From molano at ext.cnio.es Mon May 23 06:06:41 2022 From: molano at ext.cnio.es (=?iso-8859-1?Q?Olano=2EMar=EDa?=) Date: Mon, 23 May 2022 10:06:41 +0000 Subject: [Loris-dev] Uploading bulk new candidate profiles Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52E2325@DONAR.cnio.es> Good day, We were wondering if there was a way to upload a bulk of candidate profiles to LORIS (be it via a csv of sorts) instead of manually inserting every one of them. Thank you for your assistance. Mar?a [Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] Fb Amigos del CNIO | Tw @CNIOStopCancer | Youtube canalcnio **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp **LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message. Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Tue May 24 11:44:32 2022 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Tue, 24 May 2022 11:44:32 -0400 Subject: [Loris-dev] Uploading bulk new candidate profiles In-Reply-To: <1AAB0BC03205B240B7809934CFCF8DF52E2325@DONAR.cnio.es> References: <1AAB0BC03205B240B7809934CFCF8DF52E2325@DONAR.cnio.es> Message-ID: Hi Maria, Thank you for reaching out -- LORIS doesn't currently support automatic upload of candidate profiles from a CSV since there's no one-size-fits-all configuration that works across all projects. Many projects have done this by creating custom scripts using LORIS' PHP classes or API -- An example of how to Create candidate profiles automatically with the API is found in this Tutorial (see Section 3) https://github.com/xlecours/loris-api-presentation/blob/master/LORIS-API_Part2-Python-script.ipynb We hope this helps, and we'll ensure CSV upload is included in the roadmap of feature requests. Please let us know if you have further questions - Thank you, Christine Rogers on behalf of the LORIS team | LORIS.ca -- Research Project Officer christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute-Hospital McGill University | Montreal | Canada On Mon, May 23, 2022 at 6:07 AM Olano.Mar?a wrote: > Good day, > > > > We were wondering if there was a way to upload a bulk of candidate > profiles to LORIS (be it via a csv of sorts) instead of manually inserting > every one of them. > > > > Thank you for your assistance. > > > > Mar?a > > > > [image: Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] > > > *Fb* Amigos del CNIO | *Tw* > @CNIOStopCancer | *Youtube* > canalcnio > > > **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros > adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su > destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro > tipo de transmisi?n por parte de otra persona que no sea el destinatario. > Si usted recibe por error este correo, se ruega comunicarlo al remitente y > borrar el mensaje recibido. > De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a > la protecci?n de los datos personales de las personas f?sicas, la > informaci?n personal que nos pueda facilitar a trav?s de este correo > electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de > tramitar el objeto del presente correo electr?nico. El tratamiento de sus > datos personales se encuentra legitimado por ser necesario para gestionar > el objeto del presente mensaje. Estos datos personales no ser?n comunicados > a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga > exigido por una ley. Ud. podr? ejercer los derechos de acceso, > rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y > oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 > (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos > en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer > informaci?n adicional sobre el tratamiento de sus datos personales, puede > consultar dicha informaci?n adicional en el siguiente enlace dentro de > nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp > > **LEGAL NOTICE**: This email and any attached files may contain protected > information for the sole use of its intended recipient or addressee. Anyone > other than the intended recipient or addressee is strictly prohibited from > distributing, reproducing or transmitting the email and its contents in any > way. If