
<database>
<host>localhost</host>
<username>lorismysql</username>
...
Also, in the config table, `url` should be `http://localhost/` with the slash at the end. Should not be the cause to the current problem.
As for creating a new user, I don't think it will solve the problem.
Could you ensure that in MariaDB, the user `lorismysql`@`localhost` have the update permission (select, insert, update, delete) on `loris_database`.* as well as usage on these tables.
Also can you check which version of MariaDB you have? The version of MariaDB that come with CentOS 7 isn't supported for the latest versions of LORIS.
We have instructions (not quite definitive yet) on how to install MariaDB 10.3 in the documentation for Release 22 that should be out soon.
https://github.com/aces/Loris/blob/22.0-release/README.CentOS7.md
Kind regards,
Mélanie
________________________________
From: Julie Ashworth, HWNI Computing Support <support-cirl at berkeley.edu>
Sent: November 11, 2019 22:30
To: Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
Cc: Christine Rogers, Ms. <christine.rogers at mcgill.ca>; Ioannis Pappas <ioannis at berkeley.edu>; loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] loris server
thanks Christine and Melanie -
I updated the Config table settings (see below).
Ioannis,
can you please test if it works now?
Melanie,
I couldn't find a reference to dbHost in the config.xml file. The only reference to host that I could find is:
# grep -i host /srv/www/loris/project/config.xml
<host>localhost</host>
<hostname>%COUCH_HOSTNAME%</hostname>
MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www';
+----------+-------------------+-------------------+------------------+--------------------------------------+
| ConfigID | Name | Label | Value | Description |
+----------+-------------------+-------------------+------------------+--------------------------------------+
| 44 | host | Host | localhost | Host |
| 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed |
| 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url |
+----------+-------------------+-------------------+------------------+--------------------------------------+
thanks!
Julie
On 11-11-2019 17.28 +0000, Melanie Legault, Mrs wrote:
> Hello Julie,
> Yes, the '%' sign is a wildcard for 'all host'. So it should be good but I
> had problem with that in the past.
> Could you ensure the 'lorismysql'@'localhost' user proper permissions.
>
> Also, in that case, in the config.xml file, the dbHost should be
> 'localhost'. MySQL treat 127.0.0.1 and localhost as 2 different host.
>
> Mélanie
>
> --------------------------------------------------------------------------
>
> From: Julie Ashworth, HWNI Computing Support <support-cirl at berkeley.edu>
> Sent: November 11, 2019 12:03
> To: Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
> Cc: Christine Rogers, Ms. <christine.rogers at mcgill.ca>; Ioannis Pappas
> <ioannis at berkeley.edu>; loris-dev at bic.mni.mcgill.ca
> <loris-dev at bic.mni.mcgill.ca>
> Subject: Re: [Loris-dev] loris server
> Â
> thanks Melanie,
> I'm including the output below. My understanding is that '%' matches all
> hostnames. Should I specifically grant permission to 'loris.priv' from
> user lorismysql? Or perhaps you recommend changing loris_database entries
> ('host' to 'localhost' and 'url' to '[1]http://localhost')?
> thanks!
>
> MariaDB [(none)]> SELECT User, Host FROM mysql.user;
> +------------+-----------+
> | User      | Host     |
> +------------+-----------+
> | lorismysql | %Â Â Â Â Â Â Â Â |
> | root      | 127.0.0.1 |
> | root      | ::1      |
> | lorismysql | localhost |
> | root      | localhost |
> +------------+-----------+
> 5 rows in set (0.00 sec)
>
> MariaDB [(none)]> SHOW grants for 'lorismysql'@'%';
> +--------------------------------------------------------------------------------+
> | Grants for lorismysql@%
> +--------------------------------------------------------------------------------+
> | GRANT USAGE ON *.* TO 'lorismysql'@'%'
> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO
> 'lorismysql'@'%' |
> +--------------------------------------------------------------------------------+
> 2 rows in set (0.00 sec)
>
> On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote:
> >Â Â Â Hello Julie,
> >Â Â Â Could it be that your MySQL 'lorismysql' user have different
> permissions
> >Â Â Â depending on where it is connecting to the DB?
> >Â Â Â A database admin (root) can check this for you.
> >Â Â Â SELECT User, Host FROM mysql.user;
> >Â Â Â then for the user that match the Host (name or IP address) of your
> LORIS
> >Â Â Â (Apache) server
> >Â Â Â SHOW grants for 'lorismysql'@'<Host>';
> >
> >   Mélanie
> >
> >Â Â Â
> --------------------------------------------------------------------------
> >
> >Â Â Â From: Julie Ashworth, HWNI Computing Support
> <support-cirl at berkeley.edu>
> >Â Â Â Sent: November 8, 2019 21:04
> >Â Â Â To: Christine Rogers, Ms. <christine.rogers at mcgill.ca>
> >Â Â Â Cc: Ioannis Pappas <ioannis at berkeley.edu>; Melanie Legault, Mrs
> >Â Â Â <melanie.legault2 at mcgill.ca>; loris-dev at bic.mni.mcgill.ca
> >Â Â Â <loris-dev at bic.mni.mcgill.ca>
> >Â Â Â Subject: Re: [Loris-dev] loris server
> >   ÂÂ
> >Â Â Â thanks Christine,
> >
> >Â Â Â yes, it's the lorismysql user in the config.xml file.
> >   Â Â Â Â Â Â Â <username>lorismysql</username>
> >   Â Â Â Â Â Â Â <database>loris_database</database>
> >   Â Â Â Â Â Â Â <quatUser>lorismysql</quatUser>
> >
> >Â Â Â we appeciate your help troubleshooting this.
> >Â Â Â best,
> >Â Â Â Julie
> >
> >Â Â Â On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote:
> >   >   Hi Ioannis,
> >   >   Could you open your file called config.xml
> >   >   (/srv/www/loris/project/config.xml) and confirm for us --ÂÂ
> which user
> >   >   credential is stored there, and what's the name of the
> database it is
> >   >   connecting to?
> >   >   This is the mysql user which connects to the database from
> the front
> >Â Â Â end
> >   >   of LORIS.ÂÂ
> >   >   If this user has insufficient privileges on your database,
> that would
> >   >   cause the errors you are seeing. I had assumed from your
> thread it
> >Â Â Â was
> >   >   your lorismysql user but it sounds like this should be
> verified.
> >   >   Let us know, and we'll keep following up when we come back
> online
> >Â Â Â after
> >   >   the weekend,
> >   >   Best,
> >   >   Christine
> >   >   On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas
> <ioannis at berkeley.edu>
> >   >   wrote:
> >Â Â Â >
> >   >     Hi Melanie.
> >   >     Thank you for taking the time to reply to this. I took
> some to
> >Â Â Â consider
> >   >     your comments. Unfortunately as I said to Christine we
> are unable
> >Â Â Â to do
> >   >     any kind of updating to the database (either that is
> changing the
> >Â Â Â name
> >   >     or changing the small html description, etc.).
> >   >     Based on some more digging and on some of Christine's
> comments I
> >Â Â Â have a
> >   >     feeling that our lorisweb front-end, admin user cannot
> write
> >Â Â Â anything to
> >   >     the database. Along these lines could it be the case the
> lorismysql
> >Â Â Â user
> >   >     (the database, admin user with INSERT, UPDATE, etc
> privileges) is
> >Â Â Â not
> >   >     â€œtalking†to the lorisweb front end user?
> What is the
> >Â Â Â difference between
> >   >     the two and could it be a installation problem for them
> not talking
> >Â Â Â to
> >   >     each other? As Julie said, lorismysql user is working
> normally with
> >   >     MariaDB.
