galaxy-commits October 2014

galaxy-commits@lists.galaxyproject.org

2 participants
174 discussions

[galaxyproject/usegalaxy-playbook] cf32b4: Dropped survey slide; added training network slide...
by GitHub 17 Oct '14

17 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cf32b45543bd46b62761071bc2af8ca73906ea07 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf32b45543bd46b6… Author: Dave Clements <clements(a)Dave-Clementss-MacBook-Pro.local> Date: 2014-10-17 (Fri, 17 Oct 2014) Changed paths: A files/galaxy/common/static/welcome_img/GTN.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped survey slide; added training network slide.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d030de0c470/ Changeset: 3d030de0c470 User: dannon Date: 2014-10-17 12:07:24+00:00 Summary: Merge stable. Affected #: 3 files diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 +e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1336,6 +1336,7 @@ self.purged = False self.purgable = purgable self.external_filename = external_filename + self.external_extra_files_path = None self._extra_files_path = extra_files_path self.file_size = file_size if uuid is None: @@ -1359,9 +1360,20 @@ else: self.external_filename = filename file_name = property( get_file_name, set_file_name ) - @property - def extra_files_path( self ): - return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + def get_extra_files_path( self ): + # Unlike get_file_name - extrnal_extra_files_path is not backed by an + # actual database column so if SA instantiates this object - the + # attribute won't exist yet. + if not getattr( self, "external_extra_files_path", None ): + return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + else: + return os.path.abspath( self.external_extra_files_path ) + def set_extra_files_path( self, extra_files_path ): + if not extra_files_path: + self.external_extra_files_path = None + else: + self.external_extra_files_path = extra_files_path + extra_files_path = property( get_extra_files_path, set_extra_files_path) def _calculate_size( self ): if self.external_filename: try: diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -110,6 +110,8 @@ dataset = cPickle.load( open( filename_in ) ) # load DatasetInstance if dataset_filename_override: dataset.dataset.external_filename = dataset_filename_override + files_path = os.path.abspath(os.path.join( tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id) )) + dataset.dataset.external_extra_files_path = files_path if dataset.dataset.id in existing_job_metadata_dict: dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension ) # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles https://bitbucket.org/galaxy/galaxy-central/commits/acb838d9af91/ Changeset: acb838d9af91 User: dannon Date: 2014-10-17 12:08:08+00:00 Summary: Fix typo noticed by nsoranzo. Affected #: 1 file diff -r 3d030de0c4708214f7add0c6391e0bd9024c045a -r acb838d9af911cfc7c79328ffa87472913e5529c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1361,7 +1361,7 @@ self.external_filename = filename file_name = property( get_file_name, set_file_name ) def get_extra_files_path( self ): - # Unlike get_file_name - extrnal_extra_files_path is not backed by an + # Unlike get_file_name - external_extra_files_path is not backed by an # actual database column so if SA instantiates this object - the # attribute won't exist yet. if not getattr( self, "external_extra_files_path", None ): @@ -2449,7 +2449,7 @@ file_size = int( ldda.get_size() ) except OSError: file_size = 0 - + rval = dict( id = ldda.id, hda_ldda = 'ldda', model_class = self.__class__.__name__, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Upload: Handle ftp api errors on client side
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e8235a516d1/ Changeset: 0e8235a516d1 User: guerler Date: 2014-10-16 23:59:08+00:00 Summary: Upload: Handle ftp api errors on client side Affected #: 4 files diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef client/galaxy/scripts/mvc/upload/upload-ftp.js --- a/client/galaxy/scripts/mvc/upload/upload-ftp.js +++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js @@ -23,7 +23,8 @@ // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', - success : function(ftp_files) { self._fill(ftp_files); } + success : function(ftp_files) { self._fill(ftp_files); }, + error : function() { self._fill(); } }); }, @@ -34,7 +35,7 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { + if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -112,7 +112,8 @@ response.append( dict( path = path, size = statinfo.st_size, ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) - + else: + raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) # sort by path response = sorted(response, key=itemgetter("path")) return response diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -23,7 +23,8 @@ // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', - success : function(ftp_files) { self._fill(ftp_files); } + success : function(ftp_files) { self._fill(ftp_files); }, + error : function() { self._fill(); } }); }, @@ -34,7 +35,7 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { + if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef static/scripts/packed/mvc/upload/upload-ftp.js --- a/static/scripts/packed/mvc/upload/upload-ftp.js +++ b/static/scripts/packed/mvc/upload/upload-ftp.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c&&c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Api: Ftp files return empty list instead of raising error if directory is missing
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d404a6f6d01e/ Changeset: d404a6f6d01e User: guerler Date: 2014-10-16 23:47:55+00:00 Summary: Api: Ftp files return empty list instead of raising error if directory is missing Affected #: 1 file diff -r eb28a9bcb4d9ca99613b667300095ce8a52f7ae3 -r d404a6f6d01e6af5cbd35a427c474cee47fe963a lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -112,8 +112,7 @@ response.append( dict( path = path, size = statinfo.st_size, ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) - else: - raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) + # sort by path response = sorted(response, key=itemgetter("path")) return response Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Tool's command might be separated by a newline, so we should use the general form split here, not specifically on spaces. Pointed out by @kellrott.
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb28a9bcb4d9/ Changeset: eb28a9bcb4d9 User: dannon Date: 2014-10-16 23:37:30+00:00 Summary: Tool's command might be separated by a newline, so we should use the general form split here, not specifically on spaces. Pointed out by @kellrott. Affected #: 1 file diff -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 -r eb28a9bcb4d9ca99613b667300095ce8a52f7ae3 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -699,7 +699,7 @@ def load_tooldir_tag_set(self, sub_elem, elems, tool_path, integrated_elems, load_panel_dict): directory = os.path.join( tool_path, sub_elem.attrib.get("dir") ) - recursive = string_as_bool( sub_elem.attrib.get("recursive", True) ) + recursive = string_as_bool( sub_elem.attrib.get("recursive", True) ) self.__watch_directory( directory, elems, integrated_elems, load_panel_dict, recursive ) def __watch_directory( self, directory, elems, integrated_elems, load_panel_dict, recursive): @@ -825,7 +825,7 @@ tool_tup = ( os.path.abspath( tool.config_file ), os.path.split( tool.config_file )[-1] ) tarball_files.append( tool_tup ) # TODO: This feels hacky. - tool_command = tool.command.strip().split( ' ' )[0] + tool_command = tool.command.strip().split()[0] tool_path = os.path.dirname( os.path.abspath( tool.config_file ) ) # Add the tool XML to the tuple that will be used to populate the tarball. if os.path.exists( os.path.join( tool_path, tool_command ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix Circster background bug in Firefox by correctly specifying colors.
