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commit/galaxy-central: dan: Data Manager UI enhancements.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5a7edbe4905/ Changeset: a5a7edbe4905 User: dan Date: 2014-05-13 20:07:07 Summary: Data Manager UI enhancements. Affected #: 5 files diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -19,7 +19,7 @@ raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) message = kwd.get( 'message' ) status = kwd.get( 'status', 'info' ) - return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, view_only=not_is_admin, message=message, status=status ) + return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status ) @web.expose def manage_data_manager( self, trans, **kwd ): @@ -32,7 +32,7 @@ data_manager = trans.app.data_managers.get_manager( data_manager_id ) if data_manager is None: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error" ) ) - jobs = reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) + jobs = list( reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) ) return trans.fill_template( "data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status ) @web.expose diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -11,11 +11,13 @@ %if view_only: <p>Not implemented</p> +%elif not data_managers.data_managers: + ${render_msg( "You do not currently have any Data Managers installed.", "warning" ) } %else: <p>Choose your data managing option from below.</p><ul> - <li><strong>Access data managers</strong> - get data, build indexes, etc - <p/> + <li><strong>Run Data Manager Tools</strong> + <div style="margin-left:1em"><ul> %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): <li> @@ -24,10 +26,11 @@ <p/> %endfor </ul> + </div></li><p/> - <li><strong>View managed data by manager</strong> - <p/> + <li><strong>View Data Manager Jobs</strong> + <div style="margin-left:1em"><ul> %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): <li> @@ -36,11 +39,12 @@ <p/> %endfor </ul> + </div></li><p/><p/> - <li><strong>View managed data by Tool Data Table</strong> - <p/> + <li><strong>View Tool Data Table Entries</strong> + <div style="margin-left:1em"><ul> %for table_name, managers in data_managers.managed_data_tables.iteritems(): <li> @@ -48,10 +52,21 @@ </li><p/> %endfor + %for table_name in tool_data_tables.get_tables(): + %if table_name not in data_managers.managed_data_tables: + <li> + <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main">${ table_name | h }</a> + </li> + <p/> + %endif + %endfor </ul> + </div></li><p/></ul><p/><br/> %endif + +${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki.</a>', "info" ) } diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/manage_data_manager.mako --- a/templates/webapps/galaxy/data_manager/manage_data_manager.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_manager.mako @@ -18,6 +18,7 @@ <div><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"> + <td>Actions</td><td>Job ID</td><td>User</td><td>Last Update</td> @@ -27,7 +28,8 @@ <td>PID/Cluster ID</td></tr> %for job in jobs: - <td><a href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }">${ job.id | h }</a></td> + <td><a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info"></span></a></td> + <td>${ job.id | h }</td> %if job.history and job.history.user: <td>${job.history.user.email | h}</td> %else: diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -10,30 +10,36 @@ %if view_only: <p>Not implemented</p> %else: -<% column_name_list = data_table.get_column_name_list() %> -<table class="tabletip"> - <thead> - <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> - Data Manager: ${ data_table.name | h } - <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> - <span class="fa fa-refresh"></span> - </a> - </th></tr> - <tr> - - %for name in column_name_list: - <th>${name | h}</th> - %endfor - </tr> - </thead> - <tbody> - %for table_row in data_table.data: - <tr> - %for field in table_row: - <td>${field | h}</td> - %endfor - </tr> - %endfor -</table> + <p> + <% column_name_list = data_table.get_column_name_list() %> + <table class="tabletip"> + <thead> + <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> + Data Manager: ${ data_table.name | h } + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a> + </th></tr> + <tr> + + %for name in column_name_list: + <th>${name | h}</th> + %endfor + </tr> + </thead> + <tbody> + %for table_row in data_table.data: + <tr> + %for field in table_row: + <td>${field | h}</td> + %endfor + </tr> + %endfor + </tbody> + </table> + </p> + %if not data_table.data: + ${render_msg( "There are currently no entries in this Tool Data Table.", "warning" ) } + %endif %endif diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -34,7 +34,7 @@ <table class="tabletip"><thead><tr><th colspan="2" style="font-size: 120%;"> - Data Table: ${ table_name | h } + Data Table: <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}">${ table_name | h }</a></th></tr></thead><% len_json_table = len( json_table ) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add the ability for Admins to reload tool data table entries from disk without restarting the Galaxy server. This does not look for new <table> entries or contained new <file>s within XML files, but will e.g. make any changes to a .loc file become live immediately without restart.