you receive this email in error, please notify the sender and > delete the message. > Pursuant to the provisions of EU Regulation 2016/679 regarding the > protection of personal data, any personal information you provide through > this email will be registered by the CNIO Foundation in order to deal with > content of this email. Your personal data must be processed in order to be > able to deal with the content and purpose of this message. Your personal > details will not be passed on to anyone else unless you authorise us to do > so or we are required to do so by law. You may exercise your rights > regarding access, rectification, suppression, limitation of processing, > portability and opposition by writing to the following address: c/Melchor > Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection > Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If > you require further information about the processing of your personal data, > go to the following link on our webpage: > https://www.cnio.es/es/privacidad/index.asp > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.hewitt at med.uni-goettingen.de Wed May 25 09:04:05 2022 From: manuel.hewitt at med.uni-goettingen.de (Hewitt, Manuel) Date: Wed, 25 May 2022 13:04:05 +0000 Subject: [Loris-dev] Blank page after setup Message-ID: <463845cbf27147568f604c42dc577df2@med.uni-goettingen.de> Hello I'm trying to run Loris on CentOS 7.9.2009. After following the trail of outdated installation instructions and links to non-existant pages starting at loris.ca "Get Started" I think I finally found the latest set of instructions. I followed the instructions including some educated guesses and plenty of googling for all the problems that arose. In the end I managed to run installdb.php and did all those steps too. Now I open just localhost and am greeted by a blank page. In the error.log the following entry shows up and I have no clue what the problem is. Google didn't yield any fix. [Wed May 25 14:07:31.174096 2022] [php7:error] [pid 20180] [client 127.0.0.1:43398] PHP Fatal error: Uncaught Error: Interface 'Psr\\Log\\LoggerAwareInterface' not found in /var/www/loris/php/libraries/Database.class.inc:16\nStack trace:\n#0 /var/www/loris/vendor/composer/ClassLoader.php(444): include()\n#1 /var/www/loris/vendor/composer/ClassLoader.php(322): Composer\\Autoload\\includeFile()\n#2 [internal function]: Composer\\Autoload\\ClassLoader->loadClass()\n#3 /var/www/loris/php/libraries/NDB_Factory.class.inc(168): spl_autoload_call()\n#4 /var/www/loris/php/libraries/NDB_Client.class.inc(59): NDB_Factory->database()\n#5 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()\n#6 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 16 Any advice? MFG, M. Hewitt -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Wed May 25 09:11:56 2022 From: wangshen.mcin at gmail.com (Shen Wang) Date: Wed, 25 May 2022 09:11:56 -0400 Subject: [Loris-dev] Blank page after setup In-Reply-To: <463845cbf27147568f604c42dc577df2@med.uni-goettingen.de> References: <463845cbf27147568f604c42dc577df2@med.uni-goettingen.de> Message-ID: Hi Hewiitt, It seems like the "composer install" command line didn't run properly. You may try to run "composer install" manually under your Loris instance folder. Best regards Shen On Wed, May 25, 2022 at 9:04 AM Hewitt, Manuel < manuel.hewitt at med.uni-goettingen.de> wrote: > Hello > > > > I?m trying to run Loris on CentOS 7.9.2009. > > After following the trail of outdated installation instructions and links > to non-existant pages starting at loris.ca ?Get Started? I think I > finally found the latest set of instructions. > > I followed the instructions including some educated guesses and plenty of > googling for all the problems that arose. > > > > In the end I managed to run installdb.php and did all those steps too. > > Now I open just localhost and am greeted by a blank page. > > > > In the error.log the following entry shows up and I have no clue what the > problem is. Google didn?t yield any fix. > > > > [Wed May 25 14:07:31.174096 2022] [php7:error] [pid 20180] [client > 127.0.0.1:43398] PHP Fatal error: Uncaught