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d09b44c5f228/ Changeset: d09b44c5f228 User: jgoecks Date: 2014-10-16 18:15:50+00:00 Summary: Fix Circster background bug in Firefox by correctly specifying colors. Affected #: 3 files diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 client/galaxy/scripts/viz/circster.js --- a/client/galaxy/scripts/viz/circster.js +++ b/client/galaxy/scripts/viz/circster.js @@ -404,11 +404,11 @@ /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { - this.bg_stroke = 'ddd'; + this.bg_stroke = '#ddd'; // Fill color when loading data. - this.loading_bg_fill = 'ffc'; + this.loading_bg_fill = '#ffc'; // Fill color when data has been loaded. - this.bg_fill = 'ddd'; + this.bg_fill = '#ddd'; this.total_gap = options.total_gap; this.track = options.track; this.radius_bounds = options.radius_bounds; @@ -688,8 +688,8 @@ // Use a single arc for rendering data. this.innerRadius = this.radius_bounds[0]; this.radius_bounds[0] = this.radius_bounds[1]; - this.bg_stroke = 'fff'; - this.bg_fill = 'fff'; + this.bg_stroke = '#fff'; + this.bg_fill = '#fff'; // Minimum arc distance for labels to be applied. this.min_arc_len = 0.05; diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -require(["utils/utils","libs/farbtastic",],function(a){a.cssLoadFile("static/style/circster.css")});define(["libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,m,j,c){var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");return v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(Math.abs(p)<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));p=Math.abs(p);if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.genome=o.genome;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var p=this.model.get("config");p.get("arc_dataset_height").on("change:value",this.update_track_bounds,this);p.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var q=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),r=this.model.get("config").get_value("track_gap"),o=Math.min(this.$el.width(),this.$el.height())-20,u=o/2-q.length*(s+r)+r-this.label_arc_height,t=m.range(u,o/2,s+r);var p=this;return h.map(t,function(v){return[v,v+s]})},render:function(){var x=this,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),r=this.get_chord_tracks(),q=x.model.get("config").get_value("total_gap"),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new e({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:q});y.render();return y});this.chords_views=r.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:q});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new d(),radius_bounds:u,genome:x.genome,total_gap:q});this.label_track_view.render()},add_track:function(u){var p=this.model.get("config").get_value("total_gap");if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:p});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new e({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:p});o.render();this.circular_views.push(o)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})},update_track_bounds:function(){var o=this.get_tracks_bounds();h.each(this.circular_views,function(p,q){p.update_radius_bounds(o[q])});h.each(this.chords_views,function(p){p.update_radius_bounds(o[0])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ddd";this.loading_bg_fill="ffc";this.bg_fill="ddd";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=h.reject(h.map(v,function(w,x){var y=null,z=q._get_path_function(r[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});var t=p.get("config").get_value("color");o.each(function(x,w){m.select(this).transition().duration(1000).style("stroke",t).style("fill",t).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(p){var o=this.data_bounds;this.data_bounds=p||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));this._transition_chrom_data()},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);o.get("config").set_value("min_value",q.data_bounds[0],{silent:true});o.get("config").set_value("max_value",q.data_bounds[1],{silent:true});layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=2*Math.PI*this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var g=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);var p=this.track.get("config");p.get("min_value").on("change:value",this._update_min_max,this);p.get("max_value").on("change:value",this._update_min_max,this);p.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var p=this.track.get("config"),o=[p.get_value("min_value"),p.get_value("max_value")];this._update_data_bounds(o);this.parent_elt.selectAll(".min_max").text(function(r,q){return o[q]})},_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,q=function(){return"rotate(90)"};var p=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true).classed("min_max",true);h.each(p,function(r){$(r).click(function(){var s=new c.ConfigSettingCollectionView({collection:o.track.get("config")});s.render_in_modal("Configure Track")})})},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(g.prototype,i);var e=g.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var f=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config);p.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var r=new a({el:$("#center .unified-panel-body"),genome:o,model:p});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"gear",title:"Settings",on_click:function(){var s=new c.ConfigSettingCollectionView({collection:p.get("config")});s.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file +require(["utils/utils","libs/farbtastic",],function(a){a.cssLoadFile("static/style/circster.css")});define(["libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,m,j,c){var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");return v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(Math.abs(p)<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));p=Math.abs(p);if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.genome=o.genome;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var p=this.model.get("config");p.get("arc_dataset_height").on("change:value",this.update_track_bounds,this);p.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var q=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),r=this.model.get("config").get_value("track_gap"),o=Math.min(this.$el.width(),this.$el.height())-20,u=o/2-q.length*(s+r)+r-this.label_arc_height,t=m.range(u,o/2,s+r);var p=this;return h.map(t,function(v){return[v,v+s]})},render:function(){var x=this,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),r=this.get_chord_tracks(),q=x.model.get("config").get_value("total_gap"),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new e({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:q});y.render();return y});this.chords_views=r.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:q});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new d(),radius_bounds:u,genome:x.genome,total_gap:q});this.label_track_view.render()},add_track:function(u){var p=this.model.get("config").get_value("total_gap");if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:p});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new e({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:p});o.render();this.circular_views.push(o)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})},update_track_bounds:function(){var o=this.get_tracks_bounds();h.each(this.circular_views,function(p,q){p.update_radius_bounds(o[q])});h.each(this.chords_views,function(p){p.update_radius_bounds(o[0])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="#ddd";this.loading_bg_fill="#ffc";this.bg_fill="#ddd";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=h.reject(h.map(v,function(w,x){var y=null,z=q._get_path_function(r[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});var t=p.get("config").get_value("color");o.each(function(x,w){m.select(this).transition().duration(1000).style("stroke",t).style("fill",t).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(p){var o=this.data_bounds;this.data_bounds=p||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));this._transition_chrom_data()},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);o.get("config").set_value("min_value",q.data_bounds[0],{silent:true});o.get("config").set_value("max_value",q.data_bounds[1],{silent:true});layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=2*Math.PI*this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="#fff";this.bg_fill="#fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var g=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);var p=this.track.get("config");p.get("min_value").on("change:value",this._update_min_max,this);p.get("max_value").on("change:value",this._update_min_max,this);p.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var p=this.track.get("config"),o=[p.get_value("min_value"),p.get_value("max_value")];this._update_data_bounds(o);this.parent_elt.selectAll(".min_max").text(function(r,q){return o[q]})},_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,q=function(){return"rotate(90)"};var p=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true).classed("min_max",true);h.each(p,function(r){$(r).click(function(){var s=new c.ConfigSettingCollectionView({collection:o.track.get("config")});s.render_in_modal("Configure Track")})})},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(g.prototype,i);var e=g.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var f=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config);p.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var r=new a({el:$("#center .unified-panel-body"),genome:o,model:p});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"gear",title:"Settings",on_click:function(){var s=new c.ConfigSettingCollectionView({collection:p.get("config")});s.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -404,11 +404,11 @@ /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { - this.bg_stroke = 'ddd'; + this.bg_stroke = '#ddd'; // Fill color when loading data. - this.loading_bg_fill = 'ffc'; + this.loading_bg_fill = '#ffc'; // Fill color when data has been loaded. - this.bg_fill = 'ddd'; + this.bg_fill = '#ddd'; this.total_gap = options.total_gap; this.track = options.track; this.radius_bounds = options.radius_bounds; @@ -688,8 +688,8 @@ // Use a single arc for rendering data. this.innerRadius = this.radius_bounds[0]; this.radius_bounds[0] = this.radius_bounds[1]; - this.bg_stroke = 'fff'; - this.bg_fill = 'fff'; + this.bg_stroke = '#fff'; + this.bg_fill = '#fff'; // Minimum arc distance for labels to be applied. this.min_arc_len = 0.05; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: S3ObjectStore will create the bucket for you when possible if it does not exist.
