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[hg] galaxy 2953: Added 'History' column to HDA grid.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14e178f656ba changeset: 2953:14e178f656ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 16:53:14 2009 -0500 description: Added 'History' column to HDA grid. diffstat: lib/galaxy/web/controllers/dataset.py | 26 +++++++++++++++++++------- templates/dataset/grid.mako | 11 ++++++++--- templates/root/history_common.mako | 2 +- 3 files changed, 28 insertions(+), 11 deletions(-) diffs (116 lines): diff -r 6491acd0bef2 -r 14e178f656ba lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 15:39:51 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 16:53:14 2009 -0500 @@ -45,6 +45,11 @@ """ class HistoryDatasetAssociationListGrid( grids.Grid ): + # Custom columns for grid. + class HistoryColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda): + return hda.history.name + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -52,6 +57,7 @@ return "" def get_link( self, trans, grid, hda ): return None + class TagsColumn( grids.GridColumn ): def __init__(self, col_name, key, filterable): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -107,14 +113,16 @@ return accepted_filters # Grid definition - title = "Stored Datasets" + title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", - # Link name to dataset's history. + grids.GridColumn( "Name", key="name", + # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + HistoryColumn( "History", key="history", + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), TagsColumn( "Tags", key="tags", filterable=True ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), @@ -285,8 +293,9 @@ log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id ) if hdas: - - if operation == "switch": + if operation == "switch" or operation == "switch_history": + # Switch to a history that the HDA resides in. + # Convert hda to histories. histories = [] for hda in hdas: @@ -295,8 +304,11 @@ # Use history controller to switch the history. TODO: is this reasonable? status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) - # Current history changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] + # Current history changed, refresh history frame; if switching to a dataset, set hda seek. + trans.template_context['refresh_frames'] = ['history'] + if operation == "switch": + hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] + trans.template_context[ 'seek_hda_ids' ] = hda_ids # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) diff -r 6491acd0bef2 -r 14e178f656ba templates/dataset/grid.mako --- a/templates/dataset/grid.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/dataset/grid.mako Tue Nov 03 16:53:14 2009 -0500 @@ -92,8 +92,6 @@ t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); - //t.addClass("tag-input"); - return t; }); ## Can this be moved into base.mako? @@ -110,7 +108,14 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=str(ids) )}"; + ## If available, include HDA ids to seek to in history request. + <% + hda_id = None + if seek_hda_ids: + hda_id = str( seek_hda_ids[0] ) # Use only the first id. + print hda_id + %> + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=hda_id )}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } diff -r 6491acd0bef2 -r 14e178f656ba templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/root/history_common.mako Tue Nov 03 16:53:14 2009 -0500 @@ -1,6 +1,7 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> + <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: data_state = "queued" @@ -21,7 +22,6 @@ %endif ## Header row for history items (name, state, action buttons) - <a name="${trans.security.encode_id(data.id)}"></a> <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload":

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[hg] galaxy 2954: History ordering bug with SQLAlchemy 0.5 (deve...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/46791b5a653b changeset: 2954:46791b5a653b user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 17:16:40 2009 -0500 description: History ordering bug with SQLAlchemy 0.5 (developers - queries are no longer ordered by primary key by default, so order explicitly if it matters) and a <model_object>.c that slipped through. diffstat: lib/galaxy/jobs/__init__.py | 2 +- lib/galaxy/web/controllers/root.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diffs (25 lines): diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 17:16:40 2009 -0500 @@ -174,7 +174,7 @@ if self.track_jobs_in_database: for j in self.sa_session.query( model.Job ) \ .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ - .filter( model.Job.c.state == model.Job.states.NEW ): + .filter( model.Job.state == model.Job.states.NEW ): job = JobWrapper( j, self.app.toolbox.tools_by_id[ j.tool_id ], self ) new_jobs.append( job ) else: diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 17:16:40 2009 -0500 @@ -72,7 +72,8 @@ .filter( model.HistoryDatasetAssociation.history == history ) \ .options( eagerload( "children" ) ) \ .join( "dataset" ).filter( model.Dataset.purged == False ) \ - .options( eagerload_all( "dataset.actions" ) ) + .options( eagerload_all( "dataset.actions" ) ) \ + .order_by( model.HistoryDatasetAssociation.hid ) if not show_deleted: query = query.filter( model.HistoryDatasetAssociation.deleted == False ) return trans.stream_template_mako( "root/history.mako",

