From AMORALESPINZON at bwh.harvard.edu Tue Mar 5 11:37:21 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 5 Mar 2019 16:37:21 +0000 Subject: [Loris-dev] [IPMSA project] LORIS missing updates in assign_missing_instruments.php In-Reply-To: References: Message-ID: Dear LORIS-dev team, After debugging with the help of Rida, we found out a small bug in my code where I inserted an additional character in some visit labels. Thank you very much for your help. Regards, Alfredo. ________________________________ From: Morales Pinzon, Alfredo Sent: Tuesday, February 19, 2019 6:04 PM To: loris-dev at bic.mni.mcgill.ca Cc: Rozie Arnaoutelis; Douglas Arnold, Dr.; Sridar Narayanan, Dr.; Guttmann, Charles,M.D.; pistikem at gmail.com; Zografos Caramanos Subject: [IPMSA project] LORIS missing updates in assign_missing_instruments.php Dear LORIS-dev team, In the IPMSA project we are batch inserting the clinical data. I am following the steps suggested by Rida, that I successfully used for a first study but now I am stuck in one of the steps. In that step I call the script "assign_missing_instruments.php" to assign missing instruments in the system. Using the script without the option "confirm", the output is telling me that only 1053 out of the expected 32338 visits are going to be created. Could you help understanding where is the problem or if the script I am missing something? What I can see is that script is only generating the changes for 2 out the new 83 visit labels. Here is the steps I have for the uploading process of clinical data, I am stuck in step number 8: 1. Generate the labels of the visits in the system (successfully done - 83 new visit labels) a. Modify the file config.xml b. Run the script "php populate_visit_windows.php" 2. Populate the table "test_battery" (successfully done: 678 new entries were added.) a. For each visit a set of instruments is assigned. 3. Check the state of tables - session: 31027 rows - flad: 275176 rows 4. Create the visits using the LORIS-API (successfully done: 32345 visits were created.) - table "session" has now "63372" rows (32345 = 31027 previous rows + 32345 new rows) 5. Check state of "session" table (17246 entries are "In progress") - select count(*) from session where Visit='In Progress'; 6. Hack the session table (successfully done: 32345 rows were updated ) a. Update each new row in the session table (32345 new rows) like this: UPDATE session SET Visit='In Progress',Scan_done='N',Current_stage='Visit',Date_stage_change='2010-12-24',Date_visit='2010-12-24' WHERE Visit_label='VISIT_LABEL' AND CandID=123456; 7. Check state of "session" table (49584 entries are "In progress", 49584 = 17246 old entries + 32338 new entries) [7 entries were not updated for missing date] - select count(*) from session where Visit='In Progress'; 8. Run php assign missing instruments - When running assign_missing_instruments.php with no arguments I get 1053 changes but I should get 32338 changes. The changes are pointing to only 2 out of the new 83 visit labels. 9. Insert instrument-visit information 10. Add "Candidate" information Thank you very much for help. Let me know if you need more details from my side. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Thu Mar 7 15:57:26 2019 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Thu, 7 Mar 2019 15:57:26 -0500 Subject: [Loris-dev] Announcing LORIS' Google Summer of Code project : Apply March 25 - April 9th Message-ID: Hi LORIS community -- Please circulate far and wide - thanks! This year LORIS is participating in Google?s Summer of Code program. Students around the world can apply through this Google-funded paid developer program to contribute remotely to our open-source Summer of Code project: improving the LORIS testing infrastructure. Applications can be submitted to join our project between March 25 and April 9 . Project description: https://www.incf.org/gsoc2019/projectlist#LORIS Google Summer of Code program details (eligibility, timelines): https://summerofcode.withgoogle.com/ Get in touch with us before applying -- sign up for the Neurostars.org forum where we?ll be answering questions about the project and helping applicants at: https://neurostars.org/t/gsoc-project-idea-12-improve-automated-testing-suite-for-the-loris-neuroinformatics-platform/3370 LORIS is an open-source neuroscience research data sharing platform enabling researchers to seamlessly acquire, curate, and disseminate data from diverse modalities such as neuroimaging, clinical/behavioural, genetics and biobanking and electrophysiological data. It supports many Open-Science initiatives and global initiatives such as BIDS and FAIR standardization practices. Visit: LORIS.ca | Try: demo.loris.ca | Fork: github.com/aces/loris Our participation in GSoC is facilitated by INCF, the International Neuroinformatics Coordinating Facility. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Fri Mar 8 09:08:16 2019 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Fri, 8 Mar 2019 09:08:16 -0500 Subject: [Loris-dev] Announcing LORIS' Google Summer of Code project : Apply March 25 - April 9th Message-ID: Hello LORIS-dev community -- Please circulate far and wide - thanks -- This year LORIS is participating in Google?s Summer of Code program. Students around the world can apply through this Google-funded paid developer program to contribute remotely to our open-source Summer of Code project: improving the LORIS testing infrastructure. Applications can be submitted to join our project between March 25 and April 9 . Project description: https://www.incf.org/gsoc2019/projectlist#LORIS Google Summer of Code program details (eligibility, timelines): https://summerofcode.withgoogle.com/ Get in touch with us before applying -- sign up for the Neurostars.org forum where we?ll be answering questions about the project and helping applicants at: https://neurostars.org/t/gsoc-project-idea-12-improve-automated-testing-suite-for-the-loris-neuroinformatics-platform/3370 LORIS is an open-source neuroscience research data sharing platform enabling researchers to seamlessly acquire, curate, and disseminate data from diverse modalities such as neuroimaging, clinical/behavioural, genetics and biobanking and electrophysiological data. It supports many Open-Science initiatives and global initiatives such as BIDS and FAIR standardization practices. Visit: LORIS.ca | Try: demo.loris.ca | Fork: github.com/aces/loris Our participation in GSoC is facilitated by INCF , the International Neuroinformatics Coordinating Facility. -- christine.rogers at mcgill.ca | rogers at bic.mni.mcgill.ca Senior Technical Project manager LORIS Data systems | LORIS.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Fri Mar 8 09:33:55 2019 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Fri, 8 Mar 2019 09:33:55 -0500 Subject: [Loris-dev] Announcing LORIS' Google Summer of Code project : Apply March 25 - April 9th Message-ID: Hello LORIS-dev community -- Please circulate far and wide - thanks -- We are excited to announce that LORIS is participating in Google?s 2019 Summer of Code program. Students around the world can apply through this Google-funded paid developer program to contribute remotely to our open-source Summer of Code project: improving the LORIS testing infrastructure. Applications can be submitted to join our project between March 25 and April 9 . Project description: https://www.incf.org/gsoc2019/projectlist#LORIS Google Summer of Code program details (eligibility, timelines): https://summerofcode.withgoogle.com/ Get in touch with us before applying -- Sign up for the Neurostars.org forum where we?ll be answering questions about the project and helping applicants at: https://neurostars.org/t/gsoc-project-idea-12-improve-automated-testing-suite-for-the-loris-neuroinformatics-platform/3370 LORIS is an open-source neuroscience research data sharing platform enabling researchers to seamlessly acquire, curate, and disseminate data from diverse modalities such as neuroimaging, clinical/behavioural, genetics and biobanking and electrophysiological data. It supports many Open-Science initiatives and global initiatives such as BIDS and FAIR standardization practices. Visit: LORIS.ca | Try: demo.loris.ca | Fork: github.com/aces/loris Our participation in GSoC is facilitated by INCF , the International Neuroinformatics Coordinating Facility. LORIS.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Tue Mar 19 16:35:14 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 19 Mar 2019 20:35:14 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server Message-ID: Dear LorisDev Team, Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the database in the project/config.xml file the system is still not running. Are there more changes that I need to do to get the system up? Am I missing something? Thank you in advance for your help. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.abou-haidar at mcin.ca Tue Mar 19 16:43:40 2019 From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar) Date: Tue, 19 Mar 2019 16:43:40 -0400 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: Message-ID: Hi, What exact error are you getting in the apache log ? Is anything loading on the front end? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev Team, > > Our VM running Loris has been moved and a different IP was assigned. I > though the problem was the connection to the database, which is running in > a different VM, but after changing the IP of the database in the > project/config.xml file the system is still not running. > > Are there more changes that I need to do to get the system up? Am I > missing something? > > Thank you in advance for your help. > > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > 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 sylvain at bic.mni.mcgill.ca Tue Mar 19 17:23:55 2019 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Tue, 19 Mar 2019 17:23:55 -0400 (EDT) Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: Message-ID: this should