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70c404e681a0/ Changeset: 70c404e681a0 User: dannon Date: 2014-10-16 17:54:46+00:00 Summary: S3ObjectStore will create the bucket for you when possible if it does not exist. Affected #: 1 file diff -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 -r 70c404e681a0f4c347eaca75d65f23a11edcb823 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -167,8 +167,12 @@ log.debug("Using cloud object store with bucket '%s'" % bucket.name) return bucket except S3ResponseError: - log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) - time.sleep(2) + try: + log.debug("Bucket not found, creating s3 bucket with handle '%s'" % bucket_name) + self.conn.create_bucket(bucket_name) + except S3ResponseError: + log.exception("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) + time.sleep(2) # All the attempts have been exhausted and connection was not established, # raise error raise S3ResponseError Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/921aa1c775b5/ Changeset: 921aa1c775b5 User: dannon Date: 2014-10-16 17:41:10+00:00 Summary: Slightly better handling of s3 object store conf, allowing connection element to be optional Affected #: 1 file diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r 921aa1c775b54911c149fe3c8a1dc9645945a83d lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -77,7 +77,11 @@ b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') self.use_rr = b_xml.get('use_reduced_redundancy', False) - cn_xml = config_xml.findall('connection')[0] + cn_xml = config_xml.findall('connection') + if not cn_xml: + cn_xml = {} + else: + cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) self.is_secure = cn_xml.get('is_secure', True) https://bitbucket.org/galaxy/galaxy-central/commits/b1d9b4f49abb/ Changeset: b1d9b4f49abb User: dannon Date: 2014-10-16 17:41:22+00:00 Summary: Merge. Affected #: 65 files diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/collection/collection-li.js --- a/client/galaxy/scripts/mvc/collection/collection-li.js +++ b/client/galaxy/scripts/mvc/collection/collection-li.js @@ -100,8 +100,6 @@ /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", - /** jq fx speed for this view */ - fxSpeed : 'fast', /** set up */ initialize : function( attributes ){ diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/history/history-structure-view.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -0,0 +1,421 @@ +define([ + 'mvc/job/job-model', + 'mvc/job/job-li', + 'mvc/history/history-content-model', + 'mvc/history/job-dag', + 'mvc/base-mvc', + 'utils/localization', + 'libs/d3' +], function( JOB, JOB_LI, HISTORY_CONTENT, JobDAG, BASE_MVC, _l ){ +// ============================================================================ +/* TODO: +change component = this to something else + +*/ +// ============================================================================ +/** + * + */ +var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure-component', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureComponent).initialize:', attributes ); + this.component = attributes.component; + + this._jobLiMap = {}; + this._createJobModels(); + + this.layout = this._createLayout( attributes.layoutOptions ); + }, + + _createJobModels : function(){ + var view = this; + view.component.eachVertex( function( vertex ){ + var jobJSON = vertex.data.job, + job = new JOB.Job( jobJSON ); + + // get the models of the outputs for this job from the history + var outputModels = _.map( job.get( 'outputs' ), function( output ){ + //note: output is { src: 'hda/dataset_collection', id: <some id> } + // job output doesn't *quite* match up to normal typeId + var type = output.src === 'hda'? 'dataset' : 'dataset_collection', + typeId = HISTORY_CONTENT.typeIdStr( type, output.id ); + return view.model.contents.get( typeId ); + }); + // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) + job.outputCollection.reset( outputModels ); + job.outputCollection.historyId = view.model.id; + //this.debug( job.outputCollection ); + + // create the bbone view for the job (to be positioned later accrd. to the layout) and cache + var li = new JOB_LI.JobListItemView({ model: job }); + //var li = new JOB_LI.JobListItemView({ model: job }); + li.render( 0 ).$el.appendTo( view.$el ); + view._jobLiMap[ job.id ] = li; + view._setUpJobListeners( li ); + + }); + return view.jobs; + }, + + _setUpJobListeners : function( jobLi ){ + // update the layout during expansion and collapsing of job and output li's + jobLi.on( 'expanding expanded collapsing collapsed', this.render, this ); + jobLi.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', this.render, this ); + }, + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobHeight : 308, + jobWidthSpacing : 320, + linkAdjX : 4, + linkAdjY : 0 + }, + + _createLayout : function( options ){ + options = _.defaults( _.clone( options || {} ), this.layoutDefaults ); + var view = this, + vertices = _.values( view.component.vertices ), + layout = _.extend( options, { + nodeMap : {}, + links : [], + el : { width: 0, height: 0 }, + svg : { width: 0, height: 0, top: 0, left: 0 } + }); + + vertices.forEach( function( v, j ){ + var node = { name: v.name, x: 0, y: 0 }; + layout.nodeMap[ v.name ] = node; + }); + + view.component.edges( function( e ){ + var link = { + source: e.source, + target: e.target + }; + layout.links.push( link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return layout; + }, + + _updateLayout : function(){ + var view = this, + layout = view.layout; + + layout.svg.height = layout.paddingTop + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.height = layout.svg.height + layout.jobHeight; + +//TODO:?? can't we just alter the component v and e's directly? + // layout the job views putting jobWidthSpacing btwn each + var x = layout.paddingLeft, + y = layout.svg.height; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + x += layout.jobWidthSpacing; + }); + layout.el.width = layout.svg.width = Math.max( layout.el.width, x ); + + // layout the links - connecting each job by it's main coords (currently) +//TODO: somehow adjust the svg height based on the largest distance the longest connection needs + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return this.layout; + }, + + render : function( options ){ + this.debug( this + '.render:', options ); + var view = this; + + function _render(){ + view._updateLayout(); + // set up the display containers + view.$el + .width( view.layout.el.width ) + .height( view.layout.el.height ); + view.renderSVG(); + + // position the job views accrd. to the layout + view.component.eachVertex( function( v ){ +//TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ], + position = view.layout.nodeMap[ li.model.id ]; + //this.debug( position ); + li.$el.css({ top: position.y, left: position.x }); + }); + } +//TODO: hack - li's invisible in updateLayout without this delay + if( !this.$el.is( ':visible' ) ){ + _.delay( _render, 0 ); + } else { + _render(); + } + return this; + }, + + renderSVG : function(){ + var view = this, + layout = view.layout; + + var svg = d3.select( this.el ).select( 'svg' ); + if( svg.empty() ){ + svg = d3.select( this.el ).append( 'svg' ); + } + + svg + .attr( 'width', layout.svg.width ) + .attr( 'height', layout.svg.height ); + + function highlightConnect( d ){ + d3.select( this ).classed( 'highlighted', true ); + view._jobLiMap[ d.source ].$el.addClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.addClass( 'highlighted' ); + } + + function unhighlightConnect( d ){ + d3.select( this ).classed( 'highlighted', false ); + view._jobLiMap[ d.source ].