> >   >     Thank you again for your help.
> >   >     Best wishes,
> >   >     Ioannis
> >Â Â Â >
> >   >       On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs
> >   >       <melanie.legault2 at mcgill.ca> wrote:
> >   >       Hello,
> >   >       Changing the project name in the configuration page
> >   >       ([1]https://loris.url/configuration/) of LORIS, only
> change the
> >Â Â Â title of
> >   >       the project. To see this change, you have to log out
> of LORIS and
> >Â Â Â then
> >   >       go back to the login page ([2]https://.loris.url/).
> This is the
> >Â Â Â only
> >   >       place you can find the project name (except from the
> >Â Â Â configuration
> >   >       page). See ProjectName.png
> >   >       As for files permission, I would suggest a few change
> to improve
> >   >       security of you server. Some extra permissions where
> granted to
> >Â Â Â help
> >   >       you but are not needed.
> >   >         * /srv/www/loris/smarty/templates_c/ should
> have ownership of
> >   >           lorisadmin:httpd and permission 770 (or 775)
> >   >         * srv/www/loris/project/ should have ownership
> >Â Â Â lorisadmin:httpd and
> >   >           permission 770 (775)
> >   >         * All other files under loris should have
> lorisadmin:lorisadmin
> >Â Â Â 755
> >   >       Reading through this change of mail, I understand
> that you let
> >Â Â Â Apache
> >   >       store file in /srv/www/loris
> >   >          |      31 | DownloadPath  |
> Downloads  | /srv/www/loris/ ÂÂ
> >Â Â Â |
> >   >       Where
> >   >       >>    files are downloaded
> >   >       Downloaded files should not be in the same tree as
> LORIS code. It
> >   >       should be in a separate structure where Apache will
> not try and
> >Â Â Â do not
> >   >       have permission (in httpd.conf) to execute files.
> >   >       Kind regards,
> >   >       Mélanie Legault | Software developer | Faculty of
> Medicine |
> >Â Â Â McGill
> >   >       UniversityÂÂ
> >   >       3801 University, Montréal, QC H3A 2B4
> >Â Â Â >
> >   >    ÂÂ
> >Â Â Â
> ----------------------------------------------------------------------
> >Â Â Â >
> >   >       From: loris-dev-bounces at bic.mni.mcgill.ca
> >   >       <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
> Ioannis Pappas
> >   >       <ioannis at berkeley.edu>
> >   >       Sent: November 7, 2019 0:18
> >   >       To: loris-dev at bic.mni.mcgill.ca
> <loris-dev at bic.mni.mcgill.ca>
> >   >       Cc: Julie Ashworth, HWNI Computing Support
> >   >       <support-cirl at berkeley.edu>; Christine Rogers, Ms.
> >   >       <christine.rogers at mcgill.ca>
> >   >       Subject: Re: [Loris-dev] loris server
> >   >       ÂÂ
> >   >       Hi Christine and Julie.
> >Â Â Â >
> >   >       Yes it looks like that any attempt to configure
> something in the
> >   >       front-end results in the same page. I am sending this
> to the list
> >Â Â Â (as
> >   >       you requested Christine) alongside the
> troubleshooting and
> >Â Â Â discussion
> >   >       so far with Julie.
> >Â Â Â >
> >   >       Best wishes,
> >   >       Ioannis
> >Â Â Â >
> >   >       > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI
> Computing
> >Â Â Â Support
> >   >       <support-cirl at berkeley.edu> wrote:
> >   >       >
> >   >       > hi Christine and Ioannis,
> >   >       > Ioannis, can you follow-up with Christine about
> using the
> >Â Â Â front-end?
> >   >       >
> >   >       > We're using CentOS7.7 and loris-21.0.1.
> >   >       >
> >   >       > I confirmed that I could login as the mysql user
> (lorismyqsl)
> >Â Â Â and
> >   >       change the 'url' config setting from
> '[3]http://loris.priv' to
> >   >       '[4]http://localhost', and back again.
> >   >       >
> >   >       > MariaDB [loris_database]> SELECT c.ConfigID,
> cs.Name, cs.Label,
> >   >       c.Value, cs.Description FROM Config c LEFT JOIN
> ConfigSettings cs
> >Â Â Â ON
> >   >       (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON
> (cs.Parent =
> >Â Â Â csp.ID)
> >   >       WHERE csp.Name = 'www';
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       > | ConfigID | Name             |
> Label            |
> >   >       Value            |
> Description                         |
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       > |      44 | host             |
> Host             |
> >   >       loris.priv       |
> Host                                |
> >   >       > |      45 | url             ÂÂ
> | Main LORIS URL ÂÂ
> >   >       | [5]http://loris.priv | Main URL where LORIS can be
> accessed |
> >   >       > |      46 | issue_tracker_url | Issue
> tracker URL |
> >   >       /issue_tracker   | The *new* bug/issue tracker
> url     |
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       >
> >   >       > MariaDB [loris_database]> UPDATE Config SET
> >Â Â Â Value='[6]http://localhost'
> >   >       WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE
> Name='url');
> >   >       > Rows matched: 1 Changed: 1 Warnings: 0
> >   >       >
> >   >       > MariaDB [loris_database]> SELECT c.ConfigID,
> cs.Name, cs.Label,
> >   >       c.Value, cs.Description FROM Config c LEFT JOIN
> ConfigSettings cs
> >Â Â Â ON
> >   >       (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON
> (cs.Parent =
> >Â Â Â csp.ID)
> >   >       WHERE csp.Name = 'www';
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+------------------+--------------------------------------+
> >   >       > | ConfigID | Name             |
> Label            |
> >   >       Value           |
> Description                         |
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+------------------+--------------------------------------+
> >   >       > |      44 | host             |
> Host             |
> >   >       loris.priv      |
> Host                                |
> >   >       > |      45 | url             ÂÂ
> | Main LORIS URL ÂÂ
> >   >       | [7]http://localhost | Main URL where LORIS can be
> accessed |
> >   >       > |      46 | issue_tracker_url | Issue
> tracker URL |
> >   >       /issue_tracker  | The *new* bug/issue tracker
> url     |
> >   >       >
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+------------------+--------------------------------------+
> >   >       > 3 rows in set (0.00 sec)
> >   >       >
> >   >       > best,
> >   >       > Julie
> >   >       >
> >   >       >
> >   >       > On 06-11-2019 21.43 +0000, Christine Rogers, Ms.
> wrote:
> >   >       >>  Hi Julie,
> >   >       >>  Forgive my ambiguity - We run the community
> support listserv
> >Â Â Â for
> >   >       >>  developers, project administrators and
> sysadmins setting up
> >   >       LORIS, so that
> >   >       >>  these users can contact our technical team for
> exactly such
> >   >       technical
> >   >       >>  help.ÂÂ
> >   >       >>  If it's ok with you, I'd encourage you
> subscribe to the
> >Â Â Â listserv
> >   >       and
> >   >       >>  contact our technical team that way for the
> same reason.
> >   >       >>  (Note that front-end users of LORIS typically
> contact their
> >   >       project team
> >   >       >>  for support, rather than us.)
> >   >       >>  Given that your lorismysql user privileges
> seem appropriate
> >   >       ('UPDATE" is
> >   >       >>  there, I mistyped 'INSERT" before)
> >   >       >>  -- is there any other indication why the
> database record is
> >Â Â Â not
> >   >       >>  updating?ÂÂ
> >   >       >>  In the front-end, can your 'admin' user effect
> any changes
> >Â Â Â in
> >   >       (any) Config
> >   >       >>  setting?ÂÂ
> >   >       >>  In the back-end, when you tried updating a
> field using your
> >   >       >>  lorismysql credential, what happened?
