February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: add subsetting functionality to data manager and enable subsetting for line tracks.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/429103684d86/ changeset: 429103684d86 user: jgoecks date: 2013-02-21 23:10:54 summary: Trackster: add subsetting functionality to data manager and enable subsetting for line tracks. affected #: 4 files diff -r 26d7b89d9f897a28876214c88faed215973e6fcd -r 429103684d864f93563cd92c30888bd623fdb80e lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1044,9 +1044,7 @@ return all_dat is not None def get_data( self, chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs ): - # Subtract 1 because start/end are in 0-based coordinate system but BBI - # provider uses 1-based coordinate system. - start = int( start ) - 1 + start = int( start ) end = int( end ) # Helper function for getting summary data regardless of chromosome diff -r 26d7b89d9f897a28876214c88faed215973e6fcd -r 429103684d864f93563cd92c30888bd623fdb80e static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -258,7 +258,8 @@ // y becomes the bar height in pixels, which is the negated for canvas coords y = Math.round( y / vertical_range * height_px ); ctx.fillRect(x_scaled, y_zero, delta_x_px, - y ); - } else if (mode === "Intensity") { + } + else if (mode === "Intensity") { var saturation = (y - min_value) / vertical_range, // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color @@ -267,18 +268,21 @@ new_b = Math.round( pref_b + (255 - pref_b) * (1 - saturation) ); ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")"; ctx.fillRect(x_scaled, 0, delta_x_px, height_px); - } else { + } + else { // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px); y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); // console.log(canvas.get(0).height, canvas.get(0).width); if (in_path) { ctx.lineTo(x_scaled, y); - } else { + } + else { in_path = true; if (mode === "Filled") { ctx.moveTo(x_scaled, height_px); ctx.lineTo(x_scaled, y); - } else { + } + else { ctx.moveTo(x_scaled, y); } } @@ -289,7 +293,8 @@ var overflow_x; if (mode === "Histogram" || mode === "Intensity") { overflow_x = delta_x_px; - } else { // Line and Filled, which are points + } + else { // Line and Filled, which are points x_scaled -= 2; // Move it over to the left so it's centered on the point overflow_x = 4; } @@ -308,7 +313,8 @@ ctx.lineTo( 0, y_zero ); } ctx.fill(); - } else { + } + else { ctx.stroke(); } @@ -469,7 +475,7 @@ */ get_row_height: function() { var mode = this.mode, height; - if (mode === "Dense") { + if (mode === "Dense") { height = DENSE_TRACK_HEIGHT; } else if (mode === "no_detail") { diff -r 26d7b89d9f897a28876214c88faed215973e6fcd -r 429103684d864f93563cd92c30888bd623fdb80e static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3540,6 +3540,7 @@ on_resize: function() { this.request_draw(true); }, + /** * Set track minimum value. */ @@ -3549,6 +3550,7 @@ this.tile_cache.clear(); this.request_draw(); }, + /** * Set track maximum value. */ @@ -3558,6 +3560,7 @@ this.tile_cache.clear(); this.request_draw(); }, + predraw_init: function() { var track = this; track.vertical_range = undefined; @@ -3618,6 +3621,7 @@ .prependTo(track.container_div); }); }, + /** * Draw LineTrack tile. */ @@ -3632,11 +3636,12 @@ return new Tile(this, region, resolution, canvas, result.data); }, + /** - * LineTrack data cannot currently be subsetted. + * Subset line tracks only if resolution is single-base pair. */ - can_subset: function(data) { - return false; + can_subset: function(entry) { + return (entry.data[1][0] - entry.data[0][0] === 1); } }); diff -r 26d7b89d9f897a28876214c88faed215973e6fcd -r 429103684d864f93563cd92c30888bd623fdb80e static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -355,25 +355,38 @@ // var key_ary = this.get('key_ary'), obj_cache = this.get('obj_cache'), - key, entry_region; + key, entry_region, is_subregion; for (var i = 0; i < key_ary.length; i++) { key = key_ary[i]; entry_region = new GenomeRegion({from_str: key}); if (entry_region.contains(region)) { + is_subregion = true; + // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[key]; if ( is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(key, i); + + // If there's data, subset it. + if ( !is_deferred(entry) ) { + var subset_entry = this.subset_entry(entry, region); + this.set(region, subset_entry); + entry = subset_entry; + } + return entry; } } } + // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be + // subsetted. For these cases, do not increase length because region will never be found (and + // an infinite loop will occur.) // If needed, extend region to make it minimum size. - if (region.length() < this.attributes.min_region_size) { + if (!is_subregion && region.length() < this.attributes.min_region_size) { // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend. // This would prevent bad extensions when zooming in/out while still preserving the behavior // below. @@ -553,7 +566,40 @@ return deferred; }, - + + /** + * Returns entry with only data in the subregion. + */ + subset_entry: function(entry, subregion) { + // Dictionary from entry type to function for subsetting data. + var subset_fns = { + bigwig: function(data, subregion) { + return _.filter(data, function(data_point) { + return data_point[0] >= subregion.get('start') && + data_point[0] <= subregion.get('end'); + }); + }, + 'refseq': function(data, subregion) { + var seq_start = subregion.get('start') - entry.region.get('start'), + seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') ); + return entry.data.slice(seq_start, seq_end); + } + }; + + // Subset entry if there is a function for subsetting and regions are not the same. + var subregion_data = entry.data; + if (!entry.region.same(subregion) && entry.dataset_type in subset_fns) { + subregion_data = subset_fns[entry.dataset_type](entry.data, subregion); + } + + // Return entry with subregion's data. + return { + region: subregion, + data: subregion_data, + dataset_type: entry.dataset_type + }; + }, + /** * Get data from the cache. */ @@ -584,24 +630,6 @@ return { data: null }; } return GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params); - }, - - /** - * Return an entry that includes only data in the subregion. - */ - subset_entry: function(entry, subregion) { - var seq_data = entry.data; - if (!entry.region.same(subregion)) { - // Need to subset sequence data. - var seq_start = subregion.get('start') - entry.region.get('start'), - seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') ); - seq_data = entry.data.slice(seq_start, seq_end); - } - - return { - region: subregion, - data: seq_data - }; } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 21 Feb '13

21 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26d7b89d9f89/ changeset: 26d7b89d9f89 user: dan date: 2013-02-21 21:26:15 summary: Fix for display_in_upload affected #: 1 file diff -r 8717485b3c6c78f709d352a63255e50ef978f57d -r 26d7b89d9f897a28876214c88faed215973e6fcd lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -90,7 +90,7 @@ dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) - display_in_upload = elem.get( 'display_in_upload', False ) + display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) # Proprietary datatypes included in installed tool shed repositories will include two special attributes # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. @@ -107,7 +107,7 @@ in_memory_dtype = elem.get( 'type', None ) in_memory_type_extension = elem.get( 'type_extension', None ) in_memory_mimetype = elem.get( 'mimetype', None ) - in_memory_display_in_upload = elem.get( 'display_in_upload', False ) + in_memory_display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) in_memory_make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) if in_memory_dtype == dtype and in_memory_type_extension == type_extension and in_memory_mimetype == mimetype \ and in_memory_display_in_upload == display_in_upload and in_memory_make_subclass == make_subclass: https://bitbucket.org/galaxy/galaxy-central/commits/31b09605fcc3/ changeset: 31b09605fcc3 branch: stable user: dan date: 2013-02-21 21:26:15 summary: Fix for display_in_upload affected #: 1 file diff -r a0741e6798f28f05bb9bb17b572ce1ea4c62e1f0 -r 31b09605fcc313b3e93efb927ac328bfcc42ad82 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -90,7 +90,7 @@ dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) - display_in_upload = elem.get( 'display_in_upload', False ) + display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) # Proprietary datatypes included in installed tool shed repositories will include two special attributes # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. @@ -107,7 +107,7 @@ in_memory_dtype = elem.get( 'type', None ) in_memory_type_extension = elem.get( 'type_extension', None ) in_memory_mimetype = elem.get( 'mimetype', None ) - in_memory_display_in_upload = elem.get( 'display_in_upload', False ) + in_memory_display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) in_memory_make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) if in_memory_dtype == dtype and in_memory_type_extension == type_extension and in_memory_mimetype == mimetype \ and in_memory_display_in_upload == display_in_upload and in_memory_make_subclass == make_subclass: 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: greg: Minor fixes to the baseline API methods in the tool shed.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8717485b3c6c/ changeset: 8717485b3c6c user: greg date: 2013-02-21 21:04:14 summary: Minor fixes to the baseline API methods in the tool shed. affected #: 3 files diff -r 73914d7ce26131b0670f82e3596d2a56494f0480 -r 8717485b3c6c78f709d352a63255e50ef978f57d lib/galaxy/webapps/community/api/repositories.py --- a/lib/galaxy/webapps/community/api/repositories.py +++ b/lib/galaxy/webapps/community/api/repositories.py @@ -26,7 +26,9 @@ .order_by( trans.app.model.Repository.table.c.name ) \ .all() for repository in query: - item = repository.get_api_value( value_mapper={ 'id' : trans.security.encode_id( repository.id ) } ) + value_mapper={ 'id' : trans.security.encode_id( repository.id ), + 'user_id' : trans.security.encode_id( repository.user_id ) } + item = repository.get_api_value( view='collection', value_mapper=value_mapper ) item[ 'url' ] = web.url_for( 'repository_contents', repository_id=trans.security.encode_id( repository.id ) ) rval.append( item ) except Exception, e: @@ -43,7 +45,9 @@ """ try: repository = suc.get_repository_in_tool_shed( trans, id ) - repository_data = repository.get_api_value( view='element', value_mapper={ 'id' : trans.security.encode_id( repository.id ) } ) + value_mapper={ 'id' : trans.security.encode_id( repository.id ), + 'user_id' : trans.security.encode_id( repository.user_id ) } + repository_data = repository.get_api_value( view='element', value_mapper=value_mapper ) repository_data[ 'contents_url' ] = web.url_for( 'repository_contents', repository_id=id ) except Exception, e: message = "Error in the Tool Shed API at show: %s" % str( e ) diff -r 73914d7ce26131b0670f82e3596d2a56494f0480 -r 8717485b3c6c78f709d352a63255e50ef978f57d lib/galaxy/webapps/community/api/repository_revisions.py --- a/lib/galaxy/webapps/community/api/repository_revisions.py +++ b/lib/galaxy/webapps/community/api/repository_revisions.py @@ -26,7 +26,9 @@ .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ .all() for repository_metadata in query: - item = repository_metadata.get_api_value( value_mapper={ 'id' : trans.security.encode_id( repository_metadata.id ) } ) + value_mapper={ 'id' : trans.security.encode_id( repository_metadata.id ), + 'repository_id' : trans.security.encode_id( repository_metadata.repository_id ) } + item = repository_metadata.get_api_value( view='collection', value_mapper=value_mapper ) item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) rval.append( item ) except Exception, e: diff -r 73914d7ce26131b0670f82e3596d2a56494f0480 -r 8717485b3c6c78f709d352a63255e50ef978f57d lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -114,14 +114,14 @@ self.prev_session_id = prev_session_id class Repository( object, APIItem ): - api_collection_visible_keys = ( 'id', 'name', 'description', 'user_id', 'private', 'times_downloaded', 'deprecated' ) - api_element_visible_keys = ( 'id', 'name', 'description', 'long_description', 'user_id', 'private', 'times_downloaded', 'deprecated' ) + api_collection_visible_keys = ( 'id', 'name', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) + api_element_visible_keys = ( 