Galaxy fails to start after shut down
Dear Galaxy Devs, After a power shutdown of our machines, Galaxy starts up with serving on localhost:8080 (according to paster.log), but I get an error upon requesting the webpage: SyntaxError: invalid syntax (base_panels.mako.py, line 301) URL: http://localhost:8080/root File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 25 in index m_c=m_c, m_a=m_a ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 744 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 691 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 637 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/home/galaxy/galaxy-dist/database/compiled_templates/root/index.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/webapps/galaxy/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 609 in _inherit_from ret = callable_(template, lclcontext) File '/home/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/base_panels.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 596 in _inherit_from template = _lookup_template(context, uri, calling_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 626 in _lookup_template return lookup.get_template(uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 218 in get_template return self._load(srcfile, uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 283 in _load **self.template_args) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 218 in __init__ module = self._compile_from_file(path, filename) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 245 in _compile_from_file module = imp.load_source(self.module_id, path, open(path, 'rb')) SyntaxError: invalid syntax (base_panels.mako.py, line 301) I have tried replacing the database folder (which is normally on an nfs share) with the original local contents, but no luck. Further I have checked the network share's permissions, but they are all fine. Since Galaxy starts up, ending paster.log with the usual "Serving at 127.0.0.1" I am very puzzled about what's going on. Does anybody has a clue? Thanks. Regards, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
There is a problem in the syntax of the template used to produce Galaxy's main page. Specifically, it appears that templates/base_panels.mako has an error; you'll want to take a look at this file and see if changes were made it to that caused the problem. Best, J. On Jul 12, 2012, at 5:57 AM, Joachim Jacob wrote:
Dear Galaxy Devs,
After a power shutdown of our machines, Galaxy starts up with serving on localhost:8080 (according to paster.log), but I get an error upon requesting the webpage:
SyntaxError: invalid syntax (base_panels.mako.py, line 301)
URL: http://localhost:8080/root File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 25 in index m_c=m_c, m_a=m_a ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 744 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 691 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 637 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/home/galaxy/galaxy-dist/database/compiled_templates/root/index.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/webapps/galaxy/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 609 in _inherit_from ret = callable_(template, lclcontext) File '/home/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/base_panels.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 596 in _inherit_from template = _lookup_template(context, uri, calling_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 626 in _lookup_template return lookup.get_template(uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 218 in get_template return self._load(srcfile, uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 283 in _load **self.template_args) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 218 in __init__ module = self._compile_from_file(path, filename) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 245 in _compile_from_file module = imp.load_source(self.module_id, path, open(path, 'rb')) SyntaxError: invalid syntax (base_panels.mako.py, line 301)
I have tried replacing the database folder (which is normally on an nfs share) with the original local contents, but no luck. Further I have checked the network share's permissions, but they are all fine.
Since Galaxy starts up, ending paster.log with the usual "Serving at 127.0.0.1" I am very puzzled about what's going on.
Does anybody has a clue? Thanks.
Regards, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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Thanks. I was first looking at the wrong base_panels.mako: but restoring the file in <galaxyhome>/templates/base_panel.mako fixed the problem. Regards, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 07/12/2012 02:07 PM, Jeremy Goecks wrote:
There is a problem in the syntax of the template used to produce Galaxy's main page. Specifically, it appears that templates/base_panels.mako has an error; you'll want to take a look at this file and see if changes were made it to that caused the problem.
Best, J.
On Jul 12, 2012, at 5:57 AM, Joachim Jacob wrote:
Dear Galaxy Devs,
After a power shutdown of our machines, Galaxy starts up with serving on localhost:8080 (according to paster.log), but I get an error upon requesting the webpage:
SyntaxError: invalid syntax (base_panels.mako.py, line 301)
URL: http://localhost:8080/root File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 25 in index m_c=m_c, m_a=m_a ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 744 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 691 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 637 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/home/galaxy/galaxy-dist/database/compiled_templates/root/index.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/webapps/galaxy/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 609 in _inherit_from ret = callable_(template, lclcontext) File '/home/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/base_panels.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 596 in _inherit_from template = _lookup_template(context, uri, calling_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 626 in _lookup_template return lookup.get_template(uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 218 in get_template return self._load(srcfile, uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 283 in _load **self.template_args) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 218 in __init__ module = self._compile_from_file(path, filename) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 245 in _compile_from_file module = imp.load_source(self.module_id, path, open(path, 'rb')) SyntaxError: invalid syntax (base_panels.mako.py, line 301)
I have tried replacing the database folder (which is normally on an nfs share) with the original local contents, but no luck. Further I have checked the network share's permissions, but they are all fine.
Since Galaxy starts up, ending paster.log with the usual "Serving at 127.0.0.1" I am very puzzled about what's going on.
Does anybody has a clue? Thanks.
Regards, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
___________________________________________________________ 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:
participants (2)
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Jeremy Goecks -
Joachim Jacob