> >   >       >>  Your front end is loading ok, and you can log
> in there, if I
> >   >       understood
> >   >       >>  correctly.
> >   >       >>  Thanks for letting us know these details at
> >   >       >>  [1]loris-dev at bic.mni.mcgill.ca
> >   >       >>  Please also include what version of LORIS you
> are
> >Â Â Â installing, and
> >   >       on what
> >   >       >>  OS version.
> >   >       >>  Best,
> >   >       >>  Christine
> >   >       >>  On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth,
> HWNI
> >Â Â Â Computing
> >   >       Support
> >   >       >>  <[2]support-cirl at berkeley.edu> wrote:
> >   >       >>
> >   >       >>    Thank you Christine,
> >   >       >>    I'm the linux sysadmin who installed the
> loris database
> >Â Â Â for
> >   >       Ioannis.
> >   >       >>    I'm not a loris user, however, so that
> makes it a little
> >   >       awkward for
> >   >       >>    troubleshooting via the mailing list. I'm
> happy to help in
> >   >       whatever way
> >   >       >>    I can.
> >   >       >>
> >   >       >>    Regarding the database permissions, I ran:
> >   >       >>
> >   >       >>    MariaDB [(none)]> show grants for
> 'lorismysql'@'%';
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +--------------------------------------------------------------------------------+
> >   >       >>    | Grants for lorismysql@%
> >   >       >>    |
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +--------------------------------------------------------------------------------+
> >   >       >>    | GRANT USAGE ON *.* TO 'lorismysql'@'%'
> >   >       >>    |
> >   >       >>    | GRANT SELECT, INSERT, UPDATE, DELETE ON
> >Â Â Â `loris_database`.* TO
> >   >       >>    'lorismysql'@'%' |
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +--------------------------------------------------------------------------------+
> >   >       >>    2 rows in set (0.00 sec)
> >   >       >>
> >   >       >>    looking at the 'tips' section in the page
> you referred
> >Â Â Â to...
> >   >       >>
> >   >       >>    |      29 |
> base          | Base       |
> >   /srv/www/loris/  |
> >   >       The base
> >   >       >>    filesystem path where LORIS is
> >   >      ÂÂ
> installed                         |
> >   >       >>    |      31 | DownloadPath  |
> Downloads  |
> >   /srv/www/loris/  |
> >   >       Where
> >   >       >>    files are downloaded
> >   >       >>
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       >>    | ConfigID |
> Name             | Label            |
> >   >       Value            |
> >   >       >>   ÂÂ
> Description                         |
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       >>    |      44 |
> host             | Host             |
> >   >       loris.priv       |
> >   >       >>   ÂÂ
> Host                                |
> >   >       >>    |      45 |
> url              | Main LORIS URL   |
> >   >       >>    [3]http://loris.priv | Main URL where
> LORIS can be
> >Â Â Â accessed |
> >   >       >>    |      46 | issue_tracker_url |
> Issue tracker URL |
> >   >       /issue_tracker   |
> >   >       >>    The *new* bug/issue tracker url    ÂÂ
> |
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >   >       >>
> >   >       >>    apache config:
> >   >       >>
> >   >       >>    Listen 80
> >   >       >>    User apache
> >   >       >>    Group apache
> >   >       >>    DocumentRoot "/srv/www/loris/htdocs"
> >   >       >>
> >   >       >>    <Directory />
> >   >       >>        AllowOverride none
> >   >       >>        Require all denied
> >   >       >>    </Directory>
> >   >       >>
> >   >       >>    <Directory "/srv/www">
> >   >       >>        AllowOverride All
> >   >       >>        Options Indexes FollowSymLinks
> >   >       >>        Require all granted
> >   >       >>    </Directory>
> >   >       >>
> >   >       >>    <Directory "/srv/www/loris/htdocs">
> >   >       >>        Options Indexes FollowSymLinks
> >   >       >>        AllowOverride All
> >   >       >>        Require all granted
> >   >       >>    </Directory>
> >   >       >>
> >   >       >>    file permissions:
> >   >       >>
> >   >       >>    # ls -ld /srv/www/loris/smarty/templates_c
> >   >       >>    drwxrwxrwx 2 lorisadmin lorisadmin 4096
> Oct 31 09:46
> >   >       >>    /srv/www/loris/smarty/templates_c/
> >   >       >>
> >   >       >>    [root at loris loris]# ls -l
> >Â Â Â /srv/www/loris/smarty/templates_c
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 2444
> Oct 31 09:46
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 10490
> Sep 10 10:55
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 21126
> Sep 7 18:39
> >   >       >>   ÂÂ
> >Â Â Â 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 3296
> Sep 7 18:35
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 5901
> Sep 7 21:10
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 23339
> Sep 7 18:39
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin  874
> Sep 10 11:01
> >   >       >>   ÂÂ
> >Â Â Â 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 1101
> Sep 10 10:58
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 18054
> Sep 10 10:59
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 3590
> Sep 7 18:39
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 25141
> Sep 7 21:08
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin  897
> Sep 7 18:35
> >   >       >>   ÂÂ
> >Â Â Â a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 9210
> Sep 10 11:01
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 8917
> Sep 10 13:21
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 4811
> Sep 7 18:35
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 3309
> Sep 10 11:02
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 10303
> Sep 10 10:59
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php
> >   >       >>    -rw-r--r-- 1 lorisadmin lorisadmin 12273
> Sep 7 17:42
> >   >       >>   ÂÂ
> >Â Â Â fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php
> >   >       >>
> >   >       >>    thanks again!
> >   >       >>    Julie
> >   >       >>
> >   >       >>    On 06-11-2019 19.01 +0000, Christine
> Rogers, Ms. wrote:
> >   >       >>>    Hi Ioannis,Â
> >   >       >>>    Thanks for your question.Â
> >   >       >>>    Given that the URL field is not updating,
> I suspect it's
> >Â Â Â a
> >   >       database
> >   >       >>>    back-end issue.Â
> >   >       >>>    Can you verify -- Has your mysql user
> lorismysql been
> >Â Â Â granted
> >   >       the
> >   >       >>    "INSERT"
> >   >       >>>    privilege for the right database? If not,
> that would
> >Â Â Â result in
> >   >       an
> >   >       >>    error
> >   >       >>>    like the kind you are seeing.Â
> >   >       >>>    Also, if you wish to check your LORIS
> Configuration
> >Â Â Â settings
> >   >       in the
> >   >       >>>    backend database such as the URL field --
> to see what was
> >   >       actually
> >   >       >>    stored
> >   >       >>>    in a given database field and should
> display in the
> >Â Â Â Config
> >   >       >>    module:Â
> >   >       >>>    You can run the queries listed in the
> "Troubleshooting
> >   >       >>    Configuration
> >   >       >>>    settings" section of our Github-wiki
> Setup Guide (under
> >   >       Project
> >   >       >>>    Customization) :Â
> >   >       >>>  ÂÂ
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >   >       >>>    Lastly, this question is perfectly
> appropriate for the
> >   >       loris-dev
> >   >       >>    community
> >   >       >>>    support listserv -- please [2]subscribe
> here and then
> >Â Â Â email
> >   >       our
> >   >       >>    technical
> >   >       >>>    team your next question atÂ
> >Â Â Â [3][5]loris-dev at bic.mni.mcgill.ca
> >   >       >>    (after checking
> >   >       >>>    any forwarded threads for sensitive
> info).Â
> >   >       >>>    We prefer to answer technical questions
> there for the
> >Â Â Â benefit
> >   >       of
> >   >       >>    the
> >   >       >>>    community and other first-time users in
> the same position
> >Â Â Â as
> >   >       >>    yourself. Â
> >   >       >>>    Thanks and cheers,Â
> >   >       >>>    ChristineÂ
> >   >       >>>    On Mon, Nov 4, 2019 at 5:49 PM Dr.
