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commit/galaxy-central: greg: Do not allow sorting by owner on the RepositoriesReviewedByMeGrid.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c50935e70c8/ Changeset: 2c50935e70c8 User: greg Date: 2013-04-19 21:11:00 Summary: Do not allow sorting by owner on the RepositoriesReviewedByMeGrid. Affected #: 1 file diff -r 6ed903aff045656cdfb519c571627af750675aef -r 2c50935e70c8a483bcd09b358765408543a153fb lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -248,6 +248,23 @@ class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ): # This grid filters out repositories that have been marked as either deprecated or deleted. + columns = [ + RepositoriesWithReviewsGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoriesWithReviewsGrid.UserColumn( "Owner", attach_popup=False ), + RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ), + RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ), + RepositoriesWithReviewsGrid.RatingColumn( "Rating", attach_popup=False ), + RepositoriesWithReviewsGrid.ApprovedColumn( "Approved", attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[ 0 ] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, 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: Enhance several of the repository review grids to enable sorting by repository owner.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ed903aff045/ Changeset: 6ed903aff045 User: greg Date: 2013-04-19 20:59:37 Summary: Enhance several of the repository review grids to enable sorting by repository owner. Affected #: 1 file diff -r ac8f6516735f7c68859e3f0cd124e19b39c77ac7 -r 6ed903aff045656cdfb519c571627af750675aef lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -136,7 +136,10 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), - RepositoryGrid.UserColumn( "Owner", attach_popup=False ), + RepositoryGrid.UserColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), WithReviewsRevisionColumn( "Reviewed revisions" ), ReviewersColumn( "Reviewers", attach_popup=False ), RatingColumn( "Rating", attach_popup=False ), @@ -177,7 +180,9 @@ attach_popup=False ), RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), RepositoriesWithReviewsGrid.UserColumn( "Owner", - attach_popup=False ) + model_class=model.User, + attach_popup=False, + key="User.username" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[ 0 ], columns[ 1 ] ], @@ -213,7 +218,9 @@ attach_popup=False ), RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), RepositoriesWithoutReviewsGrid.UserColumn( "Owner", - attach_popup=False ) + model_class=model.User, + attach_popup=False, + key="User.username" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[ 0 ], columns[ 1 ] ], 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: Enhance the Repositories that contain tools with invalid functional tests grid to allow for sorting by repository owner.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac8f6516735f/ Changeset: ac8f6516735f User: greg Date: 2013-04-19 20:45:13 Summary: Enhance the Repositories that contain tools with invalid functional tests grid to allow for sorting by repository owner. Affected #: 1 file diff -r dd4b953f5fadb58ff427a716088c4b664ceb694e -r ac8f6516735f7c68859e3f0cd124e19b39c77ac7 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -387,7 +387,9 @@ attach_popup=False ), RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), RepositoriesWithoutReviewsGrid.UserColumn( "Owner", - attach_popup=False ) + model_class=model.User, + attach_popup=False, + key="User.username" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[ 0 ], columns[ 1 ] ], 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: use Deferreds to only drawn tiles only; this improves performance significantly.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd4b953f5fad/ Changeset: dd4b953f5fad User: jgoecks Date: 2013-04-19 20:33:11 Summary: Trackster: use Deferreds to only drawn tiles only; this improves performance significantly. Affected #: 1 file diff -r 53cf170463b4cdddf09b9cec369f2a82998d3535 -r dd4b953f5fadb58ff427a716088c4b664ceb694e static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1349,7 +1349,7 @@ view.high -= delta_chrom; view.low -= delta_chrom; } - + view.request_redraw(); // Navigate. @@ -2893,19 +2893,18 @@ var // Index of first tile that overlaps visible region. tile_index = Math.floor( low / (resolution * TILE_SIZE) ), - // If any tile could not be drawn yet, this will be set to false. - all_tiles_drawn = true, - drawn_tiles = [], - is_tile = function(o) { return (o && 'track' in o); }; + tile_region, + tile_promise, + tile_promises = [], + tiles = []; // Draw tiles. while ( ( tile_index * TILE_SIZE * resolution ) < high ) { - var tile_region = this._get_tile_bounds(tile_index, resolution), - draw_result = this.draw_helper( force, tile_region, resolution, this.tiles_div, w_scale ); - if ( is_tile(draw_result) ) { - drawn_tiles.push( draw_result ); - } else { - all_tiles_drawn = false; - } + tile_region = this._get_tile_bounds(tile_index, resolution); + tile_promise = this.draw_helper( force, tile_region, resolution, this.tiles_div, w_scale ); + tile_promises.push(tile_promise); + $.when(tile_promise).then(function(tile) { + tiles.push(tile); + }); tile_index += 1; } @@ -2914,11 +2913,15 @@ // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. var track = this; - if (all_tiles_drawn) { + $.when.apply($, tile_promises).then(function() { // Step (c) for (re)moving tiles when clear_after is true: - this.tiles_div.children(".remove").remove(); - track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); - } + track.tiles_div.children(".remove").remove(); + + // HACK: only do postdraw actions when there are tiles; ReferenceTrack may not return tiles. + if (tiles[0]) { + track.postdraw_actions(tiles, width, w_scale, clear_after); + } + }); }, /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been @@ -2970,7 +2973,8 @@ */ draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { var track = this, - key = this._gen_tile_cache_key(w_scale, region); + key = this._gen_tile_cache_key(w_scale, region), + is_tile = function(o) { return (o && 'track' in o); }; // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -2978,7 +2982,9 @@ // Check tile cache, if found show existing tile in correct position var tile = (force ? undefined : track.tile_cache.get_elt(key)); if (tile) { - track.show_tile(tile, parent_element, w_scale); + if (is_tile(tile)) { + track.show_tile(tile, parent_element, w_scale); + } return tile; } @@ -3039,15 +3045,16 @@ return tile; } - // Can't draw now, so trigger another redraw when the data is ready - var can_draw = $.Deferred(); + // Can't draw now, so put Deferred in cache and draw tile when data is available. + var tile_drawn = $.Deferred(); + track.tile_cache.set_elt(key, tile_drawn); $.when( tile_data, seq_data ).then( function() { - view.request_redraw(false, false, false, track); - can_draw.resolve(); + // Draw tile--force to clear Deferred from cache--and resolve. + tile = track.draw_helper(true, region, resolution, parent_element, w_scale, kwargs); + tile_drawn.resolve(tile); }); - // Returned Deferred is resolved when tile can be drawn. - return can_draw; + return tile_drawn; }, /** 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: inithello: Fix for incorrect path in dependent repository's env.sh when installing a repository with a complex repository dependency specifying a changeset revision that has been superseded by an updated downloadable changeset revision.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53cf170463b4/ Changeset: 53cf170463b4 User: inithello Date: 2013-04-19 20:01:51 Summary: Fix for incorrect path in dependent repository's env.sh when installing a repository with a complex repository dependency specifying a changeset revision that has been superseded by an updated downloadable changeset revision. Affected #: 1 file diff -r 7b8beadc5221774104b396d34d069a41390bc553 -r 53cf170463b4cdddf09b9cec369f2a82998d3535 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -182,14 +182,15 @@ tool_shed = package_elem.attrib[ 'toolshed' ] required_repository_name = package_elem.attrib[ 'name' ] required_repository_owner = package_elem.attrib[ 'owner' ] - required_repository_changeset_revision = package_elem.attrib[ 'changeset_revision' ] + default_required_repository_changeset_revision = package_elem.attrib[ 'changeset_revision' ] required_repository = get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, tool_shed, required_repository_name, required_repository_owner, - required_repository_changeset_revision ) + default_required_repository_changeset_revision ) tmp_filename = None if required_repository: + required_repository_changeset_revision = required_repository.installed_changeset_revision # Define the installation directory for the required tool dependency package in the required repository. required_repository_package_install_dir = \ get_tool_dependency_install_dir( app=app, @@ -257,7 +258,7 @@ install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ - ( str( required_repository_name ), str( required_repository_owner ), str( required_repository_changeset_revision ) ) + ( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) ) raise Exception( message ) elif package_elem.tag == 'install': # <install version="1.0"> 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: Be explicit about track type for Bed, Gff/Gff3/Gtf datatypes.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b8beadc5221/ Changeset: 7b8beadc5221 User: jgoecks Date: 2013-04-19 18:28:32 Summary: Be explicit about track type for Bed, Gff/Gff3/Gtf datatypes. Affected #: 1 file diff -r 26d65c9289631a10b6f5913cd74a74112ea21dff -r 7b8beadc5221774104b396d34d069a41390bc553 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -354,7 +354,8 @@ class Bed( Interval ): """Tab delimited data in BED format""" file_ext = "bed" - data_sources = {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} + data_sources = { "data": "tabix", "index": "summary_tree", "feature_search": "fli" } + track_type = Interval.track_type """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -569,6 +570,7 @@ file_ext = "gff" column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] data_sources = { "data": "interval_index", "index": "summary_tree", "feature_search": "fli" } + track_type = Interval.track_type """Add metadata elements""" MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) @@ -787,6 +789,7 @@ valid_gff3_strand = ['+', '-', '.', '?'] valid_gff3_phase = ['.', '0', '1', '2'] column_names = [ 'Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Phase', 'Attributes' ] + track_type = Interval.track_type """Add metadata elements""" MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) @@ -891,6 +894,7 @@ """Tab delimited data in Gtf format""" file_ext = "gtf" column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Attributes' ] + track_type = Interval.track_type """Add metadata elements""" MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) 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: fixes for calculating variant track height.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26d65c928963/ Changeset: 26d65c928963 User: jgoecks Date: 2013-04-19 17:53:00 Summary: Trackster: fixes for calculating variant track height. Affected #: 2 files diff -r 49305f493a907e8fbb58c2a9c57c3e3565ed9ee8 -r 26d65c9289631a10b6f5913cd74a74112ea21dff static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1571,21 +1571,13 @@ return height; }, - get_required_height: function(rows_required, width) { + /** + * Returns required height to draw a particular number of samples in a given mode. + */ + get_required_height: function(num_samples) { var height = this.prefs.summary_height; if (this.prefs.show_sample_data) { - height += this.divider_height; - if (this.data.length !== 0) { - // Sample data is separated by commas, so this computes # of samples: - var comma_match = this.data[0][7].match(/,/g); - if ( comma_match === null ) { - comma_match = 1; - } - else { - comma_match = comma_match.length + 1; - } - height += ( comma_match * this.get_row_height() ); - } + height += this.divider_height + num_samples * this.get_row_height(); } return height; }, diff -r 49305f493a907e8fbb58c2a9c57c3e3565ed9ee8 -r 26d65c9289631a10b6f5913cd74a74112ea21dff static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4226,8 +4226,8 @@ return this.summary_draw_height; } else { - var dummy_painter = new (this.painter)(result.data, null, null, this.prefs, mode); - return dummy_painter.get_required_height(); + var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); + return dummy_painter.get_required_height(this.dataset.get_metadata('sample_names').length); } }, 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: 3 new changesets
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/49305f493a90/ Changeset: 49305f493a90 User: jgoecks Date: 2013-04-19 17:01:43 Summary: Automated merge. Affected #: 1 file diff -r 6f3b665ace6b76e02ac0a5651801667cca0f50b9 -r 49305f493a907e8fbb58c2a9c57c3e3565ed9ee8 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3293,20 +3293,25 @@ } } ].concat(TiledTrack.prototype.action_icons_def), + // HACK: CompositeTrack should inherit from DrawableCollection as well. /** * Returns representation of object in a dictionary for easy saving. * Use from_dict to recreate object. */ to_dict: DrawableCollection.prototype.to_dict, + add_drawable: DrawableCollection.prototype.add_drawable, + unpack_drawables: DrawableCollection.prototype.unpack_drawables, + change_mode: function(new_mode) { TiledTrack.prototype.change_mode.call(this, new_mode); for (var i = 0; i < this.drawables.length; i++) { this.drawables[i].change_mode(new_mode); } }, + /** * Initialize component tracks and draw composite track when all components are initialized. */ @@ -3324,13 +3329,16 @@ track.request_draw(); }); }, + update_icons: function() { // For now, hide filters and tool. this.action_icons.filters_icon.hide(); this.action_icons.tools_icon.hide(); this.action_icons.param_space_viz_icon.hide(); }, + can_draw: Drawable.prototype.can_draw, + draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, @@ -3443,6 +3451,7 @@ // Returned Deferred that is resolved when tile can be drawn. return can_draw; }, + /** * Replace this track with group that includes individual tracks. */ @@ -3464,6 +3473,7 @@ var index = this.container.replace_drawable(this, group, true); group.request_draw(); }, + /** * Actions taken before drawing a tile. */ @@ -3496,6 +3506,7 @@ track.prefs.max_value = max; } }, + /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. https://bitbucket.org/galaxy/galaxy-central/commits/6f3b665ace6b/ Changeset: 6f3b665ace6b User: jgoecks Date: 2013-04-19 16:56:44 Summary: Trackster: better handling of variant track labels. Affected #: 1 file diff -r 6faaa8a10977a1cb62682e6a8156b6dc85bc338c -r 6f3b665ace6b76e02ac0a5651801667cca0f50b9 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2940,6 +2940,28 @@ } }); } + + // + // If using SummaryTree tiles, show max and make it editable. + // + this.container_div.find(".yaxislabel").remove(); + var track = this, + first_tile = tiles[0]; + if (first_tile instanceof SummaryTreeTile) { + var max_val = (this.prefs.histogram_max ? this.prefs.histogram_max : first_tile.max_val), + max_label = $("<div/>").text(max_val).make_text_editable({ + num_cols: 12, + on_finish: function(new_val) { + $(".bs-tooltip").remove(); + var new_val = parseFloat(new_val); + track.prefs.histogram_max = (!isNaN(new_val) ? new_val : null); + track.tile_cache.clear(); + track.request_draw(); + }, + help_text: "Set max value; leave blank to use default" + }).addClass('yaxislabel top').css("color", this.prefs.label_color); + this.container_div.prepend(max_label); + } }, /** @@ -3924,30 +3946,9 @@ } // - // If using SummaryTree tiles, show max and make it editable. - // - this.container_div.find(".yaxislabel").remove(); - var first_tile = tiles[0]; - if (first_tile instanceof SummaryTreeTile) { - var max_val = (this.prefs.histogram_max ? this.prefs.histogram_max : first_tile.max_val), - max_label = $("<div/>").text(max_val).make_text_editable({ - num_cols: 12, - on_finish: function(new_val) { - $(".bs-tooltip").remove(); - var new_val = parseFloat(new_val); - track.prefs.histogram_max = (!isNaN(new_val) ? new_val : null); - track.tile_cache.clear(); - track.request_draw(); - }, - help_text: "Set max value; leave blank to use default" - }).addClass('yaxislabel top').css("color", this.prefs.label_color); - this.container_div.prepend(max_label); - } - - // // If not all features slotted, show icon for showing more rows (slots). // - if (first_tile instanceof FeatureTrackTile) { + if (tiles[0] instanceof FeatureTrackTile) { var all_slotted = true; for (i = 0; i < tiles.length; i++) { if (!tiles[i].all_slotted) { @@ -4234,17 +4235,17 @@ postdraw_actions: function(tiles, width, w_scale, clear_after) { TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after); - // Add labels if needed and not already included. - if (this.prefs.show_labels) { + // Add summary/sample labels if needed and not already included. + if ( !(tiles[0] instanceof SummaryTreeTile) && this.prefs.show_labels) { // Add and/or style labels. - if (this.container_div.find('.yaxislabel').length === 0) { + if (this.container_div.find('.yaxislabel.variant').length === 0) { // Add summary and sample labels. // FIXME: label attributes could be cleaner by using CSS classes. // Add summary label. var summary_div_font_size = 10, - summary_div = $("<div/>").text('Summary').addClass('yaxislabel top').css({ + summary_div = $("<div/>").text('Summary').addClass('yaxislabel variant top').css({ 'font-size': summary_div_font_size + 'px' }); this.container_div.prepend(summary_div); @@ -4260,7 +4261,7 @@ samples_div_html += (name + '<br>'); }); - var samples_div = $("<div/>").html(samples_div_html).addClass('yaxislabel top sample').css({ + var samples_div = $("<div/>").html(samples_div_html).addClass('yaxislabel variant top sample').css({ // +2 for padding 'top': base_offset + this.prefs.summary_height + 2, }); @@ -4278,7 +4279,7 @@ } else { // Remove all labels. - this.container_div.find('.yaxislabel').remove(); + this.container_div.find('.yaxislabel.variant').remove(); } } }); https://bitbucket.org/galaxy/galaxy-central/commits/833574121ea5/ Changeset: 833574121ea5 User: jgoecks Date: 2013-04-17 16:58:19 Summary: Whitespace additions. Affected #: 1 file diff -r da5a5077ef1ebffa9e0ad9039ca4463298815de1 -r 833574121ea51428ba393d932a6391244f2a3d04 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3271,20 +3271,25 @@ } } ].concat(TiledTrack.prototype.action_icons_def), + // HACK: CompositeTrack should inherit from DrawableCollection as well. /** * Returns representation of object in a dictionary for easy saving. * Use from_dict to recreate object. */ to_dict: DrawableCollection.prototype.to_dict, + add_drawable: DrawableCollection.prototype.add_drawable, + unpack_drawables: DrawableCollection.prototype.unpack_drawables, + change_mode: function(new_mode) { TiledTrack.prototype.change_mode.call(this, new_mode); for (var i = 0; i < this.drawables.length; i++) { this.drawables[i].change_mode(new_mode); } }, + /** * Initialize component tracks and draw composite track when all components are initialized. */ @@ -3302,13 +3307,16 @@ track.request_draw(); }); }, + update_icons: function() { // For now, hide filters and tool. this.action_icons.filters_icon.hide(); this.action_icons.tools_icon.hide(); this.action_icons.param_space_viz_icon.hide(); }, + can_draw: Drawable.prototype.can_draw, + draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, @@ -3421,6 +3429,7 @@ // Returned Deferred that is resolved when tile can be drawn. return can_draw; }, + /** * Replace this track with group that includes individual tracks. */ @@ -3442,6 +3451,7 @@ var index = this.container.replace_drawable(this, group, true); group.request_draw(); }, + /** * Actions taken before drawing a tile. */ @@ -3474,6 +3484,7 @@ track.prefs.max_value = max; } }, + /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. 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: Fixes for defining the location of the env.sh file for a dependent repository that contains a complex repository dependency definition.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6faaa8a10977/ Changeset: 6faaa8a10977 User: greg Date: 2013-04-19 16:47:27 Summary: Fixes for defining the location of the env.sh file for a dependent repository that contains a complex repository dependency definition. Affected #: 1 file diff -r b92d02a6f31562a664035adc8576cff6ce6987e9 -r 6faaa8a10977a1cb62682e6a8156b6dc85bc338c lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -1,3 +1,4 @@ +import logging import os import sys import subprocess @@ -20,6 +21,8 @@ from elementtree.ElementTree import Element from elementtree.ElementTree import SubElement +log = logging.getLogger( __name__ ) + def clean_tool_shed_url( base_url ): protocol, base = base_url.split( '://' ) return base.rstrip( '/' ) @@ -172,139 +175,141 @@ # The value of package_name should match the value of the "package" type in the tool config's <requirements> tag set, but it's not required. package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) - if package_name and package_version: - if tool_dependencies: - # Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository. - install_dir = get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - if not os.path.exists( install_dir ): - for package_elem in elem: - if package_elem.tag == 'repository': - # We have a complex repository dependency definition. - tool_shed = package_elem.attrib[ 'toolshed' ] - required_repository_name = package_elem.attrib[ 'name' ] - required_repository_owner = package_elem.attrib[ 'owner' ] - required_repository_changeset_revision = package_elem.attrib[ 'changeset_revision' ] - required_repository = get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, - tool_shed, - required_repository_name, - required_repository_owner, - required_repository_changeset_revision ) - tmp_filename = None - if required_repository: - # Set this repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. - # We can get everything we need from the discovered installed required_repository. - if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED, - app.model.ToolShedRepository.installation_status.INSTALLED ]: - # Define the installation directory for the required tool dependency in the required repository. - required_repository_package_install_dir = \ - get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - if not os.path.exists( required_repository_package_install_dir ): - print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) - repo_files_dir = required_repository.repo_files_directory( app ) - tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) - if tool_dependencies_config: - config_to_use = tool_dependencies_config - else: - message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ - ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) - raise Exception( message ) - else: - # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision - # should be updated if it's not current. - text = get_updated_changeset_revisions_from_tool_shed( app=app, - tool_shed_url=tool_shed, - name=required_repository_name, - owner=required_repository_owner, - changeset_revision=required_repository_changeset_revision ) - if text: - updated_changeset_revisions = listify( text ) - # The list of changeset revisions is in reverse order, so the newest will be first. - required_repository_changeset_revision = updated_changeset_revisions[ 0 ] - # Define the installation directory for the required tool dependency in the required repository. - required_repository_package_install_dir = \ - get_tool_dependency_install_dir( app=app, - repository_name=required_repository_name, - repository_owner=required_repository_owner, - repository_changeset_revision=required_repository_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. - tmp_filename = create_temporary_tool_dependencies_config( app, - tool_shed, - required_repository_name, - required_repository_owner, - required_repository_changeset_revision ) - config_to_use = tmp_filename - tool_dependency, actions_dict = populate_actions_dict( app=app, - dependent_install_dir=install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use ) - if tmp_filename: - try: - os.remove( tmp_filename ) - except: - pass - # Install and build the package via fabric. - install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) + if tool_dependencies and package_name and package_version: + for package_elem in elem: + if package_elem.tag == 'repository': + # We have a complex repository dependency definition. + tool_shed = package_elem.attrib[ 'toolshed' ] + required_repository_name = package_elem.attrib[ 'name' ] + required_repository_owner = package_elem.attrib[ 'owner' ] + required_repository_changeset_revision = package_elem.attrib[ 'changeset_revision' ] + required_repository = get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, + tool_shed, + required_repository_name, + required_repository_owner, + required_repository_changeset_revision ) + tmp_filename = None + if required_repository: + # Define the installation directory for the required tool dependency package in the required repository. + required_repository_package_install_dir = \ + get_tool_dependency_install_dir( app=app, + repository_name=required_repository_name, + repository_owner=required_repository_owner, + repository_changeset_revision=required_repository_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + # Define the this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the + # required repository's installed tool dependency package. + dependent_install_dir = get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. + # We can get everything we need from the discovered installed required_repository. + if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED, + app.model.ToolShedRepository.installation_status.INSTALLED ]: + if not os.path.exists( required_repository_package_install_dir ): + print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) + repo_files_dir = required_repository.repo_files_directory( app ) + tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) + if tool_dependencies_config: + config_to_use = tool_dependencies_config else: - message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ - ( str( required_repository_name ), str( required_repository_owner ), str( required_repository_changeset_revision ) ) + message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ + ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) raise Exception( message ) - elif package_elem.tag == 'install': - # <install version="1.0"> - package_install_version = package_elem.get( 'version', '1.0' ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) - if package_install_version == '1.0': - # Handle tool dependency installation using a fabric method included in the Galaxy framework. - for actions_elem in package_elem: - install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=package_name ) - sa_session.refresh( tool_dependency ) - if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: - print package_name, 'version', package_version, 'installed in', install_dir - elif package_elem.tag == 'readme': - # Nothing to be done. - continue - #elif package_elem.tag == 'proprietary_fabfile': - # # TODO: This is not yet supported or functionally correct... - # # Handle tool dependency installation where the repository includes one or more proprietary fabric scripts. - # if not fabric_version_checked: - # check_fabric_version() - # fabric_version_checked = True - # fabfile_name = package_elem.get( 'name', None ) - # proprietary_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) - # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path - else: - print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n' - tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, - tool_shed_repository, - package_name, - package_version, - 'package' ) - tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() + else: + # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision + # should be updated if it's not current. + text = get_updated_changeset_revisions_from_tool_shed( app=app, + tool_shed_url=tool_shed, + name=required_repository_name, + owner=required_repository_owner, + changeset_revision=required_repository_changeset_revision ) + if text: + updated_changeset_revisions = listify( text ) + # The list of changeset revisions is in reverse order, so the newest will be first. + required_repository_changeset_revision = updated_changeset_revisions[ 0 ] + # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. + tmp_filename = create_temporary_tool_dependencies_config( app, + tool_shed, + required_repository_name, + required_repository_owner, + required_repository_changeset_revision ) + config_to_use = tmp_filename + tool_dependency, actions_dict = populate_actions_dict( app=app, + dependent_install_dir=dependent_install_dir, + required_install_dir=required_repository_package_install_dir, + tool_shed_repository=tool_shed_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use ) + if tmp_filename: + try: + os.remove( tmp_filename ) + except: + pass + # Install and build the package via fabric. + install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) + else: + message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ + ( str( required_repository_name ), str( required_repository_owner ), str( required_repository_changeset_revision ) ) + raise Exception( message ) + elif package_elem.tag == 'install': + # <install version="1.0"> + # Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository. + install_dir = get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + if os.path.exists( install_dir ): + print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n' + tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + tool_shed_repository, + package_name, + package_version, + 'package' ) + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() + + + + else: + package_install_version = package_elem.get( 'version', '1.0' ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) + if package_install_version == '1.0': + # Handle tool dependency installation using a fabric method included in the Galaxy framework. + for actions_elem in package_elem: + install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=package_name ) + sa_session.refresh( tool_dependency ) + if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: + print package_name, 'version', package_version, 'installed in', install_dir + elif package_elem.tag == 'readme': + # Nothing to be done. + continue + #elif package_elem.tag == 'proprietary_fabfile': + # # TODO: This is not yet supported or functionally correct... + # # Handle tool dependency installation where the repository includes one or more proprietary fabric scripts. + # if not fabric_version_checked: + # check_fabric_version() + # fabric_version_checked = True + # fabfile_name = package_elem.get( 'name', None ) + # proprietary_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) + # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path return tool_dependency def install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=None, proprietary_fabfile_path=None, **kwd ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: White space and import changes to comply with new Galaxy dev team standards.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b92d02a6f315/ Changeset: b92d02a6f315 User: greg Date: 2013-04-19 16:45:04 Summary: White space and import changes to comply with new Galaxy dev team standards. Affected #: 1 file diff -r a80175a97194630c1c668d3bad3cb8891d8ac219 -r b92d02a6f31562a664035adc8576cff6ce6987e9 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -1,9 +1,12 @@ # For Python 2.5 from __future__ import with_statement -import os, shutil, tempfile +import common_util +import logging +import os +import shutil +import tempfile from contextlib import contextmanager -import common_util from galaxy import eggs import pkg_resources @@ -11,7 +14,12 @@ pkg_resources.require('ssh' ) pkg_resources.require( 'Fabric' ) -from fabric.api import env, lcd, local, settings +from fabric.api import env +from fabric.api import lcd +from fabric.api import local +from fabric.api import settings + +log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' @@ -19,6 +27,7 @@ version = env.version if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) + def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): """General Galaxy environment configuration""" env.user = galaxy_user @@ -28,12 +37,14 @@ env.use_sudo = False env.safe_cmd = local return env + @contextmanager def make_tmp_dir(): work_dir = tempfile.mkdtemp() yield work_dir if os.path.exists( work_dir ): local( 'rm -rf %s' % work_dir ) + def handle_command( app, tool_dependency, install_dir, cmd ): sa_session = app.model.context.current output = local( cmd, capture=True ) @@ -44,6 +55,7 @@ sa_session.add( tool_dependency ) sa_session.flush() return output.return_code + def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" sa_session = app.model.context.current @@ -126,6 +138,7 @@ return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) if return_code: return + def log_results( command, fabric_AttributeString, file_path ): """ Write attributes of fabric.operations._AttributeString (which is the output of executing command using fabric's local() method) 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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