[Loris-dev] loris server
Melanie Legault, Mrs
melanie.legault2 at mcgill.ca
Mon Nov 11 10:47:00 EST 2019
Hello Julie,
Could it be that your MySQL 'lorismysql' user have different permissions depending on where it is connecting to the DB?
A database admin (root) can check this for you.
SELECT User, Host FROM mysql.user;
then for the user that match the Host (name or IP address) of your LORIS (Apache) server
SHOW grants for 'lorismysql'@'<Host>';
Mélanie
________________________________
From: Julie Ashworth, HWNI Computing Support <support-cirl at berkeley.edu>
Sent: November 8, 2019 21:04
To: Christine Rogers, Ms. <christine.rogers at mcgill.ca>
Cc: Ioannis Pappas <ioannis at berkeley.edu>; Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>; loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] loris server
thanks Christine,
yes, it's the lorismysql user in the config.xml file.
<username>lorismysql</username>
<database>loris_database</database>
<quatUser>lorismysql</quatUser>
we appeciate your help troubleshooting this.
best,
Julie
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 -- 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 end
> of LORIS.
> If this user has insufficient privileges on your database, that would
> cause the errors you are seeing. I had assumed from your thread it 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 after
> the weekend,
> Best,
> Christine
> On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas <ioannis at berkeley.edu>
> wrote:
>
> Hi Melanie.
> Thank you for taking the time to reply to this. I took some to consider
> your comments. Unfortunately as I said to Christine we are unable to do
> any kind of updating to the database (either that is changing the name
> or changing the small html description, etc.).
> Based on some more digging and on some of Christine's comments I have a
> feeling that our lorisweb front-end, admin user cannot write anything to
> the database. Along these lines could it be the case the lorismysql user
> (the database, admin user with INSERT, UPDATE, etc privileges) is not
> “talking†to the lorisweb front end user? What is the difference between
> the two and could it be a installation problem for them not talking to
> each other? As Julie said, lorismysql user is working normally with
> MariaDB.
> Thank you again for your help.
> Best wishes,
> Ioannis
>
> 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
> (https://loris.url/configuration/) of LORIS, only change the title of
> the project. To see this change, you have to log out of LORIS and then
> go back to the login page (https://.loris.url/). This is the only
> place you can find the project name (except from the 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 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 lorisadmin:httpd and
> permission 770 (775)
> * All other files under loris should have lorisadmin:lorisadmin 755
> Reading through this change of mail, I understand that you let Apache
> store file in /srv/www/loris
> | 31 | DownloadPath | Downloads | /srv/www/loris/ |
> 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 do not
> have permission (in httpd.conf) to execute files.
> Kind regards,
> Mélanie Legault | Software developer | Faculty of Medicine | McGill
> University
> 3801 University, Montréal, QC H3A 2B4
>
> ----------------------------------------------------------------------
>
> 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
>
> Hi Christine and Julie.
>
> 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 (as
> you requested Christine) alongside the troubleshooting and discussion
> so far with Julie.
>
> Best wishes,
> Ioannis
>
> > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support
> <support-cirl at berkeley.edu> wrote:
> >
> > hi Christine and Ioannis,
> > Ioannis, can you follow-up with Christine about using the front-end?
> >
> > We're using CentOS7.7 and loris-21.0.1.
> >
> > I confirmed that I could login as the mysql user (lorismyqsl) and
> change the 'url' config setting from 'http://loris.priv' to
> '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 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 |
> loris.priv | Host |
> > | 45 | url | Main LORIS URL
> | 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 |
> >
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >
> > MariaDB [loris_database]> UPDATE Config SET Value='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 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 |
> loris.priv | 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 |
> >
> +----------+-------------------+-------------------+------------------+--------------------------------------+
> > 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 for
> >> developers, project administrators and sysadmins setting up
> LORIS, so that
> >> these users can contact our technical team for exactly such
> technical
> >> help.
> >> If it's ok with you, I'd encourage you subscribe to the 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 not
> >> updating?
> >> In the front-end, can your 'admin' user effect any changes in
> (any) Config
> >> setting?
> >> 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 installing, and
> on what
> >> OS version.