> Ioannis Pappas PhD
> >   >       >>>    <[4][6]ioannis at berkeley.edu> wrote:
> >   >       >>>
> >   >       >>>      Hi Loris support.Â
> >   >       >>>      My name is ioannis Pappas, a post-doc
> at the D'Esposito
> >Â Â Â lab
> >   >       >>    stroke group
> >   >       >>>      at UC Berkeley. With the kind of help
> of our sys
> >   adminÂ
> >   >       Julie
> >   >       >>    (cc'ed) we
> >   >       >>>      have set up our loris database in our
> cluster (she is
> >Â Â Â the
> >   >       sudo
> >   >       >>    user and
> >   >       >>>      I am the admin user).
> >   >       >>>      If you allow me, I would like to ask
> you about the
> >Â Â Â first
> >   >       >>    configuration
> >   >       >>>      steps in the front end as they are
> described in the
> >   >       tutorial. We
> >   >       >>    can
> >   >       >>>      login to [5][7]http://loris and the
> front end normally.
> >   >       >>>      However any update that I am trying
> to perform in
> >   >       >>    Admin->Configuration
> >   >       >>>      doesn't work (e.g. updating the study
> name). It just
> >   >       refreshes
> >   >       >>    the same
> >   >       >>>      page. I am just wondering if there is
> an issue with
> >Â Â Â writing
> >   >       in
> >   >       >>    the
> >   >       >>>      configuration file.
> >   >       >>>      Here are the permissions setup for
> where Loris is
> >Â Â Â installed.
> >   >       >>>      chmod 777
> /var/www/loris/smarty/templates_c
> >   >       >>>      cd /srv/www/loris
> >   >       >>>      chown -R lorisadmin:lorisadmin .
> >   >       >>>      chmod -c -R a+r .
> >   >       >>>      Ã‚ Ã‚ this command gives
> everyone read access, and
> >Â Â Â outputs
> >   >       what
> >   >       >>    changes
> >   >       >>>      were made:
> >   >       >>>      Ã‚ Ã‚ mode of
> ¿./project¿ changed from 0770
> >Â Â Â (rwxrwx---) to
> >   >       0774
> >   >       >>>      (rwxrwxr--)
> >   >       >>>      Ã‚ Ã‚ mode of
> ¿./tools/logs¿ changed from 0770
> >Â Â Â (rwxrwx---)
> >   >       to
> >   >       >>    0774
> >   >       >>>      (rwxrwxr--)
> >   >       >>>      find . -type d -exec chmod a+x -c {}
> \;
> >   >       >>>      Ã‚ Ã‚ this command gives
> everyone permission to open
> >Â Â Â a
> >   >       directory,
> >   >       >>    and
> >   >       >>>      outputs what changes were made:
> >   >       >>>      Ã‚ Ã‚ mode of
> ¿./project¿ changed from 0774
> >Â Â Â (rwxrwxr--) to
> >   >       0775
> >   >       >>>      (rwxrwxr-x)
> >   >       >>>      Ã‚ Ã‚ mode of
> ¿./tools/logs¿ changed from 0774
> >Â Â Â (rwxrwxr--)
> >   >       to
> >   >       >>    0775
> >   >       >>>      (rwxrwxr-x)
> >   >       >>>      Hopefully you can help me with
> this. I also
> >Â Â Â subscribed to
> >   >       the
> >   >       >>    mailing
> >   >       >>>      list but I am not sure if this too
> much of a basic
> >Â Â Â question
> >   >       for
> >   >       >>    the
> >   >       >>>      list.
> >   >       >>>      Best wishes,
> >   >       >>>      Ioannis
> >   >       >>>      On Mon, Nov 4, 2019 at 1:12 PM Julie
> Ashworth, HWNI
> >   >       Computing
> >   >       >>    Support
> >   >       >>>      <[6][8]support-cirl at berkeley.edu>
> wrote:
> >   >       >>>
> >   >       >>>        Hi ioannis, maybe it's best to
> ask the developers?
> >Â Â Â You can
> >   >       cc
> >   >       >>    me if
> >   >       >>>        you'd like.
> >   >       >>>        On Mon, Nov 4, 2019, 12:37 PM
> Ioannis Pappas
> >   >       >>    <[7][9]ioannis at berkeley.edu>
> >   >       >>>        wrote:
> >   >       >>>
> >   >       >>>          That did the trick Julie.
> Thank you!
> >   >       >>>
> >   >       >>>          I am still trying to
> understand how configuration
> >Â Â Â works
> >   >       >>    though. For
> >   >       >>>          example if I just try to
> change the name of the
> >   >       >>>          study from the front end, I
> get nowhere (it just
> >   >       refreshes
> >   >       >>    the same
> >   >       >>>          page).
> >   >       >>>
> >   >       >>>          I am not sure if this
> requires write permissions
> >   >       somewhere in
> >   >       >>    a
> >   >       >>>          config file/folder and
> thatÃƒÂ¢Ã¢â€šÂ¬Ã¢â€şÂ¢s why it
> >   doesnÃƒÂ¢Ã¢â€šÂ¬Ã¢â€şÂ¢t update
> >   >       it.
> >   >       >>>
> >   >       >>>          Best wishes,
> >   >       >>>          Ioannis
> >   >       >>>
> >   >       >>>          > On Nov 4, 2019, at 12:08
> PM, Julie Ashworth, HWNI
> >   >       Computing
> >   >       >>>          Support
> <[8][10]support-cirl at berkeley.edu> wrote:
> >   >       >>>          >
> >   >       >>>          > just in case you're
> interested, these are the
> >   >       permission
> >   >       >>    changes I
> >   >       >>>          made:
> >   >       >>>          >
> >   >       >>>          > chmod 777
> /var/www/loris/smarty/templates_c
> >   >       >>>          > cd /srv/www/loris
> >   >       >>>          > chown -R
> lorisadmin:lorisadmin .
> >   >       >>>          > chmod -c -R a+r .
> >   >       >>>          > Â this command
> gives everyone read access,
> >Â Â Â and
> >   >       outputs
> >   >       >>    what
> >   >       >>>          changes were made:
> >   >       >>>          > Â mode of
> ¿./project¿ changed from
> >Â Â Â 0770
> >   >       (rwxrwx---) to
> >   >       >>    0774
> >   >       >>>          (rwxrwxr--)
> >   >       >>>          > Â mode of
> ¿./tools/logs¿ changed from
> >Â Â Â 0770
> >   >       (rwxrwx---)
> >   >       >>    to 0774
> >   >       >>>          (rwxrwxr--)
> >   >       >>>          > find . -type d -exec chmod
> a+x -c {} \;
> >   >       >>>          > Â this command
> gives everyone permission to
> >Â Â Â open a
> >   >       >>    directory, and
> >   >       >>>          outputs what changes were
> made:
> >   >       >>>          > Â mode of
> ¿./project¿ changed from
> >Â Â Â 0774
> >   >       (rwxrwxr--) to
> >   >       >>    0775
> >   >       >>>          (rwxrwxr-x)
> >   >       >>>          > Â mode of
> ¿./tools/logs¿ changed from
> >Â Â Â 0774
> >   >       (rwxrwxr--)
> >   >       >>    to 0775
> >   >       >>>          (rwxrwxr-x)
> >   >       >>>          >
> >   >       >>>          >
> >   >       >>>          >
> >   >       >>>          > On 04-11-2019 12.03 -0800,
> Ioannis Pappas wrote:
> >   >       >>>          >> Hi Julie.