$el.removeClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.removeClass( 'highlighted' ); + } + + var connections = svg.selectAll( '.connection' ) + .data( layout.links ); + + connections + .enter().append( 'path' ) + .attr( 'class', 'connection' ) + .attr( 'id', function( d ){ return d.source + '-' + d.target; }) + .on( 'mouseover', highlightConnect ) + .on( 'mouseout', unhighlightConnect ); + + connections + .attr( 'd', function( d ){ return view._connectionPath( d ); }); + +//TODO: ? can we use tick here to update the links? + + return svg.node(); + }, + + _connectionPath : function( d ){ + var CURVE_X = 0, + controlY = ( ( d.x2 - d.x1 ) / this.layout.svg.width ) * this.layout.svg.height; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 + CURVE_X, ',', d.y1 - controlY, ' ', + d.x2 - CURVE_X, ',', d.y2 - controlY, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + events : { + 'mouseover .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, true ); }, + 'mouseout .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, false ); } + }, + + highlightConnected : function( jobElement, highlight ){ + highlight = highlight !== undefined? highlight : true; + + var view = this, + component = view.component, + jobClassFn = highlight? jQuery.prototype.addClass : jQuery.prototype.removeClass, + connectionClass = highlight? 'connection highlighted' : 'connection'; + + //console.debug( 'mouseover', this ); + var $jobs = jobClassFn.call( $( jobElement ), 'highlighted' ), + id = $jobs.attr( 'id' ).replace( 'job-', '' ); + + // immed. ancestors + component.edges({ target: id }).forEach( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.source ), 'highlighted' ); + view.$( '#' + edge.source + '-' + id ).attr( 'class', connectionClass ); + }); + // descendants + component.vertices[ id ].eachEdge( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.target ), 'highlighted' ); + view.$( '#' + id + '-' + edge.target ).attr( 'class', connectionClass ); + }); + }, + + toString : function(){ + return 'HistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +/** + * + */ +var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ + + //logger : console, + + className : HistoryStructureComponent.prototype.className + ' vertical', + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobWidth : 308, + jobHeight : 308, + initialSpacing : 64, + jobSpacing : 16, + linkAdjX : 0, + linkAdjY : 4 + }, + +//TODO: how can we use the dom height of the job li's - they're not visible when this is called? + _updateLayout : function(){ + var view = this, + layout = view.layout; + //this.info( this.cid, '_updateLayout' ) + + layout.svg.width = layout.paddingLeft + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.width = layout.svg.width + layout.jobWidth; + + // reset height - we'll get the max Y below to assign to it + layout.el.height = 0; + +//TODO:?? can't we just alter the component v and e's directly? + var x = layout.svg.width, + y = layout.paddingTop; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + var li = view._jobLiMap[ jobId ]; + if( li.$el.is( ':visible' ) ){ + y += li.$el.height() + layout.jobSpacing; + } else { + y += layout.initialSpacing + layout.jobSpacing; + } + }); + layout.el.height = layout.svg.height = Math.max( layout.el.height, y ); + + // layout the links - connecting each job by it's main coords (currently) + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + view.debug( 'el:', layout.el ); + view.debug( 'svg:', layout.svg ); + return layout; + }, + + _connectionPath : function( d ){ + var CURVE_Y = 0, + controlX = ( ( d.y2 - d.y1 ) / this.layout.svg.height ) * this.layout.svg.width; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 - controlX, ',', d.y1 + CURVE_Y, ' ', + d.x2 - controlX, ',', d.y2 - CURVE_Y, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + toString : function(){ + return 'VerticalHistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +/** + * + */ +var HistoryStructureView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureView).initialize:', attributes, this.model ); +//TODO: to model + this.jobs = attributes.jobs; + this._createDAG(); + }, + + _createDAG : function(){ + this.dag = new JobDAG({ + historyContents : this.model.contents.toJSON(), + jobs : this.jobs, + excludeSetMetadata : true, + excludeErroredJobs : true + }); +//window.dag = this.dag; + this.log( this + '.dag:', this.dag ); + + this._createComponents(); + }, + + _createComponents : function(){ + this.log( this + '._createComponents' ); + var structure = this; +//window.structure = structure; + + structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ + return structure._createComponent( componentGraph ); + }); + }, + + _createComponent : function( component ){ + this.log( this + '._createComponent:', component ); + //return new HistoryStructureComponent({ + return new VerticalHistoryStructureComponent({ + model : this.model, + component : component + }); + }, + + render : function( options ){ + this.log( this + '.render:', options ); + var structure = this; + + structure.$el.html([ + '<div class="controls"></div>', + '<div class="components"></div>' + ].join( '' )); + + structure.componentViews.forEach( function( component ){ + component.render().$el.appendTo( structure.$components() ); + }); + return structure; + }, + + $components : function(){ + return this.$( '.components' ); + }, + + toString : function(){ + return 'HistoryStructureView(' + ')'; + } +}); + + +// ============================================================================ + return HistoryStructureView; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/history/job-dag.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/job-dag.js @@ -0,0 +1,219 @@ +define([ + 'utils/graph', + 'utils/add-logging' +],function( GRAPH, addLogging ){ +// ============================================================================ +var _super = GRAPH.Graph; +/** A Directed acyclic Graph built from a history's job data. + * Reads in job json, filters and process that json, and builds a graph + * using the connections between job inputs and outputs. + */ +var JobDAG = function( options ){ + var self = this; + //this.logger = console; + + // instance vars +//TODO: needed? + self._historyContentsMap = {}; + self.filters = []; + + self._idMap = {}; + self.noInputJobs = []; + self.noOutputJobs = []; + +//TODO: save these? + self.filteredSetMetadata = []; + self.filteredErroredJobs = []; + + _super.call( self, true, null, options ); +}; +JobDAG.prototype = new GRAPH.Graph(); +JobDAG.prototype.constructor = JobDAG; + +// add logging ability - turn off/on using the this.logger statement above +addLogging( JobDAG ); + +// ---------------------------------------------------------------------------- +/** process jobs, options, filters, and any history data, then create the graph */ +JobDAG.prototype.init = function _init( options ){ + options = options || {}; + _super.prototype.init.call( this, options ); + + var self = this, + historyContentsJSON = options.historyContents || []; + jobsJSON = options.jobs || []; + + historyContentsJSON.forEach( function( content, i ){ + self._historyContentsMap[ content.id ] = _.clone( content ); + }); + + self.options = _.defaults( _.omit( options, 'historyContents', 'jobs' ), { + excludeSetMetadata : false + }); + self.filters = self._initFilters(); + +//TODO: O( 3N ) + self.preprocessJobs( _.clone( jobsJSON ) ); + self.createGraph(); + + return self; +}; + +/** add job filters based on options */ +JobDAG.prototype._initFilters = function __initFilters(){ + var self = this, + filters = []; + + if( self.options.excludeSetMetadata ){ + self.filteredSetMetadata = []; + filters.push( function filterSetMetadata( jobData ){ + if( jobData.job.tool_id !