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[hg] galaxy 2956: When reseting password, if an email has not ye...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/984b1eb6c428 changeset: 2956:984b1eb6c428 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 09:32:09 2009 -0500 description: When reseting password, if an email has not yet been provided, make text box empty and not contain 'None' diffstat: lib/galaxy/web/controllers/user.py | 2 ++ 1 files changed, 2 insertions(+), 0 deletions(-) diffs (12 lines): diff -r d7c66019de13 -r 984b1eb6c428 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Tue Nov 03 19:16:01 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Wed Nov 04 09:32:09 2009 -0500 @@ -571,6 +571,8 @@ return trans.show_ok_message( "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( action='login' ) ) ) elif email != None: error = "The specified user does not exist" + elif email is None: + email = "" return trans.show_form( web.FormBuilder( web.url_for(), "Reset Password", submit_text="Submit" ) .add_text( "email", "Email", value=email, error=error ) )

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[hg] galaxy 2952: Fix a bug in streaming library tarballs. Quot...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6491acd0bef2 changeset: 2952:6491acd0bef2 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 15:39:51 2009 -0500 description: Fix a bug in streaming library tarballs. Quoth James: This bears repeating (heh, again... -nate) -- NEVER use a mutable object (like a dict) as a function parameter default. The default is evaluated once (at def time) and then used for every call to the function. This is really bad since every call, across multiple thread, are writing to that one dict. In this case, it resulted in the values of parameters that have dependencies being persisted across requests. Took me three solid days to find! diffstat: lib/galaxy/util/streamball.py | 6 ++++-- 1 files changed, 4 insertions(+), 2 deletions(-) diffs (17 lines): diff -r 2300a80d80e5 -r 6491acd0bef2 lib/galaxy/util/streamball.py --- a/lib/galaxy/util/streamball.py Tue Nov 03 13:04:35 2009 -0500 +++ b/lib/galaxy/util/streamball.py Tue Nov 03 15:39:51 2009 -0500 @@ -7,9 +7,11 @@ log = logging.getLogger( __name__ ) class StreamBall( object ): - def __init__( self, mode, members={} ): + def __init__( self, mode, members=None ): + self.members = members + if members is None: + self.members = {} self.mode = mode - self.members = members self.wsgi_status = None self.wsgi_headeritems = None def add( self, file, relpath ):

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[hg] galaxy 2948: Pack recently modified scripts.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/de764999c5af changeset: 2948:de764999c5af user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 13:00:36 2009 -0500 description: Pack recently modified scripts. diffstat: static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/trackster.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (16 lines): diff -r f776fa6045ba -r de764999c5af static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" 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de764999c5af static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/trackster.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,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")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e =this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=10,CACHED_DATA=20,CONTEXT=$("<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")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern( left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){ e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){th is.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k);if(g){this.tile_cache.set(i,g)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[ e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur eTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k= Math.floor((n.start-e)*g);k-=m.measureText(n.name).width;l=Math.ceil((n.end-e)*g)}else{k=Math.floor((n.start-e)*b);l=Math.ceil((n.end-e)*b)}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospace";v.textAlign="rig ht";var 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1 0

[hg] galaxy 2949: imported patch alchemy05_fixes_01
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/133252175425 changeset: 2949:133252175425 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:00 2009 -0500 description: imported patch alchemy05_fixes_01 diffstat: eggs.ini | 10 +- lib/galaxy/model/mapping.py | 2 +- lib/galaxy/model/migrate/check.py | 2 +- lib/galaxy/model/migrate/versions/0003_security_and_libraries.py | 4 +- lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py | 2 +- lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | 4 +- lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py | 2 +- lib/galaxy/model/migrate/versions/0008_galaxy_forms.py | 4 +- lib/galaxy/model/migrate/versions/0009_request_table.py | 2 +- lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py | 4 +- lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py | 4 +- lib/galaxy/model/migrate/versions/0012_user_address.py | 4 +- lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py | 2 +- lib/galaxy/model/migrate/versions/0017_library_item_indexes.py | 2 +- lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py | 2 +- lib/galaxy/model/migrate/versions/0019_request_library_folder.py | 4 +- lib/galaxy/model/migrate/versions/0020_library_upload_job.py | 4 +- lib/galaxy/model/orm/ext/assignmapper.py | 38 ++++++--- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/page.py | 4 +- lib/galaxy/web/controllers/workflow.py | 22 ++-- lib/galaxy/web/framework/helpers/grids.py | 4 +- 23 files changed, 73 insertions(+), 57 deletions(-) diffs (502 lines): diff -r 80915982fdb2 -r 133252175425 eggs.ini --- a/eggs.ini Tue Nov 03 11:28:34 2009 -0500 +++ b/eggs.ini Tue Nov 03 12:52:00 2009 -0500 @@ -28,6 +28,7 @@ [eggs:noplatform] amqplib = 0.6.1 Beaker = 1.4 +decorator = 3.1.2 docutils = 0.4 elementtree = 1.2.6_20050316 lrucache = 0.2 @@ -41,8 +42,8 @@ PasteScript = 1.3.6 Routes = 1.6.3 simplejson = 1.5 -SQLAlchemy = 0.4.7p1 -sqlalchemy_migrate = 0.4.5 +SQLAlchemy = 0.5.6 +sqlalchemy_migrate = 0.5.4 Tempita = 0.1 twill = 0.9 WebError = 0.8a @@ -77,6 +78,7 @@ guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz +decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz @@ -90,8 +92,8 @@ 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.… -sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… +SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.5.6.tar.gz +sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 @@ -18,7 +18,7 @@ from sqlalchemy.ext.associationproxy import association_proxy metadata = MetaData() -context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = Session = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) # For backward compatibility with "context.current" context.current = Session diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/check.py Tue Nov 03 12:52:00 2009 -0500 @@ -7,7 +7,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * -from sqlalchemy.exceptions import NoSuchTableError +from sqlalchemy.exc import NoSuchTableError log = logging.getLogger( __name__ ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0003_security_and_libraries.py --- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -20,7 +20,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) if migrate_engine.name == 'postgres': # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.ht… diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py --- a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 12:52:00 2009 -0500 @@ -12,7 +12,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) User_table = Table( "galaxy_user", metadata, autoload=True ) HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -23,7 +23,7 @@ metadata = MetaData( migrate_engine ) -context = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) ## classes @@ -662,7 +662,7 @@ log.debug( "Fixing a discrepancy concerning deleted shared history items." ) affected_items = 0 start_time = time.time() - for dataset in context.query( Dataset ).filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ): + for dataset in context.query( Dataset ).filter( and_( Dataset.deleted == True, Dataset.purged == False ) ): for dataset_instance in dataset.history_associations + dataset.library_associations: if not dataset_instance.deleted: dataset.deleted = False diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py --- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0008_galaxy_forms.py --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -11,7 +11,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -31,7 +31,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -9,7 +9,7 @@ from migrate.changeset import * import sys, logging from galaxy.model.custom_types import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -10,7 +10,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -30,7 +30,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -25,7 +25,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0012_user_address.py --- a/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 12:52:00 2009 -0500 @@ -6,7 +6,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -24,7 +24,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py --- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -17,7 +17,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import sys, logging diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0017_library_item_indexes.py --- a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) LibraryDataset_table = Table( "library_dataset", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py --- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * import migrate.changeset diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0019_request_library_folder.py --- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0020_library_upload_job.py --- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/orm/ext/assignmapper.py --- a/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 12:52:00 2009 -0500 @@ -15,22 +15,36 @@ from sqlalchemy import util, exceptions import types -from sqlalchemy.orm import mapper, Query +from sqlalchemy.orm import Query +from sqlalchemy.orm import mapper as sqla_mapper -def _monkeypatch_session_method(name, session, class_, make_list=False): - def do(self, *args, **kwargs): - if make_list: - self = [ self ] - return getattr(session, name)( self, *args, **kwargs ) +def _monkeypatch_session_method( name, session, class_ ): + # TODO: eliminate this method by fixing the session flushes + def do( self, *args, **kwargs ): + if self not in session.deleted: + session.add( self ) + return session.flush() try: do.