> >> Best,
> >> Christine
> >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing
> Support
> >> <[2]support-cirl at berkeley.edu> wrote:
> >>
> >> Thank you Christine,
> >> I'm the linux sysadmin who installed the loris database 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'@'%';
> >>
> +--------------------------------------------------------------------------------+
> >> | 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)
> >>
> >> looking at the 'tips' section in the page you referred to...
> >>
> >> | 29 | base | Base | /srv/www/loris/ |
> The base
> >> filesystem path where LORIS is
> installed |
> >> | 31 | DownloadPath | Downloads | /srv/www/loris/ |
> Where
> >> files are downloaded
> >>
> >>
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >> | ConfigID | Name | Label |
> Value |
> >> Description |
> >>
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >> | 44 | host | Host |
> loris.priv |
> >> Host |
> >> | 45 | url | Main LORIS URL |
> >> [3]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 |
> >>
> +----------+-------------------+-------------------+-------------------+--------------------------------------+
> >>
> >> 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 /srv/www/loris/smarty/templates_c
> >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46
> >>
> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55
> >>
> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39
> >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35
> >>
> 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10
> >>
> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39
> >>
> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01
> >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58
> >>
> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59
> >>
> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39
> >>
> a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08
> >>
> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35
> >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01
> >>
> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21
> >>
> ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35
> >>
> d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02
> >>
> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59
> >>
> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php
> >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42
> >> 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 a
> database
> >>> back-end issue.Â
> >>> Can you verify -- Has your mysql user lorismysql been granted
> the
> >> "INSERT"
> >>> privilege for the right database? If not, that would result in
> an
> >> error
> >>> like the kind you are seeing.Â
> >>> Also, if you wish to check your LORIS Configuration 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 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
> >>>
> >>
> [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 email
> our
> >> technical
> >>> team your next question at [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 benefit
> of
> >> the
> >>> community and other first-time users in the same position 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 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 the
> sudo
> >> user and
> >>> I am the admin user).
> >>> If you allow me, I would like to ask you about the 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 writing
> in
> >> the
> >>> configuration file.
> >>> Here are the permissions setup for where Loris is installed.
> >>> chmod 777 /var/www/loris/smarty/templates_c
> >>> cd /srv/www/loris
> >>> chown -R lorisadmin:lorisadmin .
> >>> chmod -c -R a+r .
> >>> Â Â this command gives everyone read access, and outputs
> what
> >> changes
> >>> were made:
> >>>   mode of ¿./project¿ changed from 0770 (rwxrwx---) to
> 0774
> >>> (rwxrwxr--)
> >>>   mode of ¿./tools/logs¿ changed from 0770 (rwxrwx---)
> to
> >> 0774
> >>> (rwxrwxr--)
> >>> find . -type d -exec chmod a+x -c {} \;
> >>> Â Â this command gives everyone permission to open a
> directory,
> >> and
> >>> outputs what changes were made:
> >>>   mode of ¿./project¿ changed from 0774 (rwxrwxr--) to
> 0775
> >>> (rwxrwxr-x)
> >>>   mode of ¿./tools/logs¿ changed from 0774 (rwxrwxr--)
> to
> >> 0775
> >>> (rwxrwxr-x)
> >>> Hopefully you can help me with this. I also subscribed to
> the
> >> mailing
> >>> list but I am not sure if this too much of a basic 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? 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 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 that’s why it doesn’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 Â this command gives everyone read access, and
> outputs
> >> what
> >>> changes were made:
> >>> >  mode of ¿./project¿ changed from 0770
> (rwxrwx---) to
> >> 0774
> >>> (rwxrwxr--)
> >>> >  mode of ¿./tools/logs¿ changed from 0770
> (rwxrwx---)
> >> to 0774
> >>> (rwxrwxr--)
> >>> > find . -type d -exec chmod a+x -c {} \;
> >>> >Â Â this command gives everyone permission to open a
> >> directory, and
> >>> outputs what changes were made:
> >>> >  mode of ¿./project¿ changed from 0774
> (rwxrwxr--) to
> >> 0775
> >>> (rwxrwxr-x)
> >>> >  mode of ¿./tools/logs¿ changed from 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 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, HWNI
> >> Computing
> >>> Support <[9][11]support-cirl at berkeley.edu> wrote:
> >>> >>>
> >>> >>> hi Ioannis,
> >>> >>> no worries, I changed the following directory 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 PhD
> wrote:
> >>> >>>>Â Hi Julie.
