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/
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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/
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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/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a80175a97194/
Changeset: a80175a97194
User: inithello
Date: 2013-04-19 15:33:45
Summary: Fix issue where only failures were being reported, not errors.
Affected #: 1 file
diff -r 8e78d456456f5d3cf651a6e5f2dac53e9566034f -r a80175a97194630c1c668d3bad3cb8891d8ac219 test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -694,7 +694,7 @@
log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( changeset_revision, name ) )
else:
# If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API.
- for failure in result.failures:
+ for failure in result.failures + result.errors:
# Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing.
test_id = str( failure[0] )
tool_id, tool_version = get_tool_info_from_test_id( test_id )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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