galaxy-dev January 2010

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156 discussions

[hg] galaxy 3274: trackster:
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c8ef8611841d changeset: 3274:c8ef8611841d user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 26 16:37:25 2010 -0500 description: trackster: - Fixed incorrect drawing of thick strands - Linetrack: can now set min and max values for y-axis - Featuretrack: can set color for label and block - Drawing delays 50ms so that scrolling quickly across browser does not load everything travelled through - Fixed another memory leak in arraytree provider - Made intron tracks lighter in color diffstat: lib/galaxy/visualization/tracks/data/array_tree.py | 2 + lib/galaxy/web/controllers/tracks.py | 7 + static/scripts/pack_scripts.py | 2 +- static/scripts/trackster.js | 144 ++++++++++++++---- static/trackster.css | 2 +- templates/root/history.mako | 2 +- templates/tracks/browser.mako | 162 +++++++++++++++----- templates/workflow/editor.mako | 2 +- 8 files changed, 243 insertions(+), 80 deletions(-) diffs (619 lines): diff -r 4a3a4af6be53 -r c8ef8611841d lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Jan 26 16:16:03 2010 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Jan 26 16:37:25 2010 -0500 @@ -22,6 +22,7 @@ try: chrom_array_tree = d[chrom] except KeyError: + f.close() return "no data" root_summary = chrom_array_tree.get_summary( 0, chrom_array_tree.levels ) @@ -36,6 +37,7 @@ try: chrom_array_tree = d[chrom] except KeyError: + f.close() return None block_size = chrom_array_tree.block_size diff -r 4a3a4af6be53 -r c8ef8611841d lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Jan 26 16:16:03 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Jan 26 16:37:25 2010 -0500 @@ -132,6 +132,7 @@ error( "No chromosome lengths file found for '%s'" % dataset.name ) return trans.fill_template( 'tracks/browser.mako', #dataset_ids=dataset_ids, + title = vis.title, id=id, tracks=tracks, chrom=chrom, @@ -249,3 +250,9 @@ trans.sa_session.add( assoc ) trans.sa_session.flush() return new_dataset + + @web.json + def update_config( self, trans, **kwargs ): + raise RuntimeError + + \ No newline at end of file diff -r 4a3a4af6be53 -r c8ef8611841d static/scripts/pack_scripts.py --- a/static/scripts/pack_scripts.py Tue Jan 26 16:16:03 2010 -0500 +++ b/static/scripts/pack_scripts.py Tue Jan 26 16:37:25 2010 -0500 @@ -8,7 +8,7 @@ from os import path # Scripts that should not be packed -- just copied -do_not_pack = set( [ "ie_pngfix.js", "aflax.js" ] ) +do_not_pack = set() cmd = "java -jar ../../scripts/yuicompressor.jar --type js %(fname)s -o packed/%(fname)s" diff -r 4a3a4af6be53 -r c8ef8611841d static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Jan 26 16:16:03 2010 -0500 +++ b/static/scripts/trackster.js Tue Jan 26 16:37:25 2010 -0500 @@ -4,7 +4,7 @@ var DEBUG = false; var DENSITY = 1000, - FEATURE_LEVELS = 100, + FEATURE_LEVELS = 10, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -47,8 +47,7 @@ var Cache = function( num_elements ) { this.num_elements = num_elements; - this.obj_cache = {}; - this.key_ary = []; + this.clear(); }; $.extend( Cache.prototype, { get: function( key ) { @@ -71,11 +70,16 @@ } this.obj_cache[key] = value; return value; + }, + clear: function() { + this.obj_cache = {}; + this.key_ary = []; } }); -var View = function( chrom, max_high ) { +var View = function( chrom, max_high, config ) { this.chrom = chrom; + this.config = config; this.tracks = []; this.max_low = 0; this.max_high = max_high; @@ -181,7 +185,6 @@ var w_scale = this.content_div.width() / range; - var max_height = 20; var tile_element; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); @@ -201,22 +204,30 @@ }); // Our responsibility to move the element to the new parent parent_element.append( cached ); - max_height = Math.max( max_height, cached.height() ); + this.max_height = Math.max( this.max_height, cached.height() ); } else { - tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale ); + this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale); + } + tile_index += 1; + } + }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale) { + // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data + setTimeout(function() { + if ( !(low > track.view.high || high < track.view.low) ) { + tile_element = track.draw_tile( resolution, tile_index, parent_element, w_scale ); if ( tile_element ) { - this.tile_cache.set(key, tile_element); - max_height = Math.max( max_height, tile_element.height() ); + track.tile_cache.set(key, tile_element); + track.max_height = Math.max( track.max_height, tile_element.height() ); + track.content_div.css( "height", track.max_height ); } } - this.content_div.css( "height", max_height ); - tile_index += 1; - } + }, 50); } }); var LabelTrack = function ( parent_element ) { Track.call( this, null, parent_element ); + this.hidden = true; this.container_div.addClass( "label-track" ); }; $.extend( LabelTrack.prototype, Track.prototype, { @@ -241,7 +252,7 @@ } }); -var LineTrack = function ( name, dataset_id, indexer, height ) { +var LineTrack = function ( name, dataset_id, indexer, height, minval, maxval ) { this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -251,12 +262,19 @@ this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; this.data_queue = {}; - this.cache = new Cache(CACHED_DATA); // We need to cache some data because of + this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of // asynchronous calls + if (minval !== undefined && maxval !== undefined) { + this.min_value = minval; + this.max_value = maxval; + this.vertical_range = maxval - minval; + } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { - var track = this; + var track = this, + track_id = track.view.tracks.indexOf(track); + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, @@ -274,13 +292,20 @@ } else { track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); - track.min_value = data.min; - track.max_value = data.max; - track.vertical_range = track.max_value - track.min_value; + + if (track.min_value === undefined || track.max_value === undefined) { + track.min_value = data.min; + track.max_value = data.max; + track.vertical_range = track.max_value - track.min_value; + + // Update the config + $('#track_' + track_id + '_minval').val(track.min_value); + $('#track_' + track_id + '_maxval').val(track.max_value); + } // Draw y-axis labels - var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); - var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); + var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.min_value); + var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.max_value); max_label.css({ position: "relative", top: "25px" }); max_label.prependTo(track.container_div); @@ -303,11 +328,11 @@ $.getJSON( data_url, { indexer: this.indexer, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id, resolution: this.view.resolution }, function ( data ) { - track.cache.set(key, data); + track.data_cache.set(key, data); delete track.data_queue[key]; track.draw(); }); - } + } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { if (!this.vertical_range) { // We don't have the necessary information yet @@ -319,12 +344,12 @@ canvas = $("<canvas class='tile'></canvas>"), key = resolution + "_" + tile_index; - if (!this.cache.get(key)) { + if (!this.data_cache.get(key)) { this.get_data( resolution, tile_index ); return; } - var data = this.cache.get(key); + var data = this.data_cache.get(key); canvas.css( { position: "absolute", top: 0, @@ -345,7 +370,14 @@ } else { // Translate x = x * w_scale; - y = (y - this.min_value) / this.vertical_range * this.height_px; + // console.log(y, this.min_value, this.vertical_range, (y - this.min_value) / this.vertical_range * this.height_px); + if (y <= this.min_value) { + y = this.min_value; + } else if (y >= this.max_value) { + y = this.max_value; + } + y = Math.round( this.height_px - (y - this.min_value) / this.vertical_range * this.height_px ); + // console.log(canvas.get(0).height, canvas.get(0).width); if ( in_path ) { ctx.lineTo( x, y ); } else { @@ -357,6 +389,29 @@ ctx.stroke(); parent_element.append( canvas ); return canvas; + }, gen_options: function(track_id) { + var container = $("<div></div>").addClass("form-row"); + + var minval = 'track_' + track_id + '_minval', + maxval = 'track_' + track_id + '_maxval', + min_label = $('<label></label>').attr("for", minval).text("Min value:"), + min_input = $('<input></input>').attr("id", minval).val(this.min_value || ""), + max_label = $('<label></label>').attr("for", maxval).text("Max value:"), + max_input = $('<input></input>').attr("id", maxval).val(this.max_value || ""); + + return container.append(min_label).append(min_input).append(max_label).append(max_input); + }, update_options: function(track_id) { + var min_value = $('#track_' + track_id + '_minval').val(), + max_value = $('#track_' + track_id + '_maxval').val(); + if ( min_value !== this.min_value || max_value !== this.max_value) { + this.min_value = parseFloat(min_value); + this.max_value = parseFloat(max_value); + this.vertical_range = this.max_value - this.min_value; + $('#linetrack_' + track_id + '_minval').text(this.min_value); + $('#linetrack_' + track_id + '_maxval').text(this.max_value); + this.tile_cache.clear(); + this.draw(); + } } }); @@ -374,7 +429,8 @@ this.showing_details = false; this.vertical_detail_px = 10; this.vertical_nodetail_px = 3; - this.base_color = "#2C3143"; + this.block_color = "black"; + this.label_color = "black"; this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; this.inc_slots = {}; @@ -564,7 +620,7 @@ new_canvas.get(0).height = required_height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); - ctx.fillStyle = this.base_color; + ctx.fillStyle = this.block_color; ctx.font = this.default_font; ctx.textAlign = "right"; @@ -586,10 +642,10 @@ ctx.fillRect(f_start + this.left_offset, y_center + 5, f_end - f_start, 1); } else { // Showing labels, blocks, details - if (ctx.fillText && feature.start > tile_low) { + if (feature.start > tile_low) { + ctx.fillStyle = this.label_color; ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); - // ctx.fillText(commatize(feature.start), f_start - 1 + this.left_offset, y_center + 8); - // ctx.fillText(slots[feature.uid], f_start - 1 + this.left_offset, y_center + 8); + ctx.fillStyle = this.block_color; } var blocks = feature.blocks; if (blocks) { @@ -601,7 +657,7 @@ ctx.fillStyle = LEFT_STRAND; } ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = this.base_color; + ctx.fillStyle = this.block_color; } for (var k = 0, k_len = blocks.length; k < k_len; k++) { @@ -614,7 +670,8 @@ y_start = 3; ctx.fillRect(block_start + this.left_offset, y_center + y_start, block_end - block_start, thickness); - if (thick_start !== undefined && (block_start <= thick_end || block_end >= thick_start) ) { + // Draw thick regions: check if block intersects with thick region + if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { thickness = 9; y_start = 1; var block_thick_start = Math.max(block_start, thick_start), @@ -635,7 +692,7 @@ ctx.fillStyle = LEFT_STRAND_INV; } ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = this.base_color; + ctx.fillStyle = this.block_color; } } } @@ -645,6 +702,25 @@ parent_element.append( new_canvas ); return new_canvas; + }, gen_options: function(track_id) { + var container = $("<div></div>").addClass("form-row"); + + var block_color = 'track_' + track_id + '_block_color', + block_color_label = $('<label></label>').attr("for", block_color).text("Block color:"), + block_color_input = $('<input></input>').attr("id", block_color).attr("name", block_color).val(this.block_color), + label_color = 'track_' + track_id + '_label_color', + label_color_label = $('<label></label>').attr("for", label_color).text("Label color:"), + label_color_input = $('<input></input>').attr("id", label_color).attr("name", label_color).val(this.label_color); + return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input); + }, update_options: function(track_id) { + var block_color = $('#track_' + track_id + '_block_color').val(), + label_color = $('#track_' + track_id + '_label_color').val(); + if (block_color !== this.block_color || label_color !