== '__SET_METADATA__' ){ return true; } + self.filteredSetMetadata.push( jobData.job.id ); + return false; + }); + } + + if( self.options.excludeErroredJobs ){ + self.filteredErroredJobs = []; + filters.push( function filterErrored( jobData ){ + if( jobData.job.state !== 'error' ){ return true; } + self.filteredErroredJobs.push( jobData.job.id ); + return false; + }); + } + + // all outputs deleted + // all outputs hidden + + if( _.isArray( self.options.filters ) ){ + filters = filters.concat( self.options.filters ); + } + self.debug( 'filters len:', filters.length ); + return filters; +}; + +/** sort the jobs and cache any that pass all filters into _idMap by job.id */ +JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ + this.info( 'processing jobs' ); + + var self = this; +//TODO:? sorting neccessary? + self.sort( jobs ).forEach( function( job, i ){ + var jobData = self.preprocessJob( job, i ); + if( jobData ){ + self._idMap[ job.id ] = jobData; + } + }); + return self; +}; + +/** sort the jobs based on update time */ +JobDAG.prototype.sort = function _sort( jobs ){ + function cmpCreate( a, b ){ + if( a.update_time > b.update_time ){ return 1; } + if( a.update_time < b.update_time ){ return -1; } + return 0; + } + return jobs.sort( cmpCreate ); +}; + +/** proces input/output, filter based on job data returning data if passing, null if not */ +JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ + //this.info( 'preprocessJob', job, index ); + var self = this, + jobData = { index: index, job: job }; + + jobData.inputs = self.datasetMapToIdArray( job.inputs, function( dataset, nameInJob ){ + //TODO:? store output name in self._datasets[ output.id ] from creating job? + }); + if( jobData.inputs.length === 0 ){ + self.noInputJobs.push( job.id ); + } + jobData.outputs = self.datasetMapToIdArray( job.outputs, function( dataset, nameInJob ){ + + }); + if( jobData.outputs.length === 0 ){ + self.noOutputJobs.push( job.id ); + } + + //self.debug( JSON.stringify( jobData, null, ' ' ) ); + // apply filters after processing job allowing access to the additional data above in the filters + for( var i=0; i<self.filters.length; i++ ){ + if( !self.filters[i].call( self, jobData ) ){ + self.debug( 'job', job.id, ' has been filtered out by function:\n', self.filters[i] ); + return null; + } + } + + //self.info( 'preprocessJob returning', jobData ); + return jobData; +}; + +/** make verbose input/output lists more concise, sanity checking along the way + * processFn is called on each input/output and passed the dataset obj (id,src) and the input/output name. + */ +JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ + var self = this; + return _.map( datasetMap, function( dataset, nameInJob ){ + if( !dataset.id ){ + throw new Error( 'No id on datasetMap: ', JSON.stringify( dataset ) ); + } + if( !dataset.src || dataset.src !== 'hda' ){ + throw new Error( 'Bad src on datasetMap: ', JSON.stringify( dataset ) ); + } + processFn.call( self, dataset, nameInJob ); + return dataset.id; + }); +}; + +/** Walk all the jobs (vertices), attempting to find connections + * between datasets used as both inputs and outputs (edges) + */ +JobDAG.prototype.createGraph = function _createGraph(){ + var self = this; + self.debug( 'connections:' ); + + _.each( self._idMap, function( sourceJobData, sourceJobId ){ + self.debug( '\t', sourceJobId, sourceJobData ); + self.createVertex( sourceJobId, sourceJobData ); + + sourceJobData.usedIn = []; + _.each( sourceJobData.outputs, function( outputDatasetId ){ +//TODO: O(n^2) + _.each( self._idMap, function( targetJobData, targetJobId ){ + if( targetJobData === sourceJobData ){ return; } + + if( targetJobData.inputs.indexOf( outputDatasetId ) !== -1 ){ + self.info( '\t\t\t found connection: ', sourceJobId, targetJobId ); + sourceJobData.usedIn.push({ job: targetJobId, output: outputDatasetId }); + + self.createVertex( targetJobId, targetJobData ); + + self.createEdge( sourceJobId, targetJobId, self.directed, { + dataset : outputDatasetId + }); + } + }); + }); + }); + self.debug( 'job data: ', JSON.stringify( self._idMap, null, ' ' ) ); + return self; +}; + +/** Override to re-sort (ugh) jobs in each component by update time */ +Graph.prototype.weakComponentGraphArray = function(){ + return this.weakComponents().map( function( component ){ +//TODO: this seems to belong above (in sort) - why isn't it preserved? + component.vertices.sort( function cmpCreate( a, b ){ + if( a.data.job.update_time > b.data.job.update_time ){ return 1; } + if( a.data.job.update_time < b.data.job.update_time ){ return -1; } + return 0; + }); + return new Graph( this.directed, component ); + }); +}; + + +// ============================================================================ + return JobDAG; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/job/job-li.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -0,0 +1,129 @@ +define([ + 'mvc/list/list-item', + 'mvc/dataset/dataset-list', + "mvc/base-mvc", + "utils/localization" +], function( LIST_ITEM, DATASET_LIST, BASE_MVC, _l ){ +//============================================================================== +var _super = LIST_ITEM.FoldoutListItemView; +/** @class A job view used from within a larger list of jobs. + * Each job itself is a foldout panel of history contents displaying the outputs of this job. + */ +var JobListItemView = _super.extend(/** @lends JobListItemView.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + + className : _super.prototype.className + " job", + id : function(){ + return [ 'job', this.model.get( 'id' ) ].join( '-' ); + }, + + foldoutPanelClass : DATASET_LIST.DatasetList, + + /** Set up: instance vars, options, and event handlers */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + + /** where should pages from links be displayed? (default to new tab/window) */ + this.linkTarget = attributes.linkTarget || '_blank'; + }, + + /** In this override, add the state as a class for use with state-based CSS */ + _swapNewRender : function( $newRender ){ + _super.prototype._swapNewRender.call( this, $newRender ); + if( this.model.has( 'state' ) ){ + this.$el.addClass( 'state-' + this.model.get( 'state' ) ); + } + return this.