'id', 'name', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, id=None, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, + def __init__( self, id=None, name=None, description=None, long_description=None, user_id=None, private=False, deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): self.id = id self.name = name or "Unnamed repository" @@ -129,12 +129,14 @@ self.long_description = long_description self.user_id = user_id self.private = private + self.deleted = deleted self.email_alerts = email_alerts self.times_downloaded = times_downloaded self.deprecated = deprecated def as_dict( self, trans ): - repository_dict = self.get_api_value( view='element' ) - repository_dict[ 'id' ] = trans.security.encode_id( self.id ) + value_mapper={ 'id' : trans.security.encode_id( self.id ), + 'user_id' : trans.security.encode_id( self.user_id ) } + repository_dict = self.get_api_value( view='element', value_mapper=value_mapper ) return repository_dict def get_api_value( self, view='collection', value_mapper=None ): if value_mapper is 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: greg: Baseline API methods for repositories in the tool shed.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73914d7ce261/ changeset: 73914d7ce261 user: greg date: 2013-02-21 20:38:53 summary: Baseline API methods for repositories in the tool shed. affected #: 5 files diff -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 -r 73914d7ce26131b0670f82e3596d2a56494f0480 lib/galaxy/webapps/community/api/repositories.py --- /dev/null +++ b/lib/galaxy/webapps/community/api/repositories.py @@ -0,0 +1,53 @@ +import galaxy.util.shed_util_common as suc +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.framework.helpers import is_true + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes +import logging + +log = logging.getLogger( __name__ ) + +class RepositoriesController( BaseAPIController ): + """RESTful controller for interactions with repositories in the Tool Shed.""" + @web.expose_api + def index( self, trans, deleted=False, **kwd ): + """ + GET /api/repository_revisions + Displays a collection (list) of repositories. + """ + rval = [] + deleted = util.string_as_bool( deleted ) + try: + query = trans.sa_session.query( trans.app.model.Repository ) \ + .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ + .order_by( trans.app.model.Repository.table.c.name ) \ + .all() + for repository in query: + item = repository.get_api_value( value_mapper={ 'id' : trans.security.encode_id( repository.id ) } ) + item[ 'url' ] = web.url_for( 'repository_contents', repository_id=trans.security.encode_id( repository.id ) ) + rval.append( item ) + except Exception, e: + message = "Error in the Tool Shed API at index: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + return rval + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/repositories/{encoded_repository_id} + Displays information about a repository in the Tool Shed. + """ + try: + repository = suc.get_repository_in_tool_shed( trans, id ) + repository_data = repository.get_api_value( view='element', value_mapper={ 'id' : trans.security.encode_id( repository.id ) } ) + repository_data[ 'contents_url' ] = web.url_for( 'repository_contents', repository_id=id ) + except Exception, e: + message = "Error in the Tool Shed API at show: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + return repository_data \ No newline at end of file diff -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 -r 73914d7ce26131b0670f82e3596d2a56494f0480 lib/galaxy/webapps/community/api/repository_contents.py --- /dev/null +++ b/lib/galaxy/webapps/community/api/repository_contents.py @@ -0,0 +1,32 @@ +import logging +import galaxy.util.shed_util_common as suc +from galaxy import web +from galaxy.web.base.controller import BaseAPIController + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class RepositoryContentsController( BaseAPIController ): + @web.expose_api + def index( self, trans, repository_id, **kwd ): + """ + GET /api/repositories/{encoded_repsository_id}/contents + Displays a collection (list) of repository contents. + + :param repository_id: an encoded id string of the `Repository` to