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5b545b85b83/ Changeset: e5b545b85b83 User: dan Date: 2014-05-13 19:01:47 Summary: Add the ability for Admins to reload tool data table entries from disk without restarting the Galaxy server. This does not look for new <table> entries or contained new <file>s within XML files, but will e.g. make any changes to a .loc file become live immediately without restart. Affected #: 3 files diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -141,6 +141,18 @@ out.write( '</tables>\n' ) os.chmod( full_path, 0644 ) + def reload_tables( self, table_names=None ): + tables = self.get_tables() + if not table_names: + table_names = tables.keys() + elif not isinstance( table_names, list ): + table_names = [ table_names ] + for table_name in table_names: + tables[ table_name ].reload_from_files() + log.debug( "Reloaded tool data table '%s' from files.", table_name ) + return table_names + + class ToolDataTable( object ): @classmethod @@ -160,9 +172,14 @@ # increment this variable any time a new entry is added, or when the table is totally reloaded # This value has no external meaning, and does not represent an abstract version of the underlying data self._loaded_content_version = 1 + self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config':from_shed_config } ) + self._merged_load_info = [] - def _update_version( self ): - self._loaded_content_version += 1 + def _update_version( self, version=None ): + if version is not None: + self._loaded_content_version = version + else: + self._loaded_content_version += 1 return self._loaded_content_version def get_empty_field_by_name( self, name ): @@ -187,6 +204,16 @@ def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): raise NotImplementedError( "Abstract method" ) + def reload_from_files( self ): + new_version = self._update_version() + merged_info = self._merged_load_info + self.__init__( *self._load_info[0], **self._load_info[1] ) + self._update_version( version=new_version ) + for ( tool_data_table_class, load_info ) in merged_info: + self.merge_tool_data_table( tool_data_table_class( *load_info[0], **load_info[1] ), allow_duplicates=False ) + return self._update_version() + + class TabularToolDataTable( ToolDataTable ): """ Data stored in a tabular / separated value format on disk, allows multiple @@ -278,6 +305,8 @@ for filename, info in other_table.filenames.iteritems(): if filename not in self.filenames: self.filenames[ filename ] = info + #save info about table + self._merged_load_info.append( ( other_table.__class__, other_table._load_info ) ) #add data entries and return current data table version return self.add_entries( other_table.data, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -77,3 +77,33 @@ if data_table is None: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error" ) ) return trans.fill_template( "data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status ) + + @web.expose + @web.require_admin + def reload_tool_data_tables( self, trans, table_name=None, **kwd ): + if table_name and isinstance( table_name, basestring ): + table_name = table_name.split( "," ) + # Reload the tool data tables + table_names = self.app.tool_data_tables.reload_tables( table_names=table_name ) + redirect_url = None + if table_names: + status = 'done' + if len( table_names ) == 1: + message = "The data table '%s' has been reloaded." % table_names[0] + redirect_url = web.url_for( controller='data_manager', + action='manage_data_table', + table_name=table_names[0], + message=message, + status=status ) + else: + message = "The data tables '%s' have been reloaded." % ', '.join( table_names ) + else: + message = "No data tables have been reloaded." + status = 'error' + if redirect_url is None: + redirect_url = web.url_for( controller='admin', + action='view_tool_data_tables', + message=message, + status=status ) + return trans.response.send_redirect( redirect_url ) + diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -15,6 +15,9 @@ <thead><tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> Data Manager: ${ data_table.name | h } + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a></th></tr><tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c74989f7cafe/ Changeset: c74989f7cafe User: dan Date: 2014-05-13 18:35:35 Summary: When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table. Affected #: 1 file diff -r a4bdf116d532cf18560ed2a4f1b94e84d7d9cc8b -r c74989f7cafe0605af12af8dc2303689fa674bde templates/admin/view_data_tables_registry.mako --- a/templates/admin/view_data_tables_registry.mako +++ b/templates/admin/view_data_tables_registry.mako @@ -26,7 +26,7 @@ %else: <tr class="tr"> %endif - <td>${data_table.name}</td> + <td><a href="${ h.url_for( controller="data_manager", action="manage_data_table", table_name=data_table.name ) }">${data_table.name}</a></td> %for i, ( filename, file_dict ) in enumerate( data_table.filenames.iteritems() ): %if i > 0: <tr><td></td> 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e13610643216/ Changeset: e13610643216 User: jmchilton Date: 2014-05-13 17:20:06 Summary: Remove no longer valid log message. Affected #: 1 file diff -r 953baebbd9d9f7757691b73eee3bc954570b2bbd -r e13610643216c4d59b41722516e9d4aa9b4466b8 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -210,7 +210,6 @@ destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] ) if in_directory( source_file, job_working_directory ): output_pairs.append( ( source_file, destination ) ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) https://bitbucket.org/galaxy/galaxy-central/commits/a4bdf116d532/ Changeset: a4bdf116d532 User: jmchilton Date: 2014-05-13 17:20:06 Summary: Optimize/correct LWR remote metadata generation for working directory outputs. Previously I was attempting to mimic Galaxy's behavior of copying these files to a fixed output location after execution on the remote server before setting metadata. This was an un-needed copy since it appears to easier to just send the metadata generation code the expected path on the working directory. Affected #: 1 file diff -r e13610643216c4d59b41722516e9d4aa9b4466b8 -r a4bdf116d532cf18560ed2a4f1b94e84d7d9cc8b lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -172,7 +172,6 @@ job_wrapper.prepare( **prepare_kwds ) self.__prepare_input_files_locally(job_wrapper) remote_metadata = LwrJobRunner.__remote_metadata( client ) - remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) dependency_resolution = LwrJobRunner.__dependency_resolution( client ) metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) remote_command_params = dict( @@ -184,7 +183,7 @@ self, job_wrapper=job_wrapper, include_metadata=remote_metadata, - include_work_dir_outputs=remote_work_dir_copy, + include_work_dir_outputs=False, remote_command_params=remote_command_params, ) except Exception: @@ -358,13 +357,7 @@ self.client_manager.shutdown() def __client_outputs( self, client, job_wrapper ): - remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) - if not remote_work_dir_copy: - work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) - else: - # They have already been copied over to look like regular outputs remotely, - # no need to handle them differently here. - work_dir_outputs = [] + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) output_files = self.get_output_files( job_wrapper ) client_outputs = ClientOutputs( working_directory=job_wrapper.working_directory, @@ -400,16 +393,6 @@ return remote_metadata @staticmethod - def __remote_work_dir_copy( lwr_client ): - # Right now remote metadata handling assumes from_work_dir outputs - # have been copied over before it runs. So do that remotely. This is - # not the default though because adding it to the command line is not - # cross-platform (no cp on Windows) and it's un-needed work outside - # the context of metadata settting (just as easy to download from - # either place.) - return LwrJobRunner.__remote_metadata( lwr_client ) - - @staticmethod def __use_remote_datatypes_conf( lwr_client ): """ When setting remote metadata, use integrated datatypes from this Galaxy instance or use the datatypes config configured via the remote @@ -440,7 +423,21 @@ outputs_directory = remote_job_config['outputs_directory'] configs_directory = remote_job_config['configs_directory'] working_directory = remote_job_config['working_directory'] + # For metadata calculation, we need to build a list of of output + # file objects with real path indicating location on Galaxy server + # and false path indicating location on compute server. Since the + # LWR disables from_work_dir copying as part of the job command + # line we need to take the list of output locations on the LWR + # server (produced by self.get_output_files(job_wrapper)) and for + # each work_dir output substitute the effective path on the LWR + # server relative to the remote working directory as the + # false_path to send the metadata command generation module. + work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory) outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + for output in outputs: + for lwr_workdir_path, real_path in work_dir_outputs: + if real_path == output.real_path: + output.false_path = lwr_workdir_path metadata_kwds['output_fnames'] = outputs metadata_kwds['compute_tmp_dir'] = working_directory metadata_kwds['config_root'] = remote_galaxy_home Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Ensure new_file_path exists before set_metadata.py generates metadata.