$el; + }, + + /** Stub to return proper foldout panel options */ + _getFoldoutPanelOptions : function(){ + var options = _super.prototype._getFoldoutPanelOptions.call( this ); + return _.extend( options, { + collection : this.model.outputCollection, + selecting : false + }); + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return 'JobListItemView(' + this.model + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +JobListItemView.prototype.templates = (function(){ +//TODO: move to require text! plugin + + var elTemplate = BASE_MVC.wrapTemplate([ + '<div class="list-element">', + '<div class="id"><%= model.id %></div>', + // errors, messages, etc. + '<div class="warnings"></div>', + + // multi-select checkbox + '<div class="selector">', + '<span class="fa fa-2x fa-square-o"></span>', + '</div>', + // space for title bar buttons - gen. floated to the right + '<div class="primary-actions"></div>', + '<div class="title-bar"></div>', + + // expandable area for more details + '<div class="details"></div>', + '</div>' + ]); + + var titleBarTemplate = BASE_MVC.wrapTemplate([ + // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display + '<div class="title-bar clear" tabindex="0">', + //'<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- job.tool_id %></span>', + '</div>', + '<div class="subtitle"></div>', + '</div>' + ], 'job' ); + + //var subtitleTemplate = BASE_MVC.wrapTemplate([ + // // override this + // '<div class="subtitle">', + // _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', + // _l( 'Updated' ), ': <%= new Date( job.update_time ).toString() %>', + // '</div>' + //], 'job' ); + // + //var detailsTemplate = BASE_MVC.wrapTemplate([ + // '<div class="details">', + // '<div class="params">', + // '<% _.each( job.params, function( param, paramName ){ %>', + // '<div class="param">', + // '<label class="prompt"><%= paramName %></label>', + // '<span class="value"><%= param %></span>', + // '</div>', + // '<% }) %>', + // '</div>', + // '</div>' + //], 'job' ); + + return _.extend( {}, _super.prototype.templates, { + //el : elTemplate, + titleBar : titleBarTemplate, + //subtitle : subtitleTemplate, + //details : detailsTemplate + }); +}()); + + +//============================================================================= + return { + JobListItemView : JobListItemView + }; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/job/job-model.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-model.js @@ -0,0 +1,203 @@ +define([ + "mvc/history/history-contents", + "mvc/dataset/states", + "utils/ajax-queue", + "mvc/base-mvc", + "utils/localization" +], function( HISTORY_CONTENTS, STATES, AJAX_QUEUE, BASE_MVC, _l ){ +//============================================================================== +var searchableMixin = BASE_MVC.SearchableModelMixin; +/** @class Represents a job running or ran on the server job handlers. + */ +var Job = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( + BASE_MVC.mixin( searchableMixin, /** @lends Job.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** default attributes for a model */ + defaults : { + model_class : 'Job', + + tool : null, + exit_code : null, + + inputs : {}, + outputs : {}, + params : {}, + + create_time : null, + update_time : null, + state : STATES.NEW + }, + + /** instance vars and listeners */ + initialize : function( attributes, options ){ + this.debug( this + '(Job).initialize', attributes, options ); + this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]); + this._setUpListeners(); + }, + + /** set up any event listeners + * event: state:ready fired when this DA moves into/is already in a ready state + */ + _setUpListeners : function(){ + // if the state has changed and the new state is a ready state, fire an event + this.on( 'change:state', function( currModel, newState ){ + this.log( this + ' has changed state:', currModel, newState ); + if( this.inReadyState() ){ + this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); + } + }); + }, + + // ........................................................................ common queries + /** Is this job in a 'ready' state; where 'Ready' states are states where no + * processing is left to do on the server. + */ + inReadyState : function(){ + return _.contains( STATES.READY_STATES, this.get( 'state' ) ); + }, + + /** Does this model already contain detailed data (as opposed to just summary level data)? */ + hasDetails : function(){ + //?? this may not be reliable + return _.isEmpty( this.get( 'outputs' ) ); + }, + + // ........................................................................ ajax + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + //url : function(){ return this.urlRoot; }, + + // ........................................................................ searching + // see base-mvc, SearchableModelMixin + /** what attributes of an Job will be used in a text search */ + searchAttributes : [ + 'tool' + ], + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return [ 'Job(', this.get( 'id' ), ':', this.get( 'tool_id' ), ')' ].join( '' ); + } +})); + + +//============================================================================== +/** @class Backbone collection for Jobs. + */ +var JobCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends JobCollection.prototype */{ + model : Job, + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + url : function(){ return this.urlRoot; }, + + intialize : function( models, options ){ + console.debug( models, options ); + }, + + // ........................................................................ common queries + /** Get the ids of every item in this collection + * @returns array of encoded ids + */ + ids : function(){ + return this.map( function( item ){ return item.get( 'id' ); }); + }, + + /** Get jobs that are not ready + * @returns array of content models + */ + notReady : function(){ + return this.filter( function( job ){ + return !job.inReadyState(); + }); + }, + + /** return true if any jobs don't have details */ + haveDetails : function(){ + return this.all( function( job ){ return job.hasDetails(); }); + }, + + // ........................................................................ ajax + /** fetches all details for each job in the collection using a queue */ + queueDetailFetching : function(){ + var collection = this, + queue = new AJAX_QUEUE.AjaxQueue( this.map( function( job ){ + return function(){ + return job.fetch({ silent: true }); + }; + })); + queue.done( function(){ + collection.trigger( 'details-loaded' ); + }); + return queue; + }, + + //toDAG : function(){ + // return new JobDAG( this.toJSON() ); + //}, + + // ........................................................................ sorting/filtering + /** return a new collection of jobs whose attributes contain the substring matchesWhat */ + matches : function( matchesWhat ){ + return this.filter( function( job ){ + return job.matches( matchesWhat ); + }); + }, + + // ........................................................................ misc + /** override to get a correct/smarter merge when incoming data is partial */ + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + if( !collection.get( model.id ) ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); + }, + + /** String representation. */ + toString : function(){ + return ([ 'JobCollection(', this.length, ')' ].join( '' )); + } + +//----------------------------------------------------------------------------- class vars +}, { + /** class level fn for fetching the job details for all jobs in a history */ + fromHistory : function( historyId ){ + console.debug( this ); + var Collection = this, + collection = new Collection([]); + collection.fetch({ data: { history_id: historyId }}) + .done( function(){ + window.queue = collection.queueDetailFetching(); + + }); + return collection; + } +}); + + +//============================================================================= + return { + Job : Job, + JobCollection : JobCollection + }; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/list/list-item.js --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -16,8 +16,8 @@ initialize : function( attributes ){ /** are the details of this view expanded/shown or not? */ this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; + this.log( '\t expanded:', this.expanded ); + this.fxSpeed = attributes.fxSpeed !== undefined? attributes.fxSpeed : this.fxSpeed; }, // ........................................................................ render main @@ -70,7 +70,9 @@ /** empty out the current el, move the $newRender's children in */ _swapNewRender : function( $newRender ){ - return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); + return this.$el.empty() + .attr( 'class', _.isFunction( this.className )? this.className(): this.className ) + .append( $newRender.children() ); }, /** set up js behaviors, event handlers for elements within the given container @@ -117,15 +119,8 @@ */ expand : function(){ var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); + return view._fetchModelDetails().always( function(){ + view._expand(); }); }, @@ -139,6 +134,24 @@ return jQuery.when(); }, + /** Inner fn called when expand (public) has fetched the details */ + _expand : function(){ + var view = this, + $newDetails = view._renderDetails(); + view.$details().replaceWith( $newDetails ); + // needs to be set after the above or the slide will not show + view.expanded = true; + view.$details().slideDown({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'expanding', view ); + }, + complete: function(){ + view.trigger( 'expanded', view ); + } + }); + }, + /** Hide the body/details of an HDA. * @fires collapsed when a body has been collapsed */ @@ -146,8 +159,14 @@ this.debug( this + '(ExpandableView).collapse' ); var view = this; view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); + this.$details().slideUp({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'collapsing', view ); + }, + complete: function(){ + view.trigger( 'collapsed', view ); + } }); } @@ -204,7 +223,7 @@ $newRender.children( '.warnings' ).replaceWith( this._renderWarnings() ); $newRender.children( '.title-bar' ).replaceWith( this._renderTitleBar() ); $newRender.children( '.primary-actions' ).append( this._renderPrimaryActions() ); - $newRender.find( '.title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); + $newRender.find( '> .title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); return $newRender; }, @@ -375,11 +394,13 @@ * disrespect attributes.expanded if drilldown */ initialize : function( attributes ){ - ListItemView.prototype.initialize.call( this, attributes ); //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; } this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle; this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass; + + ListItemView.prototype.initialize.call( this, attributes ); + this.foldout = this._createFoldoutPanel(); }, //TODO:?? override to exclude foldout scope? @@ -393,7 +414,7 @@ //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ return $(); } var $newDetails = ListItemView.prototype._renderDetails.call( this ); - return this._attachFoldout( this._createFoldoutPanel(), $newDetails ); + return this._attachFoldout( this.foldout, $newDetails ); }, /** In this override, handle collection expansion. */ @@ -417,7 +438,8 @@ _getFoldoutPanelOptions : function(){ return { // propagate foldout style down - foldoutStyle : this.foldoutStyle + foldoutStyle : this.foldoutStyle, + fxSpeed : this.fxSpeed }; }, @@ -436,25 +458,13 @@ return view._fetchModelDetails() .always(function(){ if( view.foldoutStyle === 'foldout' ){ - view._expandByFoldout(); + view._expand(); } else if( view.foldoutStyle === 'drilldown' ){ view._expandByDrilldown(); } }); }, - /** For foldout, call render details then slide down */ - _expandByFoldout : function(){ - var view = this; - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }, - /** For drilldown, set up close handler and fire expanded:drilldown * containing views can listen to this and handle other things * (like hiding themselves) by listening for expanded/collapsed:drilldown @@ -462,7 +472,6 @@ _expandByDrilldown : function(){ var view = this; // attachment and rendering done by listener - view.foldout = this._createFoldoutPanel(); view.foldout.on( 'close', function(){ view.trigger( 'collapsed:drilldown', view, view.foldout ); }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -22,11 +22,16 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false', + url : self.base_url + '?deleted=false&state=ok', success : function(response) { // backup summary self.summary = response; + // sort by id + self.summary.sort(function(a, b) { + return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); + }); + // log console.debug('tools-content::initialize() - Completed.'); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -27,10 +27,8 @@ this.modal = new Ui.Modal.View(); } - // link model/inputs and all options - this.options = options; - this.model = options.model; - this.inputs = options.model.inputs; + // link options + this.options = options; // set element this.setElement('<div/>'); @@ -53,9 +51,13 @@ // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - // initialize contents + // for now the initial tool model is parsed through the mako + this.model = this.options; + this.inputs = this.options.inputs; + + // request history content and build form this.content = new ToolContent({ - history_id : this.options.history_id, + history_id : self.options.history_id, success : function() { self._buildForm(); } @@ -89,6 +91,51 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, + // build tool model through api call + _buildModel: function() { + // link this + var self = this; + + // construct url + var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?'; + if (this.options.job_id) { + model_url += 'job_id=' + this.options.job_id; + } else { + if (this.options.dataset_id) { + model_url += 'dataset_id=' + this.options.dataset_id; + } else { + var loc = top.location.href; + var pos = loc.indexOf('?'); + if (loc.indexOf('tool_id=') != -1 && pos !== -1) { + model_url += loc.slice(pos + 1); + } + } + } + + // get initial model + Utils.request({ + type : 'GET', + url : model_url, + success : function(response) { + // link model data update options + self.options = $.extend(self.options, response); + self.model = response; + self.inputs = response.inputs; + + // log success + console.debug('tools-form::initialize() - Initial tool model ready.'); + console.debug(response); + + // build form + self._buildForm(); + }, + error : function(response) { + console.debug('tools-form::initialize() - Initial tool model request failed.'); + console.debug(response); + } + }); + }, + // refresh form data _refreshForm: function() { // link this @@ -97,7 +144,7 @@ // finalize data var current_state = this.tree.finalize({ data : function(dict) { - if (dict.values.length > 0 && dict.values[0].src === 'hda') { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { return self.content.get({id: dict.values[0].id}).dataset_id; } return null; @@ -111,7 +158,7 @@ // post job Utils.request({ type : 'GET', - url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); @@ -132,28 +179,31 @@ // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', - tooltip : 'Click to see a list of available operations.' + tooltip : 'Click to see a list of options.' }); - // add question option - menu.addMenu({ - icon : 'fa-question-circle', - title : 'Question?', - tooltip : 'Ask a question about this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/p/new/post/'); - } - }); - - // create search button - menu.addMenu({ - icon : 'fa-search', - title : 'Search', - tooltip : 'Search help for this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); - } - }); + // configure button selection + if(this.options.biostar_url) { + // add question option + menu.addMenu({ + icon : 'fa-question-circle', + title : 'Question?', + tooltip : 'Ask a question about this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/p/new/post/'); + } + }); + + // create search button + menu.addMenu({ + icon : 'fa-search', + title : 'Search', + tooltip : 'Search help for this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); + } + }); + }; // create share button menu.addMenu({ @@ -185,11 +235,11 @@ }); // switch to classic tool form mako if the form definition is incompatible - //if (this.incompatible) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - //} + } // create portlet this.portlet = new Portlet.View({ @@ -213,12 +263,6 @@ } }); - // configure button selection - if(!this.