> >   >       >>>          >> I just tried and I still
> don???t get anything. I
> >Â Â Â also
> >   >       >>    tried
> >   >       >>>          private mode in Firefox in
> case the empty page was
> >   >       cached.
> >   >       >>>          >> Sorry for this.
> >   >       >>>          >>
> >   >       >>>          >> Best wishes,
> >   >       >>>          >> Ioannis
> >   >       >>>          >>
> >   >       >>>          >>> On Nov 4, 2019, at 11:58
> AM, Julie Ashworth,
> >Â Â Â HWNI
> >   >       >>    Computing
> >   >       >>>          Support
> <[9][11]support-cirl at berkeley.edu> wrote:
> >   >       >>>          >>>
> >   >       >>>          >>> hi Ioannis,
> >   >       >>>          >>> no worries, I changed the
> following directory
> >Â Â Â to
> >   >       777:
> >   >       >>>          >>>
> >   >       >>>          >>>
> /var/www/loris/smarty/templates_c
> >   >       >>>          >>>
> >   >       >>>          >>> will you please check if
> that works?
> >   >       >>>          >>>
> >   >       >>>          >>> thanks!
> >   >       >>>          >>>
> >   >       >>>          >>>
> >   >       >>>          >>>
> >   >       >>>          >>>
> >   >       >>>          >>>
> >   >       >>>          >>> On 04-11-2019 11.49
> -0800, Dr. Ioannis Pappas
> >Â Â Â PhD
> >   >       wrote:
> >   >       >>>          >>>> Hi Julie.
> >   >       >>>          >>>> Apologies for
> bugging you with this again.
> >Â Â Â We
> >   >       tried
> >   >       >>    now to
> >   >       >>>          >>>> accessÂ
> [1][10][12]http://lorisÂ
> >   >       >>>          >>>> and we are
> getting a blank page. I
> >Â Â Â think the
> >   >       reason
> >   >       >>    for this
> >   >       >>>          is that we
> >   >       >>>          >>>> don't have
> read permissions to read
> >Â Â Â from the
> >   >       >>    template located
> >   >       >>>          in
> >   >       >>>          >>>>ÂÂÂ
> /var/www/loris/smarty See here bottom of
> >Â Â Â the
> >   >       >>>          >>>> pageÂ
> >   >       >>>        ÂÂ
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >>>          >>>> I think, in
> general, I am a little bit
> >Â Â Â confused
> >   >       as to
> >   >       >>    what the
> >   >       >>>          permissions
> >   >       >>>          >>>> should be for us
> that are not sudos. My
> >   >       understanding
> >   >       >>    is that
> >   >       >>>          if we don't
> >   >       >>>          >>>> have read or
> write permissions then we
> >Â Â Â can't
> >   >       access or
> >   >       >>    write
> >   >       >>>          to
> >   >       >>>          >>>> /var/www/loris,
> meaning that we can't
> >Â Â Â access or
> >   >       >>    configure.
> >   >       >>>          Should
> >   >       >>>          >>>> everything be
> chmod 777 for example?Â
> >   >       >>>          >>>> Thank you very
> much once again.
> >   >       >>>          >>>> Best wishes,
> >   >       >>>          >>>> Ioannis
> >   >       >>>          >>>> On Thu, Oct 31,
> 2019 at 1:56 PM Dr. Ioannis
> >   >       Pappas PhD
> >   >       >>>          >>>>ÂÂÂ
> <[3][12][14]ioannis at berkeley.edu> wrote:
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Thank you
> very much Julie. I appreciate
> >Â Â Â this
> >   >       and I
> >   >       >>    will dig
> >   >       >>>          into Loris
> >   >       >>>          >>>> Â given
> your changes. Thank you so much
> >Â Â Â for your
> >   >       >>    help.
> >   >       >>>          >>>> Â Best
> wishes,
> >   >       >>>          >>>> Â Ioannis
> >   >       >>>          >>>> Â On Thu,
> Oct 31, 2019 at 12:48 PM Julie
> >   >       Ashworth,
> >   >       >>    HWNI
> >   >       >>>          Computing Support
> >   >       >>>          >>>> ÂÂÂ
> <[4][13][15]support-cirl at berkeley.edu>
> >Â Â Â wrote:
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> hi Ioannis,
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> 1. I changed the permissions of
> >   >       /srv/www/loris
> >   >       >>    to be owned
> >   >       >>>          by
> >   >       >>>          >>>> Â Ã‚ÂÂ
> lorisadmin. I reivewed my
> >Â Â Â installation
> >   >       notes,
> >   >       >>    and I did
> >   >       >>>          this already
> >   >       >>>          >>>> Â Ã‚ÂÂ
> when
> >   >       >>>          >>>> Â Ã‚ I
> installed the server. I'm not
> >Â Â Â sure why
> >   >       they
> >   >       >>    changed, so
> >   >       >>>          it's
> >   >       >>>          >>>> Â Ã‚ÂÂ
> probably a
> >   >       >>>          >>>> Â Ã‚ÂÂ
> good idea to keep an eye on that.
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> 2. When I installed the loris
> >Â Â Â software, I
> >   >       also
> >   >       >>    installed a
> >   >       >>>          mysql
> >   >       >>>          >>>> Â Ã‚ÂÂ
> database as recommended in the
> >   >       instructions:
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> projectname: LORIS
> >   >       >>>          >>>> Â Ã‚ÂÂ
> databasename: loris_database
> >   >       >>>          >>>> Â Ã‚ÂÂ
> mysqluser: lorismysql
> >   >       >>>          >>>> Â Ã‚ÂÂ
> frontend: lorisweb
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> 3. A couple of weeks ago, I moved
> >Â Â Â Henrik's
> >   >       home
> >   >       >>    directory
> >   >       >>>          to
> >   >       >>>          >>>> Â Ã‚ÂÂ
> /home/despoA,
> >   >       >>>          >>>> Â Ã‚ÂÂ
> but I forgot to update loris. This
> >Â Â Â is done
> >   >       now.
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> best,
> >   >       >>>          >>>> Â Ã‚ÂÂ
> Julie
> >   >       >>>          >>>>
> >   >       >>>          >>>> Â Ã‚ÂÂ
> On 31-10-2019 11.15 -0700, Dr.
> >Â Â Â Ioannis
> >   >       Pappas
> >   >       >>    PhD wrote:
> >   >       >>>          >>>>> ÂÂÂÂ
>  Hi Julie.
> >   >       >>>          >>>>> ÂÂÂÂ
>  I hope you are well. We are
> >Â Â Â trying to
> >   >       >>    configure loris
> >   >       >>>          that you
> >   >       >>>          >>>> Â Ã‚ÂÂ
> kindly set
> >   >       >>>          >>>>> ÂÂÂÂ
>  up for us.
> >   >       >>>          >>>>> ÂÂÂÂ
>  I have a couple of
> >Â Â Â questions for you if
> >   >       you
> >   >       >>    allow me
> >   >       >>>          so.Â
> >   >       >>>          >>>>> ÂÂÂÂ
>  1) First, although we are
> >Â Â Â logging into
> >   >       the
> >   >       >>    front end
> >   >       >>>          with admin
> >   >       >>>          >>>> Â Ã‚ÂÂ
> username
> >   >       >>>          >>>>> ÂÂÂÂ
>  (lorisweb) and password, it
> >Â Â Â seems that
> >   >       any
> >   >       >>    kind of
> >   >       >>>          update of
> >   >       >>>          >>>> Â Ã‚ÂÂ
> configuration
> >   >       >>>          >>>>> ÂÂÂÂ
>  we are trying to do fails
> >Â Â Â (meaning that
> >   >       if
> >   >       >>    we, say,
> >   >       >>>          change the
> >   >       >>>          >>>> Â Ã‚ÂÂ
> name of the
> >   >       >>>          >>>>> ÂÂÂÂ
>  study and press "submit",
> >Â Â Â this doesn't
> >   >       do
> >   >       >>    anything-it
> >   >       >>>          doesn't
> >   >       >>>          >>>> Â Ã‚ÂÂ
> update).