Error: Interface > 'Psr\\Log\\LoggerAwareInterface' not found in > /var/www/loris/php/libraries/Database.class.inc:16\nStack trace:\n#0 > /var/www/loris/vendor/composer/ClassLoader.php(444): include()\n#1 > /var/www/loris/vendor/composer/ClassLoader.php(322): > Composer\\Autoload\\includeFile()\n#2 [internal function]: > Composer\\Autoload\\ClassLoader->loadClass()\n#3 > /var/www/loris/php/libraries/NDB_Factory.class.inc(168): > spl_autoload_call()\n#4 > /var/www/loris/php/libraries/NDB_Client.class.inc(59): > NDB_Factory->database()\n#5 /var/www/loris/htdocs/index.php(34): > NDB_Client->initialize()\n#6 {main}\n thrown in > /var/www/loris/php/libraries/Database.class.inc on line 16 > > > > Any advice? > > > > MFG, > > > > M. Hewitt > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.hewitt at med.uni-goettingen.de Wed May 25 09:22:36 2022 From: manuel.hewitt at med.uni-goettingen.de (Hewitt, Manuel) Date: Wed, 25 May 2022 13:22:36 +0000 Subject: [Loris-dev] Blank page after setup In-Reply-To: References: <463845cbf27147568f604c42dc577df2@med.uni-goettingen.de> Message-ID: Thanks, that did it. I had composer installed via yum and I ran the two commands in the PHP Composer section of the installtion instructions: sudo curl -sS https://getcomposer.org/installer | php sudo mv composer.phar /usr/local/bin/composer They finished without errors, but also no other significant output. I even ran them again before writing my email since a problem with composer was the only hint I got by using Google. There is no mention to run ?composer install? in the Ubunut or CentOS installations instructions. MFG, Manuel Hewitt wissenschaftlicher Mitarbeiter UNIVERSIT?TSMEDIZIN G?TTINGEN GEORG-AUGUST-UNIVERSIT?T Klinik f?r Neurologie Robert-Koch-Stra?e 40 37075 G?ttingen Briefpost 37099 G?ttingen Telefon +49 551 39-62355 Fax +49 551 39-8126 Email manuel.hewitt at med.uni-goettingen.de https://neurologie.umg.eu/ Von: Shen Wang Gesendet: Mittwoch, 25. Mai 2022 15:12 An: Hewitt, Manuel Cc: loris-dev at bic.mni.mcgill.ca Betreff: Re: [Loris-dev] Blank page after setup Hi Hewiitt, It seems like the "composer install" command line didn't run properly. You may try to run "composer install" manually under your Loris instance folder. Best regards Shen On Wed, May 25, 2022 at 9:04 AM Hewitt, Manuel > wrote: Hello I?m trying to run Loris on CentOS 7.9.2009. After following the trail of outdated installation instructions and links to non-existant pages starting at loris.ca ?Get Started? I think I finally found the latest set of instructions. I followed the instructions including some educated guesses and plenty of googling for all the problems that arose. In the end I managed to run installdb.php and did all those steps too. Now I open just localhost and am greeted by a blank page. In the error.log the following entry shows up and I have no clue what the problem is. Google didn?t yield any fix. [Wed May 25 14:07:31.174096 2022] [php7:error] [pid 20180] [client 127.0.0.1:43398] PHP Fatal error: Uncaught Error: Interface 'Psr\\Log\\LoggerAwareInterface' not found in /var/www/loris/php/libraries/Database.class.inc:16\nStack trace:\n#0 /var/www/loris/vendor/composer/ClassLoader.php(444): include()\n#1 /var/www/loris/vendor/composer/ClassLoader.php(322): Composer\\Autoload\\includeFile()\n#2 [internal function]: Composer\\Autoload\\ClassLoader->loadClass()\n#3 /var/www/loris/php/libraries/NDB_Factory.class.inc(168): spl_autoload_call()\n#4 /var/www/loris/php/libraries/NDB_Client.class.inc(59): NDB_Factory->database()\n#5 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()\n#6 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 16 Any advice? MFG, M. Hewitt _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Wed May 25 12:04:21 2022 From: wangshen.mcin at gmail.com (Shen Wang) Date: Wed, 25 May 2022 12:04:21 -0400 Subject: [Loris-dev] Blank page after setup In-Reply-To: References: <463845cbf27147568f604c42dc577df2@med.uni-goettingen.de> Message-ID: Hi, you may try this to solve the problem. Running "composer update". It will rebuild the composer.lock file and add the missing "psr/log" into the