> >>> >>>>Â Apologies for bugging you with this again. We
> tried
> >> now to
> >>> >>>> access [1][10][12]http://lorisÂ
> >>> >>>> and we are getting a blank page. I think the
> reason
> >> for this
> >>> is that we
> >>> >>>> don't have read permissions to read from the
> >> template located
> >>> in
> >>> >>>>Â /var/www/loris/smarty See here bottom of the
> >>> >>>> pageÂ
> >>>
> >>
> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >>> >>>>Â I think, in general, I am a little bit confused
> as to
> >> what the
> >>> permissions
> >>> >>>>Â should be for us that are not sudos. My
> understanding
> >> is that
> >>> if we don't
> >>> >>>>Â have read or write permissions then we can't
> access or
> >> write
> >>> to
> >>> >>>>Â /var/www/loris, meaning that we can't access or
> >> configure.
> >>> Should
> >>> >>>> everything be chmod 777 for example?Â
> >>> >>>>Â Thank you very much once again.
> >>> >>>>Â Best wishes,
> >>> >>>>Â Ioannis
> >>> >>>>Â On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis
> Pappas PhD
> >>> >>>>Â <[3][12][14]ioannis at berkeley.edu> wrote:
> >>> >>>>
> >>> >>>>Â Â Thank you very much Julie. I appreciate this
> and I
> >> will dig
> >>> into Loris
> >>> >>>>Â Â given your changes. Thank you so much for your
> >> help.
> >>> >>>>Â Â Best wishes,
> >>> >>>>Â Â Ioannis
> >>> >>>>Â Â On Thu, Oct 31, 2019 at 12:48 PM Julie
> Ashworth,
> >> HWNI
> >>> Computing Support
> >>> >>>>Â Â <[4][13][15]support-cirl at berkeley.edu> wrote:
> >>> >>>>
> >>> >>>>Â Â Â hi Ioannis,
> >>> >>>>
> >>> >>>>Â Â Â 1. I changed the permissions of
> /srv/www/loris
> >> to be owned
> >>> by
> >>> >>>>Â Â Â lorisadmin. I reivewed my installation
> notes,
> >> and I did
> >>> this already
> >>> >>>>Â Â Â when
> >>> >>>>Â Â Â I installed the server. I'm not sure why
> they
> >> changed, so
> >>> it's
> >>> >>>>Â Â Â probably a
> >>> >>>>Â Â Â good idea to keep an eye on that.
> >>> >>>>
> >>> >>>>Â Â Â 2. When I installed the loris software, I
> also
> >> installed a
> >>> mysql
> >>> >>>>Â Â Â database as recommended in the
> instructions:
> >>> >>>>
> >>> >>>>Â Â Â projectname: LORIS
> >>> >>>>Â Â Â databasename: loris_database
> >>> >>>>Â Â Â mysqluser: lorismysql
> >>> >>>>Â Â Â frontend: lorisweb
> >>> >>>>
> >>> >>>>Â Â Â 3. A couple of weeks ago, I moved Henrik's
> home
> >> directory
> >>> to
> >>> >>>>Â Â Â /home/despoA,
> >>> >>>>Â Â Â but I forgot to update loris. This is done
> now.
> >>> >>>>
> >>> >>>>Â Â Â best,
> >>> >>>>Â Â Â Julie
> >>> >>>>
> >>> >>>>Â Â Â On 31-10-2019 11.15 -0700, Dr. Ioannis
> Pappas
> >> PhD wrote:
> >>> >>>>>   Hi Julie.
> >>> >>>>>   I hope you are well. We are trying to
> >> configure loris
> >>> that you
> >>> >>>>Â Â Â kindly set
> >>> >>>>>   up for us.