give you a clue... Mar 19 16:43:37 ipmsa-mysql mysqld[13192]: refused connect from 132.216.133.49 Mar 19 16:44:13 ipmsa-mysql mysqld[13192]: refused connect from 132.216.133.49 Mar 19 16:59:11 ipmsa-mysql mysqld[13192]: refused connect from 132.216.133.49 Mar 19 17:02:24 ipmsa-mysql mysqld[13192]: refused connect from 132.216.133.49 Mar 19 17:03:06 ipmsa-mysql mysqld[13192]: refused connect from 132.216.133.50 the firewall allows it. On Tue, 19 Mar 2019, Morales Pinzon, Alfredo wrote: > Dear LorisDev Team, > > Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the database in > the project/config.xml file the system is still not running. > > Are there more changes that I need to do to get the system up? Am I missing something? > > Thank you in advance for your help. > > 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 Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) From sylvain at bic.mni.mcgill.ca Tue Mar 19 23:20:13 2019 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Tue, 19 Mar 2019 23:20:13 -0400 (EDT) Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: Message-ID: it just occurred to me that host access might be the issue and it was! problem now fixed ... $ ssh ipmsa-mysql grep mysql /etc/hosts.allow mysqld: 132.216.133.49 sorry for the trouble, Sylvain On Tue, 19 Mar 2019, Sylvain MILOT wrote: > > this should give you a clue... > > Mar 19 16:43:37 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 16:44:13 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 16:59:11 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 17:02:24 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 17:03:06 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.50 > > the firewall allows it. > > On Tue, 19 Mar 2019, Morales Pinzon, Alfredo wrote: > >> Dear LorisDev Team, >> >> Our VM running Loris has been moved and a different IP was assigned. I >> though the problem was the connection to the database, which is running in >> a different VM, but after changing the IP of the database in >> the project/config.xml file the system is still not running. >> >> Are there more changes that I need to do to get the system up? Am I missing >> something? >> >> Thank you in advance for your help. >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > > > --- > > Please join our Forum! Useful info here: > https://forum.bic.mni.mcgill.ca/c/general > > If you need services: workstation maintenance or a storage lease, please > fill out > https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form > > Other questions or requests, please contact > > Our ssh login server is login.bic.mni.mcgill.ca > ssh RSA key fingerprint is > 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b > ssh DSA key fingerprint is > 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a > ssh ECDSA key fingerprint is > 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (sylvain.milot at mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street, Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : Room NW119 (North Wing) > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) From AMORALESPINZON at bwh.harvard.edu Wed Mar 20 09:08:12 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 20 Mar 2019 13:08:12 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , Message-ID: HI Sylvain, Thank you fixing the issue, we can now access mysql from the loris VM. The server is still not working but we now know is not the database connection. Regards, Alfredo. ________________________________ From: Sylvain MILOT Sent: Tuesday, March 19, 2019 11:20 PM To: Morales Pinzon, Alfredo Cc: Sridar Narayanan, Dr.; loris-dev at bic.mni.mcgill.ca; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server External Email - Use Caution it just occurred to me that host access might be the issue and it was! problem now fixed ... $ ssh ipmsa-mysql grep mysql /etc/hosts.allow mysqld: 132.216.133.49 sorry for the trouble, Sylvain On Tue, 19 Mar 2019, Sylvain MILOT wrote: > > this should give you a clue... > > Mar 19 16:43:37 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 16:44:13 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 16:59:11 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 17:02:24 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.49 > Mar 19 17:03:06 ipmsa-mysql mysqld[13192]: refused connect from > 132.216.133.50 > > the firewall allows it. > > On Tue, 19 Mar 2019, Morales Pinzon, Alfredo wrote: > >> Dear LorisDev Team, >> >> Our VM running Loris has been moved and a different IP was assigned. I >> though the problem was the connection to the database, which is running in >> a different VM, but after changing the IP of the database in >> the project/config.xml file the system is still not running. >> >> Are there more changes that I need to do to get the system up? Am I missing >> something? >> >> Thank you in advance for your help. >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > > > --- > > Please join our Forum! Useful info here: > https://forum.bic.mni.mcgill.ca/c/general > > If you need services: workstation maintenance or a storage lease, please > fill out > https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form > > Other questions or requests, please contact > > Our ssh login server is login.bic.mni.mcgill.ca > ssh RSA key fingerprint is > 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b > ssh DSA key fingerprint is > 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a > ssh ECDSA key fingerprint is > 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (sylvain.milot at mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street, Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : Room NW119 (North Wing) > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Wed Mar 20 09:09:42 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 20 Mar 2019 13:09:42 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , Message-ID: Hi Rida, I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this is what I see in the apache log (I just restarted apache): [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: caught SIGTERM, shutting down [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: Graceful restart requested, doing restart [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' Let me know if you have any ideas. Best, Alfredo. ________________________________ From: Rida Abou-Haidar Sent: Tuesday, March 19, 2019 4:43 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server External Email - Use Caution Hi, What exact error are you getting in the apache log ? Is anything loading on the front end? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo > wrote: Dear LorisDev Team, Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the database in the project/config.xml file the system is still not running. Are there more changes that I need to do to get the system up? Am I missing something? Thank you in advance for your help. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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 AMORALESPINZON at bwh.harvard.edu Wed Mar 20 09:11:17 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 20 Mar 2019 13:11:17 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , , Message-ID: This is the correct url: https://ipmsa-loris.bic.mni.mcgill.ca/ ________________________________ From: Morales Pinzon, Alfredo Sent: Wednesday, March 20, 2019 9:09 AM To: Rida Abou-Haidar Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server Hi Rida, I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this is what I see in the apache log (I just restarted apache): [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: caught SIGTERM, shutting down [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: Graceful restart requested, doing restart [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' Let me know if you have any ideas. Best, Alfredo. ________________________________ From: Rida Abou-Haidar Sent: Tuesday, March 19, 2019 4:43 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server External Email - Use Caution Hi, What exact error are you getting in the apache log ? Is anything loading on the front end? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo > wrote: Dear LorisDev Team, Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the database in the project/config.xml file the system is still not running. Are there more changes that I need to do to get the system up? Am I missing something? Thank you in advance for your help. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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 sylvain at bic.mni.mcgill.ca Wed Mar 20 09:13:20 2019 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed, 20 Mar 2019 09:13:20 -0400 (EDT) Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , Message-ID: that's a McGill Info Security issue - they just blocked a bunch of ports ... currently in contact with them! this should soon be fixed - I'll keep you posted On Wed, 20 Mar 2019, Morales Pinzon, Alfredo wrote: > Hi Rida, > > I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this is what I see in the apache log (I just restarted apache): > > [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: caught SIGTERM, shutting down > [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations > [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' > [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: Graceful restart requested, doing restart > [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations > [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' > > Let me know if you have any ideas. > > Best, > Alfredo. > > _______________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Rida Abou-Haidar > Sent: Tuesday, March 19, 2019 4:43 PM > To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server ? > > ????????External Email - Use Caution???????? > > Hi, > > What exact error are you getting in the apache log ? > > Is anything loading on the front end? > > > Rida