__name__ = name except: pass - if not hasattr(class_, name): - setattr(class_, name, do) - + if not hasattr( class_, name ): + setattr( class_, name, do ) +def session_mapper( scoped_session, class_, *args, **kwargs ): + def mapper( cls, *arg, **kw ): + validate = kw.pop( 'validate', False ) + if cls.__init__ is object.__init__: + def __init__( self, **kwargs ): + for key, value in kwargs.items(): + if validate: + if not cls_mapper.has_property( key ): + raise TypeError( "Invalid __init__ argument: '%s'" % key ) + setattr( self, key, value ) + cls.__init__ = __init__ + cls.query = scoped_session.query_property() + _monkeypatch_session_method( 'flush', scoped_session, cls ) + return sqla_mapper( cls, *arg, **kw ) + return mapper( class_, *args, **kwargs ) def assign_mapper( session, class_, *args, **kwargs ): - m = class_.mapper = session.mapper( class_, *args, **kwargs ) - for name in ( 'flush', ): - _monkeypatch_session_method( name, session, class_, make_list=True ) + m = class_.mapper = session_mapper( session, class_, *args, **kwargs ) return m diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -450,7 +450,7 @@ # create corresponding row in the form_definition_current table fd.form_definition_current = fdc fdc.latest_form = fd - trans.sa_session.save_or_update( fdc ) + trans.sa_session.add( fdc ) trans.sa_session.flush() msg = "The new form named '%s' has been created. " % (fd.name) return fd, msg diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:52:00 2009 -0500 @@ -726,7 +726,7 @@ share.history = history share.user = send_to_user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() if history not in shared_histories: shared_histories.append( history ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/page.py Tue Nov 03 12:52:00 2009 -0500 @@ -135,7 +135,7 @@ page_revision.content = "" # Persist session = trans.sa_session - session.save_or_update( page ) + session.add( page ) session.flush() # Display the management page ## trans.set_message( "Page '%s' created" % page.title ) @@ -240,4 +240,4 @@ raise web.httpexceptions.HTTPNotFound() return trans.fill_template( "page/display.mako", page=page ) - \ No newline at end of file + diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Nov 03 12:52:00 2009 -0500 @@ -30,7 +30,7 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ @@ -53,13 +53,13 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .filter( model.StoredWorkflow.deleted == False ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, @@ -91,7 +91,7 @@ share.stored_workflow = stored share.user = other session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) ) return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) ) @@ -142,7 +142,7 @@ share.stored_workflow = stored share.user = trans.user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() # Redirect to load galaxy frames. return trans.response.send_redirect( url_for( controller='workflow' ) ) @@ -180,7 +180,7 @@ new_stored.user = user # Persist session = trans.sa_session - session.save_or_update( new_stored ) + session.add( new_stored ) session.flush() # Display the management page trans.set_message( 'Clone created with name "%s"' % new_stored.name ) @@ -205,7 +205,7 @@ stored_workflow.latest_workflow = workflow # Persist session = trans.sa_session - session.save_or_update( stored_workflow ) + session.add( stored_workflow ) session.flush() # Display the management page trans.set_message( "Workflow '%s' created" % stored_workflow.name ) @@ -514,7 +514,7 @@ stored.name = workflow_name workflow.stored_workflow = stored stored.latest_workflow = workflow - trans.sa_session.save_or_update( stored ) + trans.sa_session.add( stored ) trans.sa_session.flush() # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) @@ -656,12 +656,12 @@ ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] ) workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == False ) \ .all() return trans.fill_template( "workflow/configure_menu.mako", workflows=workflows, diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:52:00 2009 -0500 @@ -111,10 +111,10 @@ if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' - query = query.order_by( self.model_class.c.get( sort_key ).desc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).desc() ) else: sort_order = 'asc' - query = query.order_by( self.model_class.c.get( sort_key ).asc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key # There might be a current row

1 0

[hg] galaxy 2947: Improved search functionality for history grid...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f776fa6045ba changeset: 2947:f776fa6045ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 12:58:13 2009 -0500 description: Improved search functionality for history grid: (a) generic free text search box and (b) advanced search using name, tag, deleted status, and shared status. diffstat: lib/galaxy/tags/tag_handler.py | 8 +- lib/galaxy/web/controllers/history.py | 145 +++++++++++++++++--- lib/galaxy/web/framework/helpers/grids.py | 1 + static/scripts/autocomplete_tagging.js | 2 +- templates/history/grid.mako | 250 +++++++++++++++++++--------------- test/base/twilltestcase.py | 18 +- test/functional/test_history_functions.py | 2 +- 7 files changed, 278 insertions(+), 148 deletions(-) diffs (649 lines): diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Nov 03 12:58:13 