> >>> >>>>>   I have a couple of questions for you if
> you
> >> allow me
> >>> so.Â
> >>> >>>>>   1) First, although we are logging into
> the
> >> front end
> >>> with admin
> >>> >>>>Â Â Â username
> >>> >>>>>   (lorisweb) and password, it seems that
> any
> >> kind of
> >>> update of
> >>> >>>>Â Â Â configuration
> >>> >>>>>   we are trying to do fails (meaning that
> if
> >> we, say,
> >>> change the
> >>> >>>>Â Â Â name of the
> >>> >>>>>   study and press "submit", this doesn't
> do
> >> anything-it
> >>> doesn't
> >>> >>>>Â Â Â update).
> >>> >>>>>   It's almost like our lorisweb user
> doesn't
> >> have write
> >>> privileges
> >>> >>>>Â Â Â in the
> >>> >>>>>   /var/www/loris/project (where I think
> every
> >>> configuration should
> >>> >>>>Â Â Â be).
> >>> >>>>>   This generalizes for everything that we
> are
> >> trying to do
> >>> in the
> >>> >>>>Â Â Â front end.
> >>> >>>>>   Clicking any instrument/tab in the front
> end
> >> doesn't
> >>> really point
> >>> >>>>Â Â Â to
> >>> >>>>>   anything.Â
> >>> >>>>>   2) Loris suggest doing configurations
> via
> >> SQL. Is it
> >>> possible to
> >>> >>>>Â Â Â run SQL
> >>> >>>>>   scripts in the backend
> >>> >>>>>   3) For some reason typing ssh lors for
> Henrik
> >> doesn't
> >>> directly
> >>> >>>>Â Â Â take him to
> >>> >>>>>   loris (it requires a password that is
> not the
> >> password
> >>> setup for
> >>> >>>>Â Â Â the
> >>> >>>>>   lorisweb user). Will you be able to fix
> this
> >> via your
> >>> sudo
> >>> >>>>Â Â Â privileges?
> >>> >>>>>   Thank you very much in advance for all
> your
> >> help Julie.
> >>> Let us
> >>> >>>>Â Â Â know if
> >>> >>>>>   this is something that shouldn't be
> directed
> >> to you (but
> >>> instead
> >>> >>>>Â Â Â to the
> >>> >>>>>   loris people).Â
> >>> >>>>>   Best wishes,
> >>> >>>>>   Ioannis
> >>> >>>>>   On Mon, Sep 9, 2019 at 6:25 PM Julie
> >> Ashworth, HWNI
> >>> Computing
> >>> >>>>Â Â Â Support
> >>> >>>>>  ÂÂ
> <[1][5][14][16]support-cirl at berkeley.edu>
> >> wrote:
> >>> >>>>>
> >>> >>>>>    hi Henrik and Ioannis,
> >>> >>>>>    the loris server is available for
> you to
> >> use.
> >>> >>>>>
> >>> >>>>>    The servername is 'loris'. I
> created a
> >> directory
> >>> called
> >>> >>>>Â Â Â /data/loris for
> >>> >>>>>    you to store data. You may create
> new
> >> folders in
> >>> /data/loris to
> >>> >>>>Â Â Â organize
> >>> >>>>>    your data.
> >>> >>>>>
> >>> >>>>>    1) secure shell or secure copy:
> >>> >>>>>    You can log in with the 'ssh' or
> 'scp'
> >> command from
> >>> your remote
> >>> >>>>Â Â Â desktop
> >>> >>>>>    session. You don't need to
> authenticate
> >> to log in.
> >>> Maybe you'll
> >>> >>>>Â Â Â use scp
> >>> >>>>>    to transfer data between your
> cluster
> >> account and the
> >>> loris
> >>> >>>>Â Â Â server?
> >>> >>>>>    Please put the data in /data/loris,
> so I
> >> can make
> >>> backups more
> >>> >>>>Â Â Â easily.
