3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b654710d5844/ Changeset: b654710d5844 User: dannon Date: 2015-02-08 16:16:14+00:00 Summary: Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing. Affected #: 3 files diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/forms/forms.py --- a/lib/galaxy/forms/forms.py +++ b/lib/galaxy/forms/forms.py @@ -50,7 +50,7 @@ #load fields fields = [] fields_elem = elem.find( 'fields' ) - if fields_elem: + if fields_elem is not None: for field_elem in fields_elem.findall( 'field' ): field_type = field_elem.get( 'type' ) assert field_type in self.field_type_factories, 'Invalid form field type ( %s ).' % field_type diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/sample_tracking/external_service_types.py --- a/lib/galaxy/sample_tracking/external_service_types.py +++ b/lib/galaxy/sample_tracking/external_service_types.py @@ -96,9 +96,9 @@ def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' ) - if run_details_elem: + if run_details_elem is not None: results_elem = run_details_elem.find( 'results' ) - if results_elem: + if results_elem is not None: # Get the list of resulting datatypes # TODO: the 'results_urls' attribute is only useful if the transfer protocol is http(s), so check if that is the case. self.run_details[ 'results' ], self.run_details[ 'results_urls' ] = self.parse_run_details_results( results_elem ) diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -112,8 +112,7 @@ def __init_schedulers_for_element( self, plugins_element ): plugins_kwds = dict( plugins_element.items() ) self.default_scheduler_id = plugins_kwds.get( 'default', DEFAULT_SCHEDULER_ID ) - - for plugin_element in plugins_element.getchildren(): + for plugin_element in plugins_element: plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) https://bitbucket.org/galaxy/galaxy-central/commits/a02abac7d68d/ Changeset: a02abac7d68d User: dannon Date: 2015-02-08 16:21:42+00:00 Summary: Minor formatting, spelling in workflow scheduling_manager. Affected #: 1 file diff -r b654710d58445917baae8e3ec8f78acc745ef262 -r a02abac7d68dd4decd91e5a24022dc6648bf011c lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -31,11 +31,11 @@ self.app = app self.__job_config = app.job_config self.workflow_schedulers = {} - self.active_workflow_schedulers = {} # Passive workflow schedulers - # won't need to be monitored I - # guess. + self.active_workflow_schedulers = {} + # Passive workflow schedulers won't need to be monitored I guess. + self.request_monitor = None - + self.__plugin_classes = self.__plugins_dict() self.__init_schedulers() @@ -67,7 +67,7 @@ try: self.request_monitor.shutdown() except Exception: - log.exception( "Failed to shutdown worklfow request monitor." ) + log.exception( "Failed to shutdown workflow request monitor." ) def queue( self, workflow_invocation, request_params ): workflow_invocation.state = model.WorkflowInvocation.states.NEW @@ -133,7 +133,7 @@ self.workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler if isinstance( workflow_scheduler, galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin ): self.active_workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler - + def __start_request_monitor( self ): self.request_monitor = WorkflowRequestMonitor( self.app, self ) https://bitbucket.org/galaxy/galaxy-central/commits/ea23071cf22e/ Changeset: ea23071cf22e User: dannon Date: 2015-02-08 20:09:23+00:00 Summary: Merge. Affected #: 1 file diff -r a02abac7d68dd4decd91e5a24022dc6648bf011c -r ea23071cf22ea78b699264e04b59e3adf88ec619 CONTRIBUTING.md --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,93 @@ +# Contributing + +This document briefly describes how to contribute to the +galaxy-central core project - also checkout the video of our [2013 +Galaxy Community Conference +presentation](http://vimeo.com/channels/581875/73486255) on the +topic. For information on contributing more broadly to the Galaxy +ecosystem and a deeper discussion of some of these points - please see +the [Develop](https://wiki.galaxyproject.org/Develop/) section of the +[Galaxy Wiki](https://wiki.galaxyproject.org/). + +## Before you Begin + +If you have an idea for a feature to add or an approach for a bugfix - +it is best to communicate with Galaxy developers early. The most +common venue for this is the [Galaxy Trello +board](https://wiki.galaxyproject.org/Issues). Browse through existing +cards [here](http://bit.ly/gxytrello) and if one seems related comment +on it. If no existing cards seem appropriate, a new issue can be +opened using [this form](http://galaxyproject.org/trello). Galaxy +developers are also generally available via +[IRC](https://wiki.galaxyproject.org/GetInvolved#IRC_Channel) and on +the [development mailing list](http://dev.list.galaxyproject.org/). + +## How to Contribute + +* If you are new to Mercurial - please check out this [official + tutorial](http://mercurial.selenic.com/wiki/Tutorial) + +* Make sure you have a free [Bitbucket + account](https://bitbucket.org/account/signup/) + +* Fork the galaxy-central repository on + [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to + make your changes. (Many Galaxy instances target + [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active + development happens on galaxy-central and this is where pull + requests should be made). + +* Choose the correct Mercurial branch to develop your changes against. + + * Additions to the code base should be pushed to the `default` + branch (`hg checkout default`). + + * Most bug fixes to previously release components (things in + galaxy-dist) should be pushed to the `stable` branch (`hg checkout + stable`). + + * Serious security problems should not be fixed via pull request - + please responsibly disclose these by e-mailing them (with or + without patches) to galaxy-lab@bx.psu.edu. The Galaxy core + development team will issue patches to public servers before + announcing the issue to ensure there is time to patch and + highlight these fixes widely. We will provide you credit for the + discovery when publicly disclosing the issue. + +* If your changes modify code - please ensure the resulting files + conform to Galaxy [style + guidelines](https://wiki.galaxyproject.org/Develop/BestPractices). + +* Galaxy contains hundreds of tests of different types and complexity + and running each is difficult and probably not reasonable at this + time (someday we will provide a holistic test procedure to make this + possible). For now, please just review the [running tests + documentation](https://wiki.galaxyproject.org/Admin/RunningTests) + and run any that seem relevant. Developers reviewing your pull + request will be happy to help guide you to running the most relevant + tests as part of the pull request review process and may request the + output of these tests. + +* Commit and push your changes to your Bitbucket fork. + +* Open a [pull + request](https://confluence.atlassian.com/display/BITBUCKET/Fork+a+Repo,+Compare+Code...) + with these changes. You pull request message should include: + + * A description of why the change should be made. + + * A description of implementation of the change. + + * A description of how to test the change. + +## A Quick Note about Tools + + For the most part, Galaxy tools should be published to the + [ToolShed](https://wiki.galaxyproject.org/ToolShed) and not in this + repository directly. If you are looking to supply fixes for migrated + core tools that used to exist in this repository - please checkout + the [tools-devteam](https://github.com/galaxyproject/tools-devteam) + repository on GitHub. + + More information about tool development can be found [on the + wiki](https://wiki.galaxyproject.org/Develop). Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.