Abou-Haidar > CCNA Software Developer > Montreal Neurological Institute > McGill University > rida.abou-haidar at mcin.ca > > On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo wrote: > Dear LorisDev Team, > > Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the > database in the project/config.xml file the system is still not running. > > Are there more changes that I need to do to get the system up? Am I missing something? > > Thank you in advance for your help. > > 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 Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) From dave.macfarlane at mcin.ca Wed Mar 20 09:25:55 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Wed, 20 Mar 2019 09:25:55 -0400 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: Message-ID: I'm not sure if you've already fixed this, but another thing to keep in mind that I don't see mentioned in this thread is that MySQL accounts are tied to where it's connecting from, so the hostname/ip part of your MySQL account itself might need to be fixed. On Wed, Mar 20, 2019 at 9:13 AM Sylvain MILOT wrote: > > that's a McGill Info Security issue - they just blocked a bunch of ports > ... currently in contact with them! > > this should soon be fixed - I'll keep you posted > > On Wed, 20 Mar 2019, Morales Pinzon, Alfredo wrote: > > > Hi Rida, > > > > I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", > this is what I see in the apache log (I just restarted apache): > > > > [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] > AH00169: caught SIGTERM, shutting down > > [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] > AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming > normal operations > > [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: > Command line: '/usr/sbin/apache2' > > [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] > AH00171: Graceful restart requested, doing restart > > [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] > AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming > normal operations > > [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: > Command line: '/usr/sbin/apache2' > > > > Let me know if you have any ideas. > > > > Best, > > Alfredo. > > > > > _______________________________________________________________________________________________________________________________________________________________________________________________________________ > > From: Rida Abou-Haidar > > Sent: Tuesday, March 19, 2019 4:43 PM > > To: Morales Pinzon, Alfredo > > Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie > Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. > > Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in > server > > > > External Email - Use Caution > > > > Hi, > > > > What exact error are you getting in the apache log ? > > > > Is anything loading on the front end? > > > > > > Rida Abou-Haidar > > CCNA Software Developer > > Montreal Neurological Institute > > McGill University > > rida.abou-haidar at mcin.ca > > > > On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LorisDev Team, > > > > Our VM running Loris has been moved and a different IP was assigned. I > though the problem was the connection to the database, which is running in > a different VM, but after changing the IP of the > > database in the project/config.xml file the system is still not running. > > > > Are there more changes that I need to do to get the system up? Am I > missing something? > > > > Thank you in advance for your help. > > > > 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 Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > _______________________________________________ > > Loris-dev mailing list > > Loris-dev at bic.mni.mcgill.ca > > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > > > > > > --- > > Please join our Forum! Useful info here: > https://forum.bic.mni.mcgill.ca/c/general > > If you need services: workstation maintenance or a storage lease, > please fill out > > https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form > > Other questions or requests, please contact < > bicadmin at bic.mni.mcgill.ca> > > Our ssh login server is login.bic.mni.mcgill.ca > ssh RSA key fingerprint is > 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b > ssh DSA key fingerprint is > 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a > ssh ECDSA key fingerprint is > 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (sylvain.milot at mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street, Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : Room NW119 (North > Wing)_______________________________________________ > 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 AMORALESPINZON at bwh.harvard.edu Wed Mar 20 09:30:48 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 20 Mar 2019 13:30:48 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , Message-ID: Hi Dave, Yes, I fixed that. I cann login into mysql using the "mysql loris account" from