galaxy-commits November 2013

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commit/galaxy-central: jmchilton: Re-fix tool API for uploads coming through nginx.
by commits-noreply＠bitbucket.org 19 Nov '13

19 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/facb9f9d2ee4/ Changeset: facb9f9d2ee4 User: jmchilton Date: 2013-11-19 04:26:29 Summary: Re-fix tool API for uploads coming through nginx. Give tools.get_incoming_value a chance to mangle all keys and see if they appear in some other format. Thanks to @natefoo for detecting the problem, determining the source of the error, and describing the exact path through the code - i.e. doing all the work. Affected #: 1 file diff -r b0535b4864b4bf542e31af7acc027fcbb5a00a54 -r facb9f9d2ee4d614d21e4fc1a4a6d99f2668349a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2083,19 +2083,11 @@ if any_group_errors: errors[input.name] = group_errors else: - if key not in incoming \ - and "__force_update__" + key not in incoming: - # No new value provided, and we are only updating, so keep - # the old value (which should already be in the state) and - # preserve the old error message. - pass - else: - incoming_value = get_incoming_value( incoming, key, None ) - value, error = check_param( trans, input, incoming_value, context, source=source ) - # If a callback was provided, allow it to process the value - if error: - errors[ input.name ] = error - state[ input.name ] = value + incoming_value = get_incoming_value( incoming, key, None ) + value, error = check_param( trans, input, incoming_value, context, source=source ) + if error: + errors[ input.name ] = error + state[ input.name ] = value return errors def update_state( self, trans, inputs, state, incoming, source='html', prefix="", context=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: guerler: Toolshed: Fix grids
by commits-noreply＠bitbucket.org 19 Nov '13

19 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b0535b4864b4/ Changeset: b0535b4864b4 User: guerler Date: 2013-11-18 22:02:41 Summary: Toolshed: Fix grids Affected #: 2 files diff -r 32acc00ca229951afbd659281f57d93a47bcab06 -r b0535b4864b4bf542e31af7acc027fcbb5a00a54 templates/webapps/tool_shed/category/grid.mako --- a/templates/webapps/tool_shed/category/grid.mako +++ b/templates/webapps/tool_shed/category/grid.mako @@ -6,6 +6,7 @@ ## Render grid header. ## TODO: This is very similar to this directory's valid_grid.mako, so see if we can re-use this code in a better way. <%def name="render_grid_header( grid, repo_grid, render_title=True)"> + ${init()} <div class="grid-header"> %if render_title: ${grid_title()} diff -r 32acc00ca229951afbd659281f57d93a47bcab06 -r b0535b4864b4bf542e31af7acc027fcbb5a00a54 templates/webapps/tool_shed/category/valid_grid.mako --- a/templates/webapps/tool_shed/category/valid_grid.mako +++ b/templates/webapps/tool_shed/category/valid_grid.mako @@ -5,6 +5,7 @@ ## Render grid header. <%def name="render_grid_header( grid, repo_grid, render_title=True)"> + ${init()} <div class="grid-header"> %if render_title: ${grid_title()} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Nov '13

19 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe8bb4e8e3a1/ Changeset: fe8bb4e8e3a1 User: jgoecks Date: 2013-11-18 20:18:10 Summary: Trackster painters: rename y_center variable to y_start to reflect real position. Affected #: 1 file diff -r c0eb0f44b7fe80fdcb6590c4364312bbdcb286b0 -r fe8bb4e8e3a122930548c03c899fcdcaff52f484 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -466,7 +466,7 @@ f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), draw_start = f_start, draw_end = f_end, - y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width), + y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width), thickness, y_start, thick_start = null, thick_end = null, // TODO: is there any reason why block, label color cannot be set at the Painter level? // For now, assume '.' === '+' @@ -484,7 +484,7 @@ if (mode === "no_detail") { // No details for feature, so only one way to display. ctx.fillStyle = block_color; - ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT); + ctx.fillRect(f_start, y_start + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT); } else { // Mode is either Squish or Pack: // Feature details. @@ -517,7 +517,7 @@ if (!feature_blocks) { // If there are no blocks, treat the feature as one big exon. ctx.fillStyle = block_color; - ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height); + ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height); // If strand is specified, draw arrows over feature if ( feature_strand && full_height ) { if (feature_strand === "+") { @@ -525,7 +525,7 @@ } else if (feature_strand === "-") { ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' ); } - ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height); + ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height); } } else { // @@ -536,19 +536,19 @@ // a block, is visible. // - // Compute y axis center position and height - var cur_y_center, cur_height; + // Compute y axis start position and height + var cur_y_start, cur_height; if (mode === "Squish" || mode === "Dense") { - cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; + cur_y_start = y_start + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } else { // mode === "Pack" if (feature_strand) { - cur_y_center = y_center; + cur_y_start = y_start; cur_height = thick_height; } else { - cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1; + cur_y_start += (SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } } @@ -570,7 +570,7 @@ ctx.fillStyle = CONNECTOR_COLOR; } } - ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height); + ctx.fillRect(f_start, cur_y_start, f_end - f_start, cur_height); } // Draw blocks. @@ -587,14 +587,14 @@ // Draw thin block. ctx.fillStyle = block_color; - ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height); + ctx.fillRect(block_start, y_start + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height); // If block intersects with thick region, draw block as thick. // - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case if (thick_start !== undefined && feature_te > feature_ts && !(block_start > thick_end || block_end < thick_start) ) { var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height); + ctx.fillRect(block_thick_start, y_start + 1, block_thick_end - block_thick_start, thick_height); if ( feature_blocks.length === 1 && mode === "Pack") { // Exactly one block means we have no introns, but do have a distinct "thick" region, // draw arrows over it if in pack mode. @@ -608,12 +608,12 @@ block_thick_start += 2; block_thick_end -= 2; } - ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height); + ctx.fillRect(block_thick_start, y_start + 1, block_thick_end - block_thick_start, thick_height); } } // Draw individual connectors if required if ( this.draw_individual_connectors && last_block_start ) { - this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_center ); + this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_start ); } last_block_start = block_start; last_block_end = block_end; @@ -632,8 +632,8 @@ new_height = Math.ceil(thick_height * hscale_factor), ws_height = Math.round( (thick_height-new_height)/2 ); if (hscale_factor !== 1) { - ctx.fillRect(f_start, cur_y_center + 1, f_end - f_start, ws_height); - ctx.fillRect(f_start, cur_y_center + thick_height - ws_height + 1, f_end - f_start, ws_height); + ctx.fillRect(f_start, cur_y_start + 1, f_end - f_start, ws_height); + ctx.fillRect(f_start, cur_y_start + thick_height - ws_height + 1, f_end - f_start, ws_height); } } } @@ -647,11 +647,11 @@ // FIXME: assumption here that the entire view starts at 0 if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); draw_end += ctx.measureText(feature_name).width + LABEL_SPACING; } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING; } //ctx.fillStyle = block_color; @@ -741,7 +741,7 @@ /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, read_seq) { + draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) { ctx.textAlign = "center"; var tile_region = [tile_low, tile_high], base_offset = 0, @@ -793,7 +793,7 @@ // Draw read base as rectangle. ctx.fillStyle = block_color; ctx.fillRect(s_start, - y_center + (pack_mode ? 1 : 4 ), + y_start + (pack_mode ? 1 : 4 ), s_end - s_start, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); @@ -824,12 +824,12 @@ var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); ctx.fillStyle = this.base_color_fn(seq[c]); if (pack_mode && w_scale > char_width_px) { - ctx.fillText(seq[c], c_start, y_center + 9); + ctx.fillText(seq[c], c_start, y_start + 9); } // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. else if (w_scale > 0.05) { ctx.fillRect(c_start - gap, - y_center + (pack_mode ? 1 : 4), + y_start + (pack_mode ? 1 : 4), Math.max( 1, Math.round(w_scale) ), (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); } @@ -843,12 +843,12 @@ break; case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start, y_center + 5, s_end - s_start, 1); - //ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5); + ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1); + //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5); base_offset += cig_len; break; case "D": // Deletion. - paint_utils.draw_deletion(s_start, y_center, 1); + paint_utils.draw_deletion(s_start, y_start, 1); base_offset += cig_len; break; case "P": // TODO: No good way to draw insertions/padding right now, so ignore @@ -874,8 +874,8 @@ if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; - ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); - draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]}; + ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9); + draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]}; ctx.fillStyle = CONNECTOR_COLOR; // Based on overlap b/t sequence and tile, get sequence to be drawn. switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) { @@ -895,21 +895,21 @@ // Draw sequence. for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center); + ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start); } } else { // Draw block. ctx.fillStyle = "yellow"; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5), + ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5), s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); } } else { if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. - draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); + draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } ); } else { // TODO: probably can merge this case with code above. @@ -955,7 +955,7 @@ // -0.5 to put element between bases. f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), - y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, + y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, label_color = this.prefs.label_color; @@ -966,7 +966,7 @@ // Draw left/forward read. if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]); + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]); } else { connector = false; @@ -974,7 +974,7 @@ // Draw right/reverse read. if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]); + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]); } else { connector = false; @@ -989,21 +989,21 @@ b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) ); if (connector && b2_start > b1_end) { ctx.fillStyle = CONNECTOR_COLOR; - dashedLine(ctx, b1_end, y_center + 5, b2_start, y_center + 5); + dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5); } } else { // Read is single. - this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); } if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") { // Draw label. ctx.fillStyle = this.prefs.label_color; if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); } } @@ -1024,7 +1024,7 @@ /** * Draw a single read from reference-based read sequence and cigar. */ - draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, read_seq) { + draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) { ctx.textAlign = "center"; var tile_region = [tile_low, tile_high], base_offset = 0, @@ -1063,7 +1063,7 @@ // Draw read base as rectangle. ctx.fillStyle = block_color; ctx.fillRect(s_start, - y_center + (pack_mode ? 1 : 4 ), + y_start + (pack_mode ? 1 : 4 ), s_end - s_start, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); } @@ -1130,12 +1130,12 @@ var c_start = Math.floor( Math.max(0, (start_pos + c - tile_low) * w_scale) ); ctx.fillStyle = this.base_color_fn(cur_seq[c]); if (pack_mode && w_scale > char_width_px) { - ctx.fillText(cur_seq[c], c_start, y_center + 9); + ctx.fillText(cur_seq[c], c_start, y_start + 9); } // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. else if (w_scale > 0.05) { ctx.fillRect(c_start - gap, - y_center + (pack_mode ? 1 : 4), + y_start + (pack_mode ? 1 : 4), Math.max( 1, Math.round(w_scale) ), (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); } @@ -1150,14 +1150,14 @@ break; case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start, y_center + 5, s_end - s_start, 1); - //ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5); + ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1); + //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5); // No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; case "D": // Deletion. ctx.fillStyle = "black"; - ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3); + ctx.fillRect(s_start, y_start + 4, s_end - s_start, 3); base_offset += cig_len; break; case "I": // Insertion. @@ -1180,8 +1180,8 @@ if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; - ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); - draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]}; + ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9); + draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]}; ctx.fillStyle = CONNECTOR_COLOR; // Based on overlap b/t sequence and tile, get sequence to be drawn. switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) { @@ -1201,21 +1201,21 @@ // Draw sequence. for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center); + ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start); } } else { // Draw block. ctx.fillStyle = "yellow"; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5), + ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5), s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); } } else { if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. - draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); + draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } ); } else { // TODO: probably can merge this case with code above. @@ -1275,7 +1275,7 @@ return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) ); }, - draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_center ) { + draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_start ) { // Arc drawing -- from closest endpoints var x_center = ( block1_end + block2_start ) / 2, radius = block2_start - x_center; @@ -1283,7 +1283,7 @@ var angle1 = Math.PI, angle2 = 0; if ( radius > 0 ) { ctx.beginPath(); - ctx.arc( x_center, y_center, block2_start - x_center, Math.PI, 0 ); + ctx.arc( x_center, y_start, block2_start - x_center, Math.PI, 0 ); ctx.stroke(); } } https://bitbucket.org/galaxy/galaxy-central/commits/32acc00ca229/ Changeset: 32acc00ca229 User: jgoecks Date: 2013-11-18 21:57:15 Summary: Trackster: more improvements for drawing deletions in read and variant track. Affected #: 1 file diff -r fe8bb4e8e3a122930548c03c899fcdcaff52f484 -r 32acc00ca229951afbd659281f57d93a47bcab06 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -750,7 +750,7 @@ char_width_px = ctx.canvas.manager.char_width_px, block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color), pack_mode = (mode === 'Pack'), - paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale); + paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale, mode); // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -770,6 +770,10 @@ // -0.5 to offset sequence between bases. s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); + + if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) { + continue; + } // Make sure that read is drawn even if it too small to be rendered officially; in this case, // read is drawn at 1px. @@ -789,55 +793,54 @@ case "M": // Loose match with reference; can be match or mismatch. case "=": // Strict match with reference. case "X": // Strict mismatch with reference. - if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - // Draw read base as rectangle. - ctx.fillStyle = block_color; - ctx.fillRect(s_start, - y_start + (pack_mode ? 1 : 4 ), - s_end - s_start, - (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); + // Draw read base as rectangle. + ctx.fillStyle = block_color; + ctx.fillRect(s_start, + y_start + (pack_mode ? 1 : 4 ), + s_end - s_start, + (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); - // Draw sequence and/or variants. - var seq = read_seq.slice(seq_offset, seq_offset + cig_len), - ref_char, - read_char; - for (var c = 0, str_len = seq.length; c < str_len; c++) { - // Draw base if it's on tile: - if (seq_start + c >= tile_low && seq_start + c <= tile_high) { - // Get reference and read character. - ref_char = (this.ref_seq ? this.ref_seq[seq_start - tile_low + c] : null); - read_char = seq[c]; + // Draw sequence and/or variants. + var seq = read_seq.slice(seq_offset, seq_offset + cig_len), + ref_char, + read_char; + for (var c = 0, str_len = seq.length; c < str_len; c++) { + // Draw base if it's on tile: + if (seq_start + c >= tile_low && seq_start + c <= tile_high) { + // Get reference and read character. + ref_char = (this.ref_seq ? this.ref_seq[seq_start - tile_low + c] : null); + read_char = seq[c]; - // Draw base depending on (a) available reference data and (b) config options. - if ( - // If there's reference data and (a) showing all (i.e. not showing - // differences) or (b) if there is a variant. - (ref_char && - (!this.prefs.show_differences || - (read_char.toLowerCase !== 'n' && (ref_char.toLowerCase() !== read_char.toLowerCase()))) - ) || - // If there's no reference data and showing all. - (!ref_char && !this.prefs.show_differences) - ) { + // Draw base depending on (a) available reference data and (b) config options. + if ( + // If there's reference data and (a) showing all (i.e. not showing + // differences) or (b) if there is a variant. + (ref_char && + (!this.prefs.show_differences || + (read_char.toLowerCase !== 'n' && (ref_char.toLowerCase() !== read_char.toLowerCase()))) + ) || + // If there's no reference data and showing all. + (!ref_char && !this.prefs.show_differences) + ) { - // Draw base. - var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillStyle = this.base_color_fn(seq[c]); - if (pack_mode && w_scale > char_width_px) { - ctx.fillText(seq[c], c_start, y_start + 9); - } - // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. - else if (w_scale > 0.05) { - ctx.fillRect(c_start - gap, - y_start + (pack_mode ? 1 : 4), - Math.max( 1, Math.round(w_scale) ), - (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); - } + // Draw base. + var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); + ctx.fillStyle = this.base_color_fn(seq[c]); + if (pack_mode && w_scale > char_width_px) { + ctx.fillText(seq[c], c_start, y_start + 9); } + // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. + else if (w_scale > 0.05) { + ctx.fillRect(c_start - gap, + y_start + (pack_mode ? 1 : 4), + Math.max( 1, Math.round(w_scale) ), + (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); + } + } - } } } + seq_offset += cig_len; base_offset += cig_len; break; @@ -1033,6 +1036,7 @@ char_width_px = ctx.canvas.manager.char_width_px, block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color), pack_mode = (mode === 'Pack'), + paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale, mode), drawing_blocks = []; // Keep list of items that need to be drawn on top of initial drawing layer. @@ -1074,11 +1078,15 @@ var cig = cigar[cig_id], cig_op = "MIDNSHP=X"[ cig[0] ], cig_len = cig[1]; - + var seq_start = feature_start + base_offset, // -0.5 to offset sequence between bases. s_start = Math.floor( Math.max(0, -0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); + + if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) { + continue; + } // Make sure that read is drawn even if it too small to be rendered officially; in this case, // read is drawn at 1px. @@ -1100,45 +1108,43 @@ break; case "=": // Match with reference. case "X": // Mismatch with reference. - if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - // - // Draw sequence and/or variants. - // + // + // Draw sequence and/or variants. + // - // Get sequence to draw. - var cur_seq = ''; - if (cig_op === 'X') { - // Get sequence from read_seq. - cur_seq = read_seq.slice(seq_offset, seq_offset + cig_len); - } - else if (this.ref_seq) { // && cig_op === '=' - // Use reference sequence. - cur_seq = this.ref_seq.slice( - // If read starts after tile start, slice at read start. - Math.max(0, seq_start - tile_low), - // If read ends before tile end, slice at read end. - Math.min(seq_start - tile_low + cig_len, tile_high - tile_low) - ); - } + // Get sequence to draw. + var cur_seq = ''; + if (cig_op === 'X') { + // Get sequence from read_seq. + cur_seq = read_seq.slice(seq_offset, seq_offset + cig_len); + } + else if (this.ref_seq) { // && cig_op === '=' + // Use reference sequence. + cur_seq = this.ref_seq.slice( + // If read starts after tile start, slice at read start. + Math.max(0, seq_start - tile_low), + // If read ends before tile end, slice at read end. + Math.min(seq_start - tile_low + cig_len, tile_high - tile_low) + ); + } - // Draw sequence. Because cur_seq starts and read/tile start, go to there to start writing. - var start_pos = Math.max(seq_start, tile_low); - for (var c = 0; c < cur_seq.length; c++) { - // Draw base if showing all (i.e. not showing differences) or there is a mismatch. - if (cur_seq && !this.prefs.show_differences || cig_op === 'X') { - // Draw base. - var c_start = Math.floor( Math.max(0, (start_pos + c - tile_low) * w_scale) ); - ctx.fillStyle = this.base_color_fn(cur_seq[c]); - if (pack_mode && w_scale > char_width_px) { - ctx.fillText(cur_seq[c], c_start, y_start + 9); - } - // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. - else if (w_scale > 0.05) { - ctx.fillRect(c_start - gap, - y_start + (pack_mode ? 1 : 4), - Math.max( 1, Math.round(w_scale) ), - (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); - } + // Draw sequence. Because cur_seq starts and read/tile start, go to there to start writing. + var start_pos = Math.max(seq_start, tile_low); + for (var c = 0; c < cur_seq.length; c++) { + // Draw base if showing all (i.e. not showing differences) or there is a mismatch. + if (cur_seq && !this.prefs.show_differences || cig_op === 'X') { + // Draw base. + var c_start = Math.floor( Math.max(0, (start_pos + c - tile_low) * w_scale) ); + ctx.fillStyle = this.base_color_fn(cur_seq[c]); + if (pack_mode && w_scale > char_width_px) { + ctx.fillText(cur_seq[c], c_start, y_start + 9); + } + // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. + else if (w_scale > 0.05) { + ctx.fillRect(c_start - gap, + y_start + (pack_mode ? 1 : 4), + Math.max( 1, Math.round(w_scale) ), + (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); } } } @@ -1156,8 +1162,7 @@ base_offset += cig_len; break; case "D": // Deletion. - ctx.fillStyle = "black"; - ctx.fillRect(s_start, y_start + 4, s_end - s_start, 3); + paint_utils.draw_deletion(s_start, y_start + (pack_mode ? 1 : 4), cig_len); base_offset += cig_len; break; case "I": // Insertion. @@ -1509,21 +1514,24 @@ /** * Utilities for painting reads. */ -var ReadPainterUtils = function(ctx, row_height, char_width) { +var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) { this.ctx = ctx; this.row_height = row_height; - this.char_width = char_width; + this.px_per_base = px_per_base; + this.draw_details = (mode === 'Pack' || mode === 'Auto') && (px_per_base >= ctx.canvas.manager.char_width_px); + this.delete_details_thickness = 0.2; }; extend(ReadPainterUtils.prototype, { /** - * Draw deletion of base(s). + * Draw deletion of base(s). + * @param draw_detail if true, drawing in detail and deletion is drawn more subtly */ draw_deletion: function(x, y, len) { this.ctx.fillStyle = "black"; - var thickness = Math.max( 0.25 * this.row_height, 1 ); + var thickness = (this.draw_details ? this.delete_details_thickness : 1) * this.row_height; y += 0.5 * ( this.row_height - thickness ); - this.ctx.fillRect( x, y + 4, len * this.char_width, thickness); + this.ctx.fillRect(x, y, len * this.px_per_base, thickness); } }); @@ -1631,7 +1639,7 @@ (this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT) ), draw_summary = true, - paint_utils = new ReadPainterUtils(ctx, row_height, base_px), + paint_utils = new ReadPainterUtils(ctx, row_height, w_scale, this.mode), j; // If there's a single sample, update drawing variables. @@ -1738,15 +1746,15 @@ if (variant.type === 'snp') { var snp = variant.value; ctx.fillStyle = this.base_color_fn(snp); - if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { - ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + if (paint_utils.draw_details) { + ctx.fillText(snp, char_x_start, draw_y_start + row_height); } else { - ctx.fillText(snp, char_x_start, draw_y_start + row_height); + ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); } } else if (variant.type === 'deletion') { - paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start, variant.len); + paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start + 1, variant.len); } else { // TODO: handle insertions. 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commit/galaxy-central: jgoecks: Trackster: add support for detecting and drawing deletions in VCF datasets. Create shared read painter utils that are used by multiple painters.
by commits-noreply＠bitbucket.org 19 Nov '13

19 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c0eb0f44b7fe/ Changeset: c0eb0f44b7fe User: jgoecks Date: 2013-11-18 19:55:43 Summary: Trackster: add support for detecting and drawing deletions in VCF datasets. Create shared read painter utils that are used by multiple painters. Affected #: 1 file diff -r a0120448a28eeda50a0476a6d46da74ad3afa484 -r c0eb0f44b7fe80fdcb6590c4364312bbdcb286b0 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -749,7 +749,8 @@ gap = Math.round(w_scale/2), char_width_px = ctx.canvas.manager.char_width_px, block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color), - pack_mode = (mode === 'Pack'); + pack_mode = (mode === 'Pack'), + paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale); // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -847,8 +848,7 @@ base_offset += cig_len; break; case "D": // Deletion. - ctx.fillStyle = "black"; - ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3); + paint_utils.draw_deletion(s_start, y_center, 1); base_offset += cig_len; break; case "P": // TODO: No good way to draw insertions/padding right now, so ignore @@ -1507,6 +1507,27 @@ }; /** + * Utilities for painting reads. + */ +var ReadPainterUtils = function(ctx, row_height, char_width) { + this.ctx = ctx; + this.row_height = row_height; + this.char_width = char_width; +}; + +extend(ReadPainterUtils.prototype, { + /** + * Draw deletion of base(s). + */ + draw_deletion: function(x, y, len) { + this.ctx.fillStyle = "black"; + var thickness = Math.max( 0.25 * this.row_height, 1 ); + y += 0.5 * ( this.row_height - thickness ); + this.ctx.fillRect( x, y + 4, len * this.char_width, thickness); + } +}); + +/** * Paints variant data onto canvas. */ var VariantPainter = function(data, view_start, view_end, prefs, mode, base_color_fn) { @@ -1556,6 +1577,34 @@ draw: function(ctx, width, height, w_scale) { ctx.save(); + // Functions for detection insertions (TODO) and deletions. + + /** Returns dictionary of information about a deletion; returns null if there no deletion. + * Dict attributes: + * -start: where the deletion starts relative to reference start + * -len: how long the deletion is + */ + var get_deletion_info = function(ref, alt) { + var ref_len = ref.length, + alt_len = alt.length, + start = 0, + len = 1, + is_delete = false; + if (alt === '-') { + is_delete = true; + len = ref.length; + } + else if (ref.indexOf(alt) === 0 && ref_len > alt_len) { + is_delete = true; + len = ref_len = alt_len; + start += alt_len; + } + + return ( is_delete ? { start: start, len: len } : null ); + }; + + + // Draw. var locus_data, pos, id, @@ -1582,6 +1631,7 @@ (this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT) ), draw_summary = true, + paint_utils = new ReadPainterUtils(ctx, row_height, base_px), j; // If there's a single sample, update drawing variables. @@ -1605,10 +1655,31 @@ // Get locus data. locus_data = this.data[i]; pos = locus_data[1]; - alt = locus_data[4].split(','); + ref = locus_data[3]; + alt = [ locus_data[4].split(',') ]; sample_gts = locus_data[7].split(','); allele_counts = locus_data.slice(8); + // Process alterate values to derive information about each alt. + alt = _.map(_.flatten(alt), function(a) { + var type, + alt_info = {}, + delete_info = get_deletion_info(ref, a); + if (delete_info) { + type = 'deletion'; + _.extend(alt_info, delete_info); + } + // TODO: test for insertion. + else { // SNP. + type = 'snp'; + } + + return _.extend(alt_info, { + type: type, + value: a, + }); + }); + // Only draw locus data if it's in viewing region. if (pos < this.view_start || pos > this.view_end) { continue; @@ -1627,7 +1698,7 @@ draw_y_start = this.prefs.summary_height; // Draw allele fractions onto summary. for (j = 0; j < alt.length; j++) { - ctx.fillStyle = this.base_color_fn(alt[j]); + ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) ); allele_frac = allele_counts / sample_gts.length; draw_height = Math.ceil(this.prefs.summary_height * allele_frac); ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height); @@ -1664,12 +1735,21 @@ // If there's a variant, draw it. if (variant) { - ctx.fillStyle = this.base_color_fn(variant); - if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { - ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + if (variant.type === 'snp') { + var snp = variant.value; + ctx.fillStyle = this.base_color_fn(snp); + if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { + ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + } + else { + ctx.fillText(snp, char_x_start, draw_y_start + row_height); + } + } + else if (variant.type === 'deletion') { + paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start, variant.len); } else { - ctx.fillText(variant, char_x_start, draw_y_start + row_height); + // TODO: handle insertions. } } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: ensure tooltip deletion on hda view removal, add class selectors for primary action buttons; pack scripts
by commits-noreply＠bitbucket.org 19 Nov '13

19 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0120448a28e/ Changeset: a0120448a28e User: carlfeberhard Date: 2013-11-18 18:39:52 Summary: History panel: ensure tooltip deletion on hda view removal, add class selectors for primary action buttons; pack scripts Affected #: 4 files diff -r 3ebc0f5c4486cc5c207882bcea819018d23b2bf4 -r a0120448a28eeda50a0476a6d46da74ad3afa484 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -149,8 +149,8 @@ } var displayBtnData = { - icon_class : 'display', - target : 'galaxy_main' + target : 'galaxy_main', + classes : 'dataset-display' }; // show a disabled display if the data's been purged diff -r 3ebc0f5c4486cc5c207882bcea819018d23b2bf4 -r a0120448a28eeda50a0476a6d46da74ad3afa484 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -69,7 +69,7 @@ title : _l( 'Edit Attributes' ), href : this.urls.edit, target : 'galaxy_main', - icon_class : 'edit' + classes : 'dataset-edit' }; // disable if purged or deleted and explain why in the tooltip @@ -102,21 +102,18 @@ } var self = this, - delete_url = self.urls[ 'delete' ], deleteBtnData = { title : _l( 'Delete' ), - href : delete_url, - icon_class : 'delete', - onclick : function() { + classes : 'dataset-delete', + onclick : function() { // ...bler... tooltips being left behind in DOM (hover out never called on deletion) - self.$el.find( '.menu-button.delete' ).trigger( 'mouseout' ); + self.$el.find( '.icon-btn.dataset-delete' ).trigger( 'mouseout' ); self.model[ 'delete' ](); } }; if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { title : _l( 'Dataset is already deleted' ), - icon_class : 'delete', disabled : true }; } diff -r 3ebc0f5c4486cc5c207882bcea819018d23b2bf4 -r a0120448a28eeda50a0476a6d46da74ad3afa484 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:"galaxy_main",classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff -r 3ebc0f5c4486cc5c207882bcea819018d23b2bf4 -r a0120448a28eeda50a0476a6d46da74ad3afa484 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"},confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="galaxy_main">?</a>').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"},confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 18 Nov '13

18 Nov '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40d2e69e89a3/ Changeset: 40d2e69e89a3 User: jmchilton Date: 2013-11-18 07:51:54 Summary: Redo fix from 8b65e61 so it works when no Twill clicking at all occurs (e.g. all default params used). Affected #: 1 file diff -r 64cb656e95b2f40ac5f6f1f26fc484ce88a11ad1 -r 40d2e69e89a3210d1760851ea8563e1e344a0c3f test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1356,11 +1356,11 @@ tool_id = tool_id.replace(" ", "+") """Runs the tool 'tool_id' and passes it the key/values from the *kwd""" self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) ) + # Must click somewhere in tool_form, to disambiguate what form + # is being targetted. + tc.browser.clicked( tc.browser.get_form( 'tool_form' ), None ) if repeat_name is not None: repeat_button = '%s_add' % repeat_name - # Must click somewhere in tool_form, to disambiguate what form - # is being targetted. - tc.browser.clicked( tc.browser.get_form( 'tool_form' ), None ) # Submit the "repeat" form button to add an input) tc.submit( repeat_button ) tc.find( 'runtool_btn' ) https://bitbucket.org/galaxy/galaxy-central/commits/59a0ca3d48c0/ Changeset: 59a0ca3d48c0 User: jmchilton Date: 2013-11-18 07:51:54 Summary: PEP-8 fixes related to tool test parsing. Affected #: 2 files diff -r 40d2e69e89a3210d1760851ea8563e1e344a0c3f -r 59a0ca3d48c019c017d85fc780239837b2e5453d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1574,7 +1574,7 @@ # history, but we'll keep it unique per set of tests composite_data_names_counter = 0 for i, test_elem in enumerate( tests_elem.findall( 'test' ) ): - name = test_elem.get( 'name', 'Test-%d' % (i+1) ) + name = test_elem.get( 'name', 'Test-%d' % (i + 1) ) maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) test = ToolTestBuilder( self, name, maxseconds ) try: @@ -1625,6 +1625,7 @@ raise Exception( "Test output does not have a 'name'" ) assert_elem = output_elem.find("assert_contents") assert_list = None + # Trying to keep testing patch as localized as # possible, this function should be relocated # somewhere more conventional. @@ -1636,7 +1637,7 @@ converted_children = [] for child_elem in child_elems: converted_children.append( convert_elem(child_elem) ) - return {"tag" : tag, "attributes" : attributes, "children" : converted_children} + return {"tag": tag, "attributes": attributes, "children": converted_children} if assert_elem is not None: assert_list = [] for assert_child in list(assert_elem): @@ -1677,6 +1678,7 @@ test.error = True test.exception = e self.tests.append( test ) + def parse_input_page( self, input_elem, enctypes ): """ Parse a page of inputs. This basically just calls 'parse_input_elem', diff -r 40d2e69e89a3210d1760851ea8563e1e344a0c3f -r 59a0ca3d48c019c017d85fc780239837b2e5453d lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -1,20 +1,18 @@ -import new, sys import os.path -import galaxy.util -import parameters from parameters import basic from parameters import grouping -from elementtree.ElementTree import XML import logging log = logging.getLogger( __name__ ) + class ToolTestBuilder( object ): """ Encapsulates information about a tool test, and allows creation of a dynamic TestCase class (the unittest framework is very class oriented, doing dynamic tests in this way allows better integration) """ + def __init__( self, tool, name, maxseconds ): self.tool = tool self.name = name @@ -24,6 +22,7 @@ self.outputs = [] self.error = False self.exception = None + def add_param( self, name, value, extra ): try: if name not in self.tool.inputs: @@ -43,8 +42,10 @@ except Exception, e: log.debug( "Error for tool %s: could not add test parameter %s. %s" % ( self.tool.id, name, e ) ) self.inputs.append( ( name, value, extra ) ) + def add_output( self, name, file, extra ): self.outputs.append( ( name, file, extra ) ) + def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): @@ -93,20 +94,21 @@ if found_parameter: return True, new_value return False, value + def __add_uploaded_dataset( self, name, value, extra, input_parameter ): if value is None: assert input_parameter.optional, '%s is not optional. You must provide a valid filename.' % name return value if ( value, extra ) not in self.required_files: - self.required_files.append( ( value, extra ) ) #these files will be uploaded + self.required_files.append( ( value, extra ) ) # these files will be uploaded name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] if name_change: - name_change = name_change[-1].get( 'value' ) #only the last name change really matters - value = name_change #change value for select to renamed uploaded file for e.g. composite dataset + name_change = name_change[-1].get( 'value' ) # only the last name change really matters + value = name_change # change value for select to renamed uploaded file for e.g. composite dataset else: for end in [ '.zip', '.gz' ]: if value.endswith( end ): value = value[ :-len( end ) ] break - value = os.path.basename( value ) #if uploading a file in a path other than root of test-data + value = os.path.basename( value ) # if uploading a file in a path other than root of test-data return value https://bitbucket.org/galaxy/galaxy-central/commits/d9482b09663e/ Changeset: d9482b09663e User: jmchilton Date: 2013-11-18 07:51:54 Summary: Refactor tool test parsing logic out of Tool and into ToolTestBuilder. Affected #: 2 files diff -r 59a0ca3d48c019c017d85fc780239837b2e5453d -r d9482b09663e0cb7cc74adc284267fee1dc498eb lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1570,113 +1570,8 @@ store in `self.tests`. """ self.tests = [] - # Composite datasets need a unique name: each test occurs in a fresh - # history, but we'll keep it unique per set of tests - composite_data_names_counter = 0 for i, test_elem in enumerate( tests_elem.findall( 'test' ) ): - name = test_elem.get( 'name', 'Test-%d' % (i + 1) ) - maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) - test = ToolTestBuilder( self, name, maxseconds ) - try: - for param_elem in test_elem.findall( "param" ): - attrib = dict( param_elem.attrib ) - if 'values' in attrib: - value = attrib[ 'values' ].split( ',' ) - elif 'value' in attrib: - value = attrib['value'] - else: - value = None - attrib['children'] = list( param_elem.getchildren() ) - if attrib['children']: - # At this time, we can assume having children only - # occurs on DataToolParameter test items but this could - # change and would cause the below parsing to change - # based upon differences in children items - attrib['metadata'] = [] - attrib['composite_data'] = [] - attrib['edit_attributes'] = [] - # Composite datasets need to be renamed uniquely - composite_data_name = None - for child in attrib['children']: - if child.tag == 'composite_data': - attrib['composite_data'].append( child ) - if composite_data_name is None: - # Generate a unique name; each test uses a - # fresh history - composite_data_name = '_COMPOSITE_RENAMED_%i_' \ - % ( composite_data_names_counter ) - composite_data_names_counter += 1 - elif child.tag == 'metadata': - attrib['metadata'].append( child ) - elif child.tag == 'metadata': - attrib['metadata'].append( child ) - elif child.tag == 'edit_attributes': - attrib['edit_attributes'].append( child ) - if composite_data_name: - # Composite datasets need implicit renaming; - # inserted at front of list so explicit declarations - # take precedence - attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) - test.add_param( attrib.pop( 'name' ), value, attrib ) - for output_elem in test_elem.findall( "output" ): - attrib = dict( output_elem.attrib ) - name = attrib.pop( 'name', None ) - if name is None: - raise Exception( "Test output does not have a 'name'" ) - assert_elem = output_elem.find("assert_contents") - assert_list = None - - # Trying to keep testing patch as localized as - # possible, this function should be relocated - # somewhere more conventional. - def convert_elem(elem): - """ Converts and XML element to a dictionary format, used by assertion checking code. """ - tag = elem.tag - attributes = dict( elem.attrib ) - child_elems = list( elem.getchildren() ) - converted_children = [] - for child_elem in child_elems: - converted_children.append( convert_elem(child_elem) ) - return {"tag": tag, "attributes": attributes, "children": converted_children} - if assert_elem is not None: - assert_list = [] - for assert_child in list(assert_elem): - assert_list.append(convert_elem(assert_child)) - file = attrib.pop( 'file', None ) - # File no longer required if an list of assertions was present. - if assert_list is None and file is None: - raise Exception( "Test output does not have a 'file'") - attributes = {} - # Method of comparison - attributes['compare'] = attrib.pop( 'compare', 'diff' ).lower() - # Number of lines to allow to vary in logs (for dates, etc) - attributes['lines_diff'] = int( attrib.pop( 'lines_diff', '0' ) ) - # Allow a file size to vary if sim_size compare - attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) - attributes['sort'] = string_as_bool( attrib.pop( 'sort', False ) ) - attributes['extra_files'] = [] - attributes['assert_list'] = assert_list - if 'ftype' in attrib: - attributes['ftype'] = attrib['ftype'] - for extra in output_elem.findall( 'extra_files' ): - # File or directory, when directory, compare basename - # by basename - extra_type = extra.get( 'type', 'file' ) - extra_name = extra.get( 'name', None ) - assert extra_type == 'directory' or extra_name is not None, \ - 'extra_files type (%s) requires a name attribute' % extra_type - extra_value = extra.get( 'value', None ) - assert extra_value is not None, 'extra_files requires a value attribute' - extra_attributes = {} - extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() - extra_attributes['delta'] = extra.get( 'delta', '0' ) - extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) - extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) - attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) - test.add_output( name, file, attributes ) - except Exception, e: - test.error = True - test.exception = e + test = ToolTestBuilder( self, test_elem, i ) self.tests.append( test ) def parse_input_page( self, input_elem, enctypes ): diff -r 59a0ca3d48c019c017d85fc780239837b2e5453d -r d9482b09663e0cb7cc74adc284267fee1dc498eb lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -1,6 +1,7 @@ import os.path from parameters import basic from parameters import grouping +from galaxy.util import string_as_bool import logging log = logging.getLogger( __name__ ) @@ -13,7 +14,10 @@ doing dynamic tests in this way allows better integration) """ - def __init__( self, tool, name, maxseconds ): + def __init__( self, tool, test_elem, i ): + name = test_elem.get( 'name', 'Test-%d' % (i + 1) ) + maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) + self.tool = tool self.name = name self.maxseconds = maxseconds @@ -23,6 +27,114 @@ self.error = False self.exception = None + self.__parse_elem( test_elem, i ) + + def __parse_elem( self, test_elem, i ): + # Composite datasets need a unique name: each test occurs in a fresh + # history, but we'll keep it unique per set of tests - use i (test #) + # and composite_data_names_counter (instance per test #) + composite_data_names_counter = 0 + try: + for param_elem in test_elem.findall( "param" ): + attrib = dict( param_elem.attrib ) + if 'values' in attrib: + value = attrib[ 'values' ].split( ',' ) + elif 'value' in attrib: + value = attrib['value'] + else: + value = None + attrib['children'] = list( param_elem.getchildren() ) + if attrib['children']: + # At this time, we can assume having children only + # occurs on DataToolParameter test items but this could + # change and would cause the below parsing to change + # based upon differences in children items + attrib['metadata'] = [] + attrib['composite_data'] = [] + attrib['edit_attributes'] = [] + # Composite datasets need to be renamed uniquely + composite_data_name = None + for child in attrib['children']: + if child.tag == 'composite_data': + attrib['composite_data'].append( child ) + if composite_data_name is None: + # Generate a unique name; each test uses a + # fresh history + composite_data_name = '_COMPOSITE_RENAMED_t%i_d%i' \ + % ( i, composite_data_names_counter ) + composite_data_names_counter += 1 + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'edit_attributes': + attrib['edit_attributes'].append( child ) + if composite_data_name: + # Composite datasets need implicit renaming; + # inserted at front of list so explicit declarations + # take precedence + attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) + self.add_param( attrib.pop( 'name' ), value, attrib ) + for output_elem in test_elem.findall( "output" ): + attrib = dict( output_elem.attrib ) + name = attrib.pop( 'name', None ) + if name is None: + raise Exception( "Test output does not have a 'name'" ) + assert_elem = output_elem.find("assert_contents") + assert_list = None + + # Trying to keep testing patch as localized as + # possible, this function should be relocated + # somewhere more conventional. + def convert_elem(elem): + """ Converts and XML element to a dictionary format, used by assertion checking code. """ + tag = elem.tag + attributes = dict( elem.attrib ) + child_elems = list( elem.getchildren() ) + converted_children = [] + for child_elem in child_elems: + converted_children.append( convert_elem(child_elem) ) + return {"tag": tag, "attributes": attributes, "children": converted_children} + if assert_elem is not None: + assert_list = [] + for assert_child in list(assert_elem): + assert_list.append(convert_elem(assert_child)) + file = attrib.pop( 'file', None ) + # File no longer required if an list of assertions was present. + if assert_list is None and file is None: + raise Exception( "Test output does not have a 'file'") + attributes = {} + # Method of comparison + attributes['compare'] = attrib.pop( 'compare', 'diff' ).lower() + # Number of lines to allow to vary in logs (for dates, etc) + attributes['lines_diff'] = int( attrib.pop( 'lines_diff', '0' ) ) + # Allow a file size to vary if sim_size compare + attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) + attributes['sort'] = string_as_bool( attrib.pop( 'sort', False ) ) + attributes['extra_files'] = [] + attributes['assert_list'] = assert_list + if 'ftype' in attrib: + attributes['ftype'] = attrib['ftype'] + for extra in output_elem.findall( 'extra_files' ): + # File or directory, when directory, compare basename + # by basename + extra_type = extra.get( 'type', 'file' ) + extra_name = extra.get( 'name', None ) + assert extra_type == 'directory' or extra_name is not None, \ + 'extra_files type (%s) requires a name attribute' % extra_type + extra_value = extra.get( 'value', None ) + assert extra_value is not None, 'extra_files requires a value attribute' + extra_attributes = {} + extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() + extra_attributes['delta'] = extra.get( 'delta', '0' ) + extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) + extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) + attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) + self.add_output( name, file, attributes ) + except Exception, e: + self.error = True + self.exception = e + def add_param( self, name, value, extra ): try: if name not in self.tool.inputs: https://bitbucket.org/galaxy/galaxy-central/commits/b1a929a53f22/ Changeset: b1a929a53f22 User: jmchilton Date: 2013-11-18 07:51:54 Summary: Make formerly public methods in ToolTestBuilder private now that it does its own construction. Affected #: 1 file diff -r d9482b09663e0cb7cc74adc284267fee1dc498eb -r b1a929a53f22ed8e59e8ca4d75d3ab230344cd46 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -74,7 +74,7 @@ # inserted at front of list so explicit declarations # take precedence attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) - self.add_param( attrib.pop( 'name' ), value, attrib ) + self.__add_param( attrib.pop( 'name' ), value, attrib ) for output_elem in test_elem.findall( "output" ): attrib = dict( output_elem.attrib ) name = attrib.pop( 'name', None ) @@ -130,12 +130,12 @@ extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) - self.add_output( name, file, attributes ) + self.__add_output( name, file, attributes ) except Exception, e: self.error = True self.exception = e - def add_param( self, name, value, extra ): + def __add_param( self, name, value, extra ): try: if name not in self.tool.inputs: found_parameter = False @@ -155,7 +155,7 @@ log.debug( "Error for tool %s: could not add test parameter %s. %s" % ( self.tool.id, name, e ) ) self.inputs.append( ( name, value, extra ) ) - def add_output( self, name, file, extra ): + def __add_output( self, name, file, extra ): self.outputs.append( ( name, file, extra ) ) def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): https://bitbucket.org/galaxy/galaxy-central/commits/3ebc0f5c4486/ Changeset: 3ebc0f5c4486 User: jmchilton Date: 2013-11-18 07:51:54 Summary: Refactor smaller methods out of tool output test parsing. Affected #: 1 file diff -r b1a929a53f22ed8e59e8ca4d75d3ab230344cd46 -r 3ebc0f5c4486cc5c207882bcea819018d23b2bf4 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -80,29 +80,12 @@ name = attrib.pop( 'name', None ) if name is None: raise Exception( "Test output does not have a 'name'" ) - assert_elem = output_elem.find("assert_contents") - assert_list = None - # Trying to keep testing patch as localized as - # possible, this function should be relocated - # somewhere more conventional. - def convert_elem(elem): - """ Converts and XML element to a dictionary format, used by assertion checking code. """ - tag = elem.tag - attributes = dict( elem.attrib ) - child_elems = list( elem.getchildren() ) - converted_children = [] - for child_elem in child_elems: - converted_children.append( convert_elem(child_elem) ) - return {"tag": tag, "attributes": attributes, "children": converted_children} - if assert_elem is not None: - assert_list = [] - for assert_child in list(assert_elem): - assert_list.append(convert_elem(assert_child)) + assert_list = self.__parse_assert_list( output_elem ) file = attrib.pop( 'file', None ) # File no longer required if an list of assertions was present. - if assert_list is None and file is None: - raise Exception( "Test output does not have a 'file'") + if not assert_list and file is None: + raise Exception( "Test output does not have a 'file' to compare with or list of assertions to check") attributes = {} # Method of comparison attributes['compare'] = attrib.pop( 'compare', 'diff' ).lower() @@ -116,25 +99,51 @@ if 'ftype' in attrib: attributes['ftype'] = attrib['ftype'] for extra in output_elem.findall( 'extra_files' ): - # File or directory, when directory, compare basename - # by basename - extra_type = extra.get( 'type', 'file' ) - extra_name = extra.get( 'name', None ) - assert extra_type == 'directory' or extra_name is not None, \ - 'extra_files type (%s) requires a name attribute' % extra_type - extra_value = extra.get( 'value', None ) - assert extra_value is not None, 'extra_files requires a value attribute' - extra_attributes = {} - extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() - extra_attributes['delta'] = extra.get( 'delta', '0' ) - extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) - extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) - attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) + attributes['extra_files'].append( self.__parse_extra_files_elem( extra ) ) self.__add_output( name, file, attributes ) except Exception, e: self.error = True self.exception = e + def __parse_assert_list( self, output_elem ): + assert_elem = output_elem.find("assert_contents") + assert_list = None + + # Trying to keep testing patch as localized as + # possible, this function should be relocated + # somewhere more conventional. + def convert_elem(elem): + """ Converts and XML element to a dictionary format, used by assertion checking code. """ + tag = elem.tag + attributes = dict( elem.attrib ) + child_elems = list( elem.getchildren() ) + converted_children = [] + for child_elem in child_elems: + converted_children.append( convert_elem(child_elem) ) + return {"tag": tag, "attributes": attributes, "children": converted_children} + if assert_elem is not None: + assert_list = [] + for assert_child in list(assert_elem): + assert_list.append(convert_elem(assert_child)) + + return assert_list + + def __parse_extra_files_elem( self, extra ): + # File or directory, when directory, compare basename + # by basename + extra_type = extra.get( 'type', 'file' ) + extra_name = extra.get( 'name', None ) + assert extra_type == 'directory' or extra_name is not None, \ + 'extra_files type (%s) requires a name attribute' % extra_type + extra_value = extra.get( 'value', None ) + assert extra_value is not None, 'extra_files requires a value attribute' + extra_attributes = {} + extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() + extra_attributes['delta'] = extra.get( 'delta', '0' ) + extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) + extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) + return extra_type, extra_value, extra_name, extra_attributes + def __add_param( self, name, value, extra ): try: if name not in self.tool.inputs: 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: guerler: Grids: Remove console output
by commits-noreply＠bitbucket.org 17 Nov '13

17 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/64cb656e95b2/ Changeset: 64cb656e95b2 User: guerler Date: 2013-11-17 11:37:57 Summary: Grids: Remove console output Affected #: 1 file diff -r 567266a9f5ae16af522a62c0aaf3c47cab39ffc2 -r 64cb656e95b2f40ac5f6f1f26fc484ce88a11ad1 templates/webapps/galaxy/tracks/history_select_grid.mako --- a/templates/webapps/galaxy/tracks/history_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_select_grid.mako @@ -15,7 +15,6 @@ $(document).ready(function() { $(".addtracktab, #grid-table a").off(); $(".addtracktab, #grid-table a").click(function() { - console.log($(this).attr("href")); var modal_body = $(".modal-body"); if (modal_body.length !== 0) { modal_body.load($(this).attr("href")); 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: guerler: Grids: Remove console output
by commits-noreply＠bitbucket.org 17 Nov '13

17 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/567266a9f5ae/ Changeset: 567266a9f5ae User: guerler Date: 2013-11-17 11:16:54 Summary: Grids: Remove console output Affected #: 1 file diff -r f1cef709a9e5631cae2126ffff71dbba64611f87 -r 567266a9f5ae16af522a62c0aaf3c47cab39ffc2 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -222,7 +222,7 @@ $(function() { ## get configuration var grid_config = ${ h.to_json_string( self.grid_config ) }; - console.log(grid_config); + // Create grid. var grid = new Grid(grid_config); 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: guerler: Grids: Reduce mako templating to json generation, introduce GridsView, bug fixes
by commits-noreply＠bitbucket.org 17 Nov '13

17 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1cef709a9e5/ Changeset: f1cef709a9e5 User: guerler Date: 2013-11-17 11:08:25 Summary: Grids: Reduce mako templating to json generation, introduce GridsView, bug fixes iG: changed templates/webapps/galaxy/tracks/history_select_grid.mako Affected #: 14 files diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -321,7 +321,7 @@ class GridColumn( object ): def __init__( self, label, key=None, model_class=None, method=None, format=None, \ - link=None, attach_popup=False, visible=True, ncells=1, nowrap=False, \ + link=None, attach_popup=False, visible=True, nowrap=False, \ # Valid values for filterable are ['standard', 'advanced', None] filterable=None, sortable=True, label_id_prefix=None ): """Create a grid column.""" @@ -334,7 +334,6 @@ self.nowrap = nowrap self.attach_popup = attach_popup self.visible = visible - self.ncells = ncells self.filterable = filterable # Column must have a key to be sortable. self.sortable = ( self.key is not None and sortable ) diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -100,7 +100,7 @@ grids.TextColumn( "Name", key="name", # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), - HistoryColumn( "History", key="history", + HistoryColumn( "History", key="history", sortable=False, link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), @@ -113,11 +113,12 @@ key="free-text-search", visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Copy to current history", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Copy to current history", condition=( lambda item: not item.deleted ), async_compatible=True ), ] standard_filters = [] default_filter = dict( name="All", deleted="False", tags="All" ) preserve_state = False + use_async = True use_paging = True num_rows_per_page = 50 def build_initial_query( self, trans, **kwargs ): diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -30,16 +30,13 @@ def get_value( self, trans, grid, history ): state_count_dict = self.get_hda_state_counts( trans, history ) - rval = [] + rval = '' for state in ( 'ok', 'running', 'queued', 'error' ): count = state_count_dict.get( state, 0 ) if count: - rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, count ) ) - else: - rval.append( '' ) + rval += '<div class="count-box state-color-%s">%s</div>' % (state, count) return rval - class HistoryListNameColumn( NameColumn ): def get_link( self, trans, grid, history ): link = None @@ -72,7 +69,7 @@ default_sort_key = "-update_time" columns = [ HistoryListNameColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), - DatasetsByStateColumn( "Datasets", key="datasets_by_state", ncells=4, sortable=False ), + DatasetsByStateColumn( "Datasets", key="datasets_by_state", sortable=False ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), @@ -118,13 +115,11 @@ # Custom column types class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): - rval = [] + rval = '' for state in ( 'ok', 'running', 'queued', 'error' ): total = sum( 1 for d in history.active_datasets if d.state == state ) if total: - rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) - else: - rval.append( '' ) + rval += '<div class="count-box state-color-%s">%s</div>' % ( state, total ) return rval class SharedByColumn( grids.GridColumn ): @@ -138,7 +133,7 @@ default_filter = {} columns = [ grids.GridColumn( "Name", key="name", attach_popup=True ), # link=( lambda item: dict( operation="View", id=item.id ) ), attach_popup=True ), - DatasetsByStateColumn( "Datasets", ncells=4, sortable=False ), + DatasetsByStateColumn( "Datasets", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), SharedByColumn( "Shared by", key="user_id" ) diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -147,11 +147,11 @@ # Grid definition. title = "Insert into visualization" template = "/tracks/add_to_viz.mako" - async_template = "/page/select_items_grid_async.mako" model_class = model.Visualization default_sort_key = "-update_time" use_async = True use_paging = False + show_item_checkboxes = True columns = [ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ), grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -119,433 +119,456 @@ } // Add filter arguments to data, placing "f-" in front of all arguments. - // FIXME: when underscore updated, use pairs function(). var self = this; - _.each(_.keys(self.attributes.filters), function(k) { - url_data['f-' + k] = self.attributes.filters[k]; + _.each(_.pairs(self.attributes.filters), function(k) { + url_data['f-' + k[0]] = k[1]; }); return url_data; } }); -// -// Code to handle grid operations: filtering, sorting, paging, and operations. -// +// grid view +var GridView = Backbone.View.extend({ -// Initialize grid controls -function init_grid_controls() { - // Initialize submit image elements. - $('.submit-image').each( function() { - // On mousedown, add class to simulate click. - $(this).mousedown( function() { - $(this).addClass('gray-background'); + // model + grid: null, + + // Initialize + initialize: function(grid) + { + this.grid = grid; + this.init_grid_elements(); + this.init_grid_controls(); + + // Initialize text filters to select text on click and use normal font when user is typing. + $('input[type=text]').each(function() { + $(this).click(function() { $(this).select(); } ) + .keyup(function () { $(this).css("font-style", "normal"); }); + }); + }, + + // Initialize grid controls + init_grid_controls: function() { + // Initialize submit image elements. + $('.submit-image').each( function() { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); }); - // On mouseup, add class to simulate click. - $(this).mouseup( function() { - $(this).removeClass('gray-background'); + // link + var self = this; + + // Initialize sort links. + $('.sort-link').each( function() { + $(this).click( function() { + self.set_sort_condition( $(this).attr('sort_key') ); + return false; + }); }); - }); + + // Initialize page links. + $('.page-link > a').each( function() { + $(this).click( function() { + self.set_page( $(this).attr('page_num') ); + return false; + }); + }); + + // Initialize categorical filters. + $('.categorical-filter > a').each( function() { + $(this).click( function() { + self.set_categorical_filter( $(this).attr('filter_key'), $(this).attr('filter_val') ); + return false; + }); + }); + + // Initialize text filters. + $('.text-filter-form').each( function() { + $(this).submit( function() { + var column_key = $(this).attr('column_key'); + var text_input_obj = $('#input-' + column_key + '-filter'); + var text_input = text_input_obj.val(); + text_input_obj.val(''); + self.add_filter_condition(column_key, text_input, true); + return false; + }); + }); + + // Initialize autocomplete for text inputs in search UI. + var t = $("#input-tags-filter"); + if (t.length) { + t.autocomplete(this.grid.history_tag_autocomplete_url, + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }); + } + + var t2 = $("#input-name-filter"); + if (t2.length) { + t2.autocomplete(this.grid.history_name_autocomplete_url, + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }); + } + + // Initialize standard, advanced search toggles. + $('.advanced-search-toggle').each( function() { + $(this).click( function() { + $("#standard-search").slideToggle('fast'); + $('#advanced-search').slideToggle('fast'); + return false; + }); + }); + }, + + // Initialize grid elements. + init_grid_elements : function() { - // Initialize sort links. - $('.sort-link').each( function() { - $(this).click( function() { - set_sort_condition( $(this).attr('sort_key') ); - return false; + // Initialize grid selection checkboxes. + $(".grid").each( function() { + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var check_count = $(this).find("span.grid-selected-count"); + var update_checked = function() { + check_count.text( $(checkboxes).filter(":checked").length ); + }; + + $(checkboxes).each( function() { + $(this).change(update_checked); + }); + update_checked(); }); - }); - - // Initialize page links. - $('.page-link > a').each( function() { - $(this).click( function() { - set_page( $(this).attr('page_num') ); - return false; + + // Initialize item labels. + var self = this; + $(".label").each( function() { + // If href has an operation in it, do operation when clicked. Otherwise do nothing. + var href = $(this).attr('href'); + if ( href !== undefined && href.indexOf('operation=') != -1 ) { + $(this).click( function() { + self.do_operation_from_href( $(this).attr('href') ); + return false; + }); + } }); - }); + + // Initialize ratings. + if ($('.community_rating_star').length !== 0) + $('.community_rating_star').rating({}); + + // Initialize item menu operations. + make_popup_menus(); + }, - // Initialize categorical filters. - $('.categorical-filter > a').each( function() { - $(this).click( function() { - set_categorical_filter( $(this).attr('filter_key'), $(this).attr('filter_val') ); + // Go back to page one; this is useful when a filter is applied. + go_page_one: function () { + // Need to go back to page 1 if not showing all. + var cur_page = this.grid.get('cur_page'); + if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') { + this.grid.set('cur_page', 1); + } + }, + + // Add a condition to the grid filter; this adds the condition and refreshes the grid. + add_filter_condition: function (name, value, append) { + // Do nothing is value is empty. + if (value === "") { return false; + } + + // Add condition to grid. + this.grid.add_filter(name, value, append); + + // Add button that displays filter and provides a button to delete it. + var t = $("<span>" + value + "<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>"); + t.addClass('text-filter-val'); + var self = this; + t.click(function() { + // Remove filter condition. + self.grid.remove_filter(name, value); + + // Remove visible element. + $(this).remove(); + + self.go_page_one(); + self.update_grid(); }); - }); - - // Initialize text filters. - $('.text-filter-form').each( function() { - $(this).submit( function() { - var column_key = $(this).attr('column_key'); - var text_input_obj = $('#input-' + column_key + '-filter'); - var text_input = text_input_obj.val(); - text_input_obj.val(''); - add_filter_condition(column_key, text_input, true); + + var container = $('#' + name + "-filtering-criteria"); + container.append(t); + + this.go_page_one(); + this.update_grid(); + }, + + // Set sort condition for grid. + set_sort_condition: function (col_key) { + // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on + // currently sorted column, sort is reversed. + var cur_sort = this.grid.get('sort_key'); + var new_sort = col_key; + if (cur_sort.indexOf(col_key) !== -1) { + // Reverse sort. + if (cur_sort.substring(0,1) !== '-') { + new_sort = '-' + col_key; + } else { + // Sort reversed by using just col_key. + } + } + + // Remove sort arrows elements. + $('.sort-arrow').remove(); + + // Add sort arrow element to new sort column. + var sort_arrow = (new_sort.substring(0,1) == '-') ? "↑" : "↓"; + var t = $("<span>" + sort_arrow + "</span>").addClass('sort-arrow'); + var th = $("#" + col_key + '-header'); + th.append(t); + + // Update grid. + this.grid.set('sort_key', new_sort); + this.go_page_one(); + this.update_grid(); + }, + + // Set new value for categorical filter. + set_categorical_filter: function (name, new_value) { + // Update filter hyperlinks to reflect new filter value. + var category_filter = this.grid.get('categorical_filters')[name], + cur_value = this.grid.get('filters')[name]; + var self = this; + $("." + name + "-filter").each( function() { + var text = $.trim( $(this).text() ); + var filter = category_filter[text]; + var filter_value = filter[name]; + if (filter_value == new_value) { + // Remove filter link since grid will be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + $(this).empty(); + $(this).addClass("current-filter"); + $(this).append(text); + } else if (filter_value == cur_value) { + // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor. + $(this).empty(); + var t = $("<a href='#'>" + text + "</a>"); + t.click(function() { + self.set_categorical_filter( name, filter_value ); + }); + $(this).removeClass("current-filter"); + $(this).append(t); + } + }); + + // Update grid. + this.grid.add_filter(name, new_value); + this.go_page_one(); + this.update_grid(); + }, + + // Set page to view. + set_page: function (new_page) { + // Update page hyperlink to reflect new page. + var self = this; + $(".page-link").each( function() { + var id = $(this).attr('id'), + page_num = parseInt( id.split("-")[2], 10 ), // Id has form 'page-link-<page_num> + cur_page = self.grid.get('cur_page'), + text; + if (page_num === new_page) { + // Remove link to page since grid will be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + text = $(this).children().text(); + $(this).empty(); + $(this).addClass("inactive-link"); + $(this).text(text); + } + else if (page_num === cur_page) { + // Add hyperlink to this page since grid will no longer be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor. + text = $(this).text(); + $(this).empty(); + $(this).removeClass("inactive-link"); + var t = $("<a href='#'>" + text + "</a>"); + t.click(function() { + set_page(page_num); + }); + $(this).append(t); + } + }); + + var maintain_page_links = true; + if (new_page === "all") { + this.grid.set('cur_page', new_page); + maintain_page_links = false; + } else { + this.grid.set('cur_page', parseInt(new_page, 10)); + } + this.update_grid(maintain_page_links); + }, + + // Perform a grid operation. + do_operation: function (operation, item_ids) { + operation = operation.toLowerCase(); + + // Update grid. + this.grid.set({ + operation: operation, + item_ids: item_ids + }); + + // Do operation. If operation cannot be performed asynchronously, redirect to location. + if (this.grid.can_async_op(operation)) { + this.update_grid(true); + } + else { + this.go_to_URL(); + } + }, + + // Perform a hyperlink click that initiates an operation. If there is no operation, ignore click. + do_operation_from_href: function (href) { + // Get operation, id in hyperlink's href. + var href_parts = href.split("?"); + if (href_parts.length > 1) { + var href_parms_str = href_parts[1]; + var href_parms = href_parms_str.split("&"); + var operation = null; + var id = -1; + for (var index = 0; index < href_parms.length; index++) { + if (href_parms[index].indexOf('operation') != -1) { + // Found operation parm; get operation value. + operation = href_parms[index].split('=')[1]; + } else if (href_parms[index].indexOf('id') != -1) { + // Found id parm; get id value. + id = href_parms[index].split('=')[1]; + } + } + // Do operation. + this.do_operation(operation, id); return false; + } + }, + + // Navigate window to the URL defined by url_args. This method can be used to short-circuit grid AJAXing. + go_to_URL: function () { + // Not async request. + this.grid.set('async', false); + + // Go. + window.location = this.grid.get('url_base') + "?" + $.param(this.grid.get_url_data()); + + // Clear grid of transient request attributes. + this.grid.set({ + operation: undefined, + item_ids: undefined }); - }); - - // Initialize autocomplete for text inputs in search UI. - var t = $("#input-tags-filter"); - if (t.length) { - t.autocomplete(history_tag_autocomplete_url, - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }); - } - - var t2 = $("#input-name-filter"); - if (t2.length) { - t2.autocomplete(history_name_autocomplete_url, - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }); - } - - // Initialize standard, advanced search toggles. - $('.advanced-search-toggle').each( function() { - $(this).click( function() { - $("#standard-search").slideToggle('fast'); - $('#advanced-search').slideToggle('fast'); - return false; - }); - }); -} - -// Initialize grid elements. -function init_grid_elements() { - // Initialize grid selection checkboxes. - $(".grid").each( function() { - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var check_count = $(this).find("span.grid-selected-count"); - var update_checked = function() { - check_count.text( $(checkboxes).filter(":checked").length ); - }; - - $(checkboxes).each( function() { - $(this).change(update_checked); - }); - update_checked(); - }); - - // Initialize item labels. - $(".label").each( function() { - // If href has an operation in it, do operation when clicked. Otherwise do nothing. - var href = $(this).attr('href'); - if ( href !== undefined && href.indexOf('operation=') != -1 ) { - $(this).click( function() { - do_operation_from_href( $(this).attr('href') ); - return false; - }); - } - }); - - // Initialize ratings. - if ($('.community_rating_star').length !== 0) - $('.community_rating_star').rating({}); - - // Initialize item menu operations. - make_popup_menus(); -} - -// Go back to page one; this is useful when a filter is applied. -function go_page_one() { - // Need to go back to page 1 if not showing all. - var cur_page = grid.get('cur_page'); - if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') { - grid.set('cur_page', 1); - } -} - -// Add a condition to the grid filter; this adds the condition and refreshes the grid. -function add_filter_condition(name, value, append) { - // Do nothing is value is empty. - if (value === "") { - return false; - } - - // Add condition to grid. - grid.add_filter(name, value, append); - - // Add button that displays filter and provides a button to delete it. - var t = $("<span>" + value + "<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>"); - t.addClass('text-filter-val'); - t.click(function() { - // Remove filter condition. - grid.remove_filter(name, value); - - // Remove visible element. - $(this).remove(); - - go_page_one(); - update_grid(); - }); - - var container = $('#' + name + "-filtering-criteria"); - container.append(t); - - go_page_one(); - update_grid(); -} - -// Add tag to grid filter. -function add_tag_to_grid_filter(tag_name, tag_value) { - // Put tag name and value together. - var tag = tag_name + (tag_value !== undefined && tag_value !== "" ? ":" + tag_value : ""); - $('#advanced-search').show('fast'); - add_filter_condition("tags", tag, true); -} - -// Set sort condition for grid. -function set_sort_condition(col_key) { - // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on - // currently sorted column, sort is reversed. - var cur_sort = grid.get('sort_key'); - var new_sort = col_key; - if (cur_sort.indexOf(col_key) !== -1) { - // Reverse sort. - if (cur_sort.substring(0,1) !== '-') { - new_sort = '-' + col_key; - } else { - // Sort reversed by using just col_key. - } - } - - // Remove sort arrows elements. - $('.sort-arrow').remove(); - - // Add sort arrow element to new sort column. - var sort_arrow = (new_sort.substring(0,1) == '-') ? "↑" : "↓"; - var t = $("<span>" + sort_arrow + "</span>").addClass('sort-arrow'); - var th = $("#" + col_key + '-header'); - th.append(t); - - // Update grid. - grid.set('sort_key', new_sort); - go_page_one(); - update_grid(); -} - -// Set new value for categorical filter. -function set_categorical_filter(name, new_value) { - // Update filter hyperlinks to reflect new filter value. - var category_filter = grid.get('categorical_filters')[name], - cur_value = grid.get('filters')[name]; - $("." + name + "-filter").each( function() { - var text = $.trim( $(this).text() ); - var filter = category_filter[text]; - var filter_value = filter[name]; - if (filter_value == new_value) { - // Remove filter link since grid will be using this filter. It is assumed that - // this element has a single child, a hyperlink/anchor with text. - $(this).empty(); - $(this).addClass("current-filter"); - $(this).append(text); - } else if (filter_value == cur_value) { - // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that - // this element has a single child, a hyperlink/anchor. - $(this).empty(); - var t = $("<a href='#'>" + text + "</a>"); - t.click(function() { - set_categorical_filter( name, filter_value ); - }); - $(this).removeClass("current-filter"); - $(this).append(t); - } - }); - - // Update grid. - grid.add_filter(name, new_value); - go_page_one(); - update_grid(); -} - -// Set page to view. -function set_page(new_page) { - // Update page hyperlink to reflect new page. - $(".page-link").each( function() { - var id = $(this).attr('id'), - page_num = parseInt( id.split("-")[2], 10 ), // Id has form 'page-link-<page_num> - cur_page = grid.get('cur_page'), - text; - if (page_num === new_page) { - // Remove link to page since grid will be on this page. It is assumed that - // this element has a single child, a hyperlink/anchor with text. - text = $(this).children().text(); - $(this).empty(); - $(this).addClass("inactive-link"); - $(this).text(text); - } - else if (page_num === cur_page) { - // Add hyperlink to this page since grid will no longer be on this page. It is assumed that - // this element has a single child, a hyperlink/anchor. - text = $(this).text(); - $(this).empty(); - $(this).removeClass("inactive-link"); - var t = $("<a href='#'>" + text + "</a>"); - t.click(function() { - set_page(page_num); - }); - $(this).append(t); - } - }); - - var maintain_page_links = true; - if (new_page === "all") { - grid.set('cur_page', new_page); - maintain_page_links = false; - } else { - grid.set('cur_page', parseInt(new_page, 10)); - } - update_grid(maintain_page_links); -} - -// Perform a grid operation. -function do_operation(operation, item_ids) { - operation = operation.toLowerCase(); + }, // Update grid. - grid.set({ - operation: operation, - item_ids: item_ids - }); - - // Do operation. If operation cannot be performed asynchronously, redirect to location. - if (grid.can_async_op(operation)) { - update_grid(true); - } - else { - go_to_URL(); - } -} + update_grid: function (maintain_page_links) { + // If grid is not using async, then go to URL. + if (!this.grid.get('async')) { + this.go_to_URL(); + return; + } -// Perform a hyperlink click that initiates an operation. If there is no operation, ignore click. -function do_operation_from_href(href) { - // Get operation, id in hyperlink's href. - var href_parts = href.split("?"); - if (href_parts.length > 1) { - var href_parms_str = href_parts[1]; - var href_parms = href_parms_str.split("&"); - var operation = null; - var id = -1; - for (var index = 0; index < href_parms.length; index++) { - if (href_parms[index].indexOf('operation') != -1) { - // Found operation parm; get operation value. - operation = href_parms[index].split('=')[1]; - } else if (href_parms[index].indexOf('id') != -1) { - // Found id parm; get id value. - id = href_parms[index].split('=')[1]; + // If there's an operation, do POST; otherwise, do GET. + var method = (this.grid.get('operation') ? "POST" : "GET" ); + $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions. + var self = this; + $.ajax({ + type: method, + url: self.grid.get('url_base'), + data: self.grid.get_url_data(), + error: function() { alert( "Grid refresh failed" ); }, + success: function(response_text) { + // HACK: use a simple string to separate the elements in the + // response: (1) table body; (2) number of pages in table; and (3) message. + var parsed_response_text = response_text.split("*****"); + + // Update grid body and footer. + $('#grid-table-body').html(parsed_response_text[0]); + // FIXME: this does not work at all; what's needed is a function + // that updates page links when number of pages changes. + $('#grid-table-footer').html(parsed_response_text[1]); + + // Trigger custom event to indicate grid body has changed. + $('#grid-table-body').trigger('update'); + + // Init grid. + self.init_grid_elements(); + make_popup_menus(); + + // Hide loading overlay. + $('.loading-elt-overlay').hide(); + + // Show message if there is one. + var message = $.trim( parsed_response_text[2] ); + if (message !== "") { + $('#grid-message').html( message ).show(); + setTimeout( function() { $('#grid-message').hide(); }, 5000); + } + }, + complete: function() { + // Clear grid of transient request attributes. + self.grid.set({ + operation: undefined, + item_ids: undefined + }); + } + }); + }, + + check_all_items: function () { + var chk_all = document.getElementById('check_all'), + checks = document.getElementsByTagName('input'), + total = 0, + i; + if ( chk_all.checked === true ) { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) !== -1) { + checks[i].checked = true; + total++; + } } } - // Do operation. - do_operation(operation, id); - return false; - } -} + else { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) !== -1) { + checks[i].checked = false; + } -// Navigate window to the URL defined by url_args. This method can be used to short-circuit grid AJAXing. -function go_to_URL() { - // Not async request. - grid.set('async', false); - - // Go. - window.location = grid.get('url_base') + "?" + $.param(grid.get_url_data()); -} - -// Update grid. -function update_grid(maintain_page_links) { - // If grid is not using async, then go to URL. - if (!grid.get('async')) { - go_to_URL(); - return; - } - - // If there's an operation, do POST; otherwise, do GET. - var method = (grid.get('operation') ? "POST" : "GET" ); - $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions. - $.ajax({ - type: method, - url: grid.get('url_base'), - data: grid.get_url_data(), - error: function() { alert( "Grid refresh failed" ); }, - success: function(response_text) { - // HACK: use a simple string to separate the elements in the - // response: (1) table body; (2) number of pages in table; and (3) message. - var parsed_response_text = response_text.split("*****"); - - // Update grid body and footer. - $('#grid-table-body').html(parsed_response_text[0]); - // FIXME: this does not work at all; what's needed is a function - // that updates page links when number of pages changes. - $('#grid-table-footer').html(parsed_response_text[1]); - - // Trigger custom event to indicate grid body has changed. - $('#grid-table-body').trigger('update'); - - // Init grid. - init_grid_elements(); - make_popup_menus(); - - // Hide loading overlay. - $('.loading-elt-overlay').hide(); - - // Show message if there is one. - var message = $.trim( parsed_response_text[2] ); - if (message !== "") { - $('#grid-message').html( message ).show(); - setTimeout( function() { $('#grid-message').hide(); }, 5000); - } - }, - complete: function() { - // Clear grid of transient request attributes. - grid.set({ - operation: undefined, - item_ids: undefined - }); - } - }); -} - -function check_all_items() { - var chk_all = document.getElementById('check_all'), - checks = document.getElementsByTagName('input'), - total = 0, - i; - if ( chk_all.checked === true ) { - for ( i=0; i < checks.length; i++ ) { - if ( checks[i].name.indexOf( 'id' ) !== -1) { - checks[i].checked = true; - total++; } } + this.init_grid_elements(); + }, + + // confirmation/submission of operation request + submit_operation: function (selected_button, confirmation_text) + { + // verify in any item is selected + var number_of_checked_ids = $('input[name="id"]:checked').length; + if (!number_of_checked_ids > 0) + return false; + + // show confirmation box + if (confirmation_text != 'None' && confirmation_text != '') + if(!confirm(confirmation_text)) + return false; + + // collect ids + var operation_name = $(selected_button).val(); + var item_ids = []; + $('input[name=id]:checked').each(function() { + item_ids.push( $(this).val() ); + }); + this.do_operation(operation_name, item_ids); + + // return + return true; } - else { - for ( i=0; i < checks.length; i++ ) { - if ( checks[i].name.indexOf( 'id' ) !== -1) { - checks[i].checked = false; - } - } - } - init_grid_elements(); -} - - -// confirmation/submission of operation request -function submit_operation(selected_button, confirmation_text) -{ - // verify in any item is selected - var number_of_checked_ids = $('input[name="id"]:checked').length; - if (!number_of_checked_ids > 0) - return false; - - // show confirmation box - if (confirmation_text != 'None' && confirmation_text != '') - if(!confirm(confirmation_text)) - return false; - - // add ids - var operation_name = selected_button.value; - var item_ids = []; - $('input[name=id]:checked').each(function() { - item_ids.push( $(this).val() ); - }); - do_operation(operation_name, item_ids); - - // return - return true; -} +}); diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_grid_controls(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$("<span>"+e+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(d,e){var c=$('input[name="id"]:checked').length;if(!c>0){return false}if(e!="None"&&e!=""){if(!confirm(e)){return false}}var b=d.value;var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a);return true}; \ No newline at end of file +jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.pairs(b.attributes.filters),function(c){a["f-"+c[0]]=c[1]});return a}});var GridView=Backbone.View.extend({grid:null,initialize:function(a){this.grid=a;this.init_grid_elements();this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var a=this;$(".sort-link").each(function(){$(this).click(function(){a.set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){a.set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){a.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var e=$(this).attr("column_key");var d=$("#input-"+e+"-filter");var f=d.val();d.val("");a.add_filter_condition(e,f,true);return false})});var b=$("#input-tags-filter");if(b.length){b.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var c=$("#input-name-filter");if(c.length){c.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var c=$(this).find("input.grid-row-select-checkbox");var b=$(this).find("span.grid-selected-count");var d=function(){b.text($(c).filter(":checked").length)};$(c).each(function(){$(this).change(d)});d()});var a=this;$(".label").each(function(){var b=$(this).attr("href");if(b!==undefined&&b.indexOf("operation=")!=-1){$(this).click(function(){a.do_operation_from_href($(this).attr("href"));return false})}});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}make_popup_menus()},go_page_one:function(){var a=this.grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){this.grid.set("cur_page",1)}},add_filter_condition:function(d,f,a){if(f===""){return false}this.grid.add_filter(d,f,a);var e=$("<span>"+f+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");e.addClass("text-filter-val");var c=this;e.click(function(){c.grid.remove_filter(d,f);$(this).remove();c.go_page_one();c.update_grid()});var b=$("#"+d+"-filtering-criteria");b.append(e);this.go_page_one();this.update_grid()},set_sort_condition:function(f){var e=this.grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);this.grid.set("sort_key",d);this.go_page_one();this.update_grid()},set_categorical_filter:function(c,e){var b=this.grid.get("categorical_filters")[c],d=this.grid.get("filters")[c];var a=this;$("."+c+"-filter").each(function(){var i=$.trim($(this).text());var g=b[i];var h=g[c];if(h==e){$(this).empty();$(this).addClass("current-filter");$(this).append(i)}else{if(h==d){$(this).empty();var f=$("<a href='#'>"+i+"</a>");f.click(function(){a.set_categorical_filter(c,h)});$(this).removeClass("current-filter");$(this).append(f)}}});this.grid.add_filter(c,e);this.go_page_one();this.update_grid()},set_page:function(a){var b=this;$(".page-link").each(function(){var h=$(this).attr("id"),f=parseInt(h.split("-")[2],10),d=b.grid.get("cur_page"),g;if(f===a){g=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(g)}else{if(f===d){g=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var e=$("<a href='#'>"+g+"</a>");e.click(function(){set_page(f)});$(this).append(e)}}});var c=true;if(a==="all"){this.grid.set("cur_page",a);c=false}else{this.grid.set("cur_page",parseInt(a,10))}this.update_grid(c)},do_operation:function(b,a){b=b.toLowerCase();this.grid.set({operation:b,item_ids:a});if(this.grid.can_async_op(b)){this.update_grid(true)}else{this.go_to_URL()}},do_operation_from_href:function(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}this.do_operation(b,g);return false}},go_to_URL:function(){this.grid.set("async",false);window.location=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data());this.grid.set({operation:undefined,item_ids:undefined})},update_grid:function(b){if(!this.grid.get("async")){this.go_to_URL();return}var c=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var a=this;$.ajax({type:c,url:a.grid.get("url_base"),data:a.grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(e){var d=e.split("*****");$("#grid-table-body").html(d[0]);$("#grid-table-footer").html(d[1]);$("#grid-table-body").trigger("update");a.init_grid_elements();make_popup_menus();$(".loading-elt-overlay").hide();var f=$.trim(d[2]);if(f!==""){$("#grid-message").html(f).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){a.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}this.init_grid_elements()},submit_operation:function(d,e){var c=$('input[name="id"]:checked').length;if(!c>0){return false}if(e!="None"&&e!=""){if(!confirm(e)){return false}}var b=$(d).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});this.do_operation(b,a);return true}}); \ No newline at end of file diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -2,6 +2,7 @@ <!DOCTYPE HTML><html> + ${self.init()} <head><title>${self.title()}</title><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> @@ -17,6 +18,9 @@ ## Default title <%def name="title()"></%def> +## Default init +<%def name="init()"></%def> + ## Default stylesheets <%def name="stylesheets()"> ${h.css('base')} diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -12,16 +12,167 @@ return '/base.mako' %><%inherit file="${inherit(context)}"/> -<%namespace file="/display_common.mako" import="render_message" /> +<%namespace file="./grid_common.mako" import="*" /><%namespace file="/refresh_frames.mako" import="handle_refresh_frames" /> +<%namespace file="/display_common.mako" import="get_class_plural" /><%def name="init()"><% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False - self.active_view="user" - self.overlay_visible=False + self.has_left_panel = False + self.has_right_panel = False + self.message_box_visible = False + self.overlay_visible = False + self.active_view = 'user' + + self.grid_config = { + 'title' : grid.title, + 'url_base' : trans.request.path_url, + 'async' : grid.use_async, + 'async_ops' : [], + 'categorical_filters' : {}, + 'filters' : cur_filter_dict, + 'sort_key' : sort_key, + 'show_item_checkboxes' : context.get('show_item_checkboxes', False), + 'cur_page_num' : cur_page_num, + 'num_pages' : num_pages, + 'history_tag_autocomplete_url' : url( controller='tag', action='tag_autocomplete_data', item_class='History' ), + 'history_name_autocomplete_url' : url( controller='history', action='name_autocomplete_data' ), + 'status' : status, + 'message' : util.restore_text(message), + 'global_actions' : [], + 'operations' : [], + 'items' : [], + 'columns' : [], + 'multiple_item_ops_exist' : None, + 'get_class_plural' : get_class_plural( grid.model_class ).lower(), + 'use_paging' : grid.use_paging, + 'legend' : grid.legend, + 'current_item_id' : '' + } + + ## add current item if exists + if current_item: + self.grid_config['current_item_id'] = current_item.id + endif + + ## column + for column in grid.columns: + + ## add column sort links + href = None + extra = '' + if column.sortable: + if sort_key.endswith(column.key): + if not sort_key.startswith("-"): + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + + ## add to configuration + self.grid_config['columns'].append({ + 'key' : column.key, + 'visible' : column.visible, + 'nowrap' : column.nowrap, + 'attach_popup' : column.attach_popup, + 'label_id_prefix' : column.label_id_prefix, + 'sortable' : column.sortable, + 'label' : column.label, + 'href' : href, + 'extra' : extra + }) + endfor + + ## operations + for operation in grid.operations: + self.grid_config['operations'].append({ + 'allow_multiple' : operation.allow_multiple, + 'allow_popup' : operation.allow_popup, + 'target' : operation.target, + 'label' : operation.label, + 'confirm' : operation.confirm, + 'global_operation' : False + }) + if operation.allow_multiple: + self.grid_config['multiple_item_ops_exist'] = True + + if operation.global_operation: + self.grid_config['global_operation'] = url( ** (operation.global_operation()) ) + endfor + + ## global actions + for action in grid.global_actions: + self.grid_config['global_actions'].append({ + 'url_args' : url(**action.url_args), + 'label' : action.label + }) + endfor + + ## Operations that are async (AJAX) compatible. + for operation in [op for op in grid.operations if op.async_compatible]: + self.grid_config['async_ops'].append(operation.label.lower()); + endfor + + ## Filter values for categorical filters. + for column in grid.columns: + if column.filterable is not None and not isinstance( column, TextColumn ): + self.grid_config['categorical_filters'][column.key] = dict([ (filter.label, filter.args) for filter in column.get_accepted_filters() ]) + endif + endfor + + # items + for i, item in enumerate( query ): + item_dict = { + 'id' : item.id, + 'encode_id' : trans.security.encode_id(item.id), + 'link' : [], + 'operation_config' : {}, + 'column_config' : {} + } + + ## data columns + for column in grid.columns: + if column.visible: + ## get link + link = column.get_link(trans, grid, item) + if link: + link = url(**link) + else: + link = None + endif + + ## get value + value = column.get_value( trans, grid, item ) + + # Handle non-ascii chars. + if isinstance(value, str): + value = unicode(value, 'utf-8') + + # escape string + value = value.replace('/', '//') + endif + + ## Item dictionary + item_dict['column_config'][column.label] = { + 'link' : link, + 'value' : value + } + endif + endfor + ## add operation details to item + for operation in grid.operations: + item_dict['operation_config'][operation.label] = { + 'allowed' : operation.allowed(item), + 'url_args' : url( **operation.get_url_args( item ) ) + } + endfor + + ## add item to list + self.grid_config['items'].append(item_dict) + endfor %></%def> @@ -45,7 +196,7 @@ ${self.make_grid( grid )} </%def> -<%def name="title()">${grid.title}</%def> +<%def name="title()">${self.grid_config['title']}</%def><%def name="javascripts()"> ${parent.javascripts()} @@ -57,65 +208,33 @@ ${handle_refresh_frames()} <script type="text/javascript"> - - // Needed URLs for grid history searching. - var history_tag_autocomplete_url = "${url( controller='tag', action='tag_autocomplete_data', item_class='History' )}", - history_name_autocomplete_url = "${url( controller='history', action='name_autocomplete_data' )}"; - // - // Create grid object. - // + var gridView = null; - // Operations that are async (AJAX) compatible. - var async_ops = []; - %for operation in [op for op in grid.operations if op.async_compatible]: - async_ops.push('${operation.label.lower()}'); - %endfor + function add_tag_to_grid_filter (tag_name, tag_value) + { + // Put tag name and value together. + var tag = tag_name + (tag_value !== undefined && tag_value !== "" ? ":" + tag_value : ""); + $('#advanced-search').show('fast'); + gridView.add_filter_condition("tags", tag, true); + }; - // Filter values for categorical filters. - var categorical_filters = {}; - %for column in grid.columns: - %if column.filterable is not None and not isinstance( column, TextColumn ): - var ${column.key}_filters = ${ h.to_json_string( dict([ (filter.label, filter.args) for filter in column.get_accepted_filters() ]) ) }; - categorical_filters['${column.key}'] = ${column.key}_filters; - %endif - %endfor - - /** Returns true if string denotes true. */ - var is_true = function(s) { return _.indexOf(['True', 'true', 't'], s) !== -1; }; - - // Create grid. - var grid = new Grid({ - url_base: '${trans.request.path_url}', - async: is_true('${grid.use_async}'), - async_ops: async_ops, - categorical_filters: categorical_filters, - filters: ${h.to_json_string( cur_filter_dict )}, - sort_key: '${sort_key}', - show_item_checkboxes: is_true('${context.get('show_item_checkboxes', False)}'), - cur_page: ${cur_page_num}, - // persistent page="all" - //cur_page: ('${cur_page_num}' === 'all')?('all'):(Number('${cur_page_num}')), - num_pages: ${num_pages} - }); - - // Initialize grid objects on load. - // FIXME: use a grid view object eventually. - $(document).ready(function() { + $(function() { + ## get configuration + var grid_config = ${ h.to_json_string( self.grid_config ) }; + console.log(grid_config); + // Create grid. + var grid = new Grid(grid_config); // strip protocol and domain var url = grid.get('url_base'); url = url.replace(/^.*\/\/[^\/]+/, ''); grid.set('url_base', url); - - init_grid_elements(); - init_grid_controls(); - // Initialize text filters to select text on click and use normal font when user is typing. - $('input[type=text]').each(function() { - $(this).click(function() { $(this).select(); } ) - .keyup(function () { $(this).css("font-style", "normal"); }); - }); + + // Create view. + gridView = new GridView(grid); }); + </script></%def> @@ -127,17 +246,12 @@ %if context.get('use_panels'): div#center { padding: 10px; + overflow: auto; } %endif </style></%def> -## -## Custom grid methods. -## - -<%namespace file="./grid_common.mako" import="*" /> - <%def name="make_grid( grid )"><div class="loading-elt-overlay"></div><table> @@ -147,7 +261,14 @@ <td></td></tr><tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> + <td width="100%" id="grid-message" valign="top"> + %if message: + <p> + <div class="${self.grid_config['status']}message transient-message">${self.grid_config['message']}</div> + <div style="clear: both"></div> + </p> + %endif + </td><td></td><td></td></tr> @@ -157,7 +278,7 @@ </%def><%def name="grid_title()"> - <h2>${grid.title}</h2> + <h2>${self.grid_config['title']}</h2></%def> ## Render grid header. @@ -166,18 +287,18 @@ %if render_title: ${self.grid_title()} %endif - - %if grid.global_actions: + + %if self.grid_config['global_actions']: <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 3: - %for action in grid.global_actions: - <li><a class="action-button" href="${url( **action.url_args )}">${action.label}</a></li> + %if len( self.grid_config['global_actions'] ) < 3: + %for action in self.grid_config['global_actions']: + <li><a class="action-button" href="${action['url_args']}">${action['label']}</a></li> %endfor %else: <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li><div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${url( **action.url_args )}">${action.label}</a> + %for action in self.grid_config['global_actions']: + <a class="action-button" href="${action['url_args']}">${action['label']}</a> %endfor </div> %endif @@ -191,55 +312,37 @@ ## Render grid. <%def name="render_grid_table( grid, show_item_checkboxes=False)"><% - # Set flag to indicate whether grid has operations that operate on multiple items. - multiple_item_ops_exist = False - for operation in grid.operations: - if operation.allow_multiple: - multiple_item_ops_exist = True - + # get configuration + show_item_checkboxes = self.grid_config['show_item_checkboxes'] + multiple_item_ops_exist = self.grid_config['multiple_item_ops_exist'] + sort_key = self.grid_config['sort_key'] + # Show checkboxes if flag is set or if multiple item ops exist. if show_item_checkboxes or multiple_item_ops_exist: show_item_checkboxes = True %> - <form action="${url()}" method="post" onsubmit="return false;"> + <form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"><tr> %if show_item_checkboxes: <th> - %if query.count() > 0: - <input type="checkbox" id="check_all" name=select_all_checkbox value="true" onclick='check_all_items(1);'><input type="hidden" name=select_all_checkbox value="true"> + %if len(self.grid_config['items']) > 0: + <input type="checkbox" id="check_all" name=select_all_checkbox value="true" onclick='gridView.check_all_items(1);'><input type="hidden" name=select_all_checkbox value="true"> %endif </th> %endif - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key.endswith(column.key): - if not sort_key.startswith("-"): - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> + %for column in self.grid_config['columns']: + %if column['visible']: <th\ - id="${column.key}-header" - %if column.ncells > 1: - colspan="${column.ncells}" - %endif + id="${column['key']}-header" > - %if href: - <a href="${href}" class="sort-link" sort_key="${column.key}">${column.label}</a> + %if column['href']: + <a href="${column['href']}" class="sort-link" sort_key="${column['key']}">${column['label']}</a> %else: - ${column.label} + ${column['label']} %endif - <span class="sort-arrow">${extra}</span> + <span class="sort-arrow">${column['extra']}</span></th> %endif %endfor @@ -259,15 +362,16 @@ ## Render grid table body contents. <%def name="render_grid_table_body_contents(grid, show_item_checkboxes=False)"><% num_rows_rendered = 0 %> - %if query.count() == 0: + %if len(self.grid_config['items']) == 0: ## No results. <tr><td colspan="100"><em>No Items</em></td></tr><% num_rows_rendered = 1 %> %endif - %for i, item in enumerate( query ): - <% encoded_id = trans.security.encode_id( item.id ) %> + %for i, item in enumerate( self.grid_config['items'] ): + <% encoded_id = item['encode_id'] %> + <% popupmenu_id = "grid-" + str(i) + "-popup" %><tr \ - %if current_item == item: + %if self.grid_config['current_item_id'] == item['id']: class="current" \ %endif > @@ -278,71 +382,72 @@ </td> %endif ## Data columns - %for column in grid.columns: - %if column.visible: + %for column in self.grid_config['columns']: + %if column['visible']: <% - # Nowrap + ## Nowrap nowrap = "" - if column.nowrap: - nowrap = 'style="white-space:nowrap;"' - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] + if column['nowrap']: + nowrap = 'style="white-space:nowrap;"' + + # get column settings + column_settings = item['column_config'][column['label']] + + # load attributes + link = column_settings['link'] + value = column_settings['value'] + + # check if formatting is defined + value = str(value).replace('//', '/') + + # Attach popup menu? + id = "" + if column['attach_popup']: + id = 'grid-%d-popup' % i + endif + + # Determine appropriate class + cls = "" + if column['attach_popup']: + cls = "menubutton" + if link: + cls += " split" + endif + endif %> - %for cellnum, v in enumerate( value ): - <% - id = "" - # Handle non-ascii chars. - if isinstance(v, str): - v = unicode(v, 'utf-8') - # Attach popup menu? - if column.attach_popup and cellnum == 0: - id = 'grid-%d-popup' % i - # Determine appropriate class - cls = "" - if column.attach_popup: - cls = "menubutton" - if href: - cls += " split" - - %> - <td ${nowrap}> - %if href: - %if len(grid.operations) != 0: + <td ${nowrap}> + %if link: + %if len(self.grid_config['operations']) != 0: <div id="${id}" class="${cls}" style="float: left;"> - %endif - <a class="label" href="${href}">${v}</a> - %if len(grid.operations) != 0: + %endif + <a class="label" href="${link}">${value}</a> + %if len(self.grid_config['operations']) != 0: </div> - %endif - %else: - <div id="${id}" class="${cls}"><label id="${column.label_id_prefix}${encoded_id}" for="${encoded_id}">${v}</label></div> %endif - </td> - %endfor + %else: + <div id="${id}" class="${cls}"><label id="${column['label_id_prefix']}${encoded_id}" for="${encoded_id}">${value}</label></div> + %endif + </td> %endif %endfor ## Actions column <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ) and operation.allow_popup: + <div popupmenu="${popupmenu_id}"> + %for operation in self.grid_config['operations']: + <% + operation_id = operation['label'] + operation_settings = item['operation_config'][operation_id] + %> + %if operation_settings['allowed'] and operation['allow_popup']: <% target = "" - if operation.target: - target = "target='" + operation.target + "'" + if operation['target']: + target = "target='" + operation['target'] + "'" %> - %if operation.confirm: - <a class="action-button" ${target} confirm="${operation.confirm}" href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + %if operation['confirm']: + <a class="action-button" ${target} confirm="${operation['confirm']}" href="${operation_settings['url_args']}">${operation_id}</a> %else: - <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + <a class="action-button" ${target} href="${operation_settings['url_args']}">${operation_id}</a> %endif %endif %endfor @@ -351,20 +456,16 @@ </tr><% num_rows_rendered += 1 %> %endfor - ## Dummy rows to prevent table for moving too much. - ##%if grid.use_paging: - ## %for i in range( num_rows_rendered , grid.num_rows_per_page ): - ## <tr><td colspan="1000"></td></tr> - ## %endfor - ##%endif </%def> ## Render grid table footer contents. <%def name="render_grid_table_footer_contents(grid, show_item_checkboxes=False)"> - ## Row for navigating among pages. - <%namespace file="/display_common.mako" import="get_class_plural" /> - <% items_plural = get_class_plural( grid.model_class ).lower() %> - %if grid.use_paging and num_pages > 1: + <% + items_plural = self.grid_config['get_class_plural'] + num_pages = self.grid_config['num_pages'] + cur_page_num = self.grid_config['cur_page_num'] + %> + %if self.grid_config['use_paging'] and num_pages > 1: <tr id="page-links-row"> %if show_item_checkboxes: <td></td> @@ -438,33 +539,29 @@ <td></td><td colspan="100"> For <span class="grid-selected-count"></span> selected ${items_plural}: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="button" value="${operation.label}" class="action-button" onclick="submit_operation(this, '${operation.confirm}')"> + %for operation in self.grid_config['operations']: + %if operation['allow_multiple']: + <input type="button" value="${operation['label']}" class="action-button" onclick="gridView.submit_operation(this, '${operation['confirm']}')"> %endif %endfor </td></tr> %endif - %if len([o for o in grid.operations if o.global_operation]) > 0: + %if len([o for o in self.grid_config['operations'] if o['global_operation']]) > 0: <tr><td colspan="100"> - %for operation in grid.operations: - %if operation.global_operation: - <% - link = operation.global_operation() - href = url( **link ) - %> - <a class="action-button" href="${href}">${operation.label}</a> - %endif + %for operation in self.grid_config['operations']: + %if operation['global_operation']: + <a class="action-button" href="${operation['global_operation']}">${operation['label']}</a> + %endif %endfor </td></tr> %endif - %if grid.legend: + %if self.grid_config['legend']: <tr><td colspan="100"> - ${grid.legend} + ${self.grid_config['legend']} </td></tr> %endif diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/grid_base_async.mako --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,6 +1,8 @@ <%namespace file="./grid_base.mako" import="*" /><%namespace file="/display_common.mako" import="render_message" /> +${init()} + <% # Set flag to indicate whether grid has operations that operate on multiple items. multiple_item_ops_exist = False diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/webapps/galaxy/page/select_items_grid.mako --- a/templates/webapps/galaxy/page/select_items_grid.mako +++ b/templates/webapps/galaxy/page/select_items_grid.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to select items. <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${grid_javascripts()} ${stylesheets()} ${render_grid_header( grid, False )} diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/webapps/galaxy/page/select_items_grid_async.mako --- a/templates/webapps/galaxy/page/select_items_grid_async.mako +++ b/templates/webapps/galaxy/page/select_items_grid_async.mako @@ -1,6 +1,6 @@ <%namespace file="../grid_base.mako" import="*" /><%namespace file="/display_common.mako" import="render_message" /> - +${init()} ## Always show item checkboxes so that users can select items. ${render_grid_table_body_contents( grid, show_item_checkboxes=show_item_checkboxes )} ***** diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/webapps/galaxy/tracks/add_to_viz.mako --- a/templates/webapps/galaxy/tracks/add_to_viz.mako +++ b/templates/webapps/galaxy/tracks/add_to_viz.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} ${render_grid_header( grid, False )} diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/webapps/galaxy/tracks/add_tracks.mako --- a/templates/webapps/galaxy/tracks/add_tracks.mako +++ b/templates/webapps/galaxy/tracks/add_tracks.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} ${render_grid_header( grid, False )} diff -r 5e534cc8da856ad598d63b8b9f03fe20629df05f -r f1cef709a9e5631cae2126ffff71dbba64611f87 templates/webapps/galaxy/tracks/history_select_grid.mako --- a/templates/webapps/galaxy/tracks/history_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_select_grid.mako @@ -4,7 +4,7 @@ ## not make it possible to easily subclass templates. ## <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} @@ -12,18 +12,16 @@ <script type="text/javascript"> // Load all grid URLs into modal-body element so that // grid + links stays embedded. - var load_urls_into_modal_body = function() { + $(document).ready(function() { + $(".addtracktab, #grid-table a").off(); $(".addtracktab, #grid-table a").click(function() { + console.log($(this).attr("href")); var modal_body = $(".modal-body"); if (modal_body.length !== 0) { modal_body.load($(this).attr("href")); return false; } }); - }; - // Need to process label URLs when document loaded and when grid changes. - $(document).ready(function() { - load_urls_into_modal_body(); }); </script><style> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Functional tool test fix.
by commits-noreply＠bitbucket.org 17 Nov '13

17 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e534cc8da85/ Changeset: 5e534cc8da85 User: jmchilton Date: 2013-11-17 09:03:28 Summary: Functional tool test fix. No tests with a repeat and min=1 were ever going to past. Affected #: 1 file diff -r ef9968a089db28349b22c302ca07e9aa152bfe51 -r 5e534cc8da856ad598d63b8b9f03fe20629df05f test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -93,7 +93,8 @@ repeat_name = None for input_name, input_value in testdef.tool.inputs_by_page[0].items(): if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: # default behavior is to test 1 repeat, for backwards compatibility - repeat_name = input_name + if not input_value.min: # If input_value.min == 1, the element is already on the page don't add new element. + repeat_name = input_name break #check if we need to verify number of outputs created dynamically by tool 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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galaxy-commits November 2013