> >   >       >>>          >>>>> ÂÂÂÂ
>  It's almost like our
> >Â Â Â lorisweb user
> >   >       doesn't
> >   >       >>    have write
> >   >       >>>          privileges
> >   >       >>>          >>>> Â Ã‚ÂÂ
> in the
> >   >       >>>          >>>>> ÂÂÂÂ
>  /var/www/loris/project
> >Â Â Â (where I think
> >   >       every
> >   >       >>>          configuration should
> >   >       >>>          >>>> Â Ã‚ÂÂ
> be).
> >   >       >>>          >>>>> ÂÂÂÂ
>  This generalizes for
> >Â Â Â everything that we
> >   >       are
> >   >       >>    trying to do
> >   >       >>>          in the
> >   >       >>>          >>>> Â Ã‚ÂÂ
> front end.
> >   >       >>>          >>>>> ÂÂÂÂ
>  Clicking any instrument/tab
> >Â Â Â in the front
> >   >       end
> >   >       >>    doesn't
> >   >       >>>          really point
> >   >       >>>          >>>> Â Ã‚ÂÂ
> to
> >   >       >>>          >>>>> ÂÂÂÂ
>  anything.Â
> >   >       >>>          >>>>> ÂÂÂÂ
>  2) Loris suggest doing
> >Â Â Â configurations
> >   >       via
> >   >       >>    SQL. Is it
> >   >       >>>          possible to
> >   >       >>>          >>>> Â Ã‚ÂÂ
> run SQL
> >   >       >>>          >>>>> ÂÂÂÂ
>  scripts in the backend
> >   >       >>>          >>>>> ÂÂÂÂ
>  3) For some reason typing
> >Â Â Â ssh lors for
> >   >       Henrik
> >   >       >>    doesn't
> >   >       >>>          directly
> >   >       >>>          >>>> Â Ã‚ÂÂ
> take him to
> >   >       >>>          >>>>> ÂÂÂÂ
>  loris (it requires a
> >Â Â Â password that is
> >   >       not the
> >   >       >>    password
> >   >       >>>          setup for
> >   >       >>>          >>>> Â Ã‚ÂÂ
> the
> >   >       >>>          >>>>> ÂÂÂÂ
>  lorisweb user). Will you be
> >Â Â Â able to fix
> >   >       this
> >   >       >>    via your
> >   >       >>>          sudo
> >   >       >>>          >>>> Â Ã‚ÂÂ
> privileges?
> >   >       >>>          >>>>> ÂÂÂÂ
>  Thank you very much in
> >Â Â Â advance for all
> >   >       your
> >   >       >>    help Julie.
> >   >       >>>          Let us
> >   >       >>>          >>>> Â Ã‚ÂÂ
> know if
> >   >       >>>          >>>>> ÂÂÂÂ
>  this is something that
> >Â Â Â shouldn't be
> >   >       directed
> >   >       >>    to you (but
> >   >       >>>          instead
> >   >       >>>          >>>> Â Ã‚ÂÂ
> to the
> >   >       >>>          >>>>> ÂÂÂÂ
>  loris people).Â
> >   >       >>>          >>>>> ÂÂÂÂ
>  Best wishes,
> >   >       >>>          >>>>> ÂÂÂÂ
>  Ioannis
> >   >       >>>          >>>>> ÂÂÂÂ
>  On Mon, Sep 9, 2019 at 6:25
> >Â Â Â PM Julie
> >   >       >>    Ashworth, HWNI
> >   >       >>>          Computing
> >   >       >>>          >>>> Â Ã‚ÂÂ
> Support
> >   >       >>>          >>>>> ÂÂÂÂ
> ÂÂ
> >   >       <[1][5][14][16]support-cirl at berkeley.edu>
> >   >       >>    wrote:
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â hi Henrik and
> >Â Â Â Ioannis,
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â the loris server
> >Â Â Â is available for
> >   >       you to
> >   >       >>    use.
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â The servername is
> >Â Â Â 'loris'. I
> >   >       created a
> >   >       >>    directory
> >   >       >>>          called
> >   >       >>>          >>>> Â Ã‚ÂÂ
> /data/loris for
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â you to store data.
> >Â Â Â You may create
> >   >       new
> >   >       >>    folders in
> >   >       >>>          /data/loris to
> >   >       >>>          >>>> Â Ã‚ÂÂ
> organize
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â your data.
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â 1) secure shell or
> >Â Â Â secure copy:
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â You can log in
> >Â Â Â with the 'ssh' or
> >   >       'scp'
> >   >       >>    command from
> >   >       >>>          your remote
> >   >       >>>          >>>> Â Ã‚ÂÂ
> desktop
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â session. You don't
> >Â Â Â need to
> >   >       authenticate
> >   >       >>    to log in.
> >   >       >>>          Maybe you'll
> >   >       >>>          >>>> Â Ã‚ÂÂ
> use scp
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â to transfer data
> >Â Â Â between your
> >   >       cluster
> >   >       >>    account and the
> >   >       >>>          loris
> >   >       >>>          >>>> Â Ã‚ÂÂ
> server?
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Please put the
> >Â Â Â data in /data/loris,
> >   >       so I
> >   >       >>    can make
> >   >       >>>          backups more
> >   >       >>>          >>>> Â Ã‚ÂÂ
> easily.
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â secure shell:
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â $ ssh loris
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â secure copy (change the
> >   >       names
> >   >       >>    in brackets). Let
> >   >       >>>          me know if
> >   >       >>>          >>>> Â Ã‚ I
> can
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â help with syntax:
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â $ scp -r <data>
> >   >       >>    loris:/data/loris/<newfolder>
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â 2) front-end web
> >   interface.ÂÂ
> >   >       Open a
> >   >       >>    web browser in
> >   >       >>>          your remote
> >   >       >>>          >>>> Â Ã‚ÂÂ
> desktop
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â session and enter
> >Â Â Â the hostname:
> >   >       >>>          >>>>> ÂÂÂÂ
>  ÂÂÂÂ
> >Â Â Â [2][6][15][17]http://loris
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â I created an admin
> >Â Â Â user called
> >   >       >>    'lorisweb'. I put the
> >   >       >>>          password
> >   >       >>>          >>>> Â Ã‚ÂÂ
> in
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â $HOME/newuser on
> >Â Â Â the cluster. To
> >   >       see it,
> >   >       >>    open a
> >   >       >>>          terminal, and
> >   >       >>>          >>>> Â Ã‚ÂÂ
> run:
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Ã‚ÂÂÂ
> ÂÂÂÂ
> >Â Â Â $ cat $HOME/newuser
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â If other people
> >Â Â Â need shell access
> >   >       to the
> >   >       >>    webserver,
> >   >       >>>          please let
> >   >       >>>          >>>> Â Ã‚ÂÂ
> me know
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â so I can create a
> >Â Â Â home directory
> >   >       for
> >   >       >>    them.
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â We should
> >Â Â Â eventually discuss
> >   >       backups.
