Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3
Hi Nate, Thanks for the suggestion! Unfortunately, it still failed :( I got the following error message in proftp log: 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 2 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 1 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cache hit for user ' hailiang.m...@nbic.nl' 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha1' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha1' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha256' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha256' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'pbkdf2' 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: 'pbkdf2' SQLAuthType handler reports failure 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_auth The old user account generated before our code update still works. I wonder how it is configured at the Galaxy main server? Thanks, Leon On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 26, 2013, at 3:51 PM, Leon Mei wrote: Dear galaxy developers, We have tried today to upgrade our proftpd configuration to make uploading for our galaxy users possible again, both for users with old as well as new style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 and have the following SQL part in our configuration file based on the post of http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html SQLEngine on SQLLogFile /var/log/proftpd-sql.log SQLBackend postgres SQLConnectInfo galaxy@localhost:5840 galaxyftp [ourpassword] SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLPasswordUserSalt sql:/GetUserSalt SQLAuthenticate users SQLDefaultUID 108 SQLDefaultGID 116 SQLDefaultHomedir /opt/cloudman/pkg/proftpd/var SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLNamedQuery GetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U' We have executed the LookupGalaxyUser and GetUserSalt commands manually, and the results look good. Now, old users can login via ftp, but for a new user, the authentication still fails: 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: cmd_check 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'sha1' 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler reports failure 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon Hallo Leon and Rob, Thanks for working on this, when I'd looked a couple months ago I could not find an entirely-ProFTPD way to do this. I think it may have actually come about because I asked about it on their IRC channel. ;) This may work if you change SQLPasswordPBKDF2: SQLPasswordPBKDF2 SHA256 1 24 It'd be great if ProFTPD also supported pulling those values dynamically from the database, but Galaxy's PBKDF2 code currently has them hardcoded, so they will be static anyway. --nate -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce -
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Peter, The automated build prior to this email was executed incorrectly. I've resolved that status, and the current test results look correct. --Dave B. On 8/8/13 10:30:37.000, Peter Cock wrote: On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, The good news is it does seem some of the missing test results I had on Monday have been resolved. However, there are still others showing with no test results: :( No test results here (I expect some to pass and some to fail): http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a I've been updating the BLAST+ repository - currently it does show some failures due to missing test, but there seems to be test information missing here - and also I'm expecting the installation to fail with BOOST issues: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec (The other problems from 1 August look OK now) Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3
On Aug 9, 2013, at 2:38 AM, Leon Mei wrote: Hi Nate, Thanks for the suggestion! Unfortunately, it still failed :( I got the following error message in proftp log: 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 2 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 1 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cache hit for user 'hailiang.m...@nbic.nl' 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha1' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha1' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha256' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha256' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'pbkdf2' 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: 'pbkdf2' SQLAuthType handler reports failure 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_auth The old user account generated before our code update still works. I wonder how it is configured at the Galaxy main server? Thanks, Leon It isn't in use on the Main server, but now that I'm aware that ProFTPD has PBKDF2 support, I will put this on my to-do list for next week to test. --nate On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 26, 2013, at 3:51 PM, Leon Mei wrote: Dear galaxy developers, We have tried today to upgrade our proftpd configuration to make uploading for our galaxy users possible again, both for users with old as well as new style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 and have the following SQL part in our configuration file based on the post of http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html SQLEngine on SQLLogFile /var/log/proftpd-sql.log SQLBackend postgres SQLConnectInfo galaxy@localhost:5840 galaxyftp [ourpassword] SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLPasswordUserSalt sql:/GetUserSalt SQLAuthenticate users SQLDefaultUID 108 SQLDefaultGID 116 SQLDefaultHomedir /opt/cloudman/pkg/proftpd/var SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLNamedQuery GetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U' We have executed the LookupGalaxyUser and GetUserSalt commands manually, and the results look good. Now, old users can login via ftp, but for a new user, the authentication still fails: 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: cmd_check 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'sha1' 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler reports failure 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon Hallo Leon and Rob, Thanks for working on this, when I'd looked a couple months ago I could not find an entirely-ProFTPD way to do this. I think it may have actually come about because I asked about it on their IRC channel. ;) This may work if you change SQLPasswordPBKDF2: SQLPasswordPBKDF2 SHA256 1 24 It'd be great if ProFTPD also supported pulling those values dynamically from the database, but Galaxy's PBKDF2 code currently has them hardcoded, so they will be static anyway. --nate -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to
Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3
For the moment, the best solution is to disable PBKDF2 in Galaxy if you are also using FTP. That is how Galaxy main is currently configured. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Aug 9, 2013 at 10:01 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 9, 2013, at 2:38 AM, Leon Mei wrote: Hi Nate, Thanks for the suggestion! Unfortunately, it still failed :( I got the following error message in proftp log: 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 2 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 1 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cache hit for user 'hailiang.m...@nbic.nl' 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha1' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha1' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha256' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha256' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'pbkdf2' 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: 'pbkdf2' SQLAuthType handler reports failure 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_auth The old user account generated before our code update still works. I wonder how it is configured at the Galaxy main server? Thanks, Leon It isn't in use on the Main server, but now that I'm aware that ProFTPD has PBKDF2 support, I will put this on my to-do list for next week to test. --nate On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 26, 2013, at 3:51 PM, Leon Mei wrote: Dear galaxy developers, We have tried today to upgrade our proftpd configuration to make uploading for our galaxy users possible again, both for users with old as well as new style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 and have the following SQL part in our configuration file based on the post of http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html SQLEngine on SQLLogFile /var/log/proftpd-sql.log SQLBackend postgres SQLConnectInfo galaxy@localhost:5840 galaxyftp [ourpassword] SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLPasswordUserSalt sql:/GetUserSalt SQLAuthenticate users SQLDefaultUID 108 SQLDefaultGID 116 SQLDefaultHomedir /opt/cloudman/pkg/proftpd/var SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLNamedQuery GetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U' We have executed the LookupGalaxyUser and GetUserSalt commands manually, and the results look good. Now, old users can login via ftp, but for a new user, the authentication still fails: 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: cmd_check 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'sha1' 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler reports failure 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon Hallo Leon and Rob, Thanks for working on this, when I'd looked a couple months ago I could not find an entirely-ProFTPD way to do this. I think it may have actually come about because I asked about it on their IRC channel. ;) This may work if you change SQLPasswordPBKDF2: SQLPasswordPBKDF2 SHA256 1 24 It'd be great if ProFTPD also supported pulling those values dynamically from the database, but Galaxy's PBKDF2 code currently has them hardcoded, so they will be static anyway. --nate -- Hailiang (Leon) Mei Netherlands Bioinformatics Center
[galaxy-dev] One small problem for experts, one giant question for me..
Hello everyone,
Firstly, I am beginner. I am a new Galaxy user that installed the Galaxy
locally into my ubuntu (13.04) installed computer. Everything is working
perfectly right now. Galaxy is really awesome.
To learn the basics, I started the basic tutorial (Galaxy101
https://main.g2.bx.psu.edu/u/aun1/p/galaxy101) that helps too much. This
tutorial consist a step for explaning Compare Two Datasets function. I did
exactly everthing the instructor said however that module become red in History
with following error:
tool error
An error occured with dataset:
Unable to finish job (screenshot of error: http://i.imgur.com/xHqhK72.png)
I wrote the bug report at end of the mail.
Interestingly, when I press View button, I get the data that I wanted.
However, any metadata is seen. So I can not see the final results on the UCSC
browser. I replicate the same module at public server, it didn't gave an error.
What might cause this kind of problem? Does reinstalling solve this problem?
Would you please help me?
Thank you everyone.
Traceback (most recent call last):
File /home/can/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 94, in
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File /home/can/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1009, in finish
self.sa_session.flush()
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py,
line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1718, in flush
self._flush(objects)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1789, in _flush
flush_context.execute()
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 331, in execute
rec.execute(self)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 475, in execute
uow
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 59, in save_obj
mapper, table, update)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 485, in _emit_update_statements
execute(statement, params)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1449, in execute
params)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1698, in _execute_context
context)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1691, in _execute_context
context)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py,
line 331, in do_execute
cursor.execute(statement, parameters)
ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless
you use a text_factory that can interpret 8-bit bytestrings (like text_factory
= str). It is highly recommended that you instead just switch your application
to Unicode strings. u'UPDATE job SET update_time=?, stdout=?, stderr=? WHERE
job.id = ?' ('2013-08-09 09:00:48.464260', 'join (GNU coreutils)
8.20\nCopyright (C) 2012 Free Software Foundation, Inc.\nLisans GPLv3+: GNU GPL
s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1 http://gnu.org/licenses/gpl.html.\nBu
\xc3\x96zg\xc3\xbcr bir yaz\xc4\xb1l\xc4\xb1md\xc4\xb1r:
de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f\xc4\xb1tmakta
\xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4\xb1n izin verdi\xc4\x9fi
\xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir GARANT\xc4\xb0 sunulmaz.\n\nMike
Haertel taraf\xc4\xb1ndan yaz\xc4\xb1ld\xc4\xb1.\n', '', 41)
Can Holyavkin
PhD Student
Istanbul Technical University
Molecular Biology and Genetics Dept.___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] One small problem for experts, one giant question for me..
Hi Can,
something went wrong with your join utility part of your Ubuntu
installation.
Can you translate that for us?
'join (GNU coreutils) 8.20\nCopyright (C) 2012 Free Software Foundation,
Inc.\nLisans GPLv3+: GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1
http://gnu.org/licenses/gpl.html.\nBu \xc3\x96zg\xc3\xbcr bir yaz\xc4
\xb1l\xc4\xb1md\xc4\xb1r: de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f\xc4
\xb1tmakta \xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4\xb1n
izin verdi\xc4\x9fi \xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir GARANT\xc4
\xb0 sunulmaz.\n\nMike Haertel taraf\xc4\xb1ndan yaz\xc4\xb1ld\xc4
\xb1.\n'
If the data is not confidential and small enough, maybe you can send it
me. Also please make sure that no unicode character are included in the
dataset or description.
I do not think an reinstallation will solve that problem.
Cheers,
Bjoern
Hello everyone,
Firstly, I am beginner. I am a new Galaxy user that installed the
Galaxy locally into my ubuntu (13.04) installed computer. Everything
is working perfectly right now. Galaxy is really awesome.
To learn the basics, I started the basic tutorial (Galaxy101
https://main.g2.bx.psu.edu/u/aun1/p/galaxy101) that helps too much.
This tutorial consist a step for explaning Compare Two Datasets
function. I did exactly everthing the instructor said however that
module become red in History with following error:
tool error
An error occured with dataset:
Unable to finish job (screenshot of
error: http://i.imgur.com/xHqhK72.png)
I wrote the bug report at end of the mail.
Interestingly, when I press View button, I get the data that I
wanted. However, any metadata is seen. So I can not see the final
results on the UCSC browser. I replicate the same module at public
server, it didn't gave an error.
What might cause this kind of problem? Does reinstalling solve this
problem? Would you please help me?
Thank you everyone.
Traceback (most recent call last):
File /home/can/galaxy-dist/lib/galaxy/jobs/runners/local.py, line
94, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File /home/can/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1009,
in finish
self.sa_session.flush()
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py,
line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1718, in flush
self._flush(objects)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1789, in _flush
flush_context.execute()
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 331, in execute
rec.execute(self)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 475, in execute
uow
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 59, in save_obj
mapper, table, update)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 485, in _emit_update_statements
execute(statement, params)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1449, in execute
params)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1698, in _execute_context
context)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1691, in _execute_context
context)
File
/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py,
line 331, in do_execute
cursor.execute(statement, parameters)
ProgrammingError: (ProgrammingError) You must not use 8-bit
bytestrings unless you use a text_factory that can interpret 8-bit
bytestrings (like text_factory = str). It is highly recommended that
you instead just switch your application to Unicode strings. u'UPDATE
job SET update_time=?, stdout=?, stderr=? WHERE job.id
= ?' ('2013-08-09 09:00:48.464260', 'join (GNU coreutils) 8.20
\nCopyright (C) 2012 Free Software Foundation, Inc.\nLisans GPLv3+:
GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1
http://gnu.org/licenses/gpl.html.\nBu \xc3\x96zg\xc3\xbcr bir yaz
\xc4\xb1l\xc4\xb1md\xc4\xb1r: de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f
\xc4\xb1tmakta \xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4
\xb1n izin verdi\xc4\x9fi \xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Hi Dave, Progress: I can now see the test failures which suggest that the underlying binaries did not get installed properly. I guess this either means: (a) the dependency install failed but the Tool Shed doesn't say this (my hunch as recently the NCBI BLAST+ tools had stopped compiling on the Test Tool Shed due to a BOOST system library change). Or, (b) the dependency installed didn't raise any errors but failed in some way such as not setting the path (unlikely as the tool_dependencies.xml content has not changed - it has just been moved to a dependency package repository) Or, (c) there is something amiss with the dependency chain meaning that the BLAST dependencies are not being added to the PATH. This looks OK but it is the only thing I have changed recently. Or some other mode of failure I'm not guessed at yet? Is this something you can diagnose, or do I need to press ahead with a local Tool Shed to help me work out what is amiss? Thanks, Peter On Fri, Aug 9, 2013 at 1:58 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, The automated build prior to this email was executed incorrectly. I've resolved that status, and the current test results look correct. --Dave B. On 8/8/13 10:30:37.000, Peter Cock wrote: I've been updating the BLAST+ repository - currently it does show some failures due to missing test, but there seems to be test information missing here - and also I'm expecting the installation to fail with BOOST issues: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec (The other problems from 1 August look OK now) Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3
Hi Nate/James, Thanks! Where should I look into to disable PBKDF2 in the Galaxy code? Cheers, Leon On Fri, Aug 9, 2013 at 4:28 PM, James Taylor ja...@jamestaylor.org wrote: For the moment, the best solution is to disable PBKDF2 in Galaxy if you are also using FTP. That is how Galaxy main is currently configured. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Aug 9, 2013 at 10:01 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 9, 2013, at 2:38 AM, Leon Mei wrote: Hi Nate, Thanks for the suggestion! Unfortunately, it still failed :( I got the following error message in proftp log: 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 2 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_open 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: enteringpostgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: connection 'default' count is now 1 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_close 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: exiting postgres cmd_escapestring 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cache hit for user ' hailiang.m...@nbic.nl' 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,777 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha1' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha1' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'sha256' 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: 'sha256' SQLAuthType handler reports failure 2013-08-09 08:32:41,781 mod_sql/4.3[32384]: checking password using SQLAuthType 'pbkdf2' 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: 'pbkdf2' SQLAuthType handler reports failure 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_check 2013-08-09 08:32:41,841 mod_sql/4.3[32384]: cmd_auth The old user account generated before our code update still works. I wonder how it is configured at the Galaxy main server? Thanks, Leon It isn't in use on the Main server, but now that I'm aware that ProFTPD has PBKDF2 support, I will put this on my to-do list for next week to test. --nate On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 26, 2013, at 3:51 PM, Leon Mei wrote: Dear galaxy developers, We have tried today to upgrade our proftpd configuration to make uploading for our galaxy users possible again, both for users with old as well as new style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 and have the following SQL part in our configuration file based on the post of http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295.html SQLEngine on SQLLogFile /var/log/proftpd-sql.log SQLBackend postgres SQLConnectInfo galaxy@localhost:5840 galaxyftp [ourpassword] SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLPasswordUserSalt sql:/GetUserSalt SQLAuthenticate users SQLDefaultUID 108 SQLDefaultGID 116 SQLDefaultHomedir /opt/cloudman/pkg/proftpd/var SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLNamedQuery GetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U' We have executed the LookupGalaxyUser and GetUserSalt commands manually, and the results look good. Now, old users can login via ftp, but for a new user, the authentication still fails: 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: cmd_check 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'sha1' 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler reports failure 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon Hallo Leon and Rob, Thanks for working on this, when I'd looked a couple months ago I could not find an entirely-ProFTPD way to do this. I think it may have actually come about because I asked about it on their IRC channel. ;) This may work if you change SQLPasswordPBKDF2: SQLPasswordPBKDF2 SHA256 1 24 It'd be great if ProFTPD also
Re: [galaxy-dev] Upstart script to manage a multi instance load balanced installation
Dear Nate,
Adding su - galaxy as the first line of the pre-start script seems to
work reasonably well. Also it looks like the line that sets the egg cache
is not working properly. My egg cache ends up being
/tmp/${SERVER_NAME}_egg/ but things still seem to be working so I've
changed that part to use one directory in /tmp/ for all instances.
Sincerely,
Seth Sims
*galaxy.conf*
author Seth Sims seth.s...@gmail.com
version 0.0.2
description galaxy master process. Fetches eggs and spawns all of the
servers it finds configured
start on started network-services
# put galaxy root directory here
chdir /srv/galaxy-dist/
pre-start script
su - galaxy
date
echo checking python version
python ./scripts/check_python.py
[ $? -ne 0 ] exit 1
echo pre-fetching tossing out expired eggs
python ./scripts/check_eggs.py -q
if [ $? -eq 0 ]; then
echo Some eggs are out of date, attempting to fetch...
python ./scripts/fetch_eggs.py
if [ $? -eq 0 ]; then
echo Fetch Successful.
else
echo Fetch failed.
fi
fi
echo starting servers
SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini | xargs
echo`
for SERVER in ${SERVERS} ; do
echo starting server ${SERVER}
start galaxy-worker SERVER_NAME=${SERVER}
done
end script
post-stop script
SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini | xargs
echo`
date
echo stopping galaxy servers.
for SERVER in ${SERVERS} ; do
echo stopping ${SERVER}
stop galaxy-worker SERVER_NAME=${SERVER}
done
end script
---
*galaxy-worker*
author Seth Sims seth.s...@gmail.com
version 0.0.2
description Starts a galaxy server instance. This is run from the
galaxy.conf file
instance $SERVER_NAME
#make sure we are running as the galaxy user
setuid galaxy
setgid galaxy
#put the galaxy root directory here
chdir /srv/galaxy-dist/
#system users don't have /home/ directories; so point the egg unpack to a
directory in /tmp/
env PYTHON_EGG_CACHE=/tmp/galaxy_eggs/
respawn
script
exec python ./scripts/paster.py serve universe_wsgi.ini
--server-name=${SERVER_NAME}
end script
On Thu, Aug 8, 2013 at 1:52 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jul 15, 2013, at 6:29 PM, Seth Sims wrote:
After some work i've created an Upstart script which can manage a load
balanced galaxy configuration as described in the wiki. I thought that I
would put it on this list for other people to use. The script parses
universe_wsgi.ini just like run.sh and spawns all of the servers it finds.
It comes in two pieces galaxy.conf and galaxy-worker.conf. Once you place
them both in /etc/init and make the proper edits for the environment a
server can be started with sudo start galaxy. The configuration starts
the server at boot time and puts all of the instances under the management
of upstart which deals with pids, logging to syslog and respawning if an
instance crashes.
I have just gotten this working reasonably well but have done basically
no testing so there are bugs to be found. Any comments are welcome if
anyone knows a better way to do something here.
- Seth
Hi Seth,
Thanks for submitting these. I was about to commit them to the contrib/
directory along with the rest of the start scripts, but I was wondering if
you could avoid running the check/fetch scripts as root by just using `su
-c`?
--nate
*galaxy.conf*
author Seth Sims seth.s...@gmail.com
version 0.0.1 test
description galaxy master process. Fetches eggs and spawns all of the
servers it finds configured
start on started network-services
# make sure that any eggs we download are at least owned by the galaxy
group.
# we cannot use setuid in this script because only root can issue the
start galaxy-worker
# command. But this way the galaxy instances should still be able to use
their eggs.
setgid galaxy
# put galaxy root directory here
chdir /srv/galaxy-dist/
pre-start script
date
echo checking python version
python ./scripts/check_python.py
[ $? -ne 0 ] exit 1
echo pre-fetching tossing out expired eggs
python ./scripts/check_eggs.py -q
if [ $? -eq 0 ]; then
echo Some eggs are out of date, attempting to fetch...
python ./scripts/fetch_eggs.py
if [ $? -eq 0 ]; then
echo Fetch Successful.
else
echo Fetch failed.
fi
fi
echo starting servers
SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini |
xargs echo`
for SERVER in ${SERVERS} ; do
echo starting server ${SERVER}
start galaxy-worker SERVER_NAME=${SERVER}
done
end script
post-stop script
SERVERS=`sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini |
xargs echo`
date
echo
Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3
I previously tried to get this to work, too. After a lot of trial-and-error, I gave up because proFTPd always calculated a different string after salting and hashing the password with PBKDF2 than what is stored in the database. I'm sure that it extracted the correct salt and password, but something about the salthash algorithm in proFTPd is different from what Galaxy does. I ended up reverting to SHA1 for our internal instance which is behind a firewall so pw hashing isn't as critical. Just my 5c, cheers, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics ☎ +44 1865 617481 ✉ benjamin.schuster-boeck...@ludwig.ox.ac.uk Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy on cloud config issues
Hello Ravpreet, It is not working for me either. I posted a detail reply later. Best Regards, Anatoly From: Ravpreet Setia [mailto:ravpreet.se...@oicr.on.ca] Sent: Thursday, August 08, 2013 1:37 PM To: Dannon Baker; Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Galaxy on cloud config issues Anatoly, did this method work for you? It is not working for me. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Dannon Baker [dannon.ba...@gmail.com] Sent: Wednesday, August 07, 2013 8:00 PM To: Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly ulyanov_anat...@allergan.commailto:ulyanov_anat...@allergan.com wrote: Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ /prePFONT face=Verdana color=blue size=1SPAN style=FONT-SIZE: 8pt; COLOR: blue This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. /SPAN/FONT/P ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy cannot start last [server:handlerxx]
On Thu, Aug 8, 2013 at 1:31 PM, Nate Coraor n...@bx.psu.edu wrote: On Aug 5, 2013, at 6:23 PM, Rodolfo Aramayo wrote: Hi, I have a 80 core/1TB RAM Dell server. In order improve Galaxy performance I modified the universe_wsgi.ini file so as to improve the Scaling and Load Balancing as follows: # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 ... snip ... [server:handler18] use = egg:Paste#http port = 8318 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # [server:handler19] # use = egg:Paste#http # port = 8319 # host = 127.0.0.1 # use_threadpool = true # threadpool_workers = 5 # [server:handler20] # use = egg:Paste#http # port = 8320 # host = 127.0.0.1 # use_threadpool = true # threadpool_workers = 5 job_manager = manager job_handlers = handler0,handler1,,handler2,handler3,handler4,handler5,handler6,handler7,handler8,handler9,handler10,handler11,handler12,handler13,handler14,handler15,handler16,handler17,handler18 Hi Rodolfo, The job_manager and job_handlers options go under the [server:main] section, it looks like they are probably underneath the last [server:...] section right now. Please note that all of these features should now be configured via the job configuration file (job_conf.xml), and I've just updated the documentation you referred to accordingly. --nate Dear Nate, Thanks Just to be sure I understand this correctly I now have in my 'universe' file the following: # # HTTP Server -- # Configuration of the internal HTTP server. [server:main] # job_manager = manager I ASSUME THIS IS CORRECT because I get errors when it is not commented [server:manager] use = egg:Paste#http port = 8200 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 ...snip... [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # [server:handler20] # use = egg:Paste#http # port = 8320 # host = 127.0.0.1 # use_threadpool = true # threadpool_workers = 5 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 127.0.0.1 host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web1] use = egg:Paste#http port = 8401 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 ...snip... [server:web11] use = egg:Paste#http port = 8411 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web12] use = egg:Paste#http port = 8412 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # Filters -- # Filters sit between Galaxy and the HTTP server. ... # And in my job_conf.xml: handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ ...snip... handler id=handler18 tags=handlers/ handler id=handler19 tags=handlers/ # Is this correct? Also, I guess the part I do not understand is what is the magic formula between the number of threadpool_workers as configured here: # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 200 and those configured on the web servers and on the server handlers? Thanks --Rodolfo
Re: [galaxy-dev] Galaxy cannot start last [server:handlerxx]
On Aug 9, 2013, at 1:16 PM, Rodolfo Aramayo wrote: Dear Nate, Thanks Just to be sure I understand this correctly I now have in my 'universe' file the following: # # HTTP Server -- # Configuration of the internal HTTP server. [server:main] # job_manager = manager I ASSUME THIS IS CORRECT because I get errors when it is not commented [server:manager] use = egg:Paste#http port = 8200 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 ...snip... [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # [server:handler20] # use = egg:Paste#http # port = 8320 # host = 127.0.0.1 # use_threadpool = true # threadpool_workers = 5 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 127.0.0.1 host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web1] use = egg:Paste#http port = 8401 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 ...snip... [server:web11] use = egg:Paste#http port = 8411 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web12] use = egg:Paste#http port = 8412 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # Filters -- # Filters sit between Galaxy and the HTTP server. ... # And in my job_conf.xml: handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ ...snip... handler id=handler18 tags=handlers/ handler id=handler19 tags=handlers/ # Is this correct? Rodolfo, Some of this confusion might be because you have the (documented) options from the original [server:main] section orphaned underneath [server:handler19], which already has those options set. In an ini file, sections begin with [name] and all key/value pairs underneath that heading are assigned to [name] until another section heading is encountered. Removing all comments, that means your config would look like this: [server:main] [server:manager] use = egg:Paste#http port = 8200 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 use = egg:Paste#http host = 0.0.0.0 use_threadpool = True threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web1] use = egg:Paste#http port = 8401 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web11] use = egg:Paste#http port = 8411 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web12] use = egg:Paste#http port = 8412 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 - Remove [server:main], the entire [server:manager] section, and those extra options under [server:handler19], and you should be good: [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true
[galaxy-dev] Galaxy cannot start last [server:handlerxx]
It worked like a charm Thanks --R On Fri, Aug 9, 2013 at 12:32 PM, Nate Coraor n...@bx.psu.edu wrote: On Aug 9, 2013, at 1:16 PM, Rodolfo Aramayo wrote: Dear Nate, Thanks Just to be sure I understand this correctly I now have in my 'universe' file the following: # # HTTP Server -- # Configuration of the internal HTTP server. [server:main] # job_manager = manager I ASSUME THIS IS CORRECT because I get errors when it is not commented [server:manager] use = egg:Paste#http port = 8200 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 ...snip... [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # [server:handler20] # use = egg:Paste#http # port = 8320 # host = 127.0.0.1 # use_threadpool = true # threadpool_workers = 5 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 127.0.0.1 host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web1] use = egg:Paste#http port = 8401 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 ...snip... [server:web11] use = egg:Paste#http port = 8411 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web12] use = egg:Paste#http port = 8412 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # Filters -- # Filters sit between Galaxy and the HTTP server. ... # And in my job_conf.xml: handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ ...snip... handler id=handler18 tags=handlers/ handler id=handler19 tags=handlers/ # Is this correct? Rodolfo, Some of this confusion might be because you have the (documented) options from the original [server:main] section orphaned underneath [server:handler19], which already has those options set. In an ini file, sections begin with [name] and all key/value pairs underneath that heading are assigned to [name] until another section heading is encountered. Removing all comments, that means your config would look like this: [server:main] [server:manager] use = egg:Paste#http port = 8200 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler19] use = egg:Paste#http port = 8319 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 use = egg:Paste#http host = 0.0.0.0 use_threadpool = True threadpool_workers = 200 [server:web0] use = egg:Paste#http port = 8400 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web1] use = egg:Paste#http port = 8401 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web11] use = egg:Paste#http port = 8411 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 [server:web12] use = egg:Paste#http port = 8412 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 - Remove [server:main], the entire [server:manager] section, and those extra options under [server:handler19], and you should be good: [server:handler0] use = egg:Paste#http port = 8300 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8301 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler19] use = egg:Paste#http port = 8319 host =
[galaxy-dev] Public production instance page is not rendering properly
Hello dev-team,
I am experiencing a strange problem with my production instance, after I
carefully merged remote changes from galaxy-dist release to my code
repository. While restarting, It fails to load the the page properly, the
message from log file stating that serving on 0.0.0.0:8080
Here are some message found in the log file:
X.X.X.X - - [09/Aug/2013:14:30:56 -0400] GET / HTTP/1.1 500 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko)
rekonq Safari/534.34
Error - type 'exceptions.ValueError': expected only letters, got ' en'
URL: https://galaxy.cbio.mskcc.org/
File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in
__call__
app_iter = self.application(environ, sr_checker)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84
in __call__
return self.application(environ, start_response)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line
633 in __call__
return self.application(environ, start_response)
File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/codebase/lib/galaxy/web/framework/base.py', line 159 in
handle_request
trans = self.transaction_factory( environ )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in lambda
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in
transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__
self.setup_i18n()
File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in
setup_i18n
locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse
return cls(*parse_locale(identifier, sep=sep))
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in
parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got ' en'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5'
HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6'
HTTP_CACHE_CONTROL: 'max-age=0'
HTTP_CONNECTION: 'Keep-Alive'
HTTP_HOST: 'galaxy.cbio.mskcc.org'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34
(KHTML, like Gecko) rekonq Safari/534.34'
HTTP_X_FORWARDED_FOR: '172.21.50.129'
HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org'
HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org'
HTTP_X_URL_SCHEME: 'https'
ORGINAL_HTTP_HOST: 'localhost:8081'
ORGINAL_REMOTE_ADDR: '127.0.0.1'
PATH_INFO: '/'
REMOTE_ADDR: '172.21.50.129'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8081'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x7f78910
is_api_request: False
original_wsgi.url_scheme: 'http'
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object
at 0x7f78210
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x8066d90
paste.recursive.forward: paste.recursive.Forwarder from /
paste.recursive.include: paste.recursive.Includer from /
paste.recursive.include_app_iter: paste.recursive.IncluderAppIter from /
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'd4f643a8012111e3819090b11c087d99'
wsgi process: 'Multithreaded'
Any idea what is going wrong here? Please let me know if you need more get
more details.
