From christine.rogers at mcgill.ca  Wed Oct  4 10:09:01 2017
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Wed, 4 Oct 2017 10:09:01 -0400
Subject: [Loris-dev] LORIS Release v18.0.0
Message-ID: <CALbt7NDjdUaRPcBka33vW5YC3-u0MS-f1njK=s23S=NRN8UgyQ@mail.gmail.com>

Hi LORIS developer community,

*LORIS 18.0* is now available on GitHub --

Both core LORIS 18.0.0 <https://github.com/aces/Loris/releases/tag/v18.0.0a>
and Loris-MRI 18.0.0
<https://github.com/aces/Loris-MRI/releases/tag/v18.0.0> have been released.

Major features and updates are described in the Release Notes in both repos.

Upgrade Process notes are included to walk existing projects through
scripts and special patches to apply for this release.

Best,
The LORIS Team


--------------------  Release Notes from GitHub
<https://github.com/aces/Loris/releases/latest>

LORIS v18.0 is the next major release of LORIS. It adds the ability for
users and examiners to be affiliated with multiple sites, as well as adding
433 other bug fixes and minor changes.

   - Full list of changes
   <https://github.com/aces/Loris/pulls?utf8=%E2%9C%93&q=is%3Apr%20is%3Amerged%20milestone%3A17.1%20>

New Features

   - [Core] Users and Examiners may be affiliated with more than one site.
   - [Imaging Browser] A new Config module setting called "tblScanTypes"
   defines which modalities should have quality control performed. In the
   Imaging Browser, the "T1 Done" and "T2 Done" columns are now customizable
   to any set of modalities using this Config setting, and the "New Data"
   column shows only new scans from these designated modalities.
   - [LorisForm] Readonly elements and Radio button support added in
   PHP-coded instrument forms

Updates and Improvements

   - [Media] File names that are uploaded must now be unique.
   - [BrainBrowser] The version of BrainBrowser included in LORIS is
   upgraded, which should fix issues loading scans from certain scanners but
   be otherwise unnoticeable.
   - [Login] Captchas are improved by changing them to use the google
   reCAPTCHA service rather than a custom implementation

Notes for Existing Projects

   - [API] The v0.0.1 is now deprecated and will be removed in a future
   release. v0.0.1 is a proper subset of v0.0.2, so upgrading should be
   transparent and only require changing "1" to "2" in any calls to the API.
   - [Security] The old (unused) Password_MD5 column is removed. LORIS has
   used PHP's more secure password API for a number of releases, but the
   column remained so that existing users could still login (and the password
   hash would be upgraded upon login). The insecure hashes are now completely
   removed. As a result, passwords can no longer be reset via the MySQL
   commandline -- instead, run the new tools/resetpassword.php script, or
   have the user click the "Forgot your password" link.
   - [Radiological Review] The Final Radiological Review module was
   removed, as it was only used by a single LORIS project and not sufficiently
   generic to be used by others. If you were using it and need access to it,
   please contact the loris-dev mailing list for help on how to install it
   into your project/ directory.
   - [Config] In the config.xml file, the <database> subtag of CouchDB was
   renamed to <dbName> to avoid conflicts with the MySQL database config
   setting. If you have CouchDB setup in your config.xml, you'll need to
   rename this tag.

Upgrade Process

Unfortunately, due to changes in constraints in the database schema
upgrading this version of LORIS is a multistep process. After updating the
code, you must:

   1. Source the SQL file SQL/Release_patches/17.0_To_18.0_upgrade_A.sql
   2. Run the script php tools/DB_date_zeros_removal.php to remove invalid
   dates in MySQL.
   3. Run the script php tools/populate_examiners_psc_rel.php to populate
   the new multisite examiners table with existing examiners.
   4. Source the SQL file SQL/Archive/18.0/2016-06-01-
   update_zero_fields_statements.sql to add constraints on the tables
   modified by the script in step 2.
   5. Source the rest of the schema changes in the file
   SQL/Release_patches/17.0_To_18.0_upgrade_B.sql
   6. Review the file SQL/Archive/18.0/clean-up/Clean_up_patch.sql which
   removes and cleans up various columns after backing up any data in those
   tables.

?
You are receiving this because you are subscribed to this thread.
View it on GitHub <https://github.com/aces/Loris/releases/tag/v18.0.0> or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AAyg43tbG9Vt8DGO8k8Re0LMEW25fNHyks5soT7SgaJpZM4PrKJ3>
.



-- 

christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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From ncote at aviscuriosa.com  Wed Oct  4 15:20:54 2017
From: ncote at aviscuriosa.com (=?UTF-8?B?Tm9ybWFuZCBDw7R0w6k=?=)
Date: Wed, 4 Oct 2017 15:20:54 -0400
Subject: [Loris-dev] Sharing MOPs
Message-ID: <CAFkTtf9KjrcJGyyJx=MJy01Nyn5J2CP4_vDz0Cd=UbKgM_mY3w@mail.gmail.com>

Sharing MOPs from different groups using Loris was mentioned at the last
Loris meeting.  If any have been shared already, where can they be found?
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From david.macfarlane2 at mcgill.ca  Thu Oct  5 09:19:23 2017
From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr)
Date: Thu, 5 Oct 2017 13:19:23 +0000
Subject: [Loris-dev] Sharing MOPs
In-Reply-To: <CAFkTtf9KjrcJGyyJx=MJy01Nyn5J2CP4_vDz0Cd=UbKgM_mY3w@mail.gmail.com>
References: <CAFkTtf9KjrcJGyyJx=MJy01Nyn5J2CP4_vDz0Cd=UbKgM_mY3w@mail.gmail.com>
Message-ID: <YQXPR0101MB1672EEAEF08B4A717913D50EA8700@YQXPR0101MB1672.CANPRD01.PROD.OUTLOOK.COM>

I'm not aware of any that have been shared. It was a proposal (that seemed generally well-received), but as far as I know hasn't been implemented yet.


- Dave

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Normand C?t? <ncote at aviscuriosa.com>
Sent: October 4, 2017 3:20:54 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Sharing MOPs

Sharing MOPs from different groups using Loris was mentioned at the last Loris meeting.  If any have been shared already, where can they be found?
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From jordan.stirling at mail.mcgill.ca  Thu Oct  5 15:10:06 2017
From: jordan.stirling at mail.mcgill.ca (Jordan Stirling, Mr)
Date: Thu, 5 Oct 2017 19:10:06 +0000
Subject: [Loris-dev] Modifying Imported Data
In-Reply-To: <D4ABC9B1-0212-433D-8C25-0CC8A808F5C3@childmind.org>
References: <D4ABC9B1-0212-433D-8C25-0CC8A808F5C3@childmind.org>
Message-ID: <YQBPR0101MB225872C5F31F2DEAB9E32E09D3700@YQBPR0101MB2258.CANPRD01.PROD.OUTLOOK.COM>

Hi Bonhwang,


Sorry for the tardy response. Are you talking about the instrument names which show up in the Define Fields instrument dropdown?


Thanks,


Jordan

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Bonhwang Koo <Bonhwang.Koo at childmind.org>
Sent: September 20, 2017 5:26:44 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Modifying Imported Data

Hi again,

For our study, I imported the data into CouchDB using a customized script similar to tools/CouchDB_Import_Instruments.php. We?re considering changing the name of one of our instruments because of confusion among our users. Is there a way to do this other than changing the name manually for the data dictionary and each entry on Futon?

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

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

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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From ncote at aviscuriosa.com  Mon Oct  9 11:43:18 2017
From: ncote at aviscuriosa.com (=?UTF-8?B?Tm9ybWFuZCBDw7R0w6k=?=)
Date: Mon, 9 Oct 2017 11:43:18 -0400
Subject: [Loris-dev] Feedback and Behavioural QC permissions
Message-ID: <CAFkTtf8zgpZ091x2nay3nmpWPL9EPvLuh+Nxkse2yZnRpRb_nQ@mail.gmail.com>

Perhaps someone here can enlighten me on something related to the Feedback
functionality.

We would like our site users to see and respond to Feedback, but not be
able to change the BVL QC Type and Status in the left panel.  However,
these functions are both controlled by the "Behavioural QC" (internally "
bvl_feedback") permission.

Perhaps I've misunderstood the intended use for the Behavioural QC
functionality.  In our scenario, the site users would do data entry and
respond to feedback initiated by the DCC.  A clinical monitor attached to
the DCC would be responsible for hardcopy QC.  If the BVL QC is expected to
be done by the site, what would you recommend for the DCC-level QC on an
instrument instance?

Is there any documentation on the expected workflow in Loris, i.e. the
normal sequence of steps for completion of a study, from data entry to data
export, with standard permission assignment?  I can piece this together
from the available functionality, but it would be useful to see how Loris
was intended to be used.
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From Bonhwang.Koo at childmind.org  Tue Oct 10 11:14:54 2017
From: Bonhwang.Koo at childmind.org (Bonhwang Koo)
Date: Tue, 10 Oct 2017 15:14:54 +0000
Subject: [Loris-dev] Modifying Imported Data
In-Reply-To: <YQBPR0101MB225872C5F31F2DEAB9E32E09D3700@YQBPR0101MB2258.CANPRD01.PROD.OUTLOOK.COM>
References: <D4ABC9B1-0212-433D-8C25-0CC8A808F5C3@childmind.org>
	<YQBPR0101MB225872C5F31F2DEAB9E32E09D3700@YQBPR0101MB2258.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <F10A691E-89C1-4F12-83BB-97FB1F39F120@childmind.org>

Hi Jordan,

No problem. Yes, the names in the dropdown are the ones I?m trying to change.

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

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

---

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

From: "Jordan Stirling, Mr" <jordan.stirling at mail.mcgill.ca>
Date: Thursday, October 5, 2017 at 3:10 PM
To: Bonhwang Koo <Bonhwang.Koo at childmind.org>, "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>
Subject: Re: Modifying Imported Data


Hi Bonhwang,



Sorry for the tardy response. Are you talking about the instrument names which show up in the Define Fields instrument dropdown?



Thanks,



Jordan

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Bonhwang Koo <Bonhwang.Koo at childmind.org>
Sent: September 20, 2017 5:26:44 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Modifying Imported Data

Hi again,

For our study, I imported the data into CouchDB using a customized script similar to tools/CouchDB_Import_Instruments.php. We?re considering changing the name of one of our instruments because of confusion among our users. Is there a way to do this other than changing the name manually for the data dictionary and each entry on Futon?

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

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

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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From jordan.stirling at mail.mcgill.ca  Tue Oct 10 13:37:05 2017
From: jordan.stirling at mail.mcgill.ca (Jordan Stirling, Mr)
Date: Tue, 10 Oct 2017 17:37:05 +0000
Subject: [Loris-dev] Modifying Imported Data
In-Reply-To: <F10A691E-89C1-4F12-83BB-97FB1F39F120@childmind.org>
References: <D4ABC9B1-0212-433D-8C25-0CC8A808F5C3@childmind.org>
	<YQBPR0101MB225872C5F31F2DEAB9E32E09D3700@YQBPR0101MB2258.CANPRD01.PROD.OUTLOOK.COM>,
	<F10A691E-89C1-4F12-83BB-97FB1F39F120@childmind.org>
Message-ID: <YQBPR0101MB2258ACA36EE748E073C95C10D3750@YQBPR0101MB2258.CANPRD01.PROD.OUTLOOK.COM>

Hi Bonhwang,


At this point in time there is no easy way to do this because those names are so integrated on how data is fetched from the database. In order to change them you would have to modify the CouchDB_Import_Instrument.php script. That being said you're new names could not have spaces as that will break in trying to retrieve the fields associated the instrument. If you are fine with that I can guide you what you would have to do to modify the names displayed.


The ideal solution would be to modify the the entire module to use the names that are displayed in the timepoints module. This fix would be very tricky and time consuming because you would have to modify the React files on how they handle the data to the php code in how they return the data. This would be something that would be nice to add to the Core roadmap but I'm not sure where it would be placed. Hope this helps.


Thanks,


Jordan

________________________________
From: Bonhwang Koo <Bonhwang.Koo at childmind.org>
Sent: October 10, 2017 11:14:54 AM
To: Jordan Stirling, Mr; loris-dev at bic.mni.mcgill.ca
Subject: Re: Modifying Imported Data

Hi Jordan,

No problem. Yes, the names in the dropdown are the ones I?m trying to change.

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

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

---

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

From: "Jordan Stirling, Mr" <jordan.stirling at mail.mcgill.ca>
Date: Thursday, October 5, 2017 at 3:10 PM
To: Bonhwang Koo <Bonhwang.Koo at childmind.org>, "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>
Subject: Re: Modifying Imported Data


Hi Bonhwang,



Sorry for the tardy response. Are you talking about the instrument names which show up in the Define Fields instrument dropdown?



Thanks,



Jordan

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Bonhwang Koo <Bonhwang.Koo at childmind.org>
Sent: September 20, 2017 5:26:44 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Modifying Imported Data

Hi again,

For our study, I imported the data into CouchDB using a customized script similar to tools/CouchDB_Import_Instruments.php. We?re considering changing the name of one of our instruments because of confusion among our users. Is there a way to do this other than changing the name manually for the data dictionary and each entry on Futon?

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

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

---

This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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From rida.loris at gmail.com  Tue Oct 17 16:47:17 2017
From: rida.loris at gmail.com (Rida Abou-Haidar)
Date: Tue, 17 Oct 2017 20:47:17 +0000
Subject: [Loris-dev] Feedback and Behavioural QC permissions
In-Reply-To: <CAFkTtf8zgpZ091x2nay3nmpWPL9EPvLuh+Nxkse2yZnRpRb_nQ@mail.gmail.com>
References: <CAFkTtf8zgpZ091x2nay3nmpWPL9EPvLuh+Nxkse2yZnRpRb_nQ@mail.gmail.com>
Message-ID: <CAO0Avk6KNCNXS4d0Xb5OK5V=FW+dmVT_TxbqDsgdO48BEMosCQ@mail.gmail.com>

Hi Normand,

You are correct, in the current state of things, the Behavioural QC
functionality is an all-or-nothing architecture where you either can or
can't edit the QC on a specific instrument, timepoint and/or candidate.

As for the intended use, I can give you an example from a couple currently
active projects. The data-entry personnel are responsible of transferring
all the data on paper to LORIS, this constitutes the Initial Data-entry
Step.  Once that is done, the instruments are set to status:Complete. The
monitoring personnel then randomly select a certain percentage of the
completed instruments and flag them for monitoring (this step is still
manual at this point but we are hoping on automating it in a near future).
the Instrument (or even entire Timepoints) flagged for monitoring get
reviewed by the proper personnel and any encountered issues with the data
are reported using the feedback panel. This initiates a back and forth on
each specific issue until the issue is resolved and at that time it can be
set to closed (by the monitoring personnel usually) in the feedback panel.

Keep in . mind that feedback can be either at a candidate level, a
timepoint level or an instrument level. I have attached a couple of
diagrams showing our workflows for the CCNA project. Keep in mind that not
all these steps have to be linear, we chose to place them as such to
facilitate our own personal goals but some of these can be inverted and
some completely not used. I do not have any permissions default assignment
unfortunately, we manage that with an internal google sheet giving each
user a role and defining a set of permissions for that role. We are however
looking forward to incorporating a similar feature into loris 19.0 (PR:
https://github.com/aces/Loris/pull/2642)

Hopefully this answers all your questions and sorry for the delayed reply,
Best,
Rida Abou-Haidar
CCNA Software Developer
Montreal Neurological Institute
McGill University
rida.loris at gmail.com



On Mon, Oct 9, 2017 at 11:43 AM Normand C?t? <ncote at aviscuriosa.com> wrote:

> Perhaps someone here can enlighten me on something related to the Feedback
> functionality.
>
> We would like our site users to see and respond to Feedback, but not be
> able to change the BVL QC Type and Status in the left panel.  However,
> these functions are both controlled by the "Behavioural QC" (internally "
> bvl_feedback") permission.
>
> Perhaps I've misunderstood the intended use for the Behavioural QC
> functionality.  In our scenario, the site users would do data entry and
> respond to feedback initiated by the DCC.  A clinical monitor attached to
> the DCC would be responsible for hardcopy QC.  If the BVL QC is expected to
> be done by the site, what would you recommend for the DCC-level QC on an
> instrument instance?
>
> Is there any documentation on the expected workflow in Loris, i.e. the
> normal sequence of steps for completion of a study, from data entry to data
> export, with standard permission assignment?  I can piece this together
> from the available functionality, but it would be useful to see how Loris
> was intended to be used.
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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