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â best,
> >   >       >>>          >>>>> ÂÂÂÂ
>  Â Julie
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> References
> >   >       >>>          >>>>>
> >   >       >>>          >>>>> ÂÂÂÂ
>  Visible links
> >   >       >>>          >>>>> ÂÂÂÂ
>  1.
> >   >       >>   ÂÂ
> mailto:[7][16][18]support-cirl at berkeley.edu
> >   >       >>>          >>>>> ÂÂÂÂ
>  2. [8][17][19]http://loris/
> >   >       >>>          >>>> Â Ã‚ÂÂ
> ---end quoted text---
> >   >       >>>          >>>>
> >   >       >>>          >>>> References
> >   >       >>>          >>>>
> >   >       >>>          >>>> Visible links
> >   >       >>>          >>>> 1.
> [18][20]http://loris/
> >   >       >>>          >>>> 2.
> >   >       >>>        ÂÂ
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >>>          >>>> 3.
> mailto:[20][22]ioannis at berkeley.edu
> >   >       >>>          >>>> 4.
> mailto:[21][23]support-cirl at berkeley.edu
> >   >       >>>          >>>> 5.
> mailto:[22][24]support-cirl at berkeley.edu
> >   >       >>>          >>>> 6.
> [23][25]http://loris/
> >   >       >>>          >>>> 7.
> mailto:[24][26]support-cirl at berkeley.edu
> >   >       >>>          >>>> 8.
> [25][27]http://loris/
> >   >       >>>          >>> ---end quoted text---
> >   >       >>>          >>
> >   >       >>>          > ---end quoted text---
> >   >       >>>
> >   >       >>>    --
> >   >       >>>    [26][28]christine.rogers at mcgill.ca
> >   >       >>>    McGill Centre for Integrative
> Neuroscience | MCIN.ca
> >   >       >>>    Montreal Neurological Institute
> >   >       >>>    McGill University | Montreal | Canada
> >   >       >>>
> >   >       >>> References
> >   >       >>>
> >   >       >>>    Visible links
> >   >       >>>    1.
> >   >       >>  ÂÂ
> >   >      ÂÂ
> >Â Â Â
> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >   >       >>>    2.
> >   >      ÂÂ
> [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >   >       >>>    3. mailto:[31]loris-dev at bic.mni.mcgill.ca
> >   >       >>>    4. mailto:[32]ioannis at berkeley.edu
> >   >       >>>    5. [33]http://loris/
> >   >       >>>    6. mailto:[34]support-cirl at berkeley.edu
> >   >       >>>    7. mailto:[35]ioannis at berkeley.edu
> >   >       >>>    8. mailto:[36]support-cirl at berkeley.edu
> >   >       >>>    9. mailto:[37]support-cirl at berkeley.edu
> >   >       >>>   10. [38]http://xn--loris-7qa/
> >   >       >>>   11.
> >   >      ÂÂ
> [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >>>   12. mailto:[40]ioannis at berkeley.edu
> >   >       >>>   13. mailto:[41]support-cirl at berkeley.edu
> >   >       >>>   14. mailto:[42]support-cirl at berkeley.edu
> >   >       >>>   15. [43]http://loris/
> >   >       >>>   16. mailto:[44]support-cirl at berkeley.edu
> >   >       >>>   17. [45]http://loris/
> >   >       >>>   18. [46]http://loris/
> >   >       >>>   19.
> >   >      ÂÂ
> [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >>>   20. mailto:[48]ioannis at berkeley.edu
> >   >       >>>   21. mailto:[49]support-cirl at berkeley.edu
> >   >       >>>   22. mailto:[50]support-cirl at berkeley.edu
> >   >       >>>   23. [51]http://loris/
> >   >       >>>   24. mailto:[52]support-cirl at berkeley.edu
> >   >       >>>   25. [53]http://loris/
> >   >       >>>   26. mailto:[54]christine.rogers at mcgill.ca
> >   >       >>    ---end quoted text---
> >   >       >>
> >   >       >>  --
> >   >       >>  [55]christine.rogers at mcgill.ca
> >   >       >>  McGill Centre for Integrative Neuroscience |
> MCIN.ca
> >   >       >>  Montreal Neurological Institute
> >   >       >>  McGill University | Montreal | Canada
> >   >       >>
> >   >       >> References
> >   >       >>
> >   >       >>  Visible links
> >   >       >>  1. [8]mailto:loris-dev at bic.mni.mcgill.ca
> >   >       >>  2. [9]mailto:support-cirl at berkeley.edu
> >   >       >>  3. [10]http://loris.priv/
> >   >       >>ÂÂ
> >   >       4.
> >Â Â Â
> [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >   >       >>  5. [12]mailto:loris-dev at bic.mni.mcgill.ca
> >   >       >>  6. [13]mailto:ioannis at berkeley.edu
> >   >       >>  7. [14]http://loris/
> >   >       >>  8. [15]mailto:support-cirl at berkeley.edu
> >   >       >>  9. [16]mailto:ioannis at berkeley.edu
> >   >       >> 10. [17]mailto:support-cirl at berkeley.edu
> >   >       >> 11. [18]mailto:support-cirl at berkeley.edu
> >   >       >> 12. [19]http://xn--loris-era/
> >   >       >> 13.
> >Â Â Â [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >> 14. [21]mailto:ioannis at berkeley.edu
> >   >       >> 15. [22]mailto:support-cirl at berkeley.edu
> >   >       >> 16. [23]mailto:support-cirl at berkeley.edu
> >   >       >> 17. [24]http://loris/
> >   >       >> 18. [25]mailto:support-cirl at berkeley.edu
> >   >       >> 19. [26]http://loris/
> >   >       >> 20. [27]http://loris/
> >   >       >> 21.
> >Â Â Â [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >> 22. [29]mailto:ioannis at berkeley.edu
> >   >       >> 23. [30]mailto:support-cirl at berkeley.edu
> >   >       >> 24. [31]mailto:support-cirl at berkeley.edu
> >   >       >> 25. [32]http://loris/
> >   >       >> 26. [33]mailto:support-cirl at berkeley.edu
> >   >       >> 27. [34]http://loris/
> >   >       >> 28. [35]mailto:christine.rogers at mcgill.ca
> >   >       >>
> >   >       29.
> >Â Â Â
> [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >   >       >> 30.
> >Â Â Â [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >   >       >> 31. [38]mailto:loris-dev at bic.mni.mcgill.ca
> >   >       >> 32. [39]mailto:ioannis at berkeley.edu
> >   >       >> 33. [40]http://loris/
> >   >       >> 34. [41]mailto:support-cirl at berkeley.edu
> >   >       >> 35. [42]mailto:ioannis at berkeley.edu
> >   >       >> 36. [43]mailto:support-cirl at berkeley.edu
> >   >       >> 37. [44]mailto:support-cirl at berkeley.edu
> >   >       >> 38. [45]http://xn--loris-7qa/
> >   >       >> 39.
> >Â Â Â [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >> 40. [47]mailto:ioannis at berkeley.edu
> >   >       >> 41. [48]mailto:support-cirl at berkeley.edu
> >   >       >> 42. [49]mailto:support-cirl at berkeley.edu
> >   >       >> 43. [50]http://loris/
> >   >       >> 44. [51]mailto:support-cirl at berkeley.edu
> >   >       >> 45. [52]http://loris/
> >   >       >> 46. [53]http://loris/
> >   >       >> 47.