== this.label_color) { + this.block_color = block_color; + this.label_color = label_color; + this.tile_cache.clear(); + this.draw(); + } } }); @@ -684,7 +760,7 @@ new_canvas.get(0).height = required_height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); - ctx.fillStyle = this.base_color; + ctx.fillStyle = this.block_color; ctx.font = this.default_font; ctx.textAlign = "right"; var px_per_char = ctx.measureText("A").width; diff -r 4a3a4af6be53 -r c8ef8611841d static/trackster.css --- a/static/trackster.css Tue Jan 26 16:16:03 2010 -0500 +++ b/static/trackster.css Tue Jan 26 16:37:25 2010 -0500 @@ -109,7 +109,7 @@ } .track-header { - text-align: left; + text-align: center; padding: 4px; color: #666; } diff -r 4a3a4af6be53 -r c8ef8611841d templates/root/history.mako --- a/templates/root/history.mako Tue Jan 26 16:16:03 2010 -0500 +++ b/templates/root/history.mako Tue Jan 26 16:37:25 2010 -0500 @@ -20,7 +20,7 @@ <script type="text/javascript"> $(function() { // Load jStore for local storage - $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '${h.url_for("/static/jStore.Flash.html")}' }) $.jStore.load(); // Auto-select best storage $.jStore.ready(function(engine) { diff -r 4a3a4af6be53 -r c8ef8611841d templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Jan 26 16:16:03 2010 -0500 +++ b/templates/tracks/browser.mako Tue Jan 26 16:37:25 2010 -0500 @@ -11,12 +11,84 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -<link rel="stylesheet" type="text/css" href="/static/trackster.css" /> + +${h.css( "history" )} +<link rel="stylesheet" type="text/css" href="${h.url_for('/static/trackster.css')}" /> +<link rel="stylesheet" type="text/css" href="${h.url_for('/static/ui.theme.css')}" /> +<style type="text/css"> + ul#sortable-ul { + list-style: none; + padding: 0; + margin: 5px; + } + ul#sortable-ul li { + display: block; + margin: 5px 0; + background: #eee; + } + .delete-button { + background: transparent url(history-buttons.png) no-repeat scroll 0 -104px; + height: 20px; + width: 20px; + } + .delete-button:hover { + background-position: 0 -130px; + } + +</style> +</%def> + +<%def name="center_panel()"> +<div id="content"> + <div id="top-labeltrack"></div> + <div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"> + <div id="viewport"></div> + </div> + +</div> +<div id="nav-container"> + <div id="nav-labeltrack"></div> + <div id="nav"> + <div id="overview"> + <div id="overview-viewport"> + <div id="overview-box"></div> + </div> + </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 id="high" size="12" /> + ## <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 id="debug" style="float: right"></div> + </div> + </div> +</div> +</%def> + +<%def name="right_panel()"> + <div class="unified-panel-header" unselectable="on"> + <div class="unified-panel-header-inner">Configuration</div> + </div> + <form action="${h.url_for( action='update_config' )}"> +## <input name="title" id="title" value="${title}" /> + <div id="show-hide-move"> + <ul id="sortable-ul"></ul> +## <input type="submit" id="update-config" value="Save settings" /> + <input type="button" id="refresh-button" value="Refresh" /> + </div> + </form> + </%def> <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )} +${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} <script type="text/javascript"> @@ -36,7 +108,7 @@ view.redraw(); }); - $(document).bind("mousewheel", function( e, delta ) { + $("#content").bind("mousewheel", function( e, delta ) { if (delta > 0) { view.zoom_in(e.pageX); } else { @@ -45,7 +117,7 @@ e.preventDefault(); }); - $(document).bind("dblclick", function( e ) { + $("#content").bind("dblclick", function( e ) { view.zoom_in(e.pageX); }); @@ -83,7 +155,6 @@ var new_scroll = container.scrollTop() - (e.clientY - this.current_height); if ( new_scroll < container.get(0).scrollHeight - container.height() ) { container.scrollTop(new_scroll); - } this.current_height = e.clientY; this.current_x = e.offsetX; @@ -92,6 +163,17 @@ view.center -= delta_chrom; view.redraw(); }); + + $("#refresh-button").bind( "click", function(e) { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (track.update_options) { + track.update_options(track_id); + } + } + }); + + // Execute this on page load (function () { $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: "${dbkey}" }, function ( data ) { var chrom_options = '<option value="">Select Chrom/Contig</option>'; @@ -108,6 +190,39 @@ $("#chr").submit(); }); }); + + // Populate sort/move ul + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (!track.hidden) { + var label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'); + var title = $('<div class="toolFormTitle"></div>'); + var del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'); + var body = $('<div class="toolFormBody"></div>'); + // var checkbox = $('<input type="checkbox" checked="checked"></input>').attr("id", "track_" + track_id + "title"); + var li = $('<li class="sortable"></li>').attr("id", "track_" + track_id); + var div = $('<div class="toolForm"></div>'); + del_icon.prependTo(title); + label.appendTo(title); + // checkbox.prependTo(title); + if (track.gen_options) { + body.append(track.gen_options(track_id)); + } + title.prependTo(div); + body.appendTo(div); + li.append(div); + $("ul#sortable-ul").append(li); + } + } + + $("ul#sortable-ul").sortable({ + update: function(event, ui) { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + } + } + }); + })(); $(window).trigger("resize"); }); @@ -115,40 +230,3 @@ </script> </%def> -<%def name="center_panel()"> -<div id="content"> - <div id="top-labeltrack"></div> - <div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"> - <div id="viewport"></div> - </div> - -</div> -<div id="nav-container"> - <div id="nav-labeltrack"></div> - <div id="nav"> - <div id="overview"> - <div id="overview-viewport"> - <div id="overview-box"></div> - </div> - </div> - <div id="nav-controls"> - <form name="chr" id="chr" method="get"> - <select id="chrom" name="chrom" style="width: 15em;"> - <option value="">Loading</option> - </select> - <input id="low" size="12" />:<input id="high" size="12" /> - ## <input type="hidden" name="dataset_ids" value="${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 id="debug" style="float: right"></div> - </div> - </div> -</div> -</%def> - -<%def name="right_panel()"> - <div>Configs</div> - -</%def> \ No newline at end of file diff -r 4a3a4af6be53 -r c8ef8611841d templates/workflow/editor.mako --- a/templates/workflow/editor.mako Tue Jan 26 16:16:03 2010 -0500 +++ b/templates/workflow/editor.mako Tue Jan 26 16:37:25 2010 -0500 @@ -59,7 +59,7 @@ } // Load jStore for local storage - $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '${h.url_for("/static/jStore.Flash.html")}' }) $.jStore.load(); // Auto-select best storage // Canvas overview management

1 0

[hg] galaxy 3273: If a dataset is not public, populate the permi...
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4a3a4af6be53 changeset: 3273:4a3a4af6be53 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 26 16:16:03 2010 -0500 description: If a dataset is not public, populate the permissions forms for it with legitimate roles only. diffstat: lib/galaxy/model/__init__.py | 42 +----------------- lib/galaxy/security/__init__.py | 58 +++++++++++++++++++++++-- lib/galaxy/web/controllers/library_common.py | 12 ++-- lib/galaxy/web/controllers/root.py | 5 +- templates/dataset/edit_attributes.mako | 2 +- templates/dataset/security_common.mako | 2 +- templates/mobile/manage_library.mako | 2 +- test/functional/test_security_and_libraries.py | 4 +- 8 files changed, 70 insertions(+), 57 deletions(-) diffs (301 lines): diff -r 3ca480a2666b -r 4a3a4af6be53 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Jan 26 14:03:48 2010 -0500 +++ b/lib/galaxy/model/__init__.py Tue Jan 26 16:16:03 2010 -0500 @@ -5,7 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys, codecs, operator +import os.path, os, errno, sys, codecs import galaxy.datatypes from galaxy.util.bunch import Bunch from galaxy import util @@ -719,7 +719,8 @@ if isinstance(hda_name, str): hda_name = unicode(hda_name, 'utf-8') return hda_name - + def get_access_roles( self, trans ): + return self.dataset.get_access_roles( trans ) class HistoryDatasetAssociationDisplayAtAuthorization( object ): def __init__( self, hda=None, user=None, site=None ): @@ -759,43 +760,6 @@ if lp.action == trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action: roles.append( lp.role ) return roles - def get_legitimate_roles( self, trans ): - if trans.app.security_agent.library_is_public( self ): - return trans.sa_session.query( trans.app.model.Role ) \ - .filter( trans.app.model.Role.table.c.deleted==False ) \ - .order_by( trans.app.model.Role.table.c.name ) - def sort_by_attr( seq, attr ): - """ - Sort the sequence of objects by object's attribute - Arguments: - seq - the list or any sequence (including immutable one) of objects to sort. - attr - the name of attribute to sort by - """ - # Use the "Schwartzian transform" - # Create the auxiliary list of tuples where every i-th tuple has form - # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not - # only to provide stable sorting, but mainly to eliminate comparison of objects - # (which can be expensive or prohibited) in case of equal attribute values. - intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) - intermed.sort() - return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) - roles = set() - # If a library has roles associated with the LIBRARY_ACCESS permission, we need to start with them. - access_roles = self.get_access_roles( trans ) - for role in access_roles: - roles.add( role ) - # Each role potentially has users. We need to find all roles that each of those users have. - for ura in role.users: - roles.add( ura.role ) - # Each role also potentially has groups which, in turn, have members ( users ). We need to - # find all roles that each group's members have. - for gra in role.groups: - group = gra.group - for uga in group.users: - user = uga.user - for ura in user.roles: - roles.add( ura.role ) - return sort_by_attr( [ role for role in roles ], 'name' ) def get_display_name( self ): # Library name can be either a string or a unicode object. If string, # convert to unicode object assuming 'utf-8' format. diff -r 3ca480a2666b -r 4a3a4af6be53 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Jan 26 14:03:48 2010 -0500 +++ b/lib/galaxy/security/__init__.py Tue Jan 26 16:16:03 2010 -0500 @@ -2,7 +2,7 @@ Galaxy Security """ -import logging, socket +import logging, socket, operator from datetime import datetime, timedelta from galaxy.util.bunch import Bunch from galaxy.util import listify @@ -79,6 +79,8 @@ raise "Unimplemented Method" def get_permissions( self, library_dataset ): raise "Unimplemented Method" + def get_legitimate_roles( self, trans, item ): + raise "Unimplemented Method" def check_library_dataset_access( self, trans, library_id, **kwd ): raise "Unimplemented Method" def get_component_associations( self, **kwd ): @@ -107,6 +109,51 @@ def sa_session( self ): """Returns a SQLAlchemy session""" return self.model.context + def get_legitimate_roles( self, trans, item ): + """ + Return a sorted list of legitimate roles that can be associated with a permission on + item where item is a Library or a Dataset. If item is public, all roles are legitimate. + If item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS + or LIBRARY_MANAGE ) on item. + """ + if ( isinstance( item, self.model.Library ) and self.library_is_public( item ) ) or \ + ( isinstance( item, self.model.Dataset ) and self.dataset_is_public( item ) ): + return trans.sa_session.query( trans.app.model.Role ) \ + .filter( trans.app.model.Role.table.c.deleted==False ) \ + .order_by( trans.app.model.Role.table.c.name ) + def sort_by_attr( seq, attr ): + """ + Sort the sequence of objects by object's attribute + Arguments: + seq - the list or any sequence (including immutable one) of objects to sort. + attr - the name of attribute to sort by + """ + # Use the "Schwartzian transform" + # Create the auxiliary list of tuples where every i-th tuple has form + # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not + # only to provide stable sorting, but mainly to eliminate comparison of objects + # (which can be expensive or prohibited) in case of equal attribute values. + intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) + intermed.sort() + return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) + roles = set() + # If a library has roles associated with the LIBRARY_ACCESS permission, we need to start with them. + access_roles = item.get_access_roles( trans ) + for role in access_roles: + roles.add( role ) + # Each role potentially has users. We need to find all roles that each of those users have. + for ura in role.users: + roles.add( ura.role ) + # Each role also potentially has groups which, in turn, have members ( users ). We need to + # find all roles that each group's members have. + for gra in role.groups: + group = gra.group + for uga in group.users: + user = uga.user + for ura in user.roles: + roles.add( ura.role ) + return sort_by_attr( [ role for role in roles ], 'name' ) def allow_action( self, roles, action, item ): """ Method for checking a permission for the current user ( based on roles ) to perform a @@ -328,8 +375,9 @@ self.sa_session.flush() def get_permissions( self, item ): """ - Return a dictionary containing the actions and associated roles on item. - The dictionary looks like: { Action : [ Role, Role ] } + Return a dictionary containing the actions and associated roles on item + where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation, + LibraryDataset, Dataset. The dictionary looks like: { Action : [ Role, Role ] }. """ permissions = {} for item_permission in item.actions: @@ -409,7 +457,7 @@ # accessible will be True only if at least 1 user has every role in DATASET_ACCESS_in accessible = False # legitimate will be True only if all roles in DATASET_ACCESS_in are in the set - # of roles returned from library.get_legitimate_roles() + # of roles returned from self.get_legitimate_roles() legitimate = False error = None for k, v in get_permitted_actions( filter='DATASET' ).items(): @@ -422,7 +470,7 @@ # not public. This will keep ill-legitimate roles from being associated with the DATASET_ACCESS # permission on the dataset (i.e., if Role1 is associated with LIBRARY_ACCESS, then only those users # that have Role1 should be associated with DATASET_ACCESS. - legitimate_roles = library.get_legitimate_roles( trans ) + legitimate_roles = self.get_legitimate_roles( trans, library ) ill_legitimate_roles = [] for role in in_roles: if role not in legitimate_roles: diff -r 3ca480a2666b -r 4a3a4af6be53 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Jan 26 14:03:48 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Tue Jan 26 16:16:03 2010 -0500 @@ -183,7 +183,7 @@ id=trans.security.encode_id( library.id ), msg=util.sanitize_text( msg ), messagetype='done' ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) return trans.fill_template( '/library/common/library_permissions.mako', cntrller=cntrller, library=library, @@ -307,7 +307,7 @@ # If the library is public all roles are legitimate, but if the library is restricted, only those # roles associated with the LIBRARY_ACCESS permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) return trans.fill_template( '/library/common/folder_permissions.mako', cntrller=cntrller, folder=folder, @@ -492,7 +492,7 @@ # If the library is public all roles are legitimate, but if the library is restricted, only those # roles associated with the LIBRARY_ACCESS permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) if params.get( 'update_roles_button', False ): current_user_roles = trans.get_current_user_roles() if cntrller=='library_admin' or ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \ @@ -694,7 +694,7 @@ # If the library is public, all active roles are legitimate. If the library is restricted by the # LIBRARY_ACCESS permission, only those roles associated with that permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) @@ -977,7 +977,7 @@ dbkeys = get_dbkey_options( last_used_build ) # Send list of legitimate roles to the form so the dataset can be associated with 1 or more of them. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) return trans.fill_template( "/library/common/upload.mako", upload_option=upload_option, library_id=library_id, @@ -1101,7 +1101,7 @@ msg = "You are not authorized to managed the permissions of this dataset" messagetype = "error" library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = library.get_legitimate_roles( trans ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library ) return trans.fill_template( '/library/common/library_dataset_permissions.mako', cntrller=cntrller, library_dataset=library_dataset, diff -r 3ca480a2666b -r 4a3a4af6be53 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Jan 26 14:03:48 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Jan 26 16:16:03 2010 -0500 @@ -357,11 +357,12 @@ # the built-in 'id' is overwritten in lots of places as well ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] ldatatypes.sort() - trans.log_event( "Opened edit view on dataset %s" % str(id) ) + all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset ) return trans.fill_template( "/dataset/edit_attributes.mako", data=data, datatypes=ldatatypes, - current_user_roles=current_user_roles ) + current_user_roles=current_user_roles, + all_roles=all_roles ) else: return trans.show_error_message( "You do not have permission to edit this dataset's ( id: %s ) information." % str( id ) ) diff -r 3ca480a2666b -r 4a3a4af6be53 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Tue Jan 26 14:03:48 2010 -0500 +++ b/templates/dataset/edit_attributes.mako Tue Jan 26 16:16:03 2010 -0500 @@ -164,7 +164,7 @@ %if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ): <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='root', action='edit', id=data.id ), current_user_roles )} + ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='root', action='edit', id=data.id ), all_roles )} %elif trans.user: <div class="toolForm"> <div class="toolFormTitle">View Permissions</div> diff -r 3ca480a2666b -r 4a3a4af6be53 templates/dataset/security_common.mako --- a/templates/dataset/security_common.mako Tue Jan 26 14:03:48 2010 -0500 +++ b/templates/dataset/security_common.mako Tue Jan 26 16:16:03 2010 -0500 @@ -102,7 +102,7 @@ }); </script> <div class="toolForm"> - <div class="toolFormTitle">Manage ${obj_type} permissions and role associations of ${obj_str}</div> + <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div> <div class="toolFormBody"> <form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post"> <div class="form-row"></div> diff -r 3ca480a2666b -r 4a3a4af6be53 templates/mobile/manage_library.mako --- a/templates/mobile/manage_library.mako Tue Jan 26 14:03:48 2010 -0500 +++ b/templates/mobile/manage_library.mako Tue Jan 26 16:16:03 2010 -0500 @@ -50,7 +50,7 @@ </div> %endif %if trans.app.security_agent.can_manage_library_item( current_user_roles, library ): - <% roles = library.get_legitimate_roles( trans ) %> + <% roles = trans.app.security_agent.get_legitimate_roles( trans, library ) %> ${render_permission_form( library, library.name, h.url_for( controller='library_common', cntrller='mobile', action='library_permissions', id=trans.security.encode_id( library.id ) ), roles )} %endif diff -r 3ca480a2666b -r 4a3a4af6be53 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Jan 26 14:03:48 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Jan 26 16:16:03 2010 -0500 @@ -1457,7 +1457,7 @@ self.visit_url( '%s/root/edit?id=%s' % ( self.url, str( last_hda_created.id ) ) ) self.check_page_for_string( 'Edit Attributes' ) self.check_page_for_string( last_hda_created.name ) - check_str = 'Manage dataset permissions and role associations of %s' % last_hda_created.name + check_str = 'Manage dataset permissions on %s' % last_hda_created.name self.check_page_for_string( check_str ) self.check_page_for_string( 'Role members can manage the roles associated with permissions on this dataset' ) self.check_page_for_string( 'Role members can import this dataset into their history for analysis' ) @@ -1510,7 +1510,7 @@ self.check_page_for_string( last_hda_created.name ) try: # This should no longer be possible - check_str = 'Manage dataset permissions and role associations of %s' % last_hda_created.name + check_str = 'Manage dataset permissions on %s' % last_hda_created.name self.check_page_for_string( check_str ) raise AssertionError( '%s incorrectly has DATASET_MANAGE_PERMISSIONS on datasets imported from a library' % admin_user.email ) except:

1 0

[hg] galaxy 3272: Bug fix for my last commit.
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3ca480a2666b changeset: 3272:3ca480a2666b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 26 14:03:48 2010 -0500 description: Bug fix for my last commit. diffstat: lib/galaxy/security/__init__.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 166348341193 -r 3ca480a2666b lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Jan 26 13:26:42 2010 -0500 +++ b/lib/galaxy/security/__init__.py Tue Jan 26 14:03:48 2010 -0500 @@ -148,7 +148,7 @@ for action in self.get_actions(): these_perms[ action ] = [] # collect this dataset's perms - these_perms = self.get_dataset_permissions( dataset ) + these_perms = self.get_permissions( dataset ) # join or intersect this dataset's permissions with others for action, roles in these_perms.items(): if action not in perms.keys():

1 0

[hg] galaxy 3271: Fix some problems related to setting the 'mana...
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/166348341193 changeset: 3271:166348341193 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 26 13:26:42 2010 -0500 description: Fix some problems related to setting the 'manage permissions' permissin on library datasets. diffstat: lib/galaxy/security/__init__.py | 46 +++++++++++-------------- lib/galaxy/web/controllers/library_common.py | 8 ++-- templates/dataset/edit_attributes.mako | 2 +- templates/library/common/ldda_permissions.mako | 5 +- test/functional/test_security_and_libraries.py | 9 ++-- 5 files changed, 33 insertions(+), 37 deletions(-) diffs (189 lines): diff -r 04ad7a4b5c56 -r 166348341193 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Jan 26 10:23:45 2010 -0500 +++ b/lib/galaxy/security/__init__.py Tue Jan 26 13:26:42 2010 -0500 @@ -21,12 +21,12 @@ IN_ACCESSIBLE = 'access_error' ILL_LEGITIMATE = 'legitimate_error' permitted_actions = Bunch( - DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with this dataset", "grant" ), + DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with permissions on this dataset", "grant" ), DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), - LIBRARY_ACCESS = Action( "access library", "Restrict access to this library to role members only", "restrict" ), + LIBRARY_ACCESS = Action( "access library", "Restrict access to this library to only role members", "restrict" ), LIBRARY_ADD = Action( "add library item", "Role members can add library items to this library item", "grant" ), LIBRARY_MODIFY = Action( "modify library item", "Role members can modify this library item", "grant" ), - LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with this library item", "grant" ) + LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with permissions on this library item", "grant" ) ) def get_action( self, name, default=None ): """Get a permitted action by its dict key or action name""" @@ -77,7 +77,7 @@ raise "Unimplemented Method" def make_library_public( self, library ): raise "Unimplemented Method" - def get_library_dataset_permissions( self, library_dataset ): + def get_permissions( self, library_dataset ): raise "Unimplemented Method" def check_library_dataset_access( self, trans, library_id, **kwd ): raise "Unimplemented Method" @@ -326,26 +326,25 @@ if dp.action == self.permitted_actions.DATASET_ACCESS.action: self.sa_session.delete( dp ) self.sa_session.flush() - def get_dataset_permissions( self, dataset ): + def get_permissions( self, item ): """ - Return a dictionary containing the actions and associated roles on dataset. + Return a dictionary containing the actions and associated roles on item. The dictionary looks like: { Action : [ Role, Role ] } - dataset must be an instance of Dataset() - """ + """ permissions = {} - for dp in dataset.actions: - action = self.get_action( dp.action ) + for item_permission in item.actions: + action = self.get_action( item_permission.action ) if action in permissions: - permissions[ action ].append( dp.role ) + permissions[ action ].append( item_permission.role ) else: - permissions[ action ] = [ dp.role ] + permissions[ action ] = [ item_permission.role ] return permissions def copy_dataset_permissions( self, src, dst ): if not isinstance( src, self.model.Dataset ): src = src.dataset if not isinstance( dst, self.model.Dataset ): dst = dst.dataset - self.set_all_dataset_permissions( dst, self.get_dataset_permissions( src ) ) + self.set_all_dataset_permissions( dst, self.get_permissions( src ) ) def privately_share_dataset( self, dataset, users = [] ): intersect = None for user in users: @@ -385,6 +384,14 @@ action = action.action for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]: self.sa_session.add( role_assoc ) + if isinstance( library_item, self.model.LibraryDatasetDatasetAssociation ) and \ + action == self.permitted_actions.LIBRARY_MANAGE.action: + # Handle the special case when we are setting the LIBRARY_MANAGE_PERMISSION on a + # library_dataset_dataset_association since the roles need to be applied to the + # DATASET_MANAGE_PERMISSIONS permission on the associated dataset + permissions = {} + permissions[ self.permitted_actions.DATASET_MANAGE_PERMISSIONS ] = roles + self.set_dataset_permission( library_item.dataset, permissions ) self.sa_session.flush() def library_is_public( self, library ): # A library is considered public if there are no "access" actions associated with it. @@ -395,19 +402,6 @@ if lp.action == self.permitted_actions.LIBRARY_ACCESS.action: self.sa_session.delete( lp ) self.sa_session.flush() - def get_library_dataset_permissions( self, library_dataset ): - # Permissions will always be the same for LibraryDatasets and associated - # LibraryDatasetDatasetAssociations - if isinstance( library_dataset, self.model.LibraryDatasetDatasetAssociation ): - library_dataset = library_dataset.library_dataset - permissions = {} - for library_dataset_permission in library_dataset.actions: - action = self.get_action( library_dataset_permission.action ) - if action in permissions: - permissions[ action ].append( library_dataset_permission.role ) - else: - permissions[ action ] = [ library_dataset_permission.role ] - return permissions def check_library_dataset_access( self, trans, library_id, **kwd ): # library_id must be decoded before being sent msg = '' diff -r 04ad7a4b5c56 -r 166348341193 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Jan 26 10:23:45 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Tue Jan 26 13:26:42 2010 -0500 @@ -299,6 +299,7 @@ messagetype = "error" return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_permissions', + cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, msg=util.sanitize_text( msg ), @@ -542,12 +543,11 @@ for ldda in lddas: permissions = [] # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation - # will always be the same as the permissions on the associated LibraryDataset, so we only need to - # check one Library object - for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): + # will always be the same as the permissions on the associated LibraryDataset. + for library_permission in trans.app.security_agent.get_permissions( ldda.library_dataset ): if library_permission.action not in permissions: permissions.append( library_permission.action ) - for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): + for dataset_permission in trans.app.security_agent.get_permissions( ldda.dataset ): if dataset_permission.action not in permissions: permissions.append( dataset_permission.action ) permissions.sort() diff -r 04ad7a4b5c56 -r 166348341193 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Tue Jan 26 10:23:45 2010 -0500 +++ b/templates/dataset/edit_attributes.mako Tue Jan 26 13:26:42 2010 -0500 @@ -172,7 +172,7 @@ <div class="form-row"> %if data.dataset.actions: <ul> - %for action, roles in trans.app.security_agent.get_dataset_permissions( data.dataset ).items(): + %for action, roles in trans.app.security_agent.get_permissions( data.dataset ).items(): %if roles: <li>${action.description}</li> <ul> diff -r 04ad7a4b5c56 -r 166348341193 templates/library/common/ldda_permissions.mako --- a/templates/library/common/ldda_permissions.mako Tue Jan 26 10:23:45 2010 -0500 +++ b/templates/library/common/ldda_permissions.mako Tue Jan 26 13:26:42 2010 -0500 @@ -57,5 +57,6 @@ %endif <% ldda_ids = ",".join( [ trans.security.encode_id( d.id ) for d in lddas ] ) %> -## LIBRARY_ACCESS is a special permission that is set only at the library level. -${render_permission_form( lddas[0], name_str, h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ), id=ldda_ids ), roles, do_not_render=[ 'LIBRARY_ACCESS' ] )} +## LIBRARY_ACCESS is a special permission that is set only at the library level, +## and DATASET_MANAGE_PERMISSIONS is inherited to the dataset from the ldda. +${render_permission_form( lddas[0], name_str, h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ), id=ldda_ids ), roles, do_not_render=[ 'LIBRARY_ACCESS', 'DATASET_MANAGE_PERMISSIONS' ] )} diff -r 04ad7a4b5c56 -r 166348341193 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Jan 26 10:23:45 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Jan 26 13:26:42 2010 -0500 @@ -1216,7 +1216,8 @@ if not dps: raise AssertionError( 'No DatasetPermissionss created for dataset id: %d' % last_dataset_created.id ) if len( dps ) > 1: - raise AssertionError( 'More than 1 DatasetPermissionss created for dataset id: %d' % last_dataset_created.id ) + actions = [ dp.action for dp in dps ] + raise AssertionError( 'More than 1 DatasetPermissionss created for dataset id: %d, permissions: %s' % ( last_dataset_created.id, str( actions ) ) ) for dp in dps: if not dp.action == 'manage permissions': raise AssertionError( 'DatasetPermissions.action "%s" is not the DefaultHistoryPermission setting of "manage permissions"' \ @@ -1427,7 +1428,7 @@ for ldda in latest_3_lddas: ldda_ids += '%s,' % self.security.encode_id( ldda.id ) ldda_ids = ldda_ids.rstrip( ',' ) - permissions = [ 'DATASET_ACCESS', 'DATASET_MANAGE_PERMISSIONS' ] + permissions = [ 'DATASET_ACCESS', 'LIBRARY_MANAGE' ] def build_url( permissions, role ): # We'll bypass the library_admin/datasets method and directly call the library_admin/dataset method, setting # access, manage permissions, and edit metadata permissions to role_one @@ -1458,7 +1459,7 @@ self.check_page_for_string( last_hda_created.name ) check_str = 'Manage dataset permissions and role associations of %s' % last_hda_created.name self.check_page_for_string( check_str ) - self.check_page_for_string( 'Role members can manage the roles associated with this dataset' ) + self.check_page_for_string( 'Role members can manage the roles associated with permissions on this dataset' ) self.check_page_for_string( 'Role members can import this dataset into their history for analysis' ) # admin_user is associated with role_one, so should have all permissions on imported datasets check_edit_page1( latest_3_lddas ) @@ -1516,7 +1517,7 @@ pass try: # This should no longer be possible - self.check_page_for_string( 'Role members can manage the roles associated with this dataset' ) + self.check_page_for_string( 'Role members can manage roles associated with permissions on this library item' ) raise AssertionError( '%s incorrectly has DATASET_MANAGE_PERMISSIONS on datasets imported from a library' % admin_user.email ) except: pass