vendor folder. The "make" command contains "composer install", we will optimize the installation steps. Thank you. Good luck Shen On Wed, May 25, 2022 at 9:22 AM Hewitt, Manuel < manuel.hewitt at med.uni-goettingen.de> wrote: > Thanks, that did it. > > > > I had composer installed via yum and I ran the two commands in the PHP > Composer section of the installtion instructions: > > sudo curl -sS https://getcomposer.org/installer | php > > sudo mv composer.phar /usr/local/bin/composer > > > > They finished without errors, but also no other significant output. I even > ran them again before writing my email since a problem with composer was > the only hint I got by using Google. > > There is no mention to run ?composer install? in the Ubunut or CentOS > installations instructions. > > > > > > MFG, > > > > Manuel Hewitt > > wissenschaftlicher Mitarbeiter > > > > UNIVERSIT?TSMEDIZIN G?TTINGEN > > GEORG-AUGUST-UNIVERSIT?T > > Klinik f?r Neurologie > > Robert-Koch-Stra?e 40 > > 37075 G?ttingen > > Briefpost 37099 G?ttingen > > Telefon +49 551 39-62355 > > Fax +49 551 39-8126 > > Email manuel.hewitt at med.uni-goettingen.de > > https://neurologie.umg.eu/ > > > > *Von:* Shen Wang > *Gesendet:* Mittwoch, 25. Mai 2022 15:12 > *An:* Hewitt, Manuel > *Cc:* loris-dev at bic.mni.mcgill.ca > *Betreff:* Re: [Loris-dev] Blank page after setup > > > > > > Hi Hewiitt, > > It seems like the "composer install" command line didn't run properly. > > You may try to run "composer install" manually under your Loris > instance folder. > > > > Best regards > > Shen > > > > On Wed, May 25, 2022 at 9:04 AM Hewitt, Manuel < > manuel.hewitt at med.uni-goettingen.de> wrote: > > Hello > > > > I?m trying to run Loris on CentOS 7.9.2009. > > After following the trail of outdated installation instructions and links > to non-existant pages starting at loris.ca ?Get Started? I think I > finally found the latest set of instructions. > > I followed the instructions including some educated guesses and plenty of > googling for all the problems that arose. > > > > In the end I managed to run installdb.php and did all those steps too. > > Now I open just localhost and am greeted by a blank page. > > > > In the error.log the following entry shows up and I have no clue what the > problem is. Google didn?t yield any fix. > > > > [Wed May 25 14:07:31.174096 2022] [php7:error] [pid 20180] [client > 127.0.0.1:43398] PHP Fatal error: Uncaught Error: Interface > 'Psr\\Log\\LoggerAwareInterface' not found in > /var/www/loris/php/libraries/Database.class.inc:16\nStack trace:\n#0 > /var/www/loris/vendor/composer/ClassLoader.php(444): include()\n#1 > /var/www/loris/vendor/composer/ClassLoader.php(322): > Composer\\Autoload\\includeFile()\n#2 [internal function]: > Composer\\Autoload\\ClassLoader->loadClass()\n#3 > /var/www/loris/php/libraries/NDB_Factory.class.inc(168): > spl_autoload_call()\n#4 > /var/www/loris/php/libraries/NDB_Client.class.inc(59): > NDB_Factory->database()\n#5 /var/www/loris/htdocs/index.php(34): > NDB_Client->initialize()\n#6 {main}\n thrown in > /var/www/loris/php/libraries/Database.class.inc on line 16 > > > > Any advice? > > > > MFG, > > > > M. Hewitt > > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > > -- > > Shen Wang > > Loris Developer > > Montreal Neurological Institute > > McGill University > > > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue May 31 16:53:11 2022 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 31 May 2022 20:53:11 +0000 Subject: [Loris-dev] PHP Fatal error: Allowed memory size of Message-ID: Dear LorisDev team, I?m facing the following error when downloading a large minc image (~70MB) using the API ?GET /candidates/$CandID/$VisitLabel/images/$Filename?. I can download the file from the web interface with no issues. === [Tue May 31 15:25:10.697608 2022] [php7:error] [pid 20168] [client 73.219.242.88:64779] PHP Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 70594560 bytes) in /var/www/loris/htdocs/index.php on line 63 === I googled the error but couldn?t find a solution, do you know how fix this? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.