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/953baebbd9d9/ Changeset: 953baebbd9d9 User: jmchilton Date: 2014-05-13 16:29:41 Summary: Ensure new_file_path exists before set_metadata.py generates metadata. This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist. Affected #: 2 files diff -r f5f6cd1e938304094c9491da10824f93cbfb2d27 -r 953baebbd9d9f7757691b73eee3bc954570b2bbd lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -417,6 +417,16 @@ else: return default + def ensure_tempdir( self ): + self._ensure_directory( self.new_file_path ) + + def _ensure_directory( self, path ): + if path not in [ None, False ] and not os.path.isdir( path ): + try: + os.makedirs( path ) + except Exception, e: + raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) + def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] # Check that required directories exist @@ -440,11 +450,7 @@ self.whoosh_index_dir, \ self.object_store_cache_path, \ os.path.join( self.tool_data_path, 'shared', 'jars' ): - if path not in [ None, False ] and not os.path.isdir( path ): - try: - os.makedirs( path ) - except Exception, e: - raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) + self._ensure_directory( path ) # Check that required files exist tool_configs = self.tool_configs if self.migrated_tools_config not in tool_configs: diff -r f5f6cd1e938304094c9491da10824f93cbfb2d27 -r 953baebbd9d9f7757691b73eee3bc954570b2bbd scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -66,6 +66,7 @@ log.debug("Did not load option %s from %s" % (option, config_file_name)) # config object is required by ObjectStore class so create it now universe_config = config.Configuration(**conf_dict) + universe_config.ensure_tempdir() object_store = build_object_store_from_config(universe_config) galaxy.model.Dataset.object_store = object_store 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.

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commit/galaxy-central: jmchilton: Improvements to LWR documentation.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f5f6cd1e9383/ Changeset: f5f6cd1e9383 User: jmchilton Date: 2014-05-13 07:46:41 Summary: Improvements to LWR documentation. Add separate examples for MQ driven stuff - this should clear up things and make it clear which new parameters are required when using message queue and which are no longer required. Add more documentation for remote dependency resolution. Document rewrite_parameters. Affected #: 1 file diff -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 -r f5f6cd1e938304094c9491da10824f93cbfb2d27 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -23,11 +23,6 @@  -  -  - </plugin> + <plugin id="amqp_lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> + <param id="url">amqp://guest:guest@localhost:5672//</param> +  + <param id="galaxy_url">http://localhost:8080/</param> +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /><plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> @@ -116,7 +121,11 @@  + http transfers with file system copies, 'remote_transfer' to cause + the lwr to initiate HTTP transfers instead of Galaxy, or + 'remote_copy' to cause lwr to initiate file system copies. + If setting this to 'remote_transfer' be sure to specify a + 'galaxy_url' attribute on the runner plugin above. --> +  +  -  - </destination> + <destination id="amqp_lwr_dest" runner="amqp_lwr" > +  +  + <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param> +  + <param id="default_file_action">remote_transfer</param> + </destination><destination id="ssh_torque" runner="cli"><param id="shell_plugin">SecureShell</param><param id="job_plugin">Torque</param> 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48ee04030f89/ Changeset: 48ee04030f89 User: jmchilton Date: 2014-05-13 07:13:02 Summary: Implement serializable class that can describe full dependency context for remote dependency resolution. Previously LWR jut serialized tool requirements, by transitioning to this class LWR should be able to resolve tool shed installed packages as well - requiring the additional repository and tool dependency context. Affected #: 2 files diff -r 3b29b6f83d17ed07d2c3ea49d839b29d66cad580 -r 48ee04030f893a9a9657b639bb38819fb4404388 lib/galaxy/tools/deps/dependencies.py --- /dev/null +++ b/lib/galaxy/tools/deps/dependencies.py @@ -0,0 +1,68 @@ +from galaxy.tools.deps.requirements import ToolRequirement +from galaxy.util import bunch + + +class DependenciesDescription(object): + """ Capture (in a readily serializable way) context related a tool + dependencies - both the tool's listed requirements and the tool shed + related context required to resolve dependencies via the + ToolShedPackageDependencyResolver. + + This is meant to enable remote resolution of dependencies, by the LWR or + other potential remote execution mechanisms. + """ + + def __init__(self, requirements=[], installed_tool_dependencies=[]): + self.requirements = requirements + # tool shed installed tool dependencies... + self.installed_tool_dependencies = installed_tool_dependencies + + def to_dict(self): + return dict( + requirements=[r.to_dict() for r in self.requirements], + installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies] + ) + + @staticmethod + def from_dict(as_dict): + if as_dict is None: + return None + + requirements_dicts = as_dict.get('requirements', []) + requirements = [ToolRequirement.from_dict(r) for r in requirements_dicts] + installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', []) + installed_tool_dependencies = map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts) + return DependenciesDescription( + requirements=requirements, + installed_tool_dependencies=installed_tool_dependencies + ) + + @staticmethod + def _toolshed_install_dependency_from_dict(as_dict): + # Rather than requiring full models in LWR, just use simple objects + # containing only properties and associations used to resolve + # dependencies for tool execution. + repository_object = bunch.Bunch( + name=as_dict['repository_name'], + owner=as_dict['repository_owner'], + installed_changeset_revision=as_dict['repository_installed_changeset'], + ) + dependency_object = bunch.Bunch( + name=as_dict['dependency_name'], + version=as_dict['dependency_version'], + type=as_dict['dependency_type'], + tool_shed_repository=repository_object, + ) + return dependency_object + + @staticmethod + def _toolshed_install_dependency_to_dict(tool_dependency): + tool_shed_repository = tool_dependency.tool_shed_repository + return dict( + dependency_name=tool_dependency.name, + dependency_version=tool_dependency.version, + dependency_type=tool_dependency.type, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_installed_changeset=tool_shed_repository.installed_changeset_revision, + ) diff -r 3b29b6f83d17ed07d2c3ea49d839b29d66cad580 -r 48ee04030f893a9a9657b639bb38819fb4404388 test/unit/tools/test_tool_dependency_description.py --- /dev/null +++ b/test/unit/tools/test_tool_dependency_description.py @@ -0,0 +1,44 @@ +from galaxy.model import tool_shed_install +from galaxy.tools.deps import requirements +from galaxy.tools.deps import dependencies + + +def test_serialization(): + repository = tool_shed_install.ToolShedRepository( + owner="devteam", + name="tophat", + installed_changeset_revision="abcdefghijk", + ) + dependency = tool_shed_install.ToolDependency( + name="tophat", + version="2.0", + type="package", + status=tool_shed_install.ToolDependency.installation_status.INSTALLED, + ) + dependency.tool_shed_repository = repository + tool_requirement = requirements.ToolRequirement( + name="tophat", + version="2.0", + type="package", + ) + descript = dependencies.DependenciesDescription( + requirements=[tool_requirement], + installed_tool_dependencies=[dependency], + ) + result_descript = dependencies.DependenciesDescription.from_dict( + descript.to_dict() + ) + result_requirement = result_descript.requirements[0] + assert result_requirement.name == "tophat" + assert result_requirement.version == "2.0" + assert result_requirement.type == "package" + + result_tool_shed_dependency = result_descript.installed_tool_dependencies[0] + result_tool_shed_dependency.name = "tophat" + result_tool_shed_dependency.version = "2.0" + result_tool_shed_dependency.type = "package" + result_tool_shed_repository = result_tool_shed_dependency.tool_shed_repository + result_tool_shed_repository.name = "tophat" + result_tool_shed_repository.owner = "devteam" + result_tool_shed_repository.installed_changeset_revision = "abcdefghijk" + https://bitbucket.org/galaxy/galaxy-central/commits/24b5759f33f8/ Changeset: 24b5759f33f8 User: jmchilton Date: 2014-05-13 07:13:02 Summary: Update LWR client through LWR changeset 9fb7fcb. Among other smaller fixes, this update causes the LWR client/runner to pass more tool dependency context through to the remote LWR server when `dependency_resolution` is set to `remote`. This additional context allows tool shed packages to be resolved remotely (i.e. allows proper use of ToolShedPackageDependencyResolver on the remote LWR server). It remains the responsibility of the deployer to ensure identical versions of tool shed packages are installed on the remote LWR server and the local Galaxy instance. Affected #: 11 files diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -5,6 +5,7 @@ from galaxy.jobs import ComputeEnvironment from galaxy.jobs import JobDestination from galaxy.jobs.command_factory import build_command +from galaxy.tools.deps import dependencies from galaxy.util import string_as_bool_or_none from galaxy.util.bunch import Bunch @@ -118,9 +119,7 @@ return try: - dependency_resolution = LwrJobRunner.__dependency_resolution( client ) - remote_dependency_resolution = dependency_resolution == "remote" - requirements = job_wrapper.tool.requirements if remote_dependency_resolution else [] + dependencies_description = LwrJobRunner.__dependencies_description( client, job_wrapper ) rewrite_paths = not LwrJobRunner.__rewrite_parameters( client ) unstructured_path_rewrites = {} if compute_environment: @@ -133,7 +132,7 @@ working_directory=job_wrapper.working_directory, tool=job_wrapper.tool, config_files=job_wrapper.extra_filenames, - requirements=requirements, + dependencies_description=dependencies_description, env=client.env, rewrite_paths=rewrite_paths, arbitrary_files=unstructured_path_rewrites, @@ -376,6 +375,19 @@ return client_outputs @staticmethod + def __dependencies_description( lwr_client, job_wrapper ): + dependency_resolution = LwrJobRunner.__dependency_resolution( lwr_client ) + remote_dependency_resolution = dependency_resolution == "remote" + if not remote_dependency_resolution: + return None + requirements = job_wrapper.tool.requirements or [] + installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies or [] + return dependencies.DependenciesDescription( + requirements=requirements, + installed_tool_dependencies=installed_tool_dependencies, + ) + + @staticmethod def __dependency_resolution( lwr_client ): dependency_resolution = lwr_client.destination_params.get( "dependency_resolution", "local" ) if dependency_resolution not in ["none", "local", "remote"]: diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -4,6 +4,39 @@ This module contains logic for interfacing with an external LWR server. +------------------ +Configuring Galaxy +------------------ + +Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. See ``job_conf.xml.sample_advanced`` +in your Galaxy code base or on +`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanc…>`_ +for information on how to configure Galaxy to interact with the LWR. + +Galaxy also supports an older, less rich configuration of job runners directly +in its main ``universe_wsgi.ini`` file. The following section describes how to +configure Galaxy to communicate with the LWR in this legacy mode. + +Legacy +------ + +A Galaxy tool can be configured to be executed remotely via LWR by +adding a line to the ``universe_wsgi.ini`` file under the +``galaxy:tool_runners`` section with the format:: + + <tool_id> = lwr://http://<lwr_host>:<lwr_port> + +As an example, if a host named remotehost is running the LWR server +application on port ``8913``, then the tool with id ``test_tool`` can +be configured to run remotely on remotehost by adding the following +line to ``universe.ini``:: + + test_tool = lwr://http://remotehost:8913 + +Remember this must be added after the ``[galaxy:tool_runners]`` header +in the ``universe.ini`` file. + + """ from .staging.down import finish_job diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -166,8 +166,8 @@ action_type = mapper.action_type file_lister = mapper.file_lister if type in ["workdir", "output_workdir"] and action_type == "none": - ## We are changing the working_directory relative to what - ## Galaxy would use, these need to be copied over. + # We are changing the working_directory relative to what + # Galaxy would use, these need to be copied over. action_type = "copy" action_class = actions.get(action_type, None) if action_class is None: diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -13,8 +13,8 @@ DEFAULT_EXCHANGE_NAME = "lwr" DEFAULT_EXCHANGE_TYPE = "direct" -DEFAULT_TIMEOUT = 0.2 # Set timeout to periodically give up looking and check - # if polling should end. +# Set timeout to periodically give up looking and check if polling should end. +DEFAULT_TIMEOUT = 0.2 class LwrExchange(object): @@ -48,7 +48,6 @@ queue = self.__queue(queue_name) with self.connection(self.__url, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): - log.debug("Consuming queue %s" % queue) while check: try: connection.drain_events(timeout=self.__timeout) @@ -59,7 +58,6 @@ with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) - log.debug("Publishing with key %s and payload %s" % (key, payload)) producer.publish( payload, serializer='json', diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -39,9 +39,8 @@ ) else: job_directory = None - self.env = destination_params.get( "env", [] ) + self.env = destination_params.get("env", []) self.files_endpoint = destination_params.get("files_endpoint", None) - self.env = destination_params.get("env", []) self.job_directory = job_directory self.default_file_action = self.destination_params.get("default_file_action", "transfer") @@ -83,7 +82,7 @@ super(JobClient, self).__init__(destination_params, job_id) self.job_manager_interface = job_manager_interface - def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): """ Queue up the execution of the supplied `command_line` on the remote server. Called launch for historical reasons, should be renamed to @@ -98,8 +97,8 @@ submit_params_dict = submit_params(self.destination_params) if submit_params_dict: launch_params['params'] = dumps(submit_params_dict) - if requirements: - launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) + if dependencies_description: + launch_params['dependencies_description'] = dumps(dependencies_description.to_dict()) if env: launch_params['env'] = dumps(env) if remote_staging: @@ -248,8 +247,8 @@ return self._raw_execute(self._upload_file_action(args), args, contents, input_path) def _upload_file_action(self, args): - ## Hack for backward compatibility, instead of using new upload_file - ## path. Use old paths. + # Hack for backward compatibility, instead of using new upload_file + # path. Use old paths. input_type = args['input_type'] action = { # For backward compatibility just target upload_input_extra for all @@ -295,15 +294,15 @@ raise Exception(error_message) self.client_manager = client_manager - def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): """ """ launch_params = dict(command_line=command_line, job_id=self.job_id) submit_params_dict = submit_params(self.destination_params) if submit_params_dict: launch_params['params'] = submit_params_dict - if requirements: - launch_params['requirements'] = [requirement.to_dict() for requirement in requirements] + if dependencies_description: + launch_params['dependencies_description'] = dependencies_description.to_dict() if env: launch_params['env'] = env if remote_staging: diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/destination.py --- a/lib/galaxy/jobs/runners/lwr_client/destination.py +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -31,9 +31,9 @@ if not url.endswith("/"): url += "/" - ## Check for private token embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo + # Check for private token embedded in the URL. A URL of the form + # https://moo@cow:8913 will try to contact https://cow:8913 + # with a private key of moo private_token_format = "https?://(.*)@.*/?" private_token_match = match(private_token_format, url) private_token = None diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -67,8 +67,8 @@ self.object_store = object_store def __app_args(self): - ## Arguments that would be specified from LwrApp if running - ## in web server. + # Arguments that would be specified from LwrApp if running + # in web server. return { 'manager': self.job_manager, 'file_cache': self.file_cache, diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/staging/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py @@ -30,8 +30,9 @@ be transferred to remote server). working_directory : str Local path created by Galaxy for running this job. - requirements : list - List of requirements for tool execution. + dependencies_description : list + galaxy.tools.deps.dependencies.DependencyDescription object describing + tool dependency context for remote depenency resolution. env: list List of dict object describing environment variables to populate. version_file : str @@ -55,7 +56,7 @@ input_files, client_outputs, working_directory, - requirements, + dependencies_description=None, env=[], arbitrary_files=None, rewrite_paths=True, @@ -66,7 +67,7 @@ self.input_files = input_files self.client_outputs = client_outputs self.working_directory = working_directory - self.requirements = requirements + self.dependencies_description = dependencies_description self.env = env self.rewrite_paths = rewrite_paths self.arbitrary_files = arbitrary_files or {} @@ -79,6 +80,15 @@ def version_file(self): return self.client_outputs.version_file + @property + def tool_dependencies(self): + if not self.remote_dependency_resolution: + return None + return dict( + requirements=(self.tool.requirements or []), + installed_tool_dependencies=(self.tool.installed_tool_dependencies or []) + ) + class ClientOutputs(object): """ Abstraction describing the output datasets EXPECTED by the Galaxy job diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/staging/up.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py @@ -24,7 +24,7 @@ job_id = file_stager.job_id launch_kwds = dict( command_line=rebuilt_command_line, - requirements=client_job_description.requirements, + dependencies_description=client_job_description.dependencies_description, env=client_job_description.env, ) if file_stager.job_config: diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/jobs/runners/lwr_client/transport/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py @@ -15,8 +15,8 @@ def __get_transport_type(transport_type, os_module): if not transport_type: use_curl = os_module.getenv('LWR_CURL_TRANSPORT', "0") - ## If LWR_CURL_TRANSPORT is unset or set to 0, use default, - ## else use curl. + # If LWR_CURL_TRANSPORT is unset or set to 0, use default, + # else use curl. if use_curl.isdigit() and not int(use_curl): transport_type = 'urllib' else: diff -r 48ee04030f893a9a9657b639bb38819fb4404388 -r 24b5759f33f87879e945a2f14ef5e8abfce488c1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2673,12 +2673,18 @@ def build_dependency_shell_commands( self ): """Return a list of commands to be run to populate the current environment to include this tools requirements.""" + return self.app.toolbox.dependency_manager.dependency_shell_commands( + self.requirements, + installed_tool_dependencies=self.installed_tool_dependencies + ) + + @property + def installed_tool_dependencies(self): if self.tool_shed_repository: installed_tool_dependencies = self.tool_shed_repository.tool_dependencies_installed_or_in_error else: installed_tool_dependencies = None - return self.app.toolbox.dependency_manager.dependency_shell_commands( self.requirements, - installed_tool_dependencies=installed_tool_dependencies ) + return installed_tool_dependencies def build_redirect_url_params( self, param_dict ): """ 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.

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commit/galaxy-central: davebgx: Fix for retrieving job streams with the twill interactor.
by commits-noreply＠bitbucket.org 12 May '14

12 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b29b6f83d17/ Changeset: 3b29b6f83d17 User: davebgx Date: 2014-05-12 22:27:49 Summary: Fix for retrieving job streams with the twill interactor. Affected #: 1 file diff -r 246b419fc92a91f31eb7cdd5e2de4a4c15a4b631 -r 3b29b6f83d17ed07d2c3ea49d839b29d66cad580 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -386,7 +386,8 @@ self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) def get_job_stream( self, history_id, output_data, stream ): - return self.twill_test_case._get_job_stream_output( output_data.get( 'id' ), stream=stream, format=False ) + encoded_id = self.twill_test_case.security.encode_id( output_data.get( 'id' ) ) + return self.twill_test_case._get_job_stream_output( encoded_id, stream=stream, format=False ) def stage_data_async( self, test_data, history, shed_tool_id, async=True ): name = test_data.get( 'name', None ) 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.

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commit/galaxy-central: dan: When working with <conversions> in DataToolParameters, have the parsed conv_types be a list, as is now expected in subsequent usage.
by commits-noreply＠bitbucket.org 12 May '14

12 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/246b419fc92a/ Changeset: 246b419fc92a User: dan Date: 2014-05-12 21:27:36 Summary: When working with <conversions> in DataToolParameters, have the parsed conv_types be a list, as is now expected in subsequent usage. Affected #: 1 file diff -r 2b7e97a34afa6b33e9950df9213b3cb9be9026a3 -r 246b419fc92a91f31eb7cdd5e2de4a4c15a4b631 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1659,7 +1659,7 @@ conv_extensions = conv_elem.get( "type" ) # target datatype extension # FIXME: conv_extensions should be able to be an ordered list assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) - conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ) + conv_types = [ tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ) ] self.conversions.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): 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.

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commit/galaxy-central: martenson: important docs for select2 backbone view
by commits-noreply＠bitbucket.org 12 May '14

12 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b7e97a34afa/ Changeset: 2b7e97a34afa User: martenson Date: 2014-05-12 20:56:06 Summary: important docs for select2 backbone view Affected #: 2 files diff -r 8e2135ee278aa44eb5a8da04a392bfa44efc0279 -r 2b7e97a34afa6b33e9950df9213b3cb9be9026a3 static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -1,7 +1,12 @@ // dependencies define(['utils/utils'], function(Utils) { -// plugin +/** + * A plugin for initializing select2 input items. + * Make sure the select2 library itself is loaded beforehand. + * Also the element to which select2 will be appended has to + * be created before select2 initialization (and passed as option). + */ var View = Backbone.View.extend( { // options @@ -181,13 +186,13 @@ }, // element - _template: function(options) { + _template: function() { return '<input type="hidden"/>'; } }); return { View : View -} +}; }); diff -r 8e2135ee278aa44eb5a8da04a392bfa44efc0279 -r 2b7e97a34afa6b33e9950df9213b3cb9be9026a3 static/scripts/packed/mvc/ui/ui-select.js --- a/static/scripts/packed/mvc/ui/ui-select.js +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var c=this._getValue();this.$el.select2({data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder});this._setValue(c)},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var c=this._getValue();this.$el.select2({data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder});this._setValue(c)},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(){return'<input type="hidden"/>'}});return{View:b}}); 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