> >>> >>>>>
> >>> >>>>>      secure shell:
> >>> >>>>>      $ ssh loris
> >>> >>>>>
> >>> >>>>>      secure copy (change the
> names
> >> in brackets). Let
> >>> me know if
> >>> >>>>Â Â Â I can
> >>> >>>>>      help with syntax:
> >>> >>>>>      $ scp -r <data>
> >> loris:/data/loris/<newfolder>
> >>> >>>>>
> >>> >>>>>    2) front-end web interface.ÂÂ
> Open a
> >> web browser in
> >>> your remote
> >>> >>>>Â Â Â desktop
> >>> >>>>>    session and enter the hostname:
> >>> >>>>>    [2][6][15][17]http://loris
> >>> >>>>>    I created an admin user called
> >> 'lorisweb'. I put the
> >>> password
> >>> >>>>Â Â Â in
> >>> >>>>>    $HOME/newuser on the cluster. To
> see it,
> >> open a
> >>> terminal, and
> >>> >>>>Â Â Â run:
> >>> >>>>>
> >>> >>>>>      $ cat $HOME/newuser
> >>> >>>>>
> >>> >>>>>    If other people need shell access
> to the
> >> webserver,
> >>> please let
> >>> >>>>Â Â Â me know
> >>> >>>>>    so I can create a home directory
> for
> >> them.
> >>> >>>>>
> >>> >>>>>    We should eventually discuss
> backups.
> >>> >>>>>
> >>> >>>>>    best,
> >>> >>>>>    Julie
> >>> >>>>>
> >>> >>>>> References
> >>> >>>>>
> >>> >>>>>   Visible links
> >>> >>>>>   1.
> >> mailto:[7][16][18]support-cirl at berkeley.edu
> >>> >>>>>   2. [8][17][19]http://loris/
> >>> >>>>Â Â Â ---end quoted text---
> >>> >>>>
> >>> >>>> References
> >>> >>>>
> >>> >>>>Â Visible links
> >>> >>>>Â 1. [18][20]http://loris/
> >>> >>>>Â 2.
> >>>
> >>
> [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >>> >>>>Â 3. mailto:[20][22]ioannis at berkeley.edu
> >>> >>>>Â 4. mailto:[21][23]support-cirl at berkeley.edu
> >>> >>>>Â 5. mailto:[22][24]support-cirl at berkeley.edu
> >>> >>>>Â 6. [23][25]http://loris/
> >>> >>>>Â 7. mailto:[24][26]support-cirl at berkeley.edu
> >>> >>>>Â 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.
> >>
> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >>> 2.
> [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.
> [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.
> [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. mailto:loris-dev at bic.mni.mcgill.ca
> >> 2. mailto:support-cirl at berkeley.edu
> >> 3. http://loris.priv/
> >>
> 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >> 5. mailto:loris-dev at bic.mni.mcgill.ca
> >> 6. mailto:ioannis at berkeley.edu
> >> 7. http://loris/
> >> 8. mailto:support-cirl at berkeley.edu
> >> 9. mailto:ioannis at berkeley.edu
> >> 10. mailto:support-cirl at berkeley.edu
> >> 11. mailto:support-cirl at berkeley.edu
> >> 12. http://xn--loris-era/
> >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >> 14. mailto:ioannis at berkeley.edu
> >> 15. mailto:support-cirl at berkeley.edu
> >> 16. mailto:support-cirl at berkeley.edu
> >> 17. http://loris/
> >> 18. mailto:support-cirl at berkeley.edu
> >> 19. http://loris/
> >> 20. http://loris/
> >> 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. mailto:christine.rogers at mcgill.ca
> >>
> 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings
> >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> >> 31. mailto:loris-dev at bic.mni.mcgill.ca
> >> 32. mailto:ioannis at berkeley.edu
> >> 33. http://loris/
> >> 34. mailto:support-cirl at berkeley.edu
> >> 35. mailto:ioannis at berkeley.edu
> >> 36. mailto:support-cirl at berkeley.edu
> >> 37. mailto:support-cirl at berkeley.edu
> >> 38. http://xn--loris-7qa/
> >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief
> >> 40. mailto:ioannis at berkeley.edu
> >> 41. mailto:support-cirl at berkeley.edu
> >> 42. mailto:support-cirl at berkeley.edu
> >> 43. http://loris/
> >> 44. mailto:support-cirl at berkeley.edu
> >> 45. http://loris/
> >> 46. http://loris/
> >> 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. mailto:christine.rogers at mcgill.ca
> >> 55. mailto:christine.rogers at mcgill.ca
> > ---end quoted text---
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
> <ProjectName.png>
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.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
---end quoted text---
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191111/21c1f507/attachment-0001.html>
More information about the Loris-dev
mailing list