October 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2924: Require login to perform visualization (otherw...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a471575d1e4a changeset: 2924:a471575d1e4a user: James Taylor <james(a)jamestaylor.org> date: Tue Oct 27 13:39:48 2009 -0400 description: Require login to perform visualization (otherwise we have no way to store them) 2 file(s) affected in this change: lib/galaxy/web/controllers/tracks.py lib/galaxy/web/controllers/visualization.py diffs (28 lines): diff -r 734722f10df8 -r a471575d1e4a lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Oct 27 13:28:25 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Oct 27 13:39:48 2009 -0400 @@ -63,6 +63,7 @@ return trans.fill_template( "tracks/index.mako" ) @web.expose + @web.require_login() def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ): """ Build a new browser from datasets in the current history. Redirects diff -r 734722f10df8 -r a471575d1e4a lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Tue Oct 27 13:28:25 2009 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Tue Oct 27 13:39:48 2009 -0400 @@ -28,11 +28,13 @@ class VisualizationController( BaseController ): @web.expose + @web.require_login() def index( self, trans ): return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) ) list_grid = VisualizationListGrid() @web.expose + @web.require_login() def list( self, trans, *args, **kwargs ): return self.list_grid( trans, *args, **kwargs )

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[hg] galaxy 2917: trackster: fix blocks display, navigation issu...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8f57bd9b180c changeset: 2917:8f57bd9b180c user: Kanwei Li <kanwei(a)gmail.com> date: Fri Oct 23 14:57:08 2009 -0400 description: trackster: fix blocks display, navigation issues, now displays strand direction arrows 7 file(s) affected in this change: lib/galaxy/visualization/tracks/data/interval_index.py static/images/visualization/draggable_horizontal.png static/images/visualization/strand_left.png static/images/visualization/strand_right.png static/scripts/trackster.js static/trackster.css templates/tracks/browser.mako diffs (218 lines): diff -r 02127dd91492 -r 8f57bd9b180c lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Fri Oct 23 14:51:22 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Fri Oct 23 14:57:08 2009 -0400 @@ -21,19 +21,19 @@ for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3] } + payload = { 'start': start, 'end': end, 'name': feature[3], 'strand': feature[5] } try: block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip(block_sizes, block_starts) - payload['block_start_end'] = [ (chrom_start + block[1], chrom_start + block[1] + block[0]) for block in blocks] - except: + payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] + except IndexError: pass try: payload['exon_start'] = int(feature[6]) payload['exon_end'] = int(feature[7]) - except: + except IndexError: pass results.append(payload) diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/draggable_horizontal.png Binary file static/images/visualization/draggable_horizontal.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/strand_left.png Binary file static/images/visualization/strand_left.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/strand_right.png Binary file static/images/visualization/strand_right.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Oct 23 14:51:22 2009 -0400 +++ b/static/scripts/trackster.js Fri Oct 23 14:57:08 2009 -0400 @@ -6,7 +6,20 @@ DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", CACHED_TILES = 50, - CACHED_DATA = 20; + CACHED_DATA = 20, + CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), + RIGHT_STRAND, LEFT_STRAND; + +var right_img = new Image(); +right_img.src = "../images/visualization/strand_right.png"; +right_img.onload = function() { + RIGHT_STRAND = CONTEXT.createPattern(right_img, "repeat"); +} +var left_img = new Image(); +left_img.src = "../images/visualization/strand_left.png"; +left_img.onload = function() { + LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); +} function commatize( number ) { number += ''; // Convert to string @@ -101,6 +114,7 @@ var TiledTrack = function() { this.tile_cache = new Cache(CACHED_TILES); + // this.tile_cache = {}; }; $.extend( TiledTrack.prototype, Track.prototype, { draw: function() { @@ -126,20 +140,20 @@ while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.view.zoom_level + "_" + tile_index; - if ( this.tile_cache[key] ) { + var cached = this.tile_cache.getItem(key); + if ( cached ) { // console.log("cached tile"); - tile_element = this.tile_cache[key]; var tile_low = tile_index * DENSITY * resolution; - tile_element.css( { + cached.css( { left: ( tile_low - this.view.low ) * w_scale }); // Our responsibility to move the element to the new parent - parent_element.append( tile_element ); + parent_element.append( cached ); } else { tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale, h ); } if ( tile_element ) { - this.tile_cache[key] = tile_element; + this.tile_cache.setItem(key, tile_element); } tile_index += 1; } @@ -340,6 +354,7 @@ if (!this.values) { // Still loading return null; } + // console.log("drawing"); // Once we zoom in enough, show name labels if (w_scale > this.show_labels_scale && !this.showing_labels) { this.showing_labels = true; @@ -373,7 +388,7 @@ ctx.fillStyle = "#000"; ctx.font = "10px monospace"; ctx.textAlign = "right"; - + var j = 0; for (var i = 0, len = this.values.length; i < len; i++) { var feature = this.values[i]; @@ -381,9 +396,19 @@ var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), y_center = this.slots[feature.name] * this.vertical_gap; - - // console.log(feature.start, feature.end, f_start, f_end, j); - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + + if (feature.strand && this.showing_labels) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } else { + ctx.fillStyle = "#000"; + ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + } if (this.showing_labels && ctx.fillText) { ctx.fillText(feature.name, f_start, y_center + 8); @@ -393,18 +418,17 @@ if (feature.exon_start && feature.exon_end) { exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - ctx.fillRect(exon_start, y_center + 4, exon_end - exon_start, 3); } - if (feature.blocks) { + if (feature.blocks && this.showing_labels) { for (var k = 0, k_len = feature.blocks.length; k < k_len; k++) { var block = feature.blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness = 3, y_start = 4; + var thickness = 5, y_start = 3; if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 5; - y_start = 3; + thickness = 7; + y_start = 2; } ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); // console.log(block_start, block_end); diff -r 02127dd91492 -r 8f57bd9b180c static/trackster.css --- a/static/trackster.css Fri Oct 23 14:51:22 2009 -0400 +++ b/static/trackster.css Fri Oct 23 14:57:08 2009 -0400 @@ -63,7 +63,7 @@ position: absolute; margin-top: 1px; height: 16px; - background: #ddd url(images/draggable_horizontal.png) center center no-repeat; + background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; border-style: outset; border-width: 1px; } @@ -79,7 +79,6 @@ width: 100%; height: 100px; } - .track { /* border-top: solid gray 1px;*/ border-bottom: solid gray 1px; diff -r 02127dd91492 -r 8f57bd9b180c templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Oct 23 14:51:22 2009 -0400 +++ b/templates/tracks/browser.mako Fri Oct 23 14:57:08 2009 -0400 @@ -16,7 +16,7 @@ $(function() { - view.add_track( new LabelTrack( $("#viewport" ) ) ); + view.add_track( new LabelTrack( $("#top-labeltrack" ) ) ); view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); %for track in tracks: @@ -51,11 +51,6 @@ var delta_chrom = Math.round(delta / $(document).width() * view.span); view.center += delta_chrom; - if (view.center < 0) { - view.center = 0; - } else if (view.center > view.max_high) { - view.center = view.max_high; - } view.redraw(); }); @@ -79,8 +74,8 @@ this.current_height = e.clientY; this.current_x = e.offsetX; - var delta_chrom = Math.round(delta / $(document).width() * (view.max_high - view.max_low)); - view.center += delta_chrom; + var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); + view.center -= delta_chrom; view.redraw(); }); (function () { @@ -108,6 +103,7 @@ </%def> <div id="content"> + <div id="top-labeltrack"></div> <div id="viewport"></div> </div> <div id="nav">

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[hg] galaxy 2918: Tweaking trackster UI to fit Galaxy interface ...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b53985e5548c changeset: 2918:b53985e5548c user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 18:49:18 2009 -0400 description: Tweaking trackster UI to fit Galaxy interface a little better (broke something with spacing though) 3 file(s) affected in this change: static/scripts/trackster.js static/trackster.css templates/tracks/browser.mako diffs (224 lines): diff -r 8f57bd9b180c -r b53985e5548c static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Oct 23 14:57:08 2009 -0400 +++ b/static/scripts/trackster.js Fri Oct 23 18:49:18 2009 -0400 @@ -68,8 +68,8 @@ // Minimum width for usability width: Math.max( 12, ( ( this.high - this.low ) / this.span ) * $("#overview-viewport").width() ) }).show(); - $("#low").text( commatize(this.low) ); - $("#high").text( commatize(this.high) ); + $("#low").val( commatize(this.low) ); + $("#high").val( commatize(this.high) ); for ( var i = 0, len = this.tracks.length; i < len; i++ ) { this.tracks[i].draw(); } @@ -204,9 +204,11 @@ chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { - track.content_div.addClass("error").text(DATA_ERROR); + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); } else if (data == "no data") { - track.content_div.addClass("nodata").text(DATA_NONE); + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); } else { track.content_div.css( "height", track.height_px + "px" ); track.min_value = data.min; @@ -298,9 +300,11 @@ high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { - track.content_div.addClass("error").text(DATA_ERROR); + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); } else if (data.length === 0 || data == "no data") { - track.content_div.addClass("nodata").text(DATA_NONE); + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); } else { track.content_div.css( "height", track.height_px + "px" ); track.values = data; diff -r 8f57bd9b180c -r b53985e5548c static/trackster.css --- a/static/trackster.css Fri Oct 23 14:57:08 2009 -0400 +++ b/static/trackster.css Fri Oct 23 18:49:18 2009 -0400 @@ -25,9 +25,25 @@ text-align: center; } +input { + font-size: 100%; +} + +#nav { + padding: 0.5em 0; + background:#cccccc; + background-image:url(style/panel_header_bg.png); + background-position:top center; + background-repeat:repeat-x;border-top:solid #999 1px; + color:#333;font-weight:bold; + } + + +/* #nav-controls { padding: 15px 0; } +*/ #nav-controls a { color: white; padding: 0.1em 0.4em; @@ -37,6 +53,8 @@ -webkit-border-radius: 1em; -moz-border-radius: 1em; } + +/* #low { margin-left: 0.1em; float: left; @@ -45,27 +63,30 @@ margin-right: 0.1em; float: right; } +*/ #overview { width: 100%; margin: 0px; - background: #333; color: white; } #overview-viewport { - height: 20px; + position: relative; + height: 14px; /* border-top: solid #666 1px;*/ /* border-bottom: solid #aaa 1px;*/ - background: #888; + background: white; + border: solid grey 1px; + margin: 5px; } #overview-box { position: absolute; - margin-top: 1px; - height: 16px; + margin-top: 0px; + height: 14px; + background: grey; background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; - border-style: outset; - border-width: 1px; + /*border-style: outset;*/ } #viewport { @@ -80,29 +101,25 @@ height: 100px; } .track { -/* border-top: solid gray 1px;*/ - border-bottom: solid gray 1px; +/* border-top: solid gray 1px; */ +/* border-bottom: solid gray 1px; */ } .track-header { text-align: center; + padding: 2px 0; } .track-content { overflow: hidden; + text-align: center; } -.track-content.error { - text-align: center; - padding-top: 10px; +.track.error { background-color: #ECB4AF; - height: 30px; } -.track-content.nodata { - text-align: center; - padding-top: 10px; +.track.nodata { background-color: #ddd; - height: 30px; } .loading { @@ -110,12 +127,21 @@ } .label-track { - font-weight: bold; - font-size: 10px; - background-color: #333; - color: white; + /* font-weight: bold; */ + /* font-size: 10px; */ + } .label-track .label { - border-left: solid gray 1px; - padding-left: 2px; + border-left: solid #999 1px; + padding: 1px; + display: inline-block; } + +#top-labeltrack { + border-bottom: solid #999 1px; +} + +#nav-labeltrack { + border-top: solid #999 1px; + border-bottom: solid #999 1px; +} diff -r 8f57bd9b180c -r b53985e5548c templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Oct 23 14:57:08 2009 -0400 +++ b/templates/tracks/browser.mako Fri Oct 23 18:49:18 2009 -0400 @@ -105,25 +105,24 @@ <div id="content"> <div id="top-labeltrack"></div> <div id="viewport"></div> + <div id="nav-labeltrack"></div> </div> <div id="nav"> - <div id="nav-labeltrack"></div> + <div id="nav-controls"> + <form name="chr" id="chr" method="get"> + <select id="chrom" name="chrom" style="width: 15em;"> + <option value="">Loading</option> + </select> + <input id="low" size="12"></input>:<input id="high" size="12"></input> + ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> + <input type="hidden" name="id" value="${id}" /> + <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> + <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> + </form> + </div> <div id="overview"> <div id="overview-viewport"> <div id="overview-box"></div> </div> </div> - <span id="low"></span> - <span id="high"></span> - <div id="nav-controls"> - <form name="chr" id="chr" method="get"> - <select id="chrom" name="chrom"> - <option value="">Loading</option> - </select> - ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> - <input type="hidden" name="id" value="${id}" /> - <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> - <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> - </form> - </div> </div>

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[hg] galaxy 2919: Fixed a bug in viewing request type
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ef5215401458 changeset: 2919:ef5215401458 user: rc date: Mon Oct 26 14:01:46 2009 -0400 description: Fixed a bug in viewing request type 1 file(s) affected in this change: templates/admin/requests/view_request_type.mako diffs (21 lines): diff -r b53985e5548c -r ef5215401458 templates/admin/requests/view_request_type.mako --- a/templates/admin/requests/view_request_type.mako Fri Oct 23 18:49:18 2009 -0400 +++ b/templates/admin/requests/view_request_type.mako Mon Oct 26 14:01:46 2009 -0400 @@ -5,8 +5,6 @@ %if msg: ${render_msg( msg, messagetype )} %endif - -<% num_states=len(states_list) %> <div class="toolForm"> <div class="toolFormTitle">View request type details</div> @@ -38,7 +36,7 @@ <label> Possible states </label> - %for element_count, state in enumerate(states_list): + %for element_count, state in enumerate(states_list.all()): <div class="form-row"> <label>${1+element_count}. ${state.name}</label> ${state.desc}

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[hg] galaxy 2920: Samples go to to next state when bar codes are...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fa0483a31237 changeset: 2920:fa0483a31237 user: rc date: Mon Oct 26 15:05:20 2009 -0400 description: Samples go to to next state when bar codes are assigned to them 3 file(s) affected in this change: lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/admin/requests/show_request.mako diffs (58 lines): diff -r ef5215401458 -r fa0483a31237 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Oct 26 14:01:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Mon Oct 26 15:05:20 2009 -0400 @@ -460,7 +460,7 @@ select_request_type = self.__select_request_type(trans, request_type.id) # list of widgets to be rendered on the request form widgets = [] - widgets.append(dict(label='Name', + widgets.append(dict(label='Name of the Experiment', widget=TextField('name', 40, util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) diff -r ef5215401458 -r fa0483a31237 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Oct 26 14:01:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Oct 26 15:05:20 2009 -0400 @@ -358,7 +358,7 @@ widgets.append(dict(label='Select user', widget=self.__select_user(trans, user_id), helptext='The request would be submitted on behalf of this user (Required)')) - widgets.append(dict(label='Name', + widgets.append(dict(label='Name of the Experiment', widget=TextField('name', 40, util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) @@ -391,7 +391,7 @@ def __get_email(user): return user.email user_list = trans.sa_session.query( trans.app.model.User ) - user_list.sort(key=__get_email) + #user_list.sort(key=__get_email) for user in user_list: if not user.deleted: if userid == str(user.id): @@ -1038,6 +1038,12 @@ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, '')) sample.bar_code = bar_code sample.flush() + # change the state of all the samples to the next state + # get the new state + new_state = request.type.states[1] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Bar code added to this sample') + event.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='bar_codes', request_id=request.id, diff -r ef5215401458 -r fa0483a31237 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Mon Oct 26 14:01:46 2009 -0400 +++ b/templates/admin/requests/show_request.mako Mon Oct 26 15:05:20 2009 -0400 @@ -180,7 +180,7 @@ ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} %endif <td> - %if request.unsubmitted() and grid_index == 0: + %if grid_index == 0: <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> <img src="${h.url_for('/static/images/delete_icon.png')}" /> <span></span></a>

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[hg] galaxy 2914: 2 more sqlalchemy 0.5 query fixes.
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/50631e30ede2 changeset: 2914:50631e30ede2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Oct 23 13:58:56 2009 -0400 description: 2 more sqlalchemy 0.5 query fixes. 2 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/tools/__init__.py diffs (24 lines): diff -r a559bdff7fdc -r 50631e30ede2 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Oct 23 13:54:15 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Fri Oct 23 13:58:56 2009 -0400 @@ -533,7 +533,7 @@ #since if it is edited, the metadata changed on the running output will no longer match #the metadata that was stored to disk for use via the external process, #and the changes made by the user will be lost, without warning or notice - dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset ).filename_out ) + dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset, self.sa_session ).filename_out ) try: assert context.get( 'line_count', None ) is not None if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: diff -r a559bdff7fdc -r 50631e30ede2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Oct 23 13:54:15 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 23 13:58:56 2009 -0400 @@ -1568,7 +1568,7 @@ for name, dataset in inp_data.iteritems(): external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): - dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset ).filename_out ) + dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out ) # If setting external metadata has failed, how can we inform the user? # For now, we'll leave the default metadata and set the state back to its original. dataset.datatype.after_edit( dataset )

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[hg] galaxy 2915: Make Galaxy attempt to honor the user's umask ...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1ce07e82a4c1 changeset: 2915:1ce07e82a4c1 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 23 14:33:23 2009 -0400 description: Make Galaxy attempt to honor the user's umask and primary group (output datasets can have the wrong primary group if the primary group differs on the cluster). Also fixed a composite datatype files_path bug in the upload tool. 9 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/jobs/__init__.py lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/actions/upload_common.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/tool_runner.py tools/data_source/upload.py tools/data_source/upload.xml diffs (204 lines): diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/config.py --- a/lib/galaxy/config.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/config.py Fri Oct 23 14:33:23 2009 -0400 @@ -23,6 +23,10 @@ def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) + # Collect the umask and primary gid from the environment + self.umask = os.umask( 077 ) # get the current umask + os.umask( self.umask ) # can't get w/o set, so set it back + self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Fri Oct 23 14:33:23 2009 -0400 @@ -594,9 +594,10 @@ self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data, out_data=out_data, param_dict=param_dict, tool=self.tool, stdout=stdout, stderr=stderr ) - # TODO - # validate output datasets job.command_line = self.command_line + # fix permissions + for path in [ dp.real_path for dp in self.get_output_fnames() ]: + util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) self.cleanup() diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 23 14:33:23 2009 -0400 @@ -1463,6 +1463,14 @@ if len( os.listdir( temp_file_path ) ) > 0: store_file_path = os.path.join( os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), "dataset_%d_files" % hda.dataset.id ) shutil.move( temp_file_path, store_file_path ) + # fix permissions + for basedir, dirs, files in os.walk( store_file_path ): + util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid ) + for file in files: + path = os.path.join( basedir, file ) + if os.path.islink( path ): + continue # ignore symlinks + util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) except: continue diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Fri Oct 23 14:33:23 2009 -0400 @@ -202,6 +202,8 @@ trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) # Create an empty file immediately open( data.file_name, "w" ).close() + # Fix permissions + util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 ) # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Fri Oct 23 14:33:23 2009 -0400 @@ -239,7 +239,6 @@ type = uploaded_dataset.type, metadata = uploaded_dataset.metadata, primary_file = uploaded_dataset.primary_file, - extra_files_path = data.extra_files_path, composite_file_paths = uploaded_dataset.composite_files, composite_files = dict( [ ( k, v.__dict__ ) for k, v in data.datatype.get_composite_files( data ).items() ] ) ) else: diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/util/__init__.py Fri Oct 23 14:33:23 2009 -0400 @@ -3,7 +3,7 @@ """ import logging -import threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile +import threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp # Older py compatibility try: @@ -483,6 +483,38 @@ raise raise IOError, (errno.EEXIST, "No usable temporary file name found") +def umask_fix_perms( path, umask, unmasked_perms, gid=None ): + """ + umask-friendly permissions fixing + """ + perms = unmasked_perms & ~umask + st = os.stat( path ) + # fix modes + if stat.S_IMODE( st.st_mode ) != perms: + try: + os.chmod( path, perms ) + except Exception, e: + log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), \ + path, + oct( perms ), + oct( stat.S_IMODE( st.st_mode ) ), + e ) ) + # fix group + if gid is not None and st.st_gid != gid: + try: + os.chown( path, -1, gid ) + except Exception, e: + try: + desired_group = grp.getgrgid( gid ) + current_group = grp.getgrgid( st.st_gid ) + except: + desired_group = gid + current_group = st.st_gid + log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, \ + path, + current_group, + e ) ) + galaxy_root_path = os.path.join(__path__[0], "..","..","..") # The dbnames list is used in edit attributes and the upload tool dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) diff -r 50631e30ede2 -r 1ce07e82a4c1 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Fri Oct 23 13:58:56 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Fri Oct 23 14:33:23 2009 -0400 @@ -140,7 +140,6 @@ permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) def create_dataset( name ): ud = Bunch( name=name, file_type=None, dbkey=None ) - # Okay, time to make this crap actually use the upload_common functions, which means making them get called from outside the json_paramfile method. if nonfile_params.get( 'folder_id', False ): replace_id = nonfile_params.get( 'replace_id', None ) if replace_id not in [ None, 'None' ]: diff -r 50631e30ede2 -r 1ce07e82a4c1 tools/data_source/upload.py --- a/tools/data_source/upload.py Fri Oct 23 13:58:56 2009 -0400 +++ b/tools/data_source/upload.py Fri Oct 23 14:33:23 2009 -0400 @@ -119,8 +119,8 @@ def parse_outputs( args ): rval = {} for arg in args: - id, path = arg.split( ':', 1 ) - rval[int( id )] = path + id, files_path, path = arg.split( ':', 2 ) + rval[int( id )] = ( path, files_path ) return rval def add_file( dataset, json_file, output_path ): @@ -255,9 +255,9 @@ line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) -def add_composite_file( dataset, json_file, output_path ): +def add_composite_file( dataset, json_file, output_path, files_path ): if dataset.composite_files: - os.mkdir( dataset.extra_files_path ) + os.mkdir( files_path ) for name, value in dataset.composite_files.iteritems(): value = util.bunch.Bunch( **value ) if dataset.composite_file_paths[ value.name ] is None and not value.optional: @@ -269,7 +269,7 @@ sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] ) else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) - shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( files_path, name ) ) # Move the dataset to its "real" path shutil.move( dataset.primary_file, output_path ) # Write the job info @@ -290,12 +290,13 @@ dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) try: - output_path = output_paths[int( dataset.dataset_id )] + output_path = output_paths[int( dataset.dataset_id )][0] except: print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id sys.exit( 1 ) if dataset.type == 'composite': - add_composite_file( dataset, json_file, output_path ) + files_path = output_paths[int( dataset.dataset_id )][1] + add_composite_file( dataset, json_file, output_path, files_path ) else: add_file( dataset, json_file, output_path ) # clean up paramfile diff -r 50631e30ede2 -r 1ce07e82a4c1 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Fri Oct 23 13:58:56 2009 -0400 +++ b/tools/data_source/upload.xml Fri Oct 23 14:33:23 2009 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.0.3"> +<tool name="Upload File" id="upload1" version="1.0.4"> <description> from your computer </description> @@ -11,7 +11,7 @@ #while $varExists('output%i' % $outnum): #set $output = $getVar('output%i' % $outnum) #set $outnum += 1 - ${output.dataset.dataset.id}:${output} + ${output.dataset.dataset.id}:${output.files_path}:${output} #end while </command> <inputs nginx_upload="true">

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[hg] galaxy 2916: Migration script for viz
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/02127dd91492 changeset: 2916:02127dd91492 user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 14:51:22 2009 -0400 description: Migration script for viz 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0022_visualization_tables.py diffs (59 lines): diff -r 1ce07e82a4c1 -r 02127dd91492 lib/galaxy/model/migrate/versions/0022_visualization_tables.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0022_visualization_tables.py Fri Oct 23 14:51:22 2009 -0400 @@ -0,0 +1,55 @@ +""" +Migration script to add support for storing visualizations. + 1) Creates Visualization and VisualizationRevision tables +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +Visualization_table = Table( "visualization", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ), + Column( "title", TEXT ), + Column( "type", TEXT ) + ) + +VisualizationRevision_table = Table( "visualization_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "config", TEXT ) + ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + Visualization_table.create() + except: + log.debug( "Could not create page table" ) + try: + VisualizationRevision_table.create() + except: + log.debug( "Could not create page_revision table" ) + + +def downgrade(): + metadata.reflect() + Visualization_table.drop() + VisualizationRevision_table.drop() +

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[hg] galaxy 2913: Fix query style in tracks controller
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a559bdff7fdc changeset: 2913:a559bdff7fdc user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 13:54:15 2009 -0400 description: Fix query style in tracks controller 1 file(s) affected in this change: lib/galaxy/web/controllers/tracks.py diffs (15 lines): diff -r 6dcf496ad316 -r a559bdff7fdc lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Oct 23 13:31:11 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Oct 23 13:54:15 2009 -0400 @@ -122,9 +122,10 @@ vis = session.query( model.Visualization ).get( decoded_id ) tracks = [] dbkey = "" + hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] - dataset = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) + dataset = hda_query.get( dataset_id ) tracks.append( { "type": dataset.datatype.get_track_type(), "name": dataset.name,

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[hg] galaxy 2910: Tables for storing visualizations, visualizati...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/811eda31b6b3 changeset: 2910:811eda31b6b3 user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 12:47:16 2009 -0400 description: Tables for storing visualizations, visualization tab (if enable_tracks is true) 8 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/web/controllers/tracks.py lib/galaxy/web/controllers/visualization.py templates/base_panels.mako templates/panels.mako templates/tracks/browser.mako templates/tracks/new_browser.mako diffs (290 lines): diff -r 2c4ed83f76ef -r 811eda31b6b3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Oct 22 23:02:28 2009 -0400 +++ b/lib/galaxy/model/__init__.py Fri Oct 23 12:47:16 2009 -0400 @@ -1292,7 +1292,7 @@ if self.phone: html = html + '<br/>' + 'Phone: ' + self.phone return html - + class Page( object ): def __init__( self ): self.id = None @@ -1307,6 +1307,22 @@ self.user = None self.title = None self.content = None + +class Visualization( object ): + def __init__( self ): + self.id = None + self.user = None + self.type = None + self.title = None + self.latest_revision = None + self.revisions = [] + +class VisualizationRevision( object ): + def __init__( self ): + self.id = None + self.visualization = None + self.title = None + self.config = None class Tag ( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ): diff -r 2c4ed83f76ef -r 811eda31b6b3 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Oct 22 23:02:28 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri Oct 23 12:47:16 2009 -0400 @@ -556,6 +556,26 @@ Column( "content", TEXT ) ) +Visualization.table = Table( "visualization", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ), + Column( "title", TEXT ), + Column( "type", TEXT ) + ) + +VisualizationRevision.table = Table( "visualization_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "config", JSONType ) + ) + Tag.table = Table( "tag", metadata, Column( "id", Integer, primary_key=True ), Column( "type", Integer ), @@ -1012,6 +1032,18 @@ tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages") ) ) +assign_mapper( context, VisualizationRevision, VisualizationRevision.table ) + +assign_mapper( context, Visualization, Visualization.table, + properties=dict( user=relation( User ), + revisions=relation( VisualizationRevision, backref='visualization', + cascade="all, delete-orphan", + primaryjoin=( Visualization.table.c.id == VisualizationRevision.table.c.visualization_id ) ), + latest_revision=relation( VisualizationRevision, post_update=True, + primaryjoin=( Visualization.table.c.latest_revision_id == VisualizationRevision.table.c.id ), + lazy=False ) + ) ) + assign_mapper( context, Tag, Tag.table, properties=dict( children=relation(Tag, backref=backref( 'parent', remote_side=[Tag.table.c.id] ) ) ) ) diff -r 2c4ed83f76ef -r 811eda31b6b3 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Oct 22 23:02:28 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Oct 23 12:47:16 2009 -0400 @@ -63,18 +63,35 @@ return trans.fill_template( "tracks/index.mako" ) @web.expose - def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None ): + def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ): """ Build a new browser from datasets in the current history. Redirects - to 'index' once datasets to browse have been selected. + to 'browser' once datasets to browse have been selected. """ session = trans.sa_session # If the user clicked the submit button explicitly, try to build the browser - if browse and dataset_ids: + if title and browse and dataset_ids: if not isinstance( dataset_ids, list ): dataset_ids = [ dataset_ids ] - dataset_ids = ",".join( map( str, dataset_ids ) ) - trans.response.send_redirect( web.url_for( controller='tracks', action='browser', chrom="", dataset_ids=dataset_ids ) ) + # Build config + tracks = [] + for dataset_id in dataset_ids: + tracks.append( { "dataset_id": str( dataset_id ) } ) + config = { "tracks": tracks } + # Build visualization object + vis = model.Visualization() + vis.user = trans.user + vis.title = title + vis.type = "trackster" + vis_rev = model.VisualizationRevision() + vis_rev.visualization = vis + vis_rev.title = title + vis_rev.config = config + vis.latest_revision = vis_rev + session.add( vis ) + session.add( vis_rev ) + session.flush() + trans.response.send_redirect( web.url_for( controller='tracks', action='browser', id=trans.security.encode_id( vis.id ) ) ) else: # Determine the set of all dbkeys that are used in the current history dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] @@ -96,14 +113,18 @@ return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose - def browser(self, trans, dataset_ids, chrom=""): + def browser(self, trans, id, chrom=""): """ Display browser for the datasets listed in `dataset_ids`. """ + decoded_id = trans.security.decode_id( id ) + session = trans.sa_session + vis = session.query( model.Visualization ).get( decoded_id ) tracks = [] dbkey = "" - for dataset_id in dataset_ids.split( "," ): - dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) + for t in vis.latest_revision.config['tracks']: + dataset_id = t['dataset_id'] + dataset = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) tracks.append( { "type": dataset.datatype.get_track_type(), "name": dataset.name, @@ -114,7 +135,8 @@ if chrom_lengths is None: error( "No chromosome lengths file found for '%s'" % dataset.name ) return trans.fill_template( 'tracks/browser.mako', - dataset_ids=dataset_ids, + #dataset_ids=dataset_ids, + id=id, tracks=tracks, chrom=chrom, dbkey=dbkey, diff -r 2c4ed83f76ef -r 811eda31b6b3 lib/galaxy/web/controllers/visualization.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/visualization.py Fri Oct 23 12:47:16 2009 -0400 @@ -0,0 +1,47 @@ +from galaxy.web.base.controller import * +from galaxy.web.framework.helpers import time_ago, grids +from galaxy.util.sanitize_html import sanitize_html + + +class VisualizationListGrid( grids.Grid ): + # Grid definition + use_panels = True + title = "Visualizations" + model_class = model.Visualization + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Title", key="title", attach_popup=True, + link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), + grids.GridColumn( "Type", key="type" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + ## global_actions = [ + ## grids.GridAction( "Add new page", dict( action='create' ) ) + ## ] + operations = [ + grids.GridOperation( "View", allow_multiple=False, url_args=dict( controller="tracks", action='browser' ) ), + ] + def apply_default_filter( self, trans, query, **kwargs ): + return query.filter_by( user=trans.user ) + +class VisualizationController( BaseController ): + + @web.expose + def index( self, trans ): + return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) ) + + list_grid = VisualizationListGrid() + @web.expose + def list( self, trans, *args, **kwargs ): + return self.list_grid( trans, *args, **kwargs ) + + #(a)web.expose + #(a)web.require_admin + #def index( self, trans, *args, **kwargs ): + # # Build grid + # grid = self.list( trans, *args, **kwargs ) + # # Render grid wrapped in panels + # return trans.fill_template( "page/index.mako", grid=grid ) + + \ No newline at end of file diff -r 2c4ed83f76ef -r 811eda31b6b3 templates/base_panels.mako --- a/templates/base_panels.mako Thu Oct 22 23:02:28 2009 -0400 +++ b/templates/base_panels.mako Fri Oct 23 12:47:16 2009 -0400 @@ -173,11 +173,18 @@ %endif %if app.config.get_bool( 'enable_tracks', False ): - <td class="tab"> + <% + cls = "tab" + if self.active_view == 'visualization': + cls += " active" + %> + <td class="${cls}"> Visualization <div class="submenu"> <ul> <li><a href="${h.url_for( controller='tracks', action='index' )}">Build track browser</a></li> + <li><hr style="color: inherit; background-color: gray"/></li> + <li><a href="${h.url_for( controller='visualization', action='index' )}">Stored visualizations</a></li> </ul> </div> </td> diff -r 2c4ed83f76ef -r 811eda31b6b3 templates/panels.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/panels.mako Fri Oct 23 12:47:16 2009 -0400 @@ -0,0 +1,16 @@ +<%inherit file="/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view=active_view + self.message_box_visible=False +%> +</%def> + +<%def name="center_panel()"> + + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${main_url}"> </iframe> + +</%def> diff -r 2c4ed83f76ef -r 811eda31b6b3 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Oct 22 23:02:28 2009 -0400 +++ b/templates/tracks/browser.mako Fri Oct 23 12:47:16 2009 -0400 @@ -124,7 +124,8 @@ <select id="chrom" name="chrom"> <option value="">Loading</option> </select> - <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> + ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> + <input type="hidden" name="id" value="${id}" /> <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> diff -r 2c4ed83f76ef -r 811eda31b6b3 templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Thu Oct 22 23:02:28 2009 -0400 +++ b/templates/tracks/new_browser.mako Fri Oct 23 12:47:16 2009 -0400 @@ -19,10 +19,17 @@ % else: <div class="form"> - <div class="form-title">Select datasets to include in browser</div> + <div class="form-title">Create new track browser</div> <div id="dbkey" class="form-body"> <form id="form" method="POST"> + <div class="form-row"> + <label for="dbkey">Browser name:</label> + <div class="form-row-input"> + <input type="text" name="title" id="title" value="Unnamed Browser"></input> + </div> + <div style="clear: both;"></div> + </div> <div class="form-row"> <label for="dbkey">Reference genome build (dbkey): </label> <div class="form-row-input">

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