galaxy-commits June 2013

galaxy-commits@lists.galaxyproject.org

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152 discussions

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/22e18808fc58/ Changeset: 22e18808fc58 User: Dave Bouvier Date: 2013-06-24 21:41:59 Summary: Add support for optionally extracting a file downloaded with the download_file tool dependency action. Add a change_directory action. Affected #: 3 files diff -r 69797172b07930e2751dd2fe7a6e317f1e68a769 -r 22e18808fc582fba8ae3d71c8f9556792354c1be lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -216,7 +216,7 @@ return os.path.abspath( file_path ) raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) -def url_download( install_dir, downloaded_file_name, download_url ): +def url_download( install_dir, downloaded_file_name, download_url, extract=True ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None dst = None @@ -236,7 +236,22 @@ src.close() if dst: dst.close() - return os.path.abspath( file_path ) + if extract: + if istar( file_path ): + # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> + extract_tar( file_path, install_dir ) + dir = tar_extraction_directory( install_dir, file_path ) + elif isjar( file_path ): + dir = os.path.curdir + elif iszip( file_path ): + # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> + zip_archive_extracted = extract_zip( file_path, install_dir ) + dir = zip_extraction_directory( install_dir, file_path ) + else: + dir = install_dir + else: + dir = install_dir + return dir def zip_extraction_directory( file_path, file_name ): """Try to return the correct extraction directory.""" diff -r 69797172b07930e2751dd2fe7a6e317f1e68a769 -r 22e18808fc582fba8ae3d71c8f9556792354c1be lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -180,19 +180,7 @@ downloaded_filename = action_dict[ 'target_filename' ] else: downloaded_filename = os.path.split( url )[ -1 ] - downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, url ) - if common_util.istar( downloaded_file_path ): - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - common_util.extract_tar( downloaded_file_path, work_dir ) - dir = common_util.tar_extraction_directory( work_dir, downloaded_filename ) - elif common_util.isjar( downloaded_file_path ): - dir = os.path.curdir - elif common_util.iszip( downloaded_file_path ): - # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> - zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir ) - dir = common_util.zip_extraction_directory( work_dir, downloaded_filename ) - else: - dir = os.path.curdir + dir = common_util.url_download( work_dir, downloaded_filename, url, extract=True ) elif action_type == 'shell_command': # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> # Eliminate the shell_command clone action so remaining actions can be processed correctly. @@ -227,10 +215,10 @@ if not os.path.exists( full_path_to_dir ): os.makedirs( full_path_to_dir ) # The package has been down-loaded, so we can now perform all of the actions defined for building it. - with lcd( dir ): - for action_tup in filtered_actions: + for action_tup in filtered_actions: + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): action_type, action_dict = action_tup - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) if action_type == 'make_directory': common_util.make_directory( full_path=action_dict[ 'full_path' ] ) elif action_type == 'move_directory_files': @@ -316,13 +304,21 @@ if return_code: return elif action_type == 'download_file': - # Download a single file to the current directory. + # Download a single file to the current working directory. url = action_dict[ 'url' ] - if action_dict[ 'target_filename' ]: + if 'target_filename' in action_dict: filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ] - common_util.url_download( current_dir, filename, url ) + extract = action_dict.get( 'extract', False ) + common_util.url_download( current_dir, filename, url, extract=extract ) + elif action_type == 'change_directory': + target_directory = os.path.realpath( os.path.join( current_dir, dir, action_dict[ 'directory' ] ) ) + current_working_dir = os.path.realpath( dir ) + if target_directory.startswith( current_working_dir ) and os.path.exists( target_directory ): + dir = target_directory + else: + log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory ) def log_results( command, fabric_AttributeString, file_path ): """ diff -r 69797172b07930e2751dd2fe7a6e317f1e68a769 -r 22e18808fc582fba8ae3d71c8f9556792354c1be lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -13,6 +13,7 @@ from tool_shed.util import xml_util from galaxy.model.orm import and_ from galaxy.web import url_for +from galaxy.util import asbool log = logging.getLogger( __name__ ) @@ -390,15 +391,19 @@ # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> if action_elem.text: action_dict[ 'url' ] = action_elem.text - if 'target_filename' in action_elem.attrib: - action_dict[ 'target_filename' ] = action_elem.attrib[ 'target_filename' ] + target_filename = action_elem.get( 'target_filename', None ) + if target_filename: + action_dict[ 'target_filename' ] = target_filename else: continue elif action_type == 'download_file': # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> if action_elem.text: action_dict[ 'url' ] = action_elem.text - action_dict[ 'target_filename' ] = action_elem.attrib.get( 'target_filename', None ) + target_filename = action_elem.get( 'target_filename', None ) + if target_filename: + action_dict[ 'target_filename' ] = target_filename + action_dict[ 'extract' ] = asbool( action_elem.get( 'extract', False ) ) else: continue elif action_type == 'make_directory': @@ -407,6 +412,12 @@ action_dict[ 'full_path' ] = evaluate_template( action_elem.text ) else: continue + elif action_type == 'change_directory': + # <action type="change_directory">PHYLIP-3.6b</action> + if action_elem.text: + action_dict[ 'directory' ] = action_elem.text + else: + continue elif action_type in [ 'move_directory_files', 'move_file' ]: # <action type="move_file"> # <source>misc/some_file</source> https://bitbucket.org/galaxy/galaxy-central/commits/b16265a28cfc/ Changeset: b16265a28cfc User: Dave Bouvier Date: 2013-06-24 21:43:14 Summary: Add the threadpool_kill_thread_limit option to universe_wsgi.ini.sample. Affected #: 1 file diff -r 22e18808fc582fba8ae3d71c8f9556792354c1be -r b16265a28cfce30b5678dad9551f08bfdc538ad3 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -40,6 +40,9 @@ # Number of threads in the web server thread pool. #threadpool_workers = 10 +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 + # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. 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: carlfeberhard: Add new packed scripts
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/69797172b079/ Changeset: 69797172b079 User: carlfeberhard Date: 2013-06-24 21:08:23 Summary: Add new packed scripts Affected #: 2 files diff -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 -r 69797172b07930e2751dd2fe7a6e317f1e68a769 static/scripts/packed/galaxy.frame.js --- /dev/null +++ b/static/scripts/packed/galaxy.frame.js @@ -0,0 +1,1 @@ +define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){b.load_file("/static/style/galaxy.frame.css");b.load_file("/static/style/base.css");var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_load());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousedown:"event_frame_mouse_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock",mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){c.preventDefault();if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(){if(this.event.type!==null){return}this.panel_show_hide()},event_panel_active:function(){if(this.event.type!==null){return}this.panel_active_disable()},event_panel_scroll:function(c){var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(){this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(){this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var 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exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_load:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file diff -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 -r 69797172b07930e2751dd2fe7a6e317f1e68a769 static/scripts/packed/utils/galaxy.css.js --- /dev/null +++ b/static/scripts/packed/utils/galaxy.css.js @@ -0,0 +1,1 @@ +define(["libs/underscore"],function(a){function b(g,d){var e=$('<div class="'+g+'"></div>');e.appendTo(":eq(0)");var f=e.css(d).replace(/[^-\d\.]/g,"");e.remove();return f}function c(d){if(!$('link[href="'+d+'"]').length){$('<link href="'+d+'" rel="stylesheet">').appendTo("head")}}return{load_file:c,get_attribute:b}}); \ 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: carlfeberhard: data providers: add data to factory decorator to allow datasets api to parse query strings into provider settings; datasets API: allow new providers to be used in raw_data; clean up and pack scripts
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72b02995c8b1/ Changeset: 72b02995c8b1 User: carlfeberhard Date: 2013-06-24 20:06:16 Summary: data providers: add data to factory decorator to allow datasets api to parse query strings into provider settings; datasets API: allow new providers to be used in raw_data; clean up and pack scripts Affected #: 20 files diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -267,25 +267,25 @@ # bam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers #TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char? #TODO: incorporate samtools options to control output: regions first, then flags, etc. - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.line.FilteredLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.line.RegexLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.column.ColumnarDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' @@ -293,30 +293,30 @@ # these can't be used directly - may need BamColumn, BamMap (Bam metadata -> column/map) # OR - see genomic_region_dataprovider - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings ) #def dataset_column_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' # return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) #def dataset_map_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' # return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): # in this case we can use an option of samtools view to provide just what we need (w/o regex) samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset, '-H' ) return dataproviders.line.RegexLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', dataproviders.column.MapDataProvider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_types' ] = [ 'str', 'str', 'str' ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.column.ColumnarDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): # GenomicRegionDataProvider currently requires a dataset as source - may not be necc. #TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset), @@ -330,7 +330,7 @@ settings[ 'column_types' ] = [ 'str', 'int', 'int' ] return self.column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', dataproviders.column.MapDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 2, 3, 3 ] settings[ 'column_types' ] = [ 'str', 'int', 'int' ] diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -593,7 +593,6 @@ Base dataprovider factory for all datatypes that returns the proper provider for the given `data_format` or raises a `NoProviderAvailable`. """ - #TODO:?? is this handling super class providers? if self.has_dataprovider( data_format ): return self.dataproviders[ data_format ]( self, dataset, **settings ) raise dataproviders.exceptions.NoProviderAvailable( self, data_format ) @@ -603,12 +602,12 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.base.DataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'chunk' ) + @dataproviders.decorators.dataprovider_factory( 'chunk', dataproviders.chunk.ChunkDataProvider.settings ) def chunk_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.ChunkDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'chunk64' ) + @dataproviders.decorators.dataprovider_factory( 'chunk64', dataproviders.chunk.Base64ChunkDataProvider.settings ) def chunk64_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) @@ -785,7 +784,7 @@ split = classmethod(split) # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines (that have been `strip`ed) @@ -794,7 +793,7 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.line.FilteredLineDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/base.py --- a/lib/galaxy/datatypes/dataproviders/base.py +++ b/lib/galaxy/datatypes/dataproviders/base.py @@ -22,8 +22,13 @@ icorporate existing visualization/dataproviders some of the sources (esp. in datasets) don't need to be re-created +YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider -YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider +datasets API entry point: + kwargs should be parsed from strings 2 layers up (in the DatasetsAPI) - that's the 'proper' place for that. + but how would it know how/what to parse if it doesn't have access to the classes used in the provider? + Building a giant list by sweeping all possible dprov classes doesn't make sense + For now - I'm burying them in the class __init__s - but I don't like that """ import logging @@ -31,6 +36,31 @@ # ----------------------------------------------------------------------------- base classes +class HasSettings( type ): + """ + Metaclass for data providers that allows defining and inheriting + a dictionary named 'settings'. + + Useful for allowing class level access to expected variable types + passed to class `__init__` functions so they can be parsed from a query string. + """ + # yeah - this is all too acrobatic + def __new__( cls, name, base_classes, attributes ): + settings = {} + # get settings defined in base classes + for base_class in base_classes: + base_settings = getattr( base_class, 'settings', None ) + if base_settings: + settings.update( base_settings ) + # get settings defined in this class + new_settings = attributes.pop( 'settings', None ) + if new_settings: + settings.update( new_settings ) + attributes[ 'settings' ] = settings + return type.__new__( cls, name, base_classes, attributes ) + + +# ----------------------------------------------------------------------------- base classes class DataProvider( object ): """ Base class for all data providers. Data providers: @@ -39,6 +69,12 @@ (c) do not allow write methods (but otherwise implement the other file object interface methods) """ + # a definition of expected types for keyword arguments sent to __init__ + # useful for controlling how query string dictionaries can be parsed into correct types for __init__ + # empty in this base class + __metaclass__ = HasSettings + settings = {} + def __init__( self, source, **kwargs ): """ :param source: the source that this iterator will loop over. @@ -130,13 +166,16 @@ - `num_valid_data_read`: how many data have been returned from `filter`. - `num_data_returned`: how many data has this provider yielded. """ + # not useful here - we don't want functions over the query string + #settings.update({ 'filter_fn': 'function' }) + def __init__( self, source, filter_fn=None, **kwargs ): """ :param filter_fn: a lambda or function that will be passed a datum and return either the (optionally modified) datum or None. """ super( FilteredDataProvider, self ).__init__( source, **kwargs ) - self.filter_fn = filter_fn + self.filter_fn = filter_fn if hasattr( filter_fn, '__call__' ) else None # count how many data we got from the source self.num_data_read = 0 # how many valid data have we gotten from the source @@ -179,6 +218,12 @@ Useful for grabbing sections from a source (e.g. pagination). """ + # define the expected types of these __init__ arguments so they can be parsed out from query strings + settings = { + 'limit' : 'int', + 'offset': 'int' + } + #TODO: may want to squash this into DataProvider def __init__( self, source, offset=0, limit=None, **kwargs ): """ diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/chunk.py --- a/lib/galaxy/datatypes/dataproviders/chunk.py +++ b/lib/galaxy/datatypes/dataproviders/chunk.py @@ -26,6 +26,10 @@ """ MAX_CHUNK_SIZE = 2**16 DEFAULT_CHUNK_SIZE = MAX_CHUNK_SIZE + settings = { + 'chunk_index' : 'int', + 'chunk_size' : 'int' + } #TODO: subclass from LimitedOffsetDataProvider? # see web/framework/base.iterate_file, util/__init__.file_reader, and datatypes.tabular @@ -38,8 +42,8 @@ (gen. in bytes). """ super( ChunkDataProvider, self ).__init__( source, **kwargs ) - self.chunk_size = chunk_size - self.chunk_pos = chunk_index * self.chunk_size + self.chunk_size = int( chunk_size ) + self.chunk_pos = int( chunk_index ) * self.chunk_size def validate_source( self, source ): """ diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -29,6 +29,14 @@ the same number of columns as the number of indeces asked for (even if they are filled with None). """ + settings = { + 'indeces' : 'list:int', + 'column_count' : 'int', + 'column_types' : 'list:str', + 'parse_columns' : 'bool', + 'deliminator' : 'str' + } + def __init__( self, source, indeces=None, column_count=None, column_types=None, parsers=None, parse_columns=True, deliminator='\t', **kwargs ): @@ -91,11 +99,11 @@ # how/whether to parse each column value self.parsers = {} if parse_columns: - self.parsers = self._get_default_parsers() + self.parsers = self.get_default_parsers() # overwrite with user desired parsers self.parsers.update( parsers or {} ) - def _get_default_parsers( self ): + def get_default_parsers( self ): """ Return parser dictionary keyed for each columnar type (as defined in datatypes). @@ -132,7 +140,7 @@ #'gffstrand': # -, +, ?, or '.' for None, etc. } - def _parse_value( self, val, type ): + def parse_value( self, val, type ): """ Attempt to parse and return the given value based on the given type. @@ -153,7 +161,7 @@ return None return val - def _get_column_type( self, index ): + def get_column_type( self, index ): """ Get the column type for the parser from `self.column_types` or `None` if the type is unavailable. @@ -165,18 +173,18 @@ except IndexError, ind_err: return None - def _parse_column_at_index( self, columns, parser_index, index ): + def parse_column_at_index( self, columns, parser_index, index ): """ Get the column type for the parser from `self.column_types` or `None` if the type is unavailable. """ try: - return self._parse_value( columns[ index ], self._get_column_type( parser_index ) ) + return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) # if a selected index is not within columns, return None except IndexError, index_err: return None - def _parse_columns_from_line( self, line ): + def parse_columns_from_line( self, line ): """ Returns a list of the desired, parsed columns. :param line: the line to parse @@ -188,13 +196,13 @@ selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) parsed_columns = [] for parser_index, column_index in enumerate( selected_indeces ): - parsed_columns.append( self._parse_column_at_index( all_columns, parser_index, column_index ) ) + parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) return parsed_columns def __iter__( self ): parent_gen = super( ColumnarDataProvider, self ).__iter__() for line in parent_gen: - columns = self._parse_columns_from_line( line ) + columns = self.parse_columns_from_line( line ) yield columns #TODO: implement column filters here and not below - flatten hierarchy @@ -223,6 +231,10 @@ .. note: that the subclass constructors are passed kwargs - so they're params (limit, offset, etc.) are also applicable here. """ + settings = { + 'column_names' : 'list:str', + } + def __init__( self, source, column_names=None, **kwargs ): """ :param column_names: an ordered list of strings that will be used as the keys diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -141,7 +141,7 @@ """ # metadata columns are 1-based indeces column = getattr( self.dataset.metadata, name ) - return ( column - 1 ) if isinstance( column, int ) else None + return ( column - 1 ) if ( isinstance( column, int ) and column > 0 ) else None def get_genomic_region_indeces( self, check=False ): """ @@ -271,6 +271,12 @@ """ # dictionary keys when named_columns=True COLUMN_NAMES = [ 'chrom', 'start', 'end' ] + settings = { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'named_columns' : 'bool', + } def __init__( self, dataset, chrom_column=None, start_column=None, end_column=None, named_columns=False, **kwargs ): """ @@ -333,6 +339,14 @@ 'chrom', 'start', 'end' (and 'strand' and 'name' if available). """ COLUMN_NAMES = [ 'chrom', 'start', 'end', 'strand', 'name' ] + settings = { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'strand_column' : 'int', + 'name_column' : 'int', + 'named_columns' : 'bool', + } def __init__( self, dataset, chrom_column=None, start_column=None, end_column=None, strand_column=None, name_column=None, named_columns=False, **kwargs ): @@ -349,25 +363,40 @@ dataset_source = DatasetDataProvider( dataset ) # get genomic indeces and add strand and name + self.column_names = [] + indeces = [] + #TODO: this is sort of involved and oogly if chrom_column == None: chrom_column = dataset_source.get_metadata_column_index_by_name( 'chromCol' ) + if chrom_column != None: + self.column_names.append( 'chrom' ) + indeces.append( chrom_column ) if start_column == None: start_column = dataset_source.get_metadata_column_index_by_name( 'startCol' ) + if start_column != None: + self.column_names.append( 'start' ) + indeces.append( start_column ) if end_column == None: end_column = dataset_source.get_metadata_column_index_by_name( 'endCol' ) + if end_column != None: + self.column_names.append( 'end' ) + indeces.append( end_column ) if strand_column == None: strand_column = dataset_source.get_metadata_column_index_by_name( 'strandCol' ) + if strand_column != None: + self.column_names.append( 'strand' ) + indeces.append( strand_column ) if name_column == None: name_column = dataset_source.get_metadata_column_index_by_name( 'nameCol' ) - indeces = [ chrom_column, start_column, end_column, strand_column, name_column ] + if name_column != None: + self.column_names.append( 'name' ) + indeces.append( name_column ) + kwargs.update({ 'indeces' : indeces }) - if not kwargs.get( 'column_types', None ): kwargs.update({ 'column_types' : dataset_source.get_metadata_column_types( indeces=indeces ) }) self.named_columns = named_columns - if self.named_columns: - self.column_names = self.COLUMN_NAMES super( IntervalDataProvider, self ).__init__( dataset_source, **kwargs ) @@ -390,6 +419,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings = { + 'ids' : 'list:str', + } + def __init__( self, source, ids=None, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in this list. @@ -419,6 +452,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings = { + 'ids' : 'list:str', + } + def __init__( self, source, ids=None, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in this list. @@ -445,6 +482,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES = [ 'chrom', 'pos', 'value' ] + settings = { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } def __init__( self, source, named_columns=False, column_names=None, **kwargs ): """ @@ -483,6 +524,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES = [ 'chrom', 'pos', 'value' ] + settings = { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } def __init__( self, source, chrom, start, end, named_columns=False, column_names=None, **kwargs ): """ diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -87,17 +87,40 @@ # log.debug( '\t\t ', fn.__doc__ ) return cls -def dataprovider_factory( name ): +def dataprovider_factory( name, settings=None ): """ - Wraps a class method and marks it as a dataprovider factory. + Wraps a class method and marks it as a dataprovider factory and creates a + function to parse query strings to __init__ arguments as the + `parse_query_string_settings` attribute of the factory function. + + An example use of the `parse_query_string_settings`: + ..example:: + kwargs = dataset.datatype.dataproviders[ provider ].parse_query_string_settings( query_kwargs ) + return list( dataset.datatype.dataprovider( dataset, provider, **kwargs ) ) :param name: what name/key to register the factory under in `cls.dataproviders` - :param type: any hashable var + :type name: any hashable var + :param settings: dictionary containing key/type pairs for parsing query strings + to __init__ arguments + :type settings: dictionary """ + #TODO:?? use *args for settings allowing mulitple dictionaries + # make a function available through the name->provider dispatch to parse query strings + # callable like: + # settings_dict = dataproviders[ provider_name ].parse_query_string_settings( query_kwargs ) + #TODO: ugh - overly complicated but the best I could think of + def parse_query_string_settings( query_kwargs ): + return _parse_query_string_settings( query_kwargs, settings ) + #log.debug( 'dataprovider:', name ) def named_dataprovider_factory( func ): #log.debug( 'named_dataprovider_factory:', name, '->', func.__name__ ) setattr( func, _DATAPROVIDER_METHOD_NAME_KEY, name ) + + setattr( func, 'parse_query_string_settings', parse_query_string_settings ) + setattr( func, 'settings', settings ) + #TODO: I want a way to inherit settings from the previous provider( this_name ) instead of defining over and over + #log.debug( '\t setting:', getattr( func, _DATAPROVIDER_METHOD_NAME_KEY ) ) @wraps( func ) def wrapped_dataprovider_factory( self, *args, **kwargs ): @@ -105,3 +128,38 @@ return func( self, *args, **kwargs ) return wrapped_dataprovider_factory return named_dataprovider_factory + +def _parse_query_string_settings( query_kwargs, settings=None ): + """ + Parse the values in `query_kwargs` from strings to the proper types + listed in the same key in `settings`. + """ + def list_from_query_string( s ): + # assume csv + return s.split( ',' ) + + parsers = { + 'int' : int, + 'float' : float, + 'bool' : bool, + 'list:str' : lambda s: list_from_query_string( s ), + 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], + } + settings = settings or {} + # yay! yet another set of query string parsers! <-- sarcasm + # work through the keys in settings finding matching keys in query_kwargs + # if found in both, get the expected/needed type from settings and store the new parsed value + # if we can't parse it (no parser, bad value), delete the key from query_kwargs so the provider will use the defaults + for key in settings: + if key in query_kwargs: + #TODO: this would be the place to sanitize any strings + query_value = query_kwargs[ key ] + needed_type = settings[ key ] + try: + query_kwargs[ key ] = parsers[ needed_type ]( query_value ) + except ( KeyError, ValueError ): + del query_kwargs[ key ] + + #TODO:?? do we want to remove query_kwarg entries NOT in settings? + return query_kwargs + diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -27,6 +27,12 @@ to return. """ DEFAULT_COMMENT_CHAR = '#' + settings = { + 'string_lines' : 'bool', + 'provide_blank' : 'bool', + 'comment_char' : 'str', + } + def __init__( self, source, strip_lines=True, provide_blank=False, comment_char=DEFAULT_COMMENT_CHAR, **kwargs ): """ :param strip_lines: remove whitespace from the beginning an ending @@ -78,6 +84,11 @@ .. note:: the regex matches are effectively OR'd (if **any** regex matches the line it is considered valid and will be provided). """ + settings = { + 'regex_list' : 'list:str', + 'invert' : 'bool', + } + def __init__( self, source, regex_list=None, invert=False, **kwargs ): """ :param regex_list: list of strings or regular expression strings that will diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -334,20 +334,24 @@ return None # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -809,20 +813,24 @@ # ------------- Dataproviders # redefine bc super is Tabular - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 3, 4, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, 0, 3, 4, 6, 2, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -1193,12 +1201,12 @@ return resolution # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'wiggle' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle', dataproviders.dataset.WiggleDataProvider.settings ) def wiggle_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.WiggleDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'wiggle-map' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle-map', dataproviders.dataset.WiggleDataProvider.settings ) def wiggle_map_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) settings[ 'named_columns' ] = True diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -15,8 +15,6 @@ from galaxy import util from sniff import * -from galaxy.datatypes import dataproviders - import pkg_resources pkg_resources.require("simplejson") import simplejson @@ -399,15 +397,6 @@ f.close() _count_split = classmethod(_count_split) - def provider( self, dataset, data_format, **settings ): - from galaxy.dataproviders import dataset as dataset_providers - - if data_format == 'id_seq': - source = dataset_providers.DatasetDataProvider( dataset ) - return dataset_providers.FastaDataProvider( source, **settings ) - - return super( Fasta, self ).provider( dataset, data_format, **settings ) - class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """ diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -345,26 +345,25 @@ return vizs # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" - print 'Tabular.comment_char:', settings.get( 'comment_char', None ) - dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.column.ColumnarDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.ColumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetColumnarDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.column.MapDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetMapDataProvider( dataset, **settings ) @@ -502,55 +501,58 @@ # ------------- Dataproviders # sam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers #TODO:?? seems like there should be an easier way to do this - metadata.comment_char? - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).line_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).regex_line_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.ColumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) headers_source = dataproviders.line.RegexLineDataProvider( dataset_source, regex_list=[ '^@' ] ) return dataproviders.line.RegexLineDataProvider( headers_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', map_dataprovider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): # provided as an example of a specified column map (w/o metadata) settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, True, **settings ) @@ -621,11 +623,13 @@ return False # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) @@ -668,11 +672,13 @@ dataset.metadata.sample_names = line.split()[ 9: ] # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 1, 1, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -32,7 +32,7 @@ "bigwig": genome.BigWigDataProvider, "bigbed": genome.BigBedDataProvider, - "column": ColumnDataProvider + "column_with_stats": ColumnDataProvider } def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ): diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -15,22 +15,27 @@ log = logging.getLogger( __name__ ) __TODO__ = """ - BUGS: - anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ masthead) - should not show visualizations (no icon)? - newick files aren't being sniffed prop? - datatype is txt +BUGS: + anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ masthead) + should not show visualizations (no icon)? + newick files aren't being sniffed prop? - datatype is txt - have parsers create objects instead of dicts - allow data_sources with no model_class but have tests (isAdmin, etc.) - maybe that's an instance of User model_class? - some confused vocabulary in docs, var names - tests: - anding, grouping, not - data_sources: - lists of - add description element to visualization. +have parsers create objects instead of dicts +allow data_sources with no model_class but have tests (isAdmin, etc.) + maybe that's an instance of User model_class? +some confused vocabulary in docs, var names +tests: + anding, grouping, not +data_sources: + lists of +add description element to visualization. + +TESTS to add: + has dataprovider + user is admin """ +# ------------------------------------------------------------------- the registry class VisualizationsRegistry( object ): """ Main responsibilities are: @@ -93,6 +98,12 @@ """ self.listings = VisualizationsConfigParser.parse( self.configuration_filepath ) + #TODO: def get_visualization( self, trans, visualization_name, target_object ): + # """ + # Is the visualization with the given `visualization_name` applicable + # to the `target_object`? + # """ + # -- building links to visualizations from objects -- def get_visualizations( self, trans, target_object ): """ @@ -151,10 +162,11 @@ # convert datatypes to their actual classes (for use with isinstance) test_result = trans.app.datatypes_registry.get_datatype_class_by_name( test_result ) if not test_result: - # warn if can't find class, but continue + # warn if can't find class, but continue (with other tests) log.warn( 'visualizations_registry cannot find class (%s) for applicability test', test_result ) continue + #NOTE: tests are OR'd, if any test passes - the visualization can be applied if test_fn( target_object, test_result ): #log.debug( 'test passed' ) return True diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.framework.helpers import is_true +from galaxy.datatypes import dataproviders import logging log = logging.getLogger( __name__ ) @@ -217,10 +218,24 @@ return msg registry = trans.app.data_provider_registry + # allow the caller to specifiy which provider is used - if provider and provider in registry.dataset_type_name_to_data_provider: - data_provider = registry.dataset_type_name_to_data_provider[ provider ]( dataset ) - # or have it look up by datatype + # pulling from the original providers if possible, then the new providers + if provider: + if provider in registry.dataset_type_name_to_data_provider: + data_provider = registry.dataset_type_name_to_data_provider[ provider ]( dataset ) + + elif dataset.datatype.has_dataprovider( provider ): + kwargs = dataset.datatype.dataproviders[ provider ].parse_query_string_settings( kwargs ) + # use dictionary to allow more than the data itself to be returned (data totals, other meta, etc.) + return { + 'data': list( dataset.datatype.dataprovider( dataset, provider, **kwargs ) ) + } + + else: + raise dataproviders.exceptions.NoProviderAvailable( dataset.datatype, provider ) + + # no provider name: look up by datatype else: data_provider = registry.get_data_provider( trans, raw=True, original_dataset=dataset ) diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 static/scripts/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js @@ -562,7 +562,7 @@ var params = { data_type : 'raw_data', - provider : 'column', + provider : 'column_with_stats', columns : '[' + columns + ']' }; this.log( '\t data settings (url params):', params ); diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_paths.get("datasets_url")});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){(new b(i)).render()},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,initialize:function(i){var j=i.model.attributes.metadata.attributes;if(typeof j.chromCol==="undefined"||typeof j.startCol==="undefined"||typeof j.endCol==="undefined"){console.log("TabularButtonTrackster : Metadata for column identification is missing.")}else{this.col.chrom=j.chromCol-1;this.col.start=j.startCol-1;this.col.end=j.endCol-1}if(this.col.chrom===null){return}if(typeof i.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=i.model.attributes.id}if(typeof i.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=i.model.attributes.url_viz}if(typeof i.model.attributes.genome_build!=="undefined"){this.genome_build=i.model.attributes.genome_build}},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(m){if(this.col.chrom===null){return}var q=$(m.target).parent();var n=q.children().eq(this.col.chrom).html();var i=q.children().eq(this.col.start).html();var k=q.children().eq(this.col.end).html();if(n!==""&&i!==""&&k!==""){var p={dataset_id:this.dataset_id,gene_region:n+":"+i+"-"+k};var l=q.offset();var j=l.left-10;var o=l.top;$("#btn_viz").css({position:"fixed",top:o+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,p,this.genome_build));$("#btn_viz").show()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.location=i+"/trackster?"+$.param(k)})}})},"View in new visualization":function(){n.location=i+"/trackster?"+$.param(k)}})}});return false}},render:function(){var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_paths.get("datasets_url")});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){(new b(i)).render()},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,initialize:function(i){var j=i.model.attributes.metadata.attributes;if(typeof j.chromCol==="undefined"||typeof j.startCol==="undefined"||typeof j.endCol==="undefined"){console.log("TabularButtonTrackster : Metadata for column identification is missing.")}else{this.col.chrom=j.chromCol-1;this.col.start=j.startCol-1;this.col.end=j.endCol-1}if(this.col.chrom===null){return}if(typeof i.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=i.model.attributes.id}if(typeof i.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=i.model.attributes.url_viz}if(typeof i.model.attributes.genome_build!=="undefined"){this.genome_build=i.model.attributes.genome_build}},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(m){if(this.col.chrom===null){return}var q=$(m.target).parent();var n=q.children().eq(this.col.chrom).html();var i=q.children().eq(this.col.start).html();var k=q.children().eq(this.col.end).html();if(n!==""&&i!==""&&k!==""){var p={dataset_id:this.dataset_id,gene_region:n+":"+i+"-"+k};var l=q.offset();var j=l.left-10;var o=l.top;$("#btn_viz").css({position:"fixed",top:o+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,p,this.genome_build));$("#btn_viz").show()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)});n.hide_modal()})}})},"View in new visualization":function(){var o=i+"/trackster?"+$.param(k);n.frame_manager.frame_new({title:"Trackster",type:"url",content:o});n.hide_modal()}})}});return false}},render:function(){var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href="javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', center: true, content: '"+this.urls.display+"'});"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){parent.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){parent.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),center:true});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.hide_modal();f.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}})},"View in new visualization":function(){f.hide_modal();f.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})}})}});return false}}; \ No newline at end of file diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 static/scripts/packed/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js @@ -1,1 +1,1 @@ -var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file +var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file diff -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba -r 72b02995c8b188b8efe9b3ac4c5996e972e596f1 visualizations_conf.xml.sample --- a/visualizations_conf.xml.sample +++ b/visualizations_conf.xml.sample @@ -84,30 +84,30 @@ (e.g. hda_ldda can be 'hda' or 'ldda' and modifies/informs dataset_id to fetch an HDA or LDDA) --><!ELEMENT param (#PCDATA)> -  + <!ATTLIST param type CDATA #IMPLIED default CDATA #IMPLIED Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Update: Scratchbook
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ea772733c97/ Changeset: 8ea772733c97 User: guerler Date: 2013-06-24 19:47:06 Summary: Update: Scratchbook Affected #: 3 files diff -r a27c1c3a628bc0167981865b82442fc790bd8406 -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -735,7 +735,6 @@ // untoggle $(".galaxy-frame-active .icon").removeClass("f-toggle"); - } else { // activate this.active = true; @@ -1034,7 +1033,7 @@ '<div class="number f-corner">0</div>' + '<div class="icon fa-icon-2x"></div>' + '</div>'+ - '<div title="Enable/Disable Scratchbook Viewer" class="galaxy-frame-active f-corner">' + + '<div class="galaxy-frame-active f-corner">' + '<div class="icon fa-icon-2x fa-icon-th"></div>' + '</div>'; }, diff -r a27c1c3a628bc0167981865b82442fc790bd8406 -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -239,8 +239,25 @@ * @returns {jQuery} rendered DOM */ _render_visualizationsButton : function(){ + var visualizations = this.model.get( 'visualizations' ); + if( ( !this.model.hasData() ) + || ( _.isEmpty( visualizations ) ) ){ + this.visualizationsButton = null; + return null; + } + + //TODO: this is a bridge to allow the framework to be switched off + // remove this fn and use the other when fully integrated + if( _.isObject( visualizations[0] ) ){ + return this._render_visualizationsFrameworkButton( visualizations ); + } + + if( !this.urls.visualization ){ + this.visualizationsButton = null; + return null; + } + var dbkey = this.model.get( 'dbkey' ), - visualizations = this.model.get( 'visualizations' ), visualization_url = this.urls.visualization, popup_menu_dict = {}, params = { @@ -250,17 +267,10 @@ // Add dbkey to params if it exists. if( dbkey ){ params.dbkey = dbkey; } - if( !( this.model.hasData() ) - || !( visualizations && visualizations.length ) - || !( visualization_url ) ){ - this.visualizationsButton = null; - return null; - } - // render the icon from template this.visualizationsButton = new IconButtonView({ model : new IconButton({ title : _l( 'Visualize' ), - href : visualization_url, + href : this.urls.visualization, icon_class : 'chart_curve' })}); var $icon = this.visualizationsButton.render().$el; @@ -278,15 +288,14 @@ case 'scatterplot': return create_scatterplot_action_fn( visualization_url, params ); default: - return function(){ - // add widget + return function(){// add widget parent.frame_manager.frame_new( { title : "Visualization", type : "url", content : visualization_url + '/' + visualization + '?' + $.param( params ) }); - }; + }; } } @@ -306,6 +315,40 @@ } return $icon; }, + + /** Render an icon-button or popupmenu of links based on the applicable visualizations + * @returns {jQuery} rendered DOM + */ + _render_visualizationsFrameworkButton : function( visualizations ){ + if( !( this.model.hasData() ) + || !( visualizations && !_.isEmpty( visualizations ) ) ){ + this.visualizationsButton = null; + return null; + } + + // render the icon from template + this.visualizationsButton = new IconButtonView({ model : new IconButton({ + title : _l( 'Visualize' ), + icon_class : 'chart_curve' + })}); + var $icon = this.visualizationsButton.render().$el; + $icon.addClass( 'visualize-icon' ); // needed? + + // No need for popup menu because there's a single visualization. + if( _.keys( visualizations ).length === 1 ) { + $icon.attr( 'title', _.keys( visualizations )[0] ); + $icon.attr( 'href', _.values( visualizations )[0] ); + + // >1: Populate menu dict with visualization fns, make the popupmenu + } else { + var popup_menu_options = []; + _.each( visualizations, function( linkData ) { + popup_menu_options.push( linkData ); + }); + var popup = new PopupMenu( $icon, popup_menu_options ); + } + return $icon; + }, // ......................................................................... secondary actions /** Render secondary actions: currently tagging and annotation (if user is allowed). @@ -567,7 +610,6 @@ //TODO: should be imported from scatterplot.js OR abstracted to 'load this in the galaxy_main frame' function create_scatterplot_action_fn( url, params ){ action = function() { - // add widget parent.frame_manager.frame_new( { @@ -657,4 +699,4 @@ //============================================================================== //return { // HDAView : HDAView, -//};}); +//};}); \ No newline at end of file diff -r a27c1c3a628bc0167981865b82442fc790bd8406 -r 8ea772733c979a4d5578ba4c8c31dd3f47cc32ba templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -150,7 +150,7 @@ [_('New Track Browser'), "javascript:frame_manager.frame_new({title: 'Trackster', type: 'url', content: '/visualization/trackster'});"], [_('Saved Visualizations'), "javascript:frame_manager.frame_new({ type: 'url', content : '/visualization/list'});" ] ] - tab( "visualization", _("Visualization"), "javascript:frame_manager.frame_new({title: 'Trackster', type: 'url', content: '/visualization/trackster'});", menu_options=menu_options ) + tab( "visualization", _("Visualization"), "javascript:frame_manager.frame_new({title: 'Trackster', type: 'url', content: '/visualization/list'});", menu_options=menu_options ) %> ## Cloud menu. 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: Galaxy Scratchbook plugin. Allows to display multiple Trackster visualization on a single page.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a27c1c3a628b/ Changeset: a27c1c3a628b User: guerler Date: 2013-06-24 18:23:56 Summary: Galaxy Scratchbook plugin. Allows to display multiple Trackster visualization on a single page. Affected #: 10 files diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/scripts/galaxy.frame.js --- /dev/null +++ b/static/scripts/galaxy.frame.js @@ -0,0 +1,1055 @@ +/* + galaxy frames v2.0 +*/ + +// dependencies +define(["utils/galaxy.css", "libs/backbone/backbone-relational"], function(css) { + +// load required css files +css.load_file("/static/style/galaxy.frame.css"); +css.load_file("/static/style/base.css"); + +// frame manager +var GalaxyFrameManager = Backbone.View.extend( +{ + // base element + el: '#everything', + + // master head + el_header : '#masthead', + + // defaults inputs + options: + { + // default frame size + frame: + { + cols : 6, + rows : 3 + }, + + // maximum number of rows + rows: 1000, + + // cell size in px + cell: 130, + + // margin + margin: 5, + + // scroll speed + scroll: 5, + + // minimum top + top_min: 40, + + // maximum number of frames + frame_max: 10 + }, + + // number of columns + cols: 0, + + // scroll/element top + top: 0, + + // maximum viewport + top_max: 0, + + // frame counter + frame_counter: 0, + + // frame counter + frame_counter_id: 0, + + // frame list + frame_list: [], + + // frame shadow + galaxy_frame_shadow: null, + + // frame panel visible + visible: false, + + // frame active/disabled + active: false, + + // initialize + initialize : function(options) + { + // read in defaults + if (options) + this.options = _.defaults(options, this.options); + + // initialize top + this.top = this.top_max = this.options.top_min; + + // load background + $(this.el).append(this.frame_template_background()); + + // load menu buttons + $(this.el).append(this.frame_template_menu()); + + // load load button + $(this.el_header).append(this.frame_template_load()); + + // + // define shadow frame + // + var id_shadow = '#galaxy-frame-shadow'; + + // add shadow template + $(this.el).append(this.frame_template_shadow(id_shadow.substring(1))); + + // initialize frame + this.galaxy_frame_shadow = { + id : id_shadow, + screen_location : {}, + grid_location : {}, + grid_rank : null, + grid_lock : false + }; + + // initialize size + this.frame_resize(this.galaxy_frame_shadow, {width: 0, height: 0}); + + // add shadow to frame list + this.frame_list[id_shadow] = this.galaxy_frame_shadow; + + // initialize panel + this.panel_refresh(); + + // link events + this.event_initialize(); + + // catch window resize event + var self = this; + $(window).resize(function () + { + self.panel_refresh(); + }); + + // catch window close + window.onbeforeunload = function() + { + if (self.frame_counter > 0) + return "You opened " + self.frame_counter + " frame(s) which will be lost."; + }; + }, + + // check for mobile devices + is_mobile: function() + { + return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i); + }, + + /* + EVENT HANDLING + */ + + // event + event: + { + type : null, + target : null, + xy : null + }, + + // events + event_initialize: function() + { + /*if (!this.is_mobile()) + {*/ + this.events = { + 'mousedown' : 'event_frame_mouse_down', + 'mousedown .f-close' : 'event_frame_close', + 'mousedown .f-pin' : 'event_frame_lock', + 'mousemove' : 'event_frame_mouse_move', + 'mouseup' : 'event_frame_mouse_up', + 'mouseleave' : 'event_frame_mouse_up', + 'mousedown .galaxy-frame-active' : 'event_panel_active', + 'mousedown .galaxy-frame-load' : 'event_panel_load', + 'mousedown .galaxy-frame-background' : 'event_panel_load', + 'mousewheel' : 'event_panel_scroll', + 'DOMMouseScroll' : 'event_panel_scroll', + 'mousedown .galaxy-frame-scroll-up' : 'event_panel_scroll_up', + 'mousedown .galaxy-frame-scroll-down' : 'event_panel_scroll_down' + }; + /*} else { + this.events = { + 'touchstart' : 'event_frame_mouse_down', + 'touchstart .f-close' : 'event_frame_close', + 'touchstart .f-pin' : 'event_frame_lock', + 'touchmove' : 'event_frame_mouse_move', + 'touchend' : 'event_frame_mouse_up', + 'touchleave' : 'event_mouse_up', + 'touchstart .galaxy-frame-load' : 'event_frame_load' + }; + };*/ + + // delegate + this.delegateEvents(this.events); + }, + + // drag start + event_frame_mouse_down: function (e) + { + // prevent text selection + e.preventDefault(); + + // skip if event is already active + if (this.event.type !== null) + return; + + // check for drag event + if ($(e.target).hasClass('f-header') || + $(e.target).hasClass('f-title')) + this.event.type = 'drag'; + + // check for resize event + if ($(e.target).hasClass('f-resize')) + this.event.type = 'resize'; + + // skip if no event has to be handled + if (this.event.type === null) + return; + + // identify frame + this.event.target = this.event_get_frame(e.target); + + // check if frame is locked + if (this.event.target.grid_lock) + { + this.event.type = null; + return; + } + + // backup event details + this.event.xy = {x: e.originalEvent.pageX, y: e.originalEvent.pageY}; + + // prepare drag/resize + this.frame_drag_start(this.event.target); + }, + + // mouse move event + event_frame_mouse_move: function (e) + { + // check + if (this.event.type != 'drag' && this.event.type != 'resize') + return; + + // current position + var event_xy_new = {x: e.originalEvent.pageX , y: e.originalEvent.pageY}; + + // position delta + var event_xy_delta = + { + x : event_xy_new.x - this.event.xy.x, + y : event_xy_new.y - this.event.xy.y + }; + + // update + this.event.xy = event_xy_new; + + // object position / size + var p = this.frame_screen (this.event.target); + + // resize event + if (this.event.type == 'resize') + { + // update + p.width += event_xy_delta.x; + p.height += event_xy_delta.y; + + // check size + var min_dim = this.options.cell - this.options.margin - 1; + p.width = Math.max(p.width, min_dim); + p.height = Math.max(p.height, min_dim); + + // apply resize to frame + this.frame_resize(this.event.target, p); + + // break down to grid coordinates + p.width = this.to_grid_coord('width', p.width) + 1; + p.height = this.to_grid_coord('height', p.height) + 1; + + // transfer back to pixels + p.width = this.to_pixel_coord('width', p.width); + p.height = this.to_pixel_coord('height', p.height); + + // apply + this.frame_resize(this.galaxy_frame_shadow, p); + + // fix position + this.frame_insert(this.galaxy_frame_shadow, { + top : this.to_grid_coord('top', p.top), + left : this.to_grid_coord('left', p.left) + }); + } + + // drag event + if (this.event.type == 'drag') + { + // update + p.left += event_xy_delta.x; + p.top += event_xy_delta.y; + + // apply + this.frame_offset(this.event.target, p); + + // get location of shadow + var l = { + top : this.to_grid_coord('top', p.top), + left : this.to_grid_coord('left', p.left) + }; + + // increase priority of current frame + if (l.left !== 0) + l.left++; + + // fix position + this.frame_insert(this.galaxy_frame_shadow, l); + } + }, + + // mouse up + event_frame_mouse_up: function (e) + { + // check + if (this.event.type != 'drag' && this.event.type != 'resize') + return; + + // stop + this.frame_drag_stop(this.event.target); + + // reset event + this.event.type = null; + }, + + // drag start + event_frame_close: function (e) + { + // check + if (this.event.type !== null