From pierre.bellec at criugm.qc.ca Mon Oct 1 09:39:58 2018 From: pierre.bellec at criugm.qc.ca (Pierre Bellec) Date: Mon, 1 Oct 2018 09:39:58 -0400 Subject: [Loris-dev] CCNA release 1 In-Reply-To: References: Message-ID: Dear Loris-dev, See email below. I am sorry to hear that Mouna left the CCNA/LORIS team, it was a real treat to work with her. I hope this will not delay the BIDS release we had worked on together. Best, Pierre Bellec Research associate professor | Professeur agr?g? sous octroi, Psychology Department | D?partement de Psychologie Universit? de Montr?al, Montr?al, Canada Director | Directeur, Unit? de Neuroimagerie Fonctionnelle (UNF ) Researcher | Chercheur, Centre de recherche de l'institut Universitaire de g?riatrie de Montr?al (CRIUGM ) Phone | T?l?phone +1 514 713 5596 Coordinates | c oordonn?es Laboratory | Laboratoire SIMEXP ------ Please note that I am resetting my mail box on Sunday evening every week. I do my best to answer all emails, but I am sometimes not able to. If you have not heard back from me after 1 week, consider sending me a reminder. On Mon, Oct 1, 2018 at 9:37 AM Pierre Bellec wrote: > Dear Mouna, > > I hear that the first CCNA data release is on its way! > > Would it be possible to prepare a BIDS release of the T1, fMRI and > diffusion data like we did for our pilot? > > Thanks in advance. > > Best, > > Pierre Bellec > > Research associate professor | Professeur agr?g? sous octroi, > Psychology Department | D?partement de Psychologie > Universit? de Montr?al, Montr?al, Canada > Director | Directeur, Unit? de Neuroimagerie Fonctionnelle (UNF > ) > Researcher | Chercheur, Centre de recherche de l'institut Universitaire de > g?riatrie de Montr?al (CRIUGM ) > Phone | T?l?phone +1 514 713 5596 > Coordinates | c > oordonn?es > Laboratory | Laboratoire SIMEXP > ------ > > Please note that I am resetting my mail box on Sunday evening every week. > I do my best to answer all emails, but I am sometimes not able to. > If you have not heard back from me after 1 week, consider sending me a > reminder. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Lindsay.Alexander at childmind.org Thu Oct 4 09:11:01 2018 From: Lindsay.Alexander at childmind.org (Lindsay Alexander) Date: Thu, 4 Oct 2018 13:11:01 +0000 Subject: [Loris-dev] Issues accessing LORIS for HBN Message-ID: <8D8B5A79-F52C-46D2-BD4F-74338DBAE61E@childmind.org> Hello, I am having issues logging in to our Healthy Brain Network site admin account and my personal account. For the admin account, I keep getting a message that I am using the wrong username or password, but these credentials worked a few days ago. On my personal account, it does not give an error message of wrong password, but just does not move past the login screen. I tried to reset my password, but I did not receive an email to do so. Bonhwang Koo, our research assistant that installed and was maintaining our instance of LORIS is no longer with us, so I was hoping you would be able to help us get this issue resolved. Please let me know if there is any additional information I can provide. Thank you! Lindsay -- Lindsay Alexander Child Mind Institute Clinical Data Manager 646.625.4383 childmind.org | Location Facebook | Twitter | Instagram 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.loris at gmail.com Fri Oct 5 11:28:19 2018 From: rida.loris at gmail.com (Rida Abou-Haidar) Date: Fri, 5 Oct 2018 11:28:19 -0400 Subject: [Loris-dev] Issues accessing LORIS for HBN In-Reply-To: <8D8B5A79-F52C-46D2-BD4F-74338DBAE61E@childmind.org> References: <8D8B5A79-F52C-46D2-BD4F-74338DBAE61E@childmind.org> Message-ID: Hi Lindsay, Sorry to hear you are having issues. In regards to the admin account, you should be able to reset the password manually if you have access to the VM where loris is installed. I f you go to the loris root directory and then into the tools/ directory, you will find a php script calle resetpassword.php. using it is very simple `php resetpassword.php username` it should prompt you for a new password. As for your personal account, thta one is a bit strange. would you be able to provide screen shots of the webpage before you click login and after you click login (include the url in the screenshot if possible) and if we can't figure it out I might ask you to give me an account in your loris where I can go try it myself. Don't hesitate to get back to us if you have more questions, Best, Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.loris at gmail.com On Thu, Oct 4, 2018 at 11:29 AM Lindsay Alexander < Lindsay.Alexander at childmind.org> wrote: > Hello, > > > > I am having issues logging in to our Healthy Brain Network site admin > account and my personal account. For the admin account, I keep getting a > message that I am using the wrong username or password, but these > credentials worked a few days ago. On my personal account, it does not > give an error message of wrong password, but just does not move past the > login screen. I tried to reset my password, but I did not receive an email > to do so. > > > > Bonhwang Koo, our research assistant that installed and was maintaining > our instance of LORIS is no longer with us, so I was hoping you would be > able to help us get this issue resolved. > > > > Please let me know if there is any additional information I can provide. > > > > Thank you! > > Lindsay > > > > -- > > Lindsay Alexander > > Child Mind Institute > > Clinical Data Manager > > 646.625.4383 <(646)%20625-4383> > > > > childmind.org | Location > > > Facebook | Twitter > | Instagram > > > > > 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. > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cardillo at med.umich.edu Tue Oct 23 13:29:03 2018 From: cardillo at med.umich.edu (Cardillo, Garry) Date: Tue, 23 Oct 2018 17:29:03 +0000 Subject: [Loris-dev] advice on updating system Message-ID: <87a13b4e5feb412082d1f10807558101@med.umich.edu> Hello All, We are currently on Loris version 14.12.1 and are planning on updating our system. I would appreciate any insight anyone can provide. I understand we will have to upgrade to each patch and release in order, to get up to the current release. We have a lot of custom development in our system done by another programmer who is no longer here. We were not using any versioning software and documentation is limited. Referencing this page https://github.com/aces/Loris/wiki/Updating-your-LORIS: Update your LORIS in a few steps: * Download the new release codebase. Be careful of overwriting any custom code modifications that you may have added - you'll want to merge these with the code updates. What is the best way to do this? I have compared our install with the codebase for 14.12.1 and have identified all files which differ, and which are in our install only. What is the best way to merge the code? * Run composer install --no-dev and then composer dump-autoload to update dependencies and re-generate the autoload.php file Am I simply running theses two commands on command line, or do additional steps need to be taken to update dependencies and re-generate autoload.php? * Apply the MySQL release-upgrade patch found in the SQL/Release_patches directory. Carefully note modifications to data columns and data type definitions * Check your project/ directory for code that may be overriding the main Loris codebase - these files may need updating to work with the release codebase. Note that as of 16.0 release, custom module support has changed * Review all Release Notes for every release since your last version, including minor releases -- especially those in the section specifically for Existing Projects. Follow carefully the recommended steps for existing projects Upgrade tips * Ensure your admin user has all available permissions: INSERT IGNORE INTO `user_perm_rel` (userID, permID) SELECT DISTINCT 1, permID FROM permissions; To preserve custom modification we have in modules, libraries and templates, would the best course of action be to create directories in /project/modules, /project/libraries, and /project/templates and copy everything to those directories? Will that work okay with the Loris override functionality? Also, is it correct that if we are on 14.12.1, the upgrade order would be as follows: 15.04, 15.10, 15.10.1, 15.10.2, 16.0.0, 16.0.1, 16.0.2, 16.1.0, 16.1.1, 16.1.3, 17.0.0, 17.0.1, 17.0.2, 17.0.3, 17.0.4, 17.0.5, 17.0.6, 18.0.0, 18.0.1, 18.0.2, 18.0.3, 18.0.4, 18.0.5, 19.0.0, 19.0.1, 19.0.2, 19.1, 19.1.1, 19.1.2, 20.0.0, 20.0.1? Also, we are running everything from the same machine (mysql, php, loris, apache). Mysql ver 14.14 distrib 5.6.35 , php ver 5.5.9, apache/2.4.7, ubuntu 14.04. Are there any considerations that need to be taken in regards to these versions? Thanks for any help! Garry Cardillo [1523292633747_image001.png] Database Analyst/Programmer Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domino?s Farms Lobby B Suite 1000 24 Frank Lloyd Wright Dr PO BOX 362 Ann Arbor, MI 48106 t: 734-936-0630 f: 734-998-8403 e: cardillo at umich.edu ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Tue Oct 23 14:27:11 2018 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Tue, 23 Oct 2018 14:27:11 -0400 Subject: [Loris-dev] advice on updating system In-Reply-To: <87a13b4e5feb412082d1f10807558101@med.umich.edu> References: <87a13b4e5feb412082d1f10807558101@med.umich.edu> Message-ID: Hi Garry, Since you're upgrading from such an old version, since it's such an old version you're likely to encounter problems at some step of the way. You should ensure that you have a staging server to your upgrades on before doing them on production. It would be a good idea to back up your server with a recent dump of your production database before trying to ensure that you don't encounter any upgrade errors related to the data when doing it on production. I've added some notes/answers to your more specific questions below. On Tue, Oct 23, 2018 at 1:29 PM Cardillo, Garry wrote: > Hello All, > > > We are currently on Loris version 14.12.1 and are planning on updating our > system. I would appreciate any insight anyone can provide. > > > I understand we will have to upgrade to each patch and release in order, > to get up to the current release. We have a lot of custom development in > our system done by another programmer who is no longer here. We were not > using any versioning software and documentation is limited. > > > It's never too late to start. It would be a good idea to start using version control (at least for your project directory) before starting the upgrade. > Referencing this page > https://github.com/aces/Loris/wiki/Updating-your-LORIS: > > > Update your LORIS in a few steps: > > > - Download the new release codebase > . Be careful of overwriting > any custom code modifications > that you may > have added - you'll want to merge these with the code updates. *What > is the best way to do this? I have compared our install with the codebase > for 14.12.1 and have identified all files which differ, and which are in > our install only. What is the best way to merge the code? * > > You likely need to do a diff of your changes against the 14.12.1 version and then manually merge the changes into the upgraded version (in your project/libraries directory) after each upgrade. > - Run composer install --no-dev and then composer dump-autoload to > update dependencies and re-generate the autoload.php file * Am I > simply running theses two commands on command line, or do additional steps > need to be taken to update dependencies and re-generate autoload.php?* > > You should only need to run "composer install --no-dev" (but it'll have to be done after each release upgrade before testing.) > - Apply the MySQL release-upgrade patch found in the > SQL/Release_patches > directory. > Carefully note modifications to data columns and data type definitions > - Check your project/ directory for code that may be overriding > the main Loris > codebase - these files may need updating to work with the release codebase. > Note that as of 16.0 release, custom module support has changed > - Review *all* Release Notes for > every release since your last version, including minor releases -- > especially those in the section specifically for Existing Projects. Follow > carefully the recommended steps for existing projects > > *To preserve custom modification we have in modules, libraries and > templates, would the best course of action be to create directories in > /project/modules, /project/libraries, and /project/templates and copy > everything to those directories? Will that work okay with the Loris > override functionality?* > > > Any module that's overwritten should be (completely) moved to project/modules. Any libraries or templates should go into the other directories, but only the things that are modified should be put there. Putting absolutely everything there would effectively be the same as not upgrading the files at all and may lead to issues with your code being out of sync with the database schema. > *Also, is it correct that if we are on 14.12.1, the upgrade order would be > as follows:* > > *15.04, 15.10, 15.10.1, 15.10.2, 16.0.0, 16.0.1, 16.0.2, 16.1.0, 16.1.1, > 16.1.3, 17.0.0, 17.0.1, 17.0.2, 17.0.3, 17.0.4, 17.0.5, 17.0.6, 18.0.0, > 18.0.1, 18.0.2, 18.0.3, 18.0.4, 18.0.5, 19.0.0, 19.0.1, 19.0.2, 19.1, > 19.1.1, 19.1.2, 20.0.0, 20.0.1?* > > The bugfix releases (the one where the last digit of the three changes) don't need to be done, so it should be: *15.04, 15.10, 15.10.2, 16.0.2, 16.1.3, 17.0.6, 18.0.5, 19.0.2, 19.1.2, 20.0.1* (Assuming you take the highest bugfix release of each minor release so that you have the bugfixes when testing. The upgrade procedure should be the same as what's documented for the ".0" version of the minor release no matter which bugfix release you're upgrading to. ) > *Also, we are running everything from the same machine (mysql, php, loris, > apache). Mysql ver 14.14 distrib 5.6.35 **, php ver 5.5.9, apache/2.4.7, > ubuntu 14.04. Are there any considerations that need to be taken in > regards to these versions?* > > > One of the releases will mandate upgrading to PHP7 but I can't remember exactly which one (it should say in that release's release notes, hopefully.) The apache version should be fine. Officially the later versions of LORIS require MySQL 5.7, but unofficially I don't foresee any issues with 5.6 going up to 20.0 (but future versions might use features that require > 5.7) -------------- next part -------------- An HTML attachment was scrubbed... URL: