Re: [galaxy-dev] Bug report: page within help
Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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/ ___ 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] Bug report: page within help
Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually I even added the functionality of going back a page into our galaxy version... Best, Philipp On 12 Aug 2014, at 14:05, James Taylor ja...@jamestaylor.org wrote: Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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/ ___ 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] Bug report: page within help
I have applied your patch here (https://bitbucket.org/galaxy/galaxy-central/commits/19309418c86450b7f39691460eb430e100883cb4) and one correction to James' previous comment - multi-page tools actually do work through the API - this was required for multi-page tool testing via the API. -John On Tue, Aug 12, 2014 at 8:18 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually I even added the functionality of going back a page into our galaxy version... Best, Philipp On 12 Aug 2014, at 14:05, James Taylor ja...@jamestaylor.org wrote: Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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/ ___ 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/ ___ 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] Bug report
What format are the files you are trying to process with MACS in? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 23, 2013 at 3:05 PM, Jianxin Wang jianxin.w...@oicr.on.ca wrote: Hi Galaxy dev team, I'm trying to the you galaxy server to do NGS peak calling: Tools - NGS: Peak Calling - MACS Model-based Analysis of ChIP-Seq. However, the page won't allow me enter the input files: the drop-down selection box won't show anything when clicked. Same problem for the ChIP-Seq Control File selection box. Please take a look and email me back if problem is fixed. Jianxin Wang, PhD Computational Biologist jianxin.w...@oicr.on.ca Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8569 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ___ 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/ ___ 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] Bug report and patch for version_command whitespace
Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e. On Wed, Apr 17, 2013 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hello all, I recently tried adding a version_command tag as follows, version_command interpreter=python blastxml_to_top_descr.py --version /version_command This kind of white space is tolerated in the version tag, so should work here too I think. However, it resulting the Galaxy attempting to run 'python' (which stalled as there was no user input), and then 'blastxml_to_top_descr.py --version'. The following simple change fixes this bug. In the meantime, I have used the workaround to removing the white space in the XML file: version_command interpreter=pythonblastxml_to_top_descr.py --version/version_command Could someone please test this and commit it to the trunk, Regards, Peter -- $ hg diff diff -r 94e890fea3a4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Apr 17 15:03:12 2013 +0100 +++ b/lib/galaxy/tools/__init__.py Wed Apr 17 15:45:53 2013 +0100 @@ -1094,7 +1094,7 @@ self.version_string_cmd = None version_cmd = root.find(version_command) if version_cmd is not None: -self.version_string_cmd = version_cmd.text +self.version_string_cmd = version_cmd.text.strip() version_cmd_interpreter = version_cmd.get( interpreter, None ) if version_cmd_interpreter: executable = self.version_string_cmd.split()[0] ___ 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/ ___ 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] Bug report and patch for version_command whitespace
On Wed, Apr 17, 2013 at 3:56 PM, Dannon Baker dannon.ba...@gmail.com wrote: Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e. Great, thanks. https://bitbucket.org/galaxy/galaxy-central/commits/da5a5077ef1ebffa9e0ad9039ca4463298815de1 Peter (Reading my email I can see at least two grammar typos, but at least it made sense) ___ 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] Bug report : JSONDecodeError
Hi Mathieu,
As I mentioned in my previous email, here is the select that is needed. I need
to see the values of all columns for the mothur_toolsuite row.
select * from tool_shed_repository where name = 'mothur_toolsuite';
On Nov 13, 2012, at 7:33 AM, Mathieu Bahin wrote:
Hi Greg !
Running the sql command, I got that (actually, it's 'mothur_toolsuite' so I
change a bit the request but it is not deleted):
mysql select name from tool_shed_repository;
++
| name |
++
| mothur_toolsuite |
| protk |
| roche454_toolsuite |
| toolfactory|
++
4 rows in set (0.00 sec)
The mothur entries in 'shed_tool_conf.xml' file and the mothur repository are
still existing.
Cheers,
Mathieu Bahin
De: Greg Von Kuster g...@bx.psu.edu
À: Mathieu Bahin mathieu.ba...@irisa.fr
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 22:18:05
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Mathieu,
It's pretty difficult to tell you where to start looking within your
environment for the cause of the problem.
You mentioned that you attempted to uninstall the repository name mothur from
you local Galaxy instance, and that action produced this problem. What is
the result of running the following sql command in your db?
select * from tool_shed_repository where name = 'mothur';
Also, have the entries for the mothur tools been eliminated from your
shed_tool_conf.xml file?
How about the install directory for the mothur repository? Has is been
removed from disk?
Greg Von Kuster
On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote:
Hi Greg,
I kind of forgot a maybe interesting information. We found this message at
the end of the paster.log :
Exception happened during processing of request from ('127.0.0.1', 55428)
Traceback (most recent call last):
File /opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py, line
1053, in process_request_in_thread
self.finish_request(request, client_address)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 323, in
finish_request
self.RequestHandlerClass(request, client_address, self)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 641, in
__init__
self.finish()
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 694, in
finish
self.wfile.flush()
File /local/python/2.7-bis/lib/python2.7/socket.py, line 301, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Cheers,
Mathieu
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi again,
I got this with hg heads :
changeset: 7986:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
changeset: 7152:ffc20445b35e
branch: split_blast2
parent: 7058:22f545c0d412
user:Dannon Baker dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.
changeset: 7151:c94957ac5454
branch: workflow_import_menu_api
parent: 6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.
changeset: 7150:314a10ae112d
branch: split_blast
parent: 6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch
changeset: 7149:1327f2219423
branch: meme_requirement_on_fimo
parent: 6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch
And I got this with the debug at :
JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char
65522)
URL: http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories
File
'/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line
98 in __call__
environ, self.app)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539
in intercept_output
app_iter = application(environ, replacement_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80
in __call__
return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91
Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Greg !
Running the sql command, I got that (actually, it's 'mothur_toolsuite' so I
change a bit the request but it is not deleted):
mysql select name from tool_shed_repository;
++
| name |
++
| mothur_toolsuite |
| protk |
| roche454_toolsuite |
| toolfactory |
++
4 rows in set (0.00 sec)
The mothur entries in 'shed_tool_conf.xml' file and the mothur repository are
still existing.
Cheers,
Mathieu Bahin
- Mail original -
De: Greg Von Kuster g...@bx.psu.edu
À: Mathieu Bahin mathieu.ba...@irisa.fr
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 22:18:05
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Mathieu,
It's pretty difficult to tell you where to start looking within your
environment for the cause of the problem.
You mentioned that you attempted to uninstall the repository name
mothur from you local Galaxy instance, and that action produced this
problem. What is the result of running the following sql command in
your db?
select * from tool_shed_repository where name = 'mothur';
Also, have the entries for the mothur tools been eliminated from your
shed_tool_conf.xml file?
How about the install directory for the mothur repository? Has is
been removed from disk?
Greg Von Kuster
On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote:
Hi Greg,
I kind of forgot a maybe interesting information. We found this
message at the end of the paster.log :
Exception happened during processing of request from ('127.0.0.1',
55428)
Traceback (most recent call last):
File
/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line
323,
in finish_request
self.RequestHandlerClass(request, client_address, self)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line
641,
in __init__
self.finish()
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line
694,
in finish
self.wfile.flush()
File /local/python/2.7-bis/lib/python2.7/socket.py, line 301, in
flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Cheers,
Mathieu
- Mail original -
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi again,
I got this with hg heads :
changeset: 7986:12fcd068b12e
tag: tip
user: Daniel Blankenberg d...@bx.psu.edu
date: Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post
job
action.
changeset: 7152:ffc20445b35e
branch: split_blast2
parent: 7058:22f545c0d412
user: Dannon Baker dannonba...@me.com
date: Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.
changeset: 7151:c94957ac5454
branch: workflow_import_menu_api
parent: 6834:1a3d01b09f7a
user: Dannon Baker dannonba...@me.com
date: Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.
changeset: 7150:314a10ae112d
branch: split_blast
parent: 6757:ebf65c0b1e26
user: Dannon Baker dannonba...@me.com
date: Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch
changeset: 7149:1327f2219423
branch: meme_requirement_on_fimo
parent: 6662:8ba74c17e809
user: Daniel Blankenberg d...@bx.psu.edu
date: Fri Feb 03 11:15:29 2012 -0500
summary: close branch
And I got this with the debug at :
JSONDecodeError: Unterminated string starting at: line 1 column
65522
(char 65522)
URL:
http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories
File
'/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ
Re: [galaxy-dev] Bug report : JSONDecodeError
Hi again,
Sorry for the mistake in the request, but I think that now we spotted the
problem more precisely.
When I install 'mothur_toolsuite', the 'metadata' field is set with a long JSON
value (length 68,000). We noticed that when suppressing the tool, this value
is truncated around a length of 65,500. Only this value was altered in the row.
This field's type is BLOB.
Maybe this BLOB type is too short for that value but I don't understand why
there is no problem when the tool is installed (and the row inserted).
Cheers,
Mathieu
- Mail original -
De: Greg Von Kuster g...@bx.psu.edu
À: Mathieu Bahin mathieu.ba...@irisa.fr
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Envoyé: Mardi 13 Novembre 2012 14:29:39
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Mathieu,
As I mentioned in my previous email, here is the select that is
needed. I need to see the values of all columns for the
mothur_toolsuite row.
select * from tool_shed_repository where name = ' mothur_toolsuite ';
On Nov 13, 2012, at 7:33 AM, Mathieu Bahin wrote:
Hi Greg !
Running the sql command, I got that (actually, it's
'mothur_toolsuite' so I change a bit the request but it is not
deleted):
mysql select name from tool_shed_repository;
++
| name |
++
| mothur_toolsuite |
| protk |
| roche454_toolsuite |
| toolfactory |
++
4 rows in set (0.00 sec)
The mothur entries in 'shed_tool_conf.xml' file and the mothur
repository are still existing.
Cheers,
Mathieu Bahin
- Mail original -
De: Greg Von Kuster g...@bx.psu.edu
À: Mathieu Bahin mathieu.ba...@irisa.fr
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 22:18:05
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Mathieu,
It's pretty difficult to tell you where to start looking within
your
environment for the cause of the problem.
You mentioned that you attempted to uninstall the repository name
mothur from you local Galaxy instance, and that action produced
this
problem. What is the result of running the following sql command
in
your db?
select * from tool_shed_repository where name = 'mothur';
Also, have the entries for the mothur tools been eliminated from
your
shed_tool_conf.xml file?
How about the install directory for the mothur repository? Has is
been removed from disk?
Greg Von Kuster
On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote:
Hi Greg,
I kind of forgot a maybe interesting information. We found this
message at the end of the paster.log :
Exception happened during processing of request from
('127.0.0.1',
55428)
Traceback (most recent call last):
File
/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py,
line
323,
in finish_request
self.RequestHandlerClass(request, client_address, self)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py,
line
641,
in __init__
self.finish()
File /local/python/2.7-bis/lib/python2.7/SocketServer.py,
line
694,
in finish
self.wfile.flush()
File /local/python/2.7-bis/lib/python2.7/socket.py, line 301,
in
flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Cheers,
Mathieu
- Mail original -
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi again,
I got this with hg heads :
changeset: 7986:12fcd068b12e
tag: tip
user: Daniel Blankenberg d...@bx.psu.edu
date: Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction
post
job
action.
changeset: 7152:ffc20445b35e
branch: split_blast2
parent: 7058:22f545c0d412
user: Dannon Baker dannonba...@me.com
date: Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.
changeset: 7151:c94957ac5454
branch: workflow_import_menu_api
parent: 6834:1a3d01b09f7a
user: Dannon
Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Matthiew, Can you clarify the version of Galaxy you are using? What is the result of typing hg heads in your Galaxy installation directory? ALso, I noticed the following in your paster log: 131.254.16.26 - - [12/Nov/2012:10:52:26 +0200] GET /admin_toolshed/browse_repositories HTTP/1.1 500 - http://dev-galaxy.genouest.org/admin; Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 Debug at: http://dev-galaxy.genouest.org/_debug/view/1352713905 Directing your browser to the URL in the Debug at address will provide a stack trace of the exception thrown due to the problem. What is this this complete stack trace? Thanks, Greg Von Kuster On Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote: And here is the paster... De: Mathieu Bahin mathieu.ba...@irisa.fr À: Greg Von Kuster g...@bx.psu.edu Cc: galaxy-...@bx.psu.edu Envoyé: Lundi 12 Novembre 2012 10:54:21 Objet: Re: [galaxy-dev] Bug report : JSONDecodeError Hi Greg ! Thanks for the quick answer. I am using the 7720 parent version but I keep it up-to-date without any problems. Enclosed you'll find the 'paster.log' file generated when I start Galaxy and try to access the manage installed tool shed repositories page. Cheers, Mathieu Bahin De: Greg Von Kuster g...@bx.psu.edu À: Mathieu Bahin mathieu.ba...@irisa.fr Cc: galaxy-...@bx.psu.edu Envoyé: Vendredi 9 Novembre 2012 19:28:09 Objet: Re: [galaxy-dev] Bug report : JSONDecodeError Hello Mathieu, What version of Galaxy are you running? Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log? Thanks, Greg Von Kuster On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote: Hi, I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur. The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel. I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message. Cheers, Mathieu Bahin 07.png___ 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/ paster.log ___ 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/
Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Greg ! Thanks for the quick answer. I am using the 7720 parent version but I keep it up-to-date without any problems. Enclosed you'll find the 'paster.log' file generated when I start Galaxy and try to access the manage installed tool shed repositories page. Cheers, Mathieu Bahin - Mail original - De: Greg Von Kuster g...@bx.psu.edu À: Mathieu Bahin mathieu.ba...@irisa.fr Cc: galaxy-...@bx.psu.edu Envoyé: Vendredi 9 Novembre 2012 19:28:09 Objet: Re: [galaxy-dev] Bug report : JSONDecodeError Hello Mathieu, What version of Galaxy are you running? Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log? Thanks, Greg Von Kuster On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote: blockquote Hi, I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur. The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel. I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message. Cheers, Mathieu Bahin 07.png ___ 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/ /blockquote ___ 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/
Re: [galaxy-dev] Bug report : JSONDecodeError
Hi Mathieu,
It's pretty difficult to tell you where to start looking within your
environment for the cause of the problem.
You mentioned that you attempted to uninstall the repository name mothur from
you local Galaxy instance, and that action produced this problem. What is the
result of running the following sql command in your db?
select * from tool_shed_repository where name = 'mothur';
Also, have the entries for the mothur tools been eliminated from your
shed_tool_conf.xml file?
How about the install directory for the mothur repository? Has is been removed
from disk?
Greg Von Kuster
On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote:
Hi Greg,
I kind of forgot a maybe interesting information. We found this message at
the end of the paster.log :
Exception happened during processing of request from ('127.0.0.1', 55428)
Traceback (most recent call last):
File /opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py, line
1053, in process_request_in_thread
self.finish_request(request, client_address)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 323, in
finish_request
self.RequestHandlerClass(request, client_address, self)
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 641, in
__init__
self.finish()
File /local/python/2.7-bis/lib/python2.7/SocketServer.py, line 694, in
finish
self.wfile.flush()
File /local/python/2.7-bis/lib/python2.7/socket.py, line 301, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Cheers,
Mathieu
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
Hi again,
I got this with hg heads :
changeset: 7986:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
changeset: 7152:ffc20445b35e
branch: split_blast2
parent: 7058:22f545c0d412
user:Dannon Baker dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.
changeset: 7151:c94957ac5454
branch: workflow_import_menu_api
parent: 6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.
changeset: 7150:314a10ae112d
branch: split_blast
parent: 6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch
changeset: 7149:1327f2219423
branch: meme_requirement_on_fimo
parent: 6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch
And I got this with the debug at :
JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char
65522)
URL: http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories
File
'/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line
98 in __call__
environ, self.app)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539
in intercept_output
app_iter = application(environ, replacement_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80
in __call__
return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ, start_response )
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 203 in
decorator
return func( self, trans, *args, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line
381 in browse_repositories
return self.installed_repository_grid( trans, **kwd )
File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 277
in __call__
kwargs=kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 765 in
fill_template
return self.fill_template_mako( filename, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 776 in
fill_template_mako
return template.render( **data )
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako
Re: [galaxy-dev] Bug report : JSONDecodeError
Hello Mathieu, What version of Galaxy are you running? Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log? Thanks, Greg Von Kuster On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote: Hi, I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur. The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel. I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message. Cheers, Mathieu Bahin 07.png___ 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/ ___ 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/
Re: [galaxy-dev] bug report
On Sep 29, 2011, at 11:02 PM, KOH Jia Yu Jayce wrote: Hi I’d like to enquire about the bug report. Apparently when someone sends a bug report, everyone in the mailing list and the sender himself are supposed to receive the bug report (as can be seen in the to field in the email sent out). However in our case the sender never receives the bug report even though his email address is in the to field. How do we resolve the issue such that everyone including the sender receives the bug report? In the universe config file, error_email_to = galaxy_...@mailman.gis.a-star.edu.sg was set. Hi, I've just submitted a fix for this to the in-development source tree, and it'll be part of our next stable release. Thanks for reporting this issue and for using Galaxy. --nate Thanks so much! ___ 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/ ___ 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/
Re: [galaxy-dev] bug report submission bug
Got another problem with the bug reporting tool: POST /dataset/report_error HTTP/1.1 500 - http://galaxy.hpc.ufl.edu/dataset/errors?id=775; Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.1; Trident/5.0)Error - type 'exceptions.UnboundLocalError': local variable 'dataset_id' referenced before assignmentURL: http://galaxy.hpc.ufl.edu/dataset/report_error File '/galaxy/prod/galaxy/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/prod/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response)File '/galaxy/prod/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/galaxy/prod/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/prod/galaxy/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/prod/galaxy/lib/galaxy/web/controllers/dataset.py', line 176 in report_error body = string.Template( error_report_template ) \ UnboundLocalError: local variable 'dataset_id' referenced before assignment I suppose that since I got no replies to the first message on the 3rd of October that it's likely my local instance's problem and nobody else run into any trouble with the bug reporting tool? OM___ 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/