1 0

[hg] galaxy 3270: merge
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/04ad7a4b5c56 changeset: 3270:04ad7a4b5c56 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 26 10:23:45 2010 -0500 description: merge diffstat: eggs.ini | 4 +--- lib/galaxy/web/buildapp.py | 7 +------ lib/galaxy/web/framework/base.py | 5 +---- lib/galaxy/web/framework/memdebug.py | 26 -------------------------- 4 files changed, 3 insertions(+), 39 deletions(-) diffs (96 lines): diff -r 8b4e25dc5d08 -r 04ad7a4b5c56 eggs.ini --- a/eggs.ini Mon Jan 25 13:05:41 2010 -0500 +++ b/eggs.ini Tue Jan 26 10:23:45 2010 -0500 @@ -24,7 +24,6 @@ python_lzo = 1.08 threadframe = 0.2 guppy = 0.1.8 -PSI = 0.3b1.1 [eggs:noplatform] amqplib = 0.6.1 @@ -93,7 +92,6 @@ Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.6.tar.gz PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.… PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.7.… -PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.11.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… SQLAlchemy = http://dist.g2.bx.psu.edu/SQLAlchemy-0.5.6_r6498.tar.bz2 @@ -106,4 +104,4 @@ wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip Babel = http://ftp.edgewall.com/pub/babel/Babel-0.9.4.zip wchartype = http://ginstrom.com/code/wchartype-0.1.zip -boto = http://boto.googlecode.com/files/boto-1.8d.tar.gz \ No newline at end of file +boto = http://boto.googlecode.com/files/boto-1.8d.tar.gz diff -r 8b4e25dc5d08 -r 04ad7a4b5c56 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Mon Jan 25 13:05:41 2010 -0500 +++ b/lib/galaxy/web/buildapp.py Tue Jan 26 10:23:45 2010 -0500 @@ -65,12 +65,7 @@ sys.exit( 1 ) atexit.register( app.shutdown ) # Create the universe WSGI application - if app.config.log_memory_usage: - from galaxy.web.framework.memdebug import MemoryLoggingWebApplication - webapp = MemoryLoggingWebApplication( app, session_cookie='galaxysession' ) - else: - webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) - # Find controllers + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) add_controllers( webapp, app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) diff -r 8b4e25dc5d08 -r 04ad7a4b5c56 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Mon Jan 25 13:05:41 2010 -0500 +++ b/lib/galaxy/web/framework/base.py Tue Jan 26 10:23:45 2010 -0500 @@ -122,7 +122,7 @@ # Special key for AJAX debugging, remove to avoid confusing methods kwargs.pop( '_', None ) try: - body = self.call_body_method( method, trans, kwargs ) + body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) if not body: @@ -140,9 +140,6 @@ trans.response.wsgi_headeritems() ) return self.make_body_iterable( trans, body ) - def call_body_method( self, method, trans, kwargs ): - return method( trans, **kwargs ) - def make_body_iterable( self, trans, body ): if isinstance( body, ( types.GeneratorType, list, tuple ) ): # Recursively stream the iterable diff -r 8b4e25dc5d08 -r 04ad7a4b5c56 lib/galaxy/web/framework/memdebug.py --- a/lib/galaxy/web/framework/memdebug.py Mon Jan 25 13:05:41 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -""" -Implementation of WebApplication that logs memory usage before and after -calling each controller method. -""" - -import pkg_resources -pkg_resources.require( "PSI" ) -import psi.process - -import os -import logging - -from galaxy.web.framework import WebApplication - -log = logging.getLogger( __name__ ) -pid = os.getpid() - -class MemoryLoggingWebApplication( WebApplication ): - def call_body_method( self, method, trans, kwargs ): - cls = method.im_class - process = psi.process.Process( pid ) - log.debug( "before controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) - rval = method( trans, **kwargs ) - process = psi.process.Process( pid ) - log.debug( "after controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) - return rval \ No newline at end of file

1 0

[hg] galaxy 3269: Backed out changeset 72020a46127e. Removes me...
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/76f6e26fd4f6 changeset: 3269:76f6e26fd4f6 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 26 10:20:46 2010 -0500 description: Backed out changeset 72020a46127e. Removes memory logging and PSI dependency. diffstat: eggs.ini | 2 -- lib/galaxy/web/buildapp.py | 7 +------ lib/galaxy/web/framework/base.py | 5 +---- lib/galaxy/web/framework/memdebug.py | 26 -------------------------- 4 files changed, 2 insertions(+), 38 deletions(-) diffs (89 lines): diff -r 72020a46127e -r 76f6e26fd4f6 eggs.ini --- a/eggs.ini Fri Oct 02 09:36:07 2009 -0400 +++ b/eggs.ini Tue Jan 26 10:20:46 2010 -0500 @@ -23,7 +23,6 @@ python_lzo = 1.08 threadframe = 0.2 guppy = 0.1.8 -PSI = 0.3b1.1 [eggs:noplatform] amqplib = 0.6.1 @@ -87,7 +86,6 @@ Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.… PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.… -PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.… diff -r 72020a46127e -r 76f6e26fd4f6 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Fri Oct 02 09:36:07 2009 -0400 +++ b/lib/galaxy/web/buildapp.py Tue Jan 26 10:20:46 2010 -0500 @@ -64,12 +64,7 @@ sys.exit( 1 ) atexit.register( app.shutdown ) # Create the universe WSGI application - if app.config.log_memory_usage: - from galaxy.web.framework.memdebug import MemoryLoggingWebApplication - webapp = MemoryLoggingWebApplication( app, session_cookie='galaxysession' ) - else: - webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) - # Find controllers + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) add_controllers( webapp, app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) diff -r 72020a46127e -r 76f6e26fd4f6 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Fri Oct 02 09:36:07 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Tue Jan 26 10:20:46 2010 -0500 @@ -122,7 +122,7 @@ # Special key for AJAX debugging, remove to avoid confusing methods kwargs.pop( '_', None ) try: - body = self.call_body_method( method, trans, kwargs ) + body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) if not body: @@ -140,9 +140,6 @@ trans.response.wsgi_headeritems() ) return self.make_body_iterable( trans, body ) - def call_body_method( self, method, trans, kwargs ): - return method( trans, **kwargs ) - def make_body_iterable( self, trans, body ): if isinstance( body, ( types.GeneratorType, list, tuple ) ): # Recursively stream the iterable diff -r 72020a46127e -r 76f6e26fd4f6 lib/galaxy/web/framework/memdebug.py --- a/lib/galaxy/web/framework/memdebug.py Fri Oct 02 09:36:07 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -""" -Implementation of WebApplication that logs memory usage before and after -calling each controller method. -""" - -import pkg_resources -pkg_resources.require( "PSI" ) -import psi.process - -import os -import logging - -from galaxy.web.framework import WebApplication - -log = logging.getLogger( __name__ ) -pid = os.getpid() - -class MemoryLoggingWebApplication( WebApplication ): - def call_body_method( self, method, trans, kwargs ): - cls = method.im_class - process = psi.process.Process( pid ) - log.debug( "before controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) - rval = method( trans, **kwargs ) - process = psi.process.Process( pid ) - log.debug( "after controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) - return rval \ No newline at end of file