2009 -0500 @@ -3,6 +3,12 @@ class TagHandler( object ): + # Minimum tag length. + min_tag_len = 2 + + # Maximum tag length. + max_tag_len = 255 + # Tag separator. tag_separators = ',;' @@ -215,7 +221,7 @@ scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. - if len(scrubbed_name) < 3 or len(scrubbed_name) > 255: + if len(scrubbed_name) < self.min_tag_len or len(scrubbed_name) > self.max_tag_len: return None return scrubbed_name diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:58:13 2009 -0500 @@ -5,6 +5,7 @@ from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.odict import odict from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -19,12 +20,29 @@ class HistoryListGrid( grids.Grid ): # Custom column types class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup ): + def __init( self, key, link, attach_popup, filterable ): grids.GridColumn.__init__(self, key, link, attach_popup) def get_value( self, trans, grid, history ): return history.get_display_name() + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by name. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -48,6 +66,7 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -61,7 +80,7 @@ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): - """ Modify query to include only histories with tags in column_filter. """ + """ Modify query to filter histories by tag. """ if column_filter == "All": pass elif column_filter: @@ -69,52 +88,115 @@ tag_handler = TagHandler() raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( History.tags.any( tag_id=tag.id ) ) + if name: + # Search for tag names. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - query = query.filter( History.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( History.tags.any( user_tname=name ) ) + # Search for tag values. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) return query def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - - + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } accepted_filters = [] for label, val in accepted_filter_labels_and_vals.items(): args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters + + class SharingColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( History.users_shared_with == None ) + query = query.filter( History.importable == False ) + elif column_filter == "shared": + query = query.filter( History.users_shared_with != None ) + elif column_filter == "importable": + query = query.filter( History.importable == True ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["importable"] = "importable" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class FreeTextSearchColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to search tags and history names. """ + if column_filter == "All": + pass + elif column_filter: + # Build tags filter. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + tags_filter = None + for name, value in raw_tags.items(): + if name: + # Search for tag names. + tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) + if value: + # Search for tag values. + tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) + + # Build history name filter. + history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) + + # Apply filters to query. + if tags_filter: + query = query.filter( or_( tags_filter, history_name_filter ) ) + else: + query = query.filter( history_name_filter ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition - title = "Stored histories" + title = "Saved Histories" model_class = model.History template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True ), + attach_popup=True, filterable=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Valid for filtering but invisible - DeletedColumn( "Status", key="deleted", visible=False, filterable=True ) + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), + SharingColumn( "Shared", key="shared", visible=False, filterable=True ), + FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), @@ -131,7 +213,7 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False use_paging = True @@ -160,6 +242,7 @@ template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" + default_filter = {} columns = [ grids.GridColumn( "Name", key="name" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), @@ -374,6 +457,18 @@ trans.sa_session.flush() @web.expose + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for history names""" + user = trans.get_user() + if not user: + return + + ac_data = "" + for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + ac_data = ac_data + history.name + "\n" + return ac_data + + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" msg = "" diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:58:13 2009 -0500 @@ -183,6 +183,7 @@ query=query, cur_page_num = page_num, num_pages = num_pages, + default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r 80915982fdb2 -r f776fa6045ba static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Tue Nov 03 11:28:34 2009 -0500 +++ b/static/scripts/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 @@ -309,7 +309,7 @@ new_value = new_value.replace(/^\s+|\s+$/g,""); // Too short? - if (new_value.length < 3) + if (new_value.length < 2) return false; // diff -r 80915982fdb2 -r f776fa6045ba templates/history/grid.mako --- a/templates/history/grid.mako Tue Nov 03 11:28:34 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 03 12:58:13 2009 -0500 @@ -29,71 +29,20 @@ }); // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); + var t = $("#input-tags-filter"); - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - $("#page-select").change(navigate_to_page); + // Set up autocomplete for name filter input. + var t2 = $("#input-name-filter"); + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -125,21 +74,52 @@ %endif %endif + // Filter and sort args for grid. + var filter_args = ${h.to_json_string(cur_filter_dict)}; + var sort_key = "${sort_key}"; + // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // Add tag to grid filter. // function add_tag_to_grid_filter(tag_name, tag_value) { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + add_condition_to_grid_filter("tags", tag, true); + } + + // + // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. + // + function add_condition_to_grid_filter(name, value, append) + { + // Update filter arg with new condition. + if (append) + { + // Append value. + var cur_val = filter_args[name]; + if (cur_val != "All") + cur_val = cur_val + ", " + value; + else + cur_val = value; + filter_args[name] = cur_val; + } + else + { + // Replace value. + filter_args[name] = value; + } + + // Build URL with filter args, sort key. + var filter_arg_value_strs = new Array(); + var i = 0; + for (arg in filter_args) + { + filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; + } + var filter_str = filter_arg_value_strs.join("&"); + var url_base = "${h.url_for( controller='history', action='list')}"; + var url = url_base + "?" + filter_str + "&sort=" + sort_key; self.location = url; } @@ -154,7 +134,7 @@ var url = url_base.replace("PAGE", page_num); self.location = url; } - + </script> </%def> @@ -175,47 +155,95 @@ <div class="grid-header"> <h2>${grid.title}</h2> - - ## Print grid filter. - <form name="history_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> + + ## Search box and more options filter at top of grid. + <div> + ## Grid search. TODO: use more elegant way to get free text search column. + <% column = grid.columns[-1] %> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" + action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" + method="get" > + ${column.label}: + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> %endif %endfor - - ## Link to clear all filters. TODO: this should be the default filter or an empty filter. - <% - args = { "deleted" : "False", "tags" : "All" } - no_filter = GridColumnFilter("Clear Filter", args) - %> - <span><a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a></span> - </form> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if use_form: + </form> + %endif + </div> + + ## Advanced Search + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable: + <tr> + ## Show div if current filter has value that is different from the default filter. + %if cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + <td style="padding-left: 10px">${column.label.lower()}:</td> + <td> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" + method="get" > + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %if use_form: + </form> + %endif + </td> + </tr> + %endif + %endfor + </table> + </div> </div> <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> @@ -291,7 +319,7 @@ extra = "" %> %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> %else: <td >${v}${extra}</td> %endif diff -r 80915982fdb2 -r f776fa6045ba test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/base/twilltestcase.py Tue Nov 03 12:58:13 2009 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile, re from itertools import * import twill @@ -311,20 +311,20 @@ def view_stored_active_histories( self, check_str='' ): self.home() self.visit_page( "history/list" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) + self.check_page_for_string( 'operation=Rename' ) + self.check_page_for_string( 'operation=Switch' ) + self.check_page_for_string( 'operation=Delete' ) if check_str: self.check_page_for_string( check_str ) self.home() def view_stored_deleted_histories( self, check_str='' ): self.home() self.visit_page( "history/list?f-deleted=True" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Undelete&id' ) + self.check_page_for_string( 'operation=Undelete' ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -723,14 +723,14 @@ # Functions associated with browsers, cookies, HTML forms and page visits def check_page_for_string( self, patt ): - """Looks for 'patt' in the current browser page""" + """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) - + def write_temp_file( self, content ): fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) f = os.fdopen( fd, "w" ) diff -r 80915982fdb2 -r f776fa6045ba test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/functional/test_history_functions.py Tue Nov 03 12:58:13 2009 -0500 @@ -179,7 +179,7 @@ self.share_current_history( regular_user1.email, check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing">shared' ) + self.view_stored_active_histories( check_str='operation=sharing' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare',

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[hg] galaxy 2946: Fix new functional tests script return code (f...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80915982fdb2 changeset: 2946:80915982fdb2 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 11:28:34 2009 -0500 description: Fix new functional tests script return code (for buildbot) diffstat: scripts/functional_tests.py | 11 +++++++---- 1 files changed, 7 insertions(+), 4 deletions(-) diffs (34 lines): diff -r c96e886f883f -r 80915982fdb2 scripts/functional_tests.py --- a/scripts/functional_tests.py Tue Nov 03 10:26:42 2009 -0500 +++ b/scripts/functional_tests.py Tue Nov 03 11:28:34 2009 -0500 @@ -155,7 +155,7 @@ log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) - rval = False + success = False try: @@ -186,7 +186,7 @@ result = test_runner.run( tests ) - rval = result.wasSuccessful() + success = result.wasSuccessful() except: log.exception( "Failure running tests" ) @@ -206,7 +206,10 @@ app = None log.info( "Embedded Universe application stopped" ) - return rval + if success: + return 0 + else: + return 1 if __name__ == "__main__": - main() + sys.exit( main() )

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[hg] galaxy 2945: Fixed a bug in the user selectbox in new reque...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c96e886f883f changeset: 2945:c96e886f883f user: rc date: Tue Nov 03 10:26:42 2009 -0500 description: Fixed a bug in the user selectbox in new requests page diffstat: lib/galaxy/web/controllers/requests_admin.py | 9 +++------ 1 files changed, 3 insertions(+), 6 deletions(-) diffs (34 lines): diff -r 7594fc81bdfc -r c96e886f883f lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 07:58:24 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 10:26:42 2009 -0500 @@ -377,8 +377,10 @@ msg=msg, messagetype=messagetype) def __select_user(self, trans, userid): + user_list = trans.sa_session.query( trans.app.model.User )\ + .order_by( trans.app.model.User.email.asc() ) user_ids = ['none'] - for user in trans.sa_session.query( trans.app.model.User ): + for user in user_list: if not user.deleted: user_ids.append(str(user.id)) select_user = SelectField('select_user', @@ -388,10 +390,6 @@ select_user.add_option('Select one', 'none', selected=True) else: select_user.add_option('Select one', 'none') - def __get_email(user): - return user.email - user_list = trans.sa_session.query( trans.app.model.User ) - #user_list.sort(key=__get_email) for user in user_list: if not user.deleted: if userid == str(user.id): @@ -399,7 +397,6 @@ else: select_user.add_option(user.email, user.id) return select_user - def __library_ui(self, trans, user, request=None, **kwd): ''' This method creates the data library & folder selectbox for new &

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[hg] galaxy 2944: Changed the test user emails in the user_info ...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7594fc81bdfc changeset: 2944:7594fc81bdfc user: rc date: Tue Nov 03 07:58:24 2009 -0500 description: Changed the test user emails in the user_info functional tests diffstat: test/functional/test_user_info.py | 18 +++++++++--------- 1 files changed, 9 insertions(+), 9 deletions(-) diffs (60 lines): diff -r 6e657b4aa837 -r 7594fc81bdfc test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Nov 02 16:52:32 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 07:58:24 2009 -0500 @@ -75,7 +75,7 @@ # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test1(a)bx.psu.edu', 'testuser', 'test1', + self.create_user_with_info( 'test11(a)bx.psu.edu', 'testuser', 'test11', user_info_forms='multiple', user_info_form_id=form_one.id, user_info_values=user_info_values ) @@ -98,7 +98,7 @@ # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test2(a)bx.psu.edu', 'testuser', 'test2', + self.create_user_with_info( 'test12(a)bx.psu.edu', 'testuser', 'test12', user_info_forms='single', user_info_form_id=form_one.id, user_info_values=user_info_values ) @@ -110,31 +110,31 @@ def test_015_edit_user_info( self ): """Testing editing user info as a regular user""" self.logout() - self.login( 'test1(a)bx.psu.edu' ) + self.login( 'test11(a)bx.psu.edu' ) user = sa_session.query( galaxy.model.User ) \ - .filter( and_( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) ).first() - self.edit_login_info( new_email='test1_new(a)bx.psu.edu', new_username='test1_new' ) + .filter( and_( galaxy.model.User.table.c.email=='test11(a)bx.psu.edu' ) ).first() + self.edit_login_info( new_email='test11_new(a)bx.psu.edu', new_username='test11_new' ) self.change_password('testuser', 'new_testuser') self.edit_user_info( ['Research', 'PSU'] ) def test_020_create_user_as_admin( self ): ''' Testing creating users as an admin ''' self.logout() - self.login( 'test2(a)bx.psu.edu' ) + self.login( 'test(a)bx.psu.edu' ) form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test3(a)bx.psu.edu', 'testuser', 'test3', + self.create_user_with_info( 'test13(a)bx.psu.edu', 'testuser', 'test13', user_info_forms='single', user_info_form_id=form_one.id, user_info_values=user_info_values ) self.logout() self.login( 'test(a)bx.psu.edu' ) user = sa_session.query( galaxy.model.User ) \ - .filter( and_( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ) ).first() + .filter( and_( galaxy.model.User.table.c.email=='test13(a)bx.psu.edu' ) ).first() self.home() page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id( user.id ) self.visit_page( page ) self.check_page_for_string( 'Manage User Information' ) - self.check_page_for_string( 'test3(a)bx.psu.edu' ) + self.check_page_for_string( 'test13(a)bx.psu.edu' ) for value in user_info_values: self.check_page_for_string( value ) # lets delete the 'Student' user info form

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