inspect + """ + rval = [] + try: + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repository_dict = repository.as_dict( trans ) + repository_dict[ 'url' ] = web.url_for( 'repository_contents', repository_id=repository_id ) + rval.append( repository_dict ) + except Exception, e: + message = "Error in repository_contents API: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + return rval diff -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 -r 73914d7ce26131b0670f82e3596d2a56494f0480 lib/galaxy/webapps/community/api/repository_revisions.py --- a/lib/galaxy/webapps/community/api/repository_revisions.py +++ b/lib/galaxy/webapps/community/api/repository_revisions.py @@ -1,5 +1,6 @@ +import galaxy.util.shed_util_common as suc from galaxy import web, util -from galaxy.web.base.controller import BaseController, BaseAPIController +from galaxy.web.base.controller import BaseAPIController from galaxy.web.framework.helpers import is_true import pkg_resources @@ -10,7 +11,7 @@ log = logging.getLogger( __name__ ) class RepositoryRevisionsController( BaseAPIController ): - """RESTful controller for interactions with tool shed repositories.""" + """RESTful controller for interactions with tool shed repository revisions.""" @web.expose_api def index( self, trans, downloadable=True, **kwd ): """ @@ -25,11 +26,11 @@ .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ .all() for repository_metadata in query: - item = repository_metadata.get_api_value( value_mapper={ 'id' : trans.security.encode_id } ) + item = repository_metadata.get_api_value( value_mapper={ 'id' : trans.security.encode_id( repository_metadata.id ) } ) item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) rval.append( item ) except Exception, e: - rval = "Error in repository_revisions API" + rval = "Error in repository_revisions API at index: " + str( e ) log.error( rval + ": %s" % str( e ) ) trans.response.status = 500 return rval diff -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 -r 73914d7ce26131b0670f82e3596d2a56494f0480 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py +++ b/lib/galaxy/webapps/community/buildapp.py @@ -69,8 +69,15 @@ webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) - # Add the web API + # Add the web API. webapp.add_api_controllers( 'galaxy.webapps.community.api', app ) + webapp.api_mapper.resource( 'content', + 'contents', + controller='repository_contents', + name_prefix='repository_', + path_prefix='/api/repositories/:repository_id', + parent_resources=dict( member_name='repository', collection_name='repositories' ) ) + webapp.api_mapper.resource( 'repository', 'repositories', path_prefix='/api' ) webapp.api_mapper.resource( 'repository_revision', 'repository_revisions', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 -r 73914d7ce26131b0670f82e3596d2a56494f0480 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -114,14 +114,16 @@ self.prev_session_id = prev_session_id class Repository( object, APIItem ): - api_collection_visible_keys = ( 'id', 'name' ) - api_element_visible_keys = ( 'id', 'name', 'description' ) + api_collection_visible_keys = ( 'id', 'name', 'description', 'user_id', 'private', 'times_downloaded', 'deprecated' ) + api_element_visible_keys = ( 'id', 'name', 'description', 'long_description', 'user_id', 'private', 'times_downloaded', 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, times_downloaded=0, deprecated=False ): + def __init__( self, id=None, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, + times_downloaded=0, deprecated=False ): + self.id = id self.name = name or "Unnamed repository" self.description = description self.long_description = long_description @@ -130,6 +132,28 @@ self.email_alerts = email_alerts self.times_downloaded = times_downloaded self.deprecated = deprecated + def as_dict( self, trans ): + repository_dict = self.get_api_value( view='element' ) + repository_dict[ 'id' ] = trans.security.encode_id( self.id ) + return repository_dict + def get_api_value( self, view='collection', value_mapper=None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[ key ] = self.__getattribute__( key ) + if key in value_mapper: + rval[ key ] = value_mapper.get( key, rval[ key ] ) + except AttributeError: + rval[ key ] = None + if 'user_id' in rval: + rval[ 'owner' ] = self.user.username + return rval def repo_path( self, app ): return app.hgweb_config_manager.get_entry( os.path.join( "repos", self.user.username, self.name ) ) def revision( self, app ): @@ -194,7 +218,7 @@ try: rval[ key ] = self.__getattribute__( key ) if key in value_mapper: - rval[ key ] = value_mapper.get( key )( rval[ key ] ) + rval[ key ] = value_mapper.get( key, rval[ key ] ) except AttributeError: rval[ key ] = None return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: performance improvements for drawing reference track data.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c32f70e92aa4/ changeset: c32f70e92aa4 user: jgoecks date: 2013-02-21 20:37:38 summary: Trackster: performance improvements for drawing reference track data. affected #: 2 files diff -r b7b000557d128c537dfeb5bb4a9260853463793b -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -803,6 +803,7 @@ } } } else { + // Not enough detail to draw sequence data. ctx.fillStyle = block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT); diff -r b7b000557d128c537dfeb5bb4a9260853463793b -r c32f70e92aa428dcab3d753ef88a5d255272e4f9 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3465,11 +3465,11 @@ */ draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { if (w_scale > this.view.canvas_manager.char_width_px) { - this.show_contents(); + this.tiles_div.show(); return TiledTrack.prototype.draw_helper.call(this, force, region, resolution, parent_element, w_scale, kwargs); } else { - this.hide_contents(); + this.tiles_div.hide(); return null; } }, @@ -3480,22 +3480,18 @@ * Draw ReferenceTrack tile. */ draw_tile: function(data, ctx, mode, resolution, region, w_scale) { - if (w_scale > this.view.canvas_manager.char_width_px) { - // Try to subset data. - var subset = this.data_manager.subset_entry(data, region), - seq_data = subset.data; - - // Draw sequence data. - var canvas = ctx.canvas; - ctx.font = ctx.canvas.manager.default_font; - ctx.textAlign = "center"; - for (var c = 0, str_len = seq_data.length; c < str_len; c++) { - ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10); - } - return new Tile(this, region, resolution, canvas, subset); + // Try to subset data. + var subset = this.data_manager.subset_entry(data, region), + seq_data = subset.data; + + // Draw sequence data. + var canvas = ctx.canvas; + ctx.font = ctx.canvas.manager.default_font; + ctx.textAlign = "center"; + for (var c = 0, str_len = seq_data.length; c < str_len; c++) { + ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10); } - - this.hide_contents(); + return new Tile(this, region, resolution, canvas, subset); } }); 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: jgoecks: Trackster: subset reference data when available.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7b000557d12/ changeset: b7b000557d12 user: jgoecks date: 2013-02-21 20:11:09 summary: Trackster: subset reference data when available. affected #: 2 files diff -r 5a910304b25466d3781821bc35f7d0a6c1eae28a -r b7b000557d128c537dfeb5bb4a9260853463793b static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2915,6 +2915,10 @@ if ( is_deferred( seq_data ) ) { can_draw_now = false; } + else { + // Sequence data is available, subset to get only data in region. + seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); + } } // If we can draw now, do so. @@ -3440,7 +3444,8 @@ this.data_url = reference_url + "/" + this.view.dbkey; this.data_url_extra_params = {reference: true}; this.data_manager = new visualization.ReferenceTrackDataManager({ - data_url: this.data_url + data_url: this.data_url, + can_subset: this.can_subset }); this.hide_contents(); }; @@ -3456,10 +3461,11 @@ can_draw: Drawable.prototype.can_draw, /** - * Only retrieves data and draws tile if reference data can be displayed. + * Retrieves data and draws tile if reference data can be displayed. */ draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { if (w_scale > this.view.canvas_manager.char_width_px) { + this.show_contents(); return TiledTrack.prototype.draw_helper.call(this, force, region, resolution, parent_element, w_scale, kwargs); } else { @@ -3468,28 +3474,27 @@ } }, + can_subset: function(data) { return true; }, + /** * Draw ReferenceTrack tile. */ - draw_tile: function(seq, ctx, mode, resolution, region, w_scale) { - var track = this; - + draw_tile: function(data, ctx, mode, resolution, region, w_scale) { if (w_scale > this.view.canvas_manager.char_width_px) { - if (seq.data === null) { - this.hide_contents(); - return; - } + // Try to subset data. + var subset = this.data_manager.subset_entry(data, region), + seq_data = subset.data; + + // Draw sequence data. var canvas = ctx.canvas; ctx.font = ctx.canvas.manager.default_font; - ctx.textAlign = "center"; - seq = seq.data; - for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.floor(c * w_scale); - ctx.fillText(seq[c], c_start, 10); + ctx.textAlign = "center"; + for (var c = 0, str_len = seq_data.length; c < str_len; c++) { + ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10); } - this.show_contents(); - return new Tile(track, region, resolution, canvas, seq); + return new Tile(this, region, resolution, canvas, subset); } + this.hide_contents(); } }); diff -r 5a910304b25466d3781821bc35f7d0a6c1eae28a -r b7b000557d128c537dfeb5bb4a9260853463793b static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -318,6 +318,8 @@ // Do request. var manager = this, entry = $.getJSON(dataset.url(), params, function (result) { + // Add region to the result. + result.region = region; manager.set_data(region, result); }); @@ -582,7 +584,25 @@ return { data: null }; } return GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params); - } + }, + + /** + * Return an entry that includes only data in the subregion. + */ + subset_entry: function(entry, subregion) { + var seq_data = entry.data; + if (!entry.region.same(subregion)) { + // Need to subset sequence data. + var seq_start = subregion.get('start') - entry.region.get('start'), + seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') ); + seq_data = entry.data.slice(seq_start, seq_end); + } + + return { + region: subregion, + data: seq_data + }; + } }); /** @@ -639,6 +659,16 @@ end: 0, genome: null }, + + /** + * Returns true if this region is the same as a given region. + * It does not test the genome right now. + */ + same: function(region) { + return this.attributes.chrom === region.get('chrom') && + this.attributes.start === region.get('start') && + this.attributes.end === region.get('end'); + }, /** * If from_str specified, use it to initialize attributes. 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: greg: Add styles to the readme container.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0741e6798f2/ changeset: a0741e6798f2 branch: stable user: greg date: 2013-02-21 17:49:21 summary: Add styles to the readme container. affected #: 1 file diff -r 04b4efed14bab6a322c3c93d1785cc3cd398e91f -r a0741e6798f28f05bb9bb17b572ce1ea4c62e1f0 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -349,13 +349,25 @@ from galaxy.util.shed_util_common import to_safe_string encoded_id = trans.security.encode_id( readme.id ) %> + <style type="text/css"> + #readme_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - ${ to_safe_string( readme.text, to_html=True ) } + <table id="readme_table"> + <tr><td>${ to_safe_string( readme.text, to_html=True ) }</td></tr> + </table></td></tr><% 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: Fix for displaying job_id when preparing a job fails.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a910304b254/ changeset: 5a910304b254 user: dan date: 2013-02-21 17:53:32 summary: Fix for displaying job_id when preparing a job fails. affected #: 1 file diff -r bf84118d56670484db09986435bb79376e8fb52b -r 5a910304b25466d3781821bc35f7d0a6c1eae28a lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -112,7 +112,7 @@ job_wrapper.prepare() job_wrapper.runner_command_line = self.build_command_line( job_wrapper ) except: - log.exception("(%d) Failure preparing job" % job_id) + log.exception("(%s) Failure preparing job" % job_id) job_wrapper.fail( "failure preparing job", exception=True ) return 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: greg: Add styles to the readme container.
by Bitbucket 21 Feb '13

21 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf84118d5667/ changeset: bf84118d5667 user: greg date: 2013-02-21 17:49:21 summary: Add styles to the readme container. affected #: 1 file diff -r 45f1d93124ad4cadff01d8ae0fadfb1db5d8fcb2 -r bf84118d56670484db09986435bb79376e8fb52b templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -462,13 +462,25 @@ from galaxy.util.shed_util_common import to_safe_string encoded_id = trans.security.encode_id( readme.id ) %> + <style type="text/css"> + #readme_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - ${ to_safe_string( readme.text, to_html=True ) } + <table id="readme_table"> + <tr><td>${ to_safe_string( readme.text, to_html=True ) }</td></tr> + </table></td></tr><% 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 Bitbucket 21 Feb '13

21 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04b4efed14ba/ changeset: 04b4efed14ba branch: stable user: inithello date: 2013-02-21 17:06:11 summary: Changed to_safe_string to use markupsafe.escape for unsafe characters. affected #: 1 file diff -r 7c3df0bcbc222f478b1e21886fbb384d3dc96f31 -r 04b4efed14bab6a322c3c93d1785cc3cd398e91f lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -30,17 +30,11 @@ log = logging.getLogger( __name__ ) INITIAL_CHANGELOG_HASH = '000000000000' -# Characters that must be html escaped -MAPPED_CHARS = { '>' :'>', - '<' :'<', - '"' : '"', - '&' : '&', - '\'' : ''' } MAX_CONTENT_SIZE = 32768 NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'repository_dependencies.xml', 'tool_dependencies.xml' ] GALAXY_ADMIN_TOOL_SHED_CONTROLLER = 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER' TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER' -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) new_repo_email_alert_template = """ Repository name: ${repository_name} @@ -3420,12 +3414,14 @@ def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text: + if to_html: + escaped_text = str( markupsafe.escape( text ) ) + else: + escaped_text = str( text ) translated = [] - for c in text: + for c in escaped_text: if c in VALID_CHARS: translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) elif c in [ '\n' ]: if to_html: translated.append( '<br/>' ) @@ -3437,8 +3433,6 @@ translated.append( c ) else: translated.append( '' ) - if to_html: - str( markupsafe.escape( ''.join( translated ) ) ) return ''.join( translated ) return text def tool_shed_from_repository_clone_url( repository_clone_url ): https://bitbucket.org/galaxy/galaxy-central/commits/45f1d93124ad/ changeset: 45f1d93124ad user: inithello date: 2013-02-21 17:06:11 summary: Changed to_safe_string to use markupsafe.escape for unsafe characters. affected #: 1 file diff -r 1adf6fdd9c49bda204e5d90f70f10e7ef4ec06bd -r 45f1d93124ad4cadff01d8ae0fadfb1db5d8fcb2 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -32,18 +32,12 @@ INITIAL_CHANGELOG_HASH = '000000000000' REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = "data_manager_conf.xml" -# Characters that must be html escaped -MAPPED_CHARS = { '>' :'>', - '<' :'<', - '"' : '"', - '&' : '&', - '\'' : ''' } MAX_CONTENT_SIZE = 32768 NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'repository_dependencies.xml', 'tool_dependencies.xml', REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] GALAXY_ADMIN_TOOL_SHED_CONTROLLER = 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER' TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER' TOOL_TYPES_NOT_IN_TOOL_PANEL = [ 'manage_data' ] -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) new_repo_email_alert_template = """ Sharable link: ${sharable_link} @@ -3802,12 +3796,14 @@ def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text: + if to_html: + escaped_text = str( markupsafe.escape( text ) ) + else: + escaped_text = str( text ) translated = [] - for c in text: + for c in escaped_text: if c in VALID_CHARS: translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) elif c in [ '\n' ]: if to_html: translated.append( '<br/>' ) @@ -3825,8 +3821,6 @@ translated.append( c ) else: translated.append( '' ) - if to_html: - str( markupsafe.escape( ''.join( translated ) ) ) return ''.join( translated ) return text def tool_shed_from_repository_clone_url( repository_clone_url ): 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.

1 0