Re: [galaxy-dev] [galaxy-user] postgres version 9.0.3
Martin, There were a few issues with postgres 9 that were fixed in changeset 5074, what revision is your galaxy instance running? If you are running something newer than that, could you explain more explicitly the steps to reproduce the server error? Also, I've moved the thread to galaxy-dev since this involves a local instance. -Dannon On Mar 19, 2011, at 4:45 AM, Martin Senger wrote: Hi, Our system changed from postgres 8.3 to postgres 9.0.3 - and since I am getting Server error on Galaxy. I am still investigating (because the server error is not there always, specifically it does not occur for an anonymous user) but I wonder if there are some known issues with Galaxy running with postgres 8.3. It would definitely help in my error tracking. Thanks, Martin -- Martin Senger email: martin.sen...@gmail.com,martin.sen...@kaust.edu.sa skype: martinsenger ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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] [galaxy-user] postgres version 9.0.3
Thanks for an answer and for moving it to the proper mailing list. There were a few issues with postgres 9 that were fixed in changeset 5074, what revision is your galaxy instance running? I am still running the stable version (galaxy-dist branch). I guess that with this version I need to stick with the older postgres 8.x. And I will try now, separately, to use the development version (galaxy-central branch). If you are running something newer than that, could you explain more explicitly the steps to reproduce the server error? Even though perhaps there is no need to investigate further - all I need is to use the fixes introduced in 5074 - but still I am attaching the error I got. Mainly because it is only my guess that the error was caused by the new postgres (because it does not occur when I switch back to sqlite). Thanks, Martin URL: http://cluster.cbrc.kaust.edu.sa:8080/tool_runner/index File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.5.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-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.5.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 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 933 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 1225 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 288 in execute data.dbkey = str(input_dbkey) File '/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 656 in set_dbkey self.metadata.dbkey = [value] File '/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 85 in __setattr__ self.parent._metadata[name] = self.spec[name].unwrap( value ) TypeError: 'NoneType' object does not support item assignment -- Martin Senger email: martin.sen...@gmail.com,martin.sen...@kaust.edu.sa skype: martinsenger ___ 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/
[galaxy-dev] Galaxy prone to XSS and HTML injection attacks
We recently ran a Nessus vulnerability scan against our server that hosts a local installation of Galaxy. The scan report showed that the web application is vulnerable to XSS and HTML injection attacks. In order to determine if/when these vulnerabilities will be fixed, where should I either send or post the scan results? -Rohit ___ 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] Galaxy prone to XSS and HTML injection attacks
I'd be happy to review the scan results, feel free to send them to me. I'll share it with the rest of the team as well. Thanks! -Dannon On Mar 19, 2011, at 11:37 AM, Paul, Rohit (NIH/NCI) [C] wrote: We recently ran a Nessus vulnerability scan against our server that hosts a local installation of Galaxy. The scan report showed that the web application is vulnerable to XSS and HTML injection attacks. In order to determine if/when these vulnerabilities will be fixed, where should I either send or post the scan results? -Rohit ___ 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/
[galaxy-dev] DB access and passowrd field
Hi All, I have some tools that generate some tabular output. The next step is to aggregate the data for some filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Tools and cmd line wrappers can easily connect to this DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password. Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages.Or is this a bad thing to pursue anyway? Thanks for any directions. Alex ___ 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/