> >Â Â Â [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >   >       >> 48. [55]mailto:ioannis at berkeley.edu
> >   >       >> 49. [56]mailto:support-cirl at berkeley.edu
> >   >       >> 50. [57]mailto:support-cirl at berkeley.edu
> >   >       >> 51. [58]http://loris/
> >   >       >> 52. [59]mailto:support-cirl at berkeley.edu
> >   >       >> 53. [60]http://loris/
> >   >       >> 54. [61]mailto:christine.rogers at mcgill.ca
> >   >       >> 55. [62]mailto:christine.rogers at mcgill.ca
> >   >       > ---end quoted text---
> >Â Â Â >
> >   >       _______________________________________________
> >   >       Loris-dev mailing list
> >   >       Loris-dev at bic.mni.mcgill.ca
> >   >      ÂÂ
> [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >   >       <ProjectName.png>
> >Â Â Â >
> >   >     _______________________________________________
> >   >     Loris-dev mailing list
> >   >     Loris-dev at bic.mni.mcgill.ca
> >   >    ÂÂ
> [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >Â Â Â >
> >   >   --
> >   >   christine.rogers at mcgill.ca
> >   >   McGill Centre for Integrative Neuroscience | MCIN.ca
> >   >   Montreal Neurological Institute
> >   >   McGill University | Montreal | Canada
> >Â Â Â ---end quoted text---
> >
> > References
> >
> >Â Â Â Visible links
> >Â Â Â 1. [2]https://loris.url/configuration/
> >Â Â Â 2. [3]https://.loris.url/
> >Â Â Â 3. [4]http://loris.priv/
> >Â Â Â 4. [5]http://localhost/
> >Â Â Â 5. [6]http://loris.priv/
> >Â Â Â 6. [7]http://localhost/
> >Â Â Â 7. [8]http://localhost/
> >Â Â Â 8. [9]mailto:loris-dev at bic.mni.mcgill.ca
> >Â Â Â 9. [10]mailto:support-cirl at berkeley.edu
> >Â Â 10. [11]http://loris.priv/
> >Â Â 11.
> [12]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >Â Â 12. [13]mailto:loris-dev at bic.mni.mcgill.ca
> >Â Â 13. [14]mailto:ioannis at berkeley.edu
> >Â Â 14. [15]http://loris/
> >Â Â 15. [16]mailto:support-cirl at berkeley.edu
> >Â Â 16. [17]mailto:ioannis at berkeley.edu
> >Â Â 17. [18]mailto:support-cirl at berkeley.edu
> >Â Â 18. [19]mailto:support-cirl at berkeley.edu
> >Â Â 19. [20]http://xn--loris-era/
> >Â Â 20. [21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >Â Â 21. [22]mailto:ioannis at berkeley.edu
> >Â Â 22. [23]mailto:support-cirl at berkeley.edu
> >Â Â 23. [24]mailto:support-cirl at berkeley.edu
> >Â Â 24. [25]http://loris/
> >Â Â 25. [26]mailto:support-cirl at berkeley.edu
> >Â Â 26. [27]http://loris/
> >Â Â 27. [28]http://loris/
> >Â Â 28. [29]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >Â Â 29. [30]mailto:ioannis at berkeley.edu
> >Â Â 30. [31]mailto:support-cirl at berkeley.edu
> >Â Â 31. [32]mailto:support-cirl at berkeley.edu
> >Â Â 32. [33]http://loris/
> >Â Â 33. [34]mailto:support-cirl at berkeley.edu
> >Â Â 34. [35]http://loris/
> >Â Â 35. [36]mailto:christine.rogers at mcgill.ca
> >Â Â 36.
> [37]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >Â Â 37. [38]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >Â Â 38. [39]mailto:loris-dev at bic.mni.mcgill.ca
> >Â Â 39. [40]mailto:ioannis at berkeley.edu
> >Â Â 40. [41]http://loris/
> >Â Â 41. [42]mailto:support-cirl at berkeley.edu
> >Â Â 42. [43]mailto:ioannis at berkeley.edu
> >Â Â 43. [44]mailto:support-cirl at berkeley.edu
> >Â Â 44. [45]mailto:support-cirl at berkeley.edu
> >Â Â 45. [46]http://xn--loris-7qa/
> >Â Â 46. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >Â Â 47. [48]mailto:ioannis at berkeley.edu
> >Â Â 48. [49]mailto:support-cirl at berkeley.edu
> >Â Â 49. [50]mailto:support-cirl at berkeley.edu
> >Â Â 50. [51]http://loris/
> >Â Â 51. [52]mailto:support-cirl at berkeley.edu
> >Â Â 52. [53]http://loris/
> >Â Â 53. [54]http://loris/
> >Â Â 54. [55]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >Â Â 55. [56]mailto:ioannis at berkeley.edu
> >Â Â 56. [57]mailto:support-cirl at berkeley.edu
> >Â Â 57. [58]mailto:support-cirl at berkeley.edu
> >Â Â 58. [59]http://loris/
> >Â Â 59. [60]mailto:support-cirl at berkeley.edu
> >Â Â 60. [61]http://loris/
> >Â Â 61. [62]mailto:christine.rogers at mcgill.ca
> >Â Â 62. [63]mailto:christine.rogers at mcgill.ca
> >Â Â 63. [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >Â Â 64. [65]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> ---end quoted text---
>
> References
>
> Visible links
> 1. http://localhost/
> 2. https://loris.url/configuration/
> 3. https://.loris.url/
> 4. http://loris.priv/
> 5. http://localhost/
> 6. http://loris.priv/
> 7. http://localhost/
> 8. http://localhost/
> 9. mailto:loris-dev at bic.mni.mcgill.ca
> 10. mailto:support-cirl at berkeley.edu
> 11. http://loris.priv/
> 12. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> 13. mailto:loris-dev at bic.mni.mcgill.ca
> 14. mailto:ioannis at berkeley.edu
> 15. http://loris/
> 16. mailto:support-cirl at berkeley.edu
> 17. mailto:ioannis at berkeley.edu
> 18. mailto:support-cirl at berkeley.edu
> 19. mailto:support-cirl at berkeley.edu
> 20. http://xn--loris-era/
> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> 22. mailto:ioannis at berkeley.edu
> 23. mailto:support-cirl at berkeley.edu
> 24. mailto:support-cirl at berkeley.edu
> 25. http://loris/
> 26. mailto:support-cirl at berkeley.edu
> 27. http://loris/
> 28. http://loris/
> 29. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> 30. mailto:ioannis at berkeley.edu
> 31. mailto:support-cirl at berkeley.edu
> 32. mailto:support-cirl at berkeley.edu
> 33. http://loris/
> 34. mailto:support-cirl at berkeley.edu
> 35. http://loris/
> 36. mailto:christine.rogers at mcgill.ca
> 37. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> 38. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> 39. mailto:loris-dev at bic.mni.mcgill.ca
> 40. mailto:ioannis at berkeley.edu
> 41. http://loris/
> 42. mailto:support-cirl at berkeley.edu
> 43. mailto:ioannis at berkeley.edu
> 44. mailto:support-cirl at berkeley.edu
> 45. mailto:support-cirl at berkeley.edu
> 46. http://xn--loris-7qa/
> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> 48. mailto:ioannis at berkeley.edu
> 49. mailto:support-cirl at berkeley.edu
> 50. mailto:support-cirl at berkeley.edu
> 51. http://loris/
> 52. mailto:support-cirl at berkeley.edu
> 53. http://loris/
> 54. http://loris/
> 55. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> 56. mailto:ioannis at berkeley.edu
> 57. mailto:support-cirl at berkeley.edu
> 58. mailto:support-cirl at berkeley.edu
> 59. http://loris/
> 60. mailto:support-cirl at berkeley.edu
> 61. http://loris/
> 62. mailto:christine.rogers at mcgill.ca
> 63. mailto:christine.rogers at mcgill.ca
> 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> 65. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
---end quoted text---
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