Many thanks,
--/Vipin
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[galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)
Hi, Regarding the error I experienced with [galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable) Two things: FIRST The error I reported, in short, it was my fault as I failed to to set up the: cmdline = '/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 21/dev/null' line properly in the oases_optimiser.py script properly I guess it would help for developers to state exactly the customization required for each package installed via ToolShed for the tool to work properly or better yet, it would be really nice if we could set up environmental variables like: TOOL_SHED_REPOS=/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos so that scripts could invoke them upon installation: cmdline = '$TOOL_SHED_REPOS/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 21/dev/null' SECOND I still am experiencing errors with this tool When I run oases_optimiser on either fasta or fastq files the jobs start, run and then fail In all cases the problem is the lack of an ''splicing_events.txt' file Help will be appreciated Thanks --R # The stderr is as follows: Traceback (most recent call last): File /usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py, line 120, in module if __name__ == __main__: __main__() File /usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py, line 76, in __main__ for line in open(path ): IOError: [Errno 2] No such file or directory: 'splicing_events.txt' # The stdout is as follows: [0.00] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [13.354877] 8855297 sequences found [13.354879] Done [13.354940] Reading read set file ./Sequences; [14.405160] 8855297 sequences found [20.956147] Done [20.956153] 8855297 sequences in total. [20.956229] Writing into roadmap file ./Roadmaps... [23.008558] Inputting sequences... [23.008571] Inputting sequence 0 / 8855297 [25.835351] Inputting sequence 100 / 8855297 [28.835964] Inputting sequence 200 / 8855297 [31.938277] Inputting sequence 300 / 8855297 [35.129436] Inputting sequence 400 / 8855297 [38.384093] Inputting sequence 500 / 8855297 [41.660153] Inputting sequence 600 / 8855297 [44.905326] Inputting sequence 700 / 8855297 [48.168615] Inputting sequence 800 / 8855297 [50.969068] === Sequences loaded in 28.188442 s [50.969101] Done inputting sequences [50.969103] Destroying splay table [51.018112] Splay table destroyed [0.00] Reading roadmap file ./Roadmaps [13.140830] 8855297 roadmaps read [13.144978] Creating insertion markers [15.796233] Ordering insertion markers [21.652798] Counting preNodes [22.631404] 2753107 preNodes counted, creating them now [24.516794] Sequence 100 / 8855297 [25.609456] Sequence 200 / 8855297 [26.585862] Sequence 300 / 8855297 [27.501523] Sequence 400 / 8855297 [28.375045] Sequence 500 / 8855297 [29.217391] Sequence 600 / 8855297 [30.037355] Sequence 700 / 8855297 [30.838062] Sequence 800 / 8855297 [31.514315] Adjusting marker info... [32.498044] Connecting preNodes [32.734023] Connecting 100 / 8855297 [33.029694] Connecting 200 / 8855297 [33.36] Connecting 300 / 8855297 [33.712200] Connecting 400 / 8855297 [34.080947] Connecting 500 / 8855297 [34.464629] Connecting 600 / 8855297 [34.853754] Connecting 700 / 8855297 [35.256476] Connecting 800 / 8855297 [35.604610] Cleaning up memory [35.622205] Done creating preGraph [35.622208] Concatenation... [36.944164] Renumbering preNodes [36.944174] Initial preNode count 2753107 [36.992738] Destroyed 2139761 preNodes [36.992745] Concatenation over! [36.992747] Clipping short tips off preGraph [37.241017] Concatenation... [37.561728] Renumbering preNodes [37.561735] Initial preNode count 613346 [37.564816] Destroyed 602327 preNodes [37.564818] Concatenation over! [37.564819] 565869 tips cut off [37.564820] 11019 nodes left [37.564908] Writing into pregraph file ./PreGraph... [37.628994] Reading read set file ./Sequences; [38.666026] 8855297 sequences found [45.262765] Done [47.287358] Reading pre-graph file ./PreGraph [47.287449] Graph has 11019 nodes and 8855297 sequences [47.320337] Scanning pre-graph file ./PreGraph for k-mers [47.345965] 587492 kmers found [47.410094] Sorting kmer occurence table ... [47.807351] Sorting done. [47.807356] Computing acceleration table... [47.839961] Computing offsets... [47.856571] Ghost Threading through reads 0 / 8855297 [49.327252] Ghost Threading through reads 100 / 8855297 [50.789941] Ghost Threading through reads 200 / 8855297
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Vipin,
This has been fixed in the stable branch of galaxy-central
https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but has not
made it on to galaxy-dist yet.
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 2:33 PM, Vipin TS wrote:
Hello dev-team,
I am experiencing a strange problem with my production instance, after I
carefully merged remote changes from galaxy-dist release to my code
repository. While restarting, It fails to load the the page properly, the
message from log file stating that serving on 0.0.0.0:8080
Here are some message found in the log file:
X.X.X.X - - [09/Aug/2013:14:30:56 -0400] GET / HTTP/1.1 500 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko)
rekonq Safari/534.34
Error - type 'exceptions.ValueError': expected only letters, got ' en'
URL: https://galaxy.cbio.mskcc.org/
File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in
__call__
app_iter = self.application(environ, sr_checker)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in
__call__
return self.application(environ, start_response)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line
633 in __call__
return self.application(environ, start_response)
File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/codebase/lib/galaxy/web/framework/base.py', line 159 in handle_request
trans = self.transaction_factory( environ )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in lambda
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in
transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__
self.setup_i18n()
File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in setup_i18n
locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse
return cls(*parse_locale(identifier, sep=sep))
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in
parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got ' en'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5'
HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6'
HTTP_CACHE_CONTROL: 'max-age=0'
HTTP_CONNECTION: 'Keep-Alive'
HTTP_HOST: 'galaxy.cbio.mskcc.org'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34
(KHTML, like Gecko) rekonq Safari/534.34'
HTTP_X_FORWARDED_FOR: '172.21.50.129'
HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org'
HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org'
HTTP_X_URL_SCHEME: 'https'
ORGINAL_HTTP_HOST: 'localhost:8081'
ORGINAL_REMOTE_ADDR: '127.0.0.1'
PATH_INFO: '/'
REMOTE_ADDR: '172.21.50.129'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8081'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x7f78910
is_api_request: False
original_wsgi.url_scheme: 'http'
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object at
0x7f78210
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x8066d90
paste.recursive.forward: paste.recursive.Forwarder from /
paste.recursive.include: paste.recursive.Includer from /
paste.recursive.include_app_iter: paste.recursive.IncluderAppIter from /
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'd4f643a8012111e3819090b11c087d99'
wsgi process: 'Multithreaded'
Any idea what is going wrong here? Please let me know if you need more get
more details.
