Strange behaviour with galaxy history
Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.*sample* file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot@wur.nl>wrote:
Hi,
First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause...
I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either.
In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed!
Thanks!
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl<; http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; Ambrose.Andongabo@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot@wur.nl<mailto:philip.degroot@wur.nl>> wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl><mailto:Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
Nice catch! I'll see where this leads. On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de <philip.degroot@wur.nl>wrote:
Hi Carl,
Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem.
The moment I UNCOMMENT the following line: #log_actions = True
I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now!
Thank you for your help!
Regards,
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; Ambrose.Andongabo@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history
Hello, Phillip
I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"?
Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy
That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate.
Thanks, Carl
On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot@wur.nl <mailto:philip.degroot@wur.nl>> wrote: Hi,
First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause...
I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either.
In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed!
Thanks!
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl><mailto: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<; http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
Hello, This should be working now in stable's branch, revision: 9ebd773<https://bitbucket.org/galaxy/galaxy-central/commits/9ebd7732e616492f4570587496f1b9074cb2eac7>. You should be able to use the saved histories list *and* log_actions=True together. Let me know if you see any more trouble. Thanks for the reports and the help in tracking it down. Carl On Tue, Jul 16, 2013 at 4:06 PM, Carl Eberhard <carlfeberhard@gmail.com>wrote:
Nice catch!
I'll see where this leads.
On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de <philip.degroot@wur.nl>wrote:
Hi Carl,
Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem.
The moment I UNCOMMENT the following line: #log_actions = True
I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now!
Thank you for your help!
Regards,
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; Ambrose.Andongabo@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history
Hello, Phillip
I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"?
Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy
That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate.
Thanks, Carl
On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot@wur.nl <mailto:philip.degroot@wur.nl>> wrote: Hi,
First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause...
I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either.
In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed!
Thanks!
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl><mailto: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<; http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
Thanks Carl, Happy you got to the bottom of it. Shane On 19/07/2013, at 2:28 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello,
This should be working now in stable's branch, revision: 9ebd773. You should be able to use the saved histories list and log_actions=True together. Let me know if you see any more trouble.
Thanks for the reports and the help in tracking it down. Carl
On Tue, Jul 16, 2013 at 4:06 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote: Nice catch!
I'll see where this leads.
On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de <philip.degroot@wur.nl> wrote: Hi Carl,
Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem.
The moment I UNCOMMENT the following line: #log_actions = True
I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now!
Thank you for your help!
Regards,
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; Ambrose.Andongabo@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history
Hello, Phillip
I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"?
Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy
That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate.
Thanks, Carl
On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot@wur.nl<mailto:philip.degroot@wur.nl>> wrote: Hi,
First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause...
I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either.
In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed!
Thanks!
Dr. Philip de Groot Ph.D. Bioinformatics Researcher
Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl><mailto:Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
-- For urgent cases, contact support@biomatters.com Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
participants (3)
-
Carl Eberhard -
Groot, Philip de -
Shane Sturrock