1 0

psi module
by Davide Cittaro 26 Jan '10

26 Jan '10

Hi all, is the "psi" module only imported in galaxy/web/framework/memdebug.py to get memory usage for the process itself? psi is not supported by *BSD OS and I wonder if I can replace it with psutils d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

2 1

Galaxy-GenomeBrowser integration for BAM files
by Assaf Gordon 26 Jan '10

26 Jan '10

Hello, The UCSC Genome Browser team announced today their support for display BAM files ( http://genome.ucsc.edu/goldenPath/help/bam.html ). With this feature, we can have BAM files stored on Galaxy and transparently uploaded in the Genome Browser. This will be even better than with BED files, because Galaxy sends the entire BED file to the Genome Browser, but it only needs to send the URL of the BAM dataset to the genome browser (the GB later on download only the file portions it needs). This has the potential of making Galaxy the fastest, easiest way to handle next-gen libraries: Upload a FASTQ file, Map it with BWA, Get results as BAM files, click on a link and view the entire library in genome browser. Without it - users needs to have a public storage space (FTP/HTTP), to know how to use it, and how to construct "bigDataURL"s (not too hard, but the whole point of Galaxy is to hide these technicalities). I have a working prototype that with a single click sends the BAM track to the Genome Browser (with correct bigDataURL that the Genome Browser can use). The real pain is that the Genome Browser assumes the "bai" (bam index) file has the same URL as the BAM file (with ".bai" extension added), whereas galaxy saves the "bai" files as completely separated metadata files (with their own IDs and naming scheme). You can test it here: http://cancan.cshl.edu/bamgalaxy/history/imp?id=d38c5ae01427bcab (import the history, expand the BAM dataset, and click "display at UCSC main", I hope it won't crash) It's a very ugly hack, but if you're willing to consider this feature, I'll be happy to try and improve it. Comments are welcomed, - gordon

1 0

[hg] galaxy 3268: Fix functional tests for postgres by explicitl...
by Greg Von Kuster 26 Jan '10

26 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8b4e25dc5d08 changeset: 3268:8b4e25dc5d08 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Jan 25 13:05:41 2010 -0500 description: Fix functional tests for postgres by explicitly setting username for created users. diffstat: test/base/twilltestcase.py | 3 ++- 1 files changed, 2 insertions(+), 1 deletions(-) diffs (13 lines): diff -r 217da764cd50 -r 8b4e25dc5d08 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jan 25 12:45:55 2010 -0500 +++ b/test/base/twilltestcase.py Mon Jan 25 13:05:41 2010 -0500 @@ -608,7 +608,8 @@ # Functions associated with user accounts def create( self, email='test(a)bx.psu.edu', password='testuser' ): self.home() - self.visit_page( "user/create?email=%s&password=%s&confirm=%s&create_user_button=Submit" % ( email, password, password ) ) + # Create user, setting username to email. + self.visit_page( "user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( email, email, password, password ) ) self.check_page_for_string( "Now logged in as %s" %email ) self.home() # Make sure a new private role was created for the user

1 0

[hg] galaxy 3267: Merge
by Greg Von Kuster 26 Jan '10

26 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/217da764cd50 changeset: 3267:217da764cd50 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Jan 25 12:45:55 2010 -0500 description: Merge diffstat: lib/galaxy/tools/__init__.py | 9 +++++---- lib/galaxy/web/controllers/library.py | 3 +++ lib/galaxy/web/controllers/library_admin.py | 4 ++++ lib/galaxy/web/controllers/library_common.py | 9 ++++++++- 4 files changed, 20 insertions(+), 5 deletions(-) diffs (67 lines): diff -r b4c62757393a -r 217da764cd50 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Jan 25 12:43:45 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Mon Jan 25 12:45:55 2010 -0500 @@ -5,7 +5,7 @@ pkg_resources.require( "simplejson" ) -import logging, os, string, sys, tempfile, glob, shutil, types +import logging, os, string, sys, tempfile, glob, shutil, types, urllib import simplejson import binascii from UserDict import DictMixin @@ -432,10 +432,11 @@ # Handle properties of the input form self.check_values = util.string_as_bool( input_elem.get("check_values", "true") ) self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) ) + self.action = input_elem.get( 'action', '/tool_runner/index' ) if self.nginx_upload and self.app.config.nginx_upload_path: - self.action = input_elem.get( "action", self.app.config.nginx_upload_path + "?nginx_redir=/tool_runner/index" ) - else: - self.action = input_elem.get( "action", "/tool_runner/index") + if '?' in urllib.unquote_plus( self.action ): + raise Exception( 'URL parameters in a non-default tool action can not be used in conjunction with nginx upload. Please convert them to hidden POST parameters' ) + self.action = self.app.config.nginx_upload_path + '?nginx_redir=' + urllib.unquote_plus( self.action ) self.target = input_elem.get( "target", "galaxy_main" ) self.method = input_elem.get( "method", "post" ) # Parse the actual parameters diff -r b4c62757393a -r 217da764cd50 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Mon Jan 25 12:43:45 2010 -0500 +++ b/lib/galaxy/web/controllers/library.py Mon Jan 25 12:45:55 2010 -0500 @@ -34,3 +34,6 @@ default_action=params.get( 'default_action', None ), msg=msg, messagetype=messagetype ) + @web.expose + def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): + return trans.webapp.controllers[ 'library_common' ].upload_library_dataset( trans, 'library', library_id, folder_id, **kwd ) diff -r b4c62757393a -r 217da764cd50 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Jan 25 12:43:45 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Jan 25 12:45:55 2010 -0500 @@ -239,3 +239,7 @@ id=library_id, msg=msg, messagetype=status ) ) + @web.expose + @web.require_admin + def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): + return trans.webapp.controllers[ 'library_common' ].upload_library_dataset( trans, 'library_admin', library_id, folder_id, **kwd ) diff -r b4c62757393a -r 217da764cd50 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Jan 25 12:43:45 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Jan 25 12:45:55 2010 -0500 @@ -701,7 +701,14 @@ # If we're using nginx upload, override the form action action = web.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller ) if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: - action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action + # url_for is intentionally not used on the base URL here - + # nginx_upload_path is expected to include the proxy prefix if the + # administrator intends for it to be part of the URL. We also + # redirect to the library or library_admin controller rather than + # library_common because GET arguments can't be used in conjunction + # with nginx upload (nginx can't do percent decoding without a + # bunch of hacky rewrite rules). + action = trans.app.config.nginx_upload_path + '?nginx_redir=' + web.url_for( controller=cntrller, action='upload_library_dataset' ) return trans.fill_template( '/library/common/upload.mako', cntrller=cntrller, upload_option=upload_option,

1 0

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galaxy-dev January 2010