Many thanks,
--/Vipin
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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http://lists.bx.psu.edu/
To search Galaxy
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an empty
sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1 404
- https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line
84, in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319, in
render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line
73, in render_body
if bool( [ data for data in history.active_datasets if data.state in
['running', 'queued', '', None ] ] ):
AttributeError: 'Undefined' object has no attribute 'active_datasets'
Do you have any quick way to fix the same? Or update to galaxy-central
stable branch?
Thank you, Vipin
On Fri, Aug 9, 2013 at 2:57 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
This has been fixed in the stable branch of galaxy-central
https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but has
not made it on to galaxy-dist yet.
Thanks for
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Vipin,
Can you try deleting the contents of your compiled templates directory (i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an empty
sequence. This results in a contradiction, which nonetheless can be expensive
to evaluate. Consider alternative strategies for improved performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML,
like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1 404 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203, in
__call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159, in
__call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149, in
__call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line 84,
in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py, line
633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319, in
render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line 73,
in render_body
if bool( [ data for data in history.active_datasets if data.state in
['running', 'queued', '', None ] ] ):
AttributeError: 'Undefined' object has no attribute 'active_datasets'
Do you have any quick way to fix the
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance, still
no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac
OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line
84, in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in
render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319,
in render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line
73, in render_body
if bool( [ data for data in
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Vipin,
Strange, are you running the latest galaxy-dist? That line doesn't exist in
e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default.
Can you compare your file to the file in the repository? What is the output of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the contents from /codebase/database/complied_templates/* and
restarted the instance, still no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory (i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an empty
sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1 404
- https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line 84,
in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in render
template.render_context(
[galaxy-dev] Fwd: Public production instance page is not rendering properly
--/Vipin
-- Forwarded message --
From: Vipin TS vipin...@gmail.com
Date: Fri, Aug 9, 2013 at 5:04 PM
Subject: Re: [galaxy-dev] Public production instance page is not rendering
properly
To: Daniel Blankenberg d...@bx.psu.edu
Hi Dan,
Thanks for your support, Hmm, I can see that there are changes:
but here is the out come from the below commands:
$$
hg diff templates/webapps/galaxy/root/history.mako
empty
$$
hg summary
parent: 10218:ff0bd4a811d9 tip
merged the changes from stable release version July 2013 from bx.psu.edu
branch: default
commit: 5 modified, 5 removed, 452 deleted
update: 1663 new changesets, 2 branch heads (merge)
$$hg config
Sorry, it says unknown option.
Do you think I have mixed up something ?
Thank you, Vipin
On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Strange, are you running the latest galaxy-dist? That line doesn't exist
in e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default.
Can you compare your file to the file in the repository? What is the output
of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance, still
no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository
manually. Now I can invoke the page but the frames were not loaded
correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel
Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line
203, in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py,
line 12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line
159, in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 67, in replacement_start_response
return start_response( status, headers,
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Dan,
hg config for our repository is:
cat .hg/hgrc
[paths]
default = http://www.bx.psu.edu/hg/galaxy
[ui]
username = Galaxy RaetschLab gal...@raetschlab.org
verbose = True
merge = vimdiff
[merge-tools]
vimdiff.executable = vim
vimdiff.args = -d $base $local $output $other +close +close
Thanks, Vipin
Hi Dan,
Thanks for your support, Hmm, I can see that there are changes:
but here is the out come from the below commands:
$$
hg diff templates/webapps/galaxy/root/history.mako
empty
$$
hg summary
parent: 10218:ff0bd4a811d9 tip
merged the changes from stable release version July 2013 from bx.psu.edu
branch: default
commit: 5 modified, 5 removed, 452 deleted
update: 1663 new changesets, 2 branch heads (merge)
$$hg config
Sorry, it says unknown option.
Do you think I have mixed up something ?
Thank you, Vipin
On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Strange, are you running the latest galaxy-dist? That line doesn't exist
in e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default.
Can you compare your file to the file in the repository? What is the output
of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance,
still no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.eduwrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository
manually. Now I can invoke the page but the frames were not loaded
correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel
Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in
finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line
203, in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py,
line 12, in __call__
return self.app( environ, start_response )
File
/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py, line 21,
in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line
159, in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