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - // append form this.$el.append(this.portlet.$el); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -37,7 +37,7 @@ console.debug(job_def); // show progress modal - this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }}); + this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }}); // post job Utils.request({ @@ -55,10 +55,20 @@ var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); + break; } } else { // show error message with details console.debug(response); + self.app.modal.show({ + title : 'Job submission failed', + body : ToolTemplate.error(job_def), + buttons : { + 'Close' : function() { + self.app.modal.hide(); + } + } + }); } } }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -529,22 +529,12 @@ /** Slider field */ _fieldSlider: function(input_def) { - // set min/max - input_def.min = input_def.min || 0; - input_def.max = input_def.max || 100000; - - // calculate step size - var step = 1; - if (input_def.type == 'float') { - step = (input_def.max - input_def.min) / 10000; - } - // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, + precise : input_def.type == 'float', min : input_def.min, - max : input_def.max, - step : step + max : input_def.max }); }, diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -40,7 +40,7 @@ var dataset_options = []; for (var i in datasets) { dataset_options.push({ - label: datasets[i].name, + label: datasets[i].hid + ': ' + datasets[i].name, value: datasets[i].id }); } @@ -67,7 +67,7 @@ var collection_options = []; for (var i in collections) { collection_options.push({ - label: collections[i].name, + label: collections[i].hid + ': ' + collections[i].name, value: collections[i].id }); } @@ -103,20 +103,36 @@ }, /** Return the currently selected dataset values */ - value : function () { - // identify select element - var select = null; - switch(this.current) { - case 'hda': - select = this.select_datasets; - break; - case 'hdca': - select = this.select_collection; - break; + value : function (dict) { + // update current value + if (dict !== undefined) { + try { + // set source + this.current = dict.values[0].src; + this.refresh(); + + // create list + var list = []; + for (var i in dict.values) { + list.push(dict.values[i].id); + } + + // identify select element + switch(this.current) { + case 'hda': + this.select_datasets.value(list); + break; + case 'hdca': + this.select_collection.value(list[0]); + break; + } + } catch (err) { + console.debug('tools-select-content::value() - Skipped.'); + } } // transform into an array - var id_list = select.value(); + var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } @@ -142,12 +158,7 @@ /** Validate current selection */ validate: function() { - switch(this.current) { - case 'hda': - return this.select_datasets.validate(); - case 'hdca': - return this.select_collection.validate(); - } + return this._select().validate(); }, /** Refreshes data selection view */ @@ -162,6 +173,16 @@ this.select_collection.$el.fadeIn(); break; } + }, + + /** Assists in selecting the current field */ + _select: function() { + switch(this.current) { + case 'hdca': + return this.select_collection; + default: + return this.select_datasets; + } } }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -49,7 +49,7 @@ error: function(job_def) { return '<div>' + '<p>' + - 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + JSON.stringify(job_def, undefined, 4) + diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -6,9 +6,11 @@ // options optionsDefault: { value : '', - min : 1, - max : 100, - step : 1 + min : null, + max : null, + step : null, + precise : false, + split : 10000 }, // initialize @@ -18,19 +20,35 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement(this._template(this.options)); - // backup slider - this.$slider = this.$el.find('#slider'); + // determine wether to use the slider + this.useslider = this.options.max !== null && this.options.min !== null && this.options.max > this.options.min; + + // set default step size + if (this.options.step === null) { + this.options.step = 1; + if (this.options.precise && this.useslider) { + this.options.step = (this.options.max - this.options.min) / this.options.split; + } + } + + // create slider if min and max are defined properly + if (this.useslider) { + this.$slider = this.$el.find('#slider'); + this.$slider.slider(this.options); + this.$slider.on('slide', function (event, ui) { + self.value(ui.value); + }); + } else { + this.$el.find('.ui-form-slider-text').css('width', '100%'); + } // backup integer field this.$text = this.$el.find('#text'); - // load slider plugin - this.$slider.slider(this.options); - // add text field event this.$text.on('change', function () { self.value($(this).val()); @@ -39,24 +57,23 @@ // add text field event this.$text.on('keydown', function (event) { var v = event.which; - console.log(v); if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57) - || (self.options.step != 1 && $(this).val().indexOf('.') == -1) && v == 190)) { + || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) { event.preventDefault(); } }); - - // add slider event - this.$slider.on('slide', function (event, ui) { - self.value(ui.value); - }); }, // value value : function (new_val) { if (new_val !== undefined) { - // limit - new_val = Math.max(Math.min(new_val, this.options.max), this.options.min); + // apply limit + if (this.options.max !== null) { + new_val = Math.min(new_val, this.options.max); + } + if (this.options.min !== null) { + new_val = Math.max(new_val, this.options.min); + } // trigger on change event if (this.options.onchange) { @@ -64,7 +81,7 @@ } // set values - this.$slider.slider('value', new_val); + this.$slider && this.$slider.slider('value', new_val); this.$text.val(new_val); } This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: SelectToolParameter: Fix type check before split operation.
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20882e294f92/ Changeset: 20882e294f92 User: guerler Date: 2014-10-16 17:42:17+00:00 Summary: SelectToolParameter: Fix type check before split operation. Affected #: 1 file diff -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 -r 20882e294f925cb4c895e194d508bc15306e4403 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -818,7 +818,7 @@ if value == '': value = None else: - if not isinstance( value, list ): + if isinstance( value, basestring ): # Split on all whitespace. This not only provides flexibility # in interpreting values but also is needed because many browsers # use \r\n to separate lines. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset e1404e285ccb
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78c9a97be4b6/ Changeset: 78c9a97be4b6 Branch: stable User: natefoo Date: 2014-10-16 17:00:13+00:00 Summary: Update tag latest_2014.10.06 for changeset e1404e285ccb Affected #: 1 file diff -r e1404e285ccb9e52bd09c5827934cd0da1974acc -r 78c9a97be4b6bfe55136b055477fd1b9f22fd848 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -1744b7d8e9ab619d78c0516f9ccb093b0a814163 latest_2014.10.06 +e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits October 2014