the loris VM. Alfredo. ________________________________ From: Dave MacFarlane Sent: Wednesday, March 20, 2019 9:25 AM To: Sylvain MILOT Cc: Morales Pinzon, Alfredo; Sridar Narayanan, Dr.; loris-dev at bic.mni.mcgill.ca; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server External Email - Use Caution I'm not sure if you've already fixed this, but another thing to keep in mind that I don't see mentioned in this thread is that MySQL accounts are tied to where it's connecting from, so the hostname/ip part of your MySQL account itself might need to be fixed. On Wed, Mar 20, 2019 at 9:13 AM Sylvain MILOT > wrote: that's a McGill Info Security issue - they just blocked a bunch of ports ... currently in contact with them! this should soon be fixed - I'll keep you posted On Wed, 20 Mar 2019, Morales Pinzon, Alfredo wrote: > Hi Rida, > > I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this is what I see in the apache log (I just restarted apache): > > [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: caught SIGTERM, shutting down > [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations > [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' > [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: Graceful restart requested, doing restart > [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations > [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: Command line: '/usr/sbin/apache2' > > Let me know if you have any ideas. > > Best, > Alfredo. > > _______________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Rida Abou-Haidar > > Sent: Tuesday, March 19, 2019 4:43 PM > To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server > > External Email - Use Caution > > Hi, > > What exact error are you getting in the apache log ? > > Is anything loading on the front end? > > > Rida Abou-Haidar > CCNA Software Developer > Montreal Neurological Institute > McGill University > rida.abou-haidar at mcin.ca > > On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo > wrote: > Dear LorisDev Team, > > Our VM running Loris has been moved and a different IP was assigned. I though the problem was the connection to the database, which is running in a different VM, but after changing the IP of the > database in the project/config.xml file the system is still not running. > > Are there more changes that I need to do to get the system up? Am I missing something? > > Thank you in advance for your help. > > 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 Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact > Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing)_______________________________________________ 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 sylvain at bic.mni.mcgill.ca Wed Mar 20 09:32:42 2019 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed, 20 Mar 2019 09:32:42 -0400 (EDT) Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , Message-ID: ok the InfoSec issue is fixed... from outside McGill, you have... nmap -PN ipmsa-loris.bic.mni.mcgill.ca Starting Nmap 6.40 ( http://nmap.org ) at 2019-03-20 09:30 EDT Nmap scan report for ipmsa-loris.bic.mni.mcgill.ca (132.216.133.49) Host is up (0.0087s latency). Not shown: 998 filtered ports PORT STATE SERVICE 80/tcp open http 443/tcp open https On Wed, 20 Mar 2019, Sylvain MILOT wrote: > > that's a McGill Info Security issue - they just blocked a bunch of ports ... > currently in contact with them! > > this should soon be fixed - I'll keep you posted > > On Wed, 20 Mar 2019, Morales Pinzon, Alfredo wrote: > >> Hi Rida, >> >> I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this >> is what I see in the apache log (I just restarted apache): >> >> [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: >> caught SIGTERM, shutting down >> [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: >> Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal >> operations >> [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: >> Command line: '/usr/sbin/apache2' >> [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: >> Graceful restart requested, doing restart >> [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: >> Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal >> operations >> [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: >> Command line: '/usr/sbin/apache2' >> >> Let me know if you have any ideas. >> >> Best, >> Alfredo. >> >> _______________________________________________________________________________________________________________________________________________________________________________________________________________ >> From: Rida Abou-Haidar >> Sent: Tuesday, March 19, 2019 4:43 PM >> To: Morales Pinzon, Alfredo >> Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; >> Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. >> Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server >> ? >> >> ????????External Email - Use Caution???????? >> >> Hi, >> >> What exact error are you getting in the apache log ? >> >> Is anything loading on the front end? >> >> >> Rida Abou-Haidar >> CCNA Software Developer >> Montreal Neurological Institute >> McGill University >> rida.abou-haidar at mcin.ca >> >> On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo >> wrote: >> Dear LorisDev Team, >> >> Our VM running Loris has been moved and a different IP was assigned. I >> though the problem was the connection to the database, which is running in >> a different VM, but after changing the IP of the >> database in the project/config.xml file the system is still not running. >> >> Are there more changes that I need to do to get the system up? Am I missing >> something? >> >> Thank you in advance for your help. >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> > > > --- > > Please join our Forum! Useful info here: > https://forum.bic.mni.mcgill.ca/c/general > > If you need services: workstation maintenance or a storage lease, please > fill out > https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form > > Other questions or requests, please contact > > Our ssh login server is login.bic.mni.mcgill.ca > ssh RSA key fingerprint is > 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b > ssh DSA key fingerprint is > 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a > ssh ECDSA key fingerprint is > 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (sylvain.milot at mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street, Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : Room NW119 (North Wing) --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) From AMORALESPINZON at bwh.harvard.edu Wed Mar 20 10:13:25 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 20 Mar 2019 14:13:25 +0000 Subject: [Loris-dev] [IPMSA] System down due to change of IP in server In-Reply-To: References: , , Message-ID: Hi Sylvain, Daven and Rida, I also fixed a typo in the ip of the database in the config.xml, now LORIS is running. Thank you for your help. Regards, Alfredo. ________________________________ From: Sylvain MILOT Sent: Wednesday, March 20, 2019 9:32 AM To: Morales Pinzon, Alfredo Cc: Sridar Narayanan, Dr.; loris-dev at bic.mni.mcgill.ca; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server External Email - Use Caution ok the InfoSec issue is fixed... from outside McGill, you have... nmap -PN ipmsa-loris.bic.mni.mcgill.ca Starting Nmap 6.40 ( http://nmap.org ) at 2019-03-20 09:30 EDT Nmap scan report for ipmsa-loris.bic.mni.mcgill.ca (132.216.133.49) Host is up (0.0087s latency). Not shown: 998 filtered ports PORT STATE SERVICE 80/tcp open http 443/tcp open https On Wed, 20 Mar 2019, Sylvain MILOT wrote: > > that's a McGill Info Security issue - they just blocked a bunch of ports ... > currently in contact with them! > > this should soon be fixed - I'll keep you posted > > On Wed, 20 Mar 2019, Morales Pinzon, Alfredo wrote: > >> Hi Rida, >> >> I cannot even reach the site "https://ipmsa-spine.bic.mni.mcgill.ca/", this >> is what I see in the apache log (I just restarted apache): >> >> [Wed Mar 20 09:01:22.401358 2019] [mpm_prefork:notice] [pid 31256] AH00169: >> caught SIGTERM, shutting down >> [Wed Mar 20 09:01:23.655172 2019] [mpm_prefork:notice] [pid 29025] AH00163: >> Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal >> operations >> [Wed Mar 20 09:01:23.655330 2019] [core:notice] [pid 29025] AH00094: >> Command line: '/usr/sbin/apache2' >> [Wed Mar 20 09:01:39.651730 2019] [mpm_prefork:notice] [pid 29025] AH00171: >> Graceful restart requested, doing restart >> [Wed Mar 20 09:01:40.102377 2019] [mpm_prefork:notice] [pid 29025] AH00163: >> Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal >> operations >> [Wed Mar 20 09:01:40.102407 2019] [core:notice] [pid 29025] AH00094: >> Command line: '/usr/sbin/apache2' >> >> Let me know if you have any ideas. >> >> Best, >> Alfredo. >> >> _______________________________________________________________________________________________________________________________________________________________________________________________________________ >> From: Rida Abou-Haidar >> Sent: Tuesday, March 19, 2019 4:43 PM >> To: Morales Pinzon, Alfredo >> Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; >> Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. >> Subject: Re: [Loris-dev] [IPMSA] System down due to change of IP in server >> >> >> External Email - Use Caution >> >> Hi, >> >> What exact error are you getting in the apache log ? >> >> Is anything loading on the front end? >> >> >> Rida Abou-Haidar >> CCNA Software Developer >> Montreal Neurological Institute >> McGill University >> rida.abou-haidar at mcin.ca >> >> On Tue., Mar. 19, 2019, 4:35 p.m. Morales Pinzon, Alfredo >> wrote: >> Dear LorisDev Team, >> >> Our VM running Loris has been moved and a different IP was assigned. I >> though the problem was the connection to the database, which is running in >> a different VM, but after changing the IP of the >> database in the project/config.xml file the system is still not running. >> >> Are there more changes that I need to do to get the system up? Am I missing >> something? >> >> Thank you in advance for your help. >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> > > > --- > > Please join our Forum! Useful info here: > https://forum.bic.mni.mcgill.ca/c/general > > If you need services: workstation maintenance or a storage lease, please > fill out > https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form > > Other questions or requests, please contact > > Our ssh login server is login.bic.mni.mcgill.ca > ssh RSA key fingerprint is > 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b > ssh DSA key fingerprint is > 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a > ssh ECDSA key fingerprint is > 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (sylvain.milot at mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street, Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : Room NW119 (North Wing) --- Please join our Forum! Useful info here: https://forum.bic.mni.mcgill.ca/c/general If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form Other questions or requests, please contact Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street, Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : Room NW119 (North Wing) -------------- next part -------------- An HTML attachment was scrubbed... URL: From rolando.acosta at cnbp.ca Thu Mar 21 14:21:05 2019 From: rolando.acosta at cnbp.ca (Rolando Acosta) Date: Thu, 21 Mar 2019 14:21:05 -0400 Subject: [Loris-dev] Need of a refresh token mechanism for the LORIS API. In-Reply-To: References: Message-ID: Hi loris-dev team, At CNBP we're wondering if there is a possibility of developing a refresh token for the Loris-API. The demand comes from the following situation: Currently API token expires in 24 hours. When an app authenticate and get the access token, must do the re-authentication process (via user, pass) before 24hours to get the new token in the case of continuous communication needs. We have in place a service that takes MRIs from the scanner and push it into the LORIS instances automatically via the API. The issue comes then because LORIS users have a password expiration after 6months of creation/modification. So every 6 months the automatic uploading system crash (as the password expiry) and the sysadmin should manually change the password and feed it back into the automatic system. Having a refresh token two issues could be solved from the automation perspective: - The user and pass will not longer have to be provided to the system every 24 hours. (of course the refresh token must) - The automatic system for uploading content will not break and need human intervention every 6 months. Thank you very much in advance for the help you can provide us, Rolando Acosta Canadian Neonatal Brain Platform (CHU Sainte-Justine) -------------- next part -------------- An HTML attachment was scrubbed... URL: From john.saigle at mcin.ca Thu Mar 21 17:16:44 2019 From: john.saigle at mcin.ca (John Saigle) Date: Thu, 21 Mar 2019 17:16:44 -0400 Subject: [Loris-dev] Need of a refresh token mechanism for the LORIS API. In-Reply-To: References: Message-ID: Hi Rolando, Thanks for the suggestion -- it's a very good idea. I've opened a ticket on GitHub containing the body of your email. We don't have a plan to implement this feature yet but we can put it on our roadmap as we sort out priorities for upcoming releases. You can track the status of this request by checking on on the ticket every so often. All the best, John Saigle On Thu, Mar 21, 2019 at 2:21 PM Rolando Acosta wrote: > Hi loris-dev team, > > At CNBP we're wondering if there is a possibility of developing a refresh > token for the Loris-API. The demand comes from the following situation: > > Currently API token expires in 24 hours. When an app authenticate and get > the access token, must do the re-authentication process (via user, pass) > before 24hours to get the new token in the case of continuous communication > needs. We have in place a service that takes MRIs from the scanner and push > it into the LORIS instances automatically via the API. The issue comes then > because LORIS users have a password expiration after 6months of > creation/modification. So every 6 months the automatic uploading system > crash (as the password expiry) and the sysadmin should manually change the > password and feed it back into the automatic system. > > Having a refresh token two issues could be solved from the automation > perspective: > - The user and pass will not longer have to be provided to the system > every 24 hours. (of course the refresh token must) > - The automatic system for uploading content will not break and need > human intervention every 6 months. > > Thank you very much in advance for the help you can provide us, > > Rolando Acosta > Canadian Neonatal Brain Platform (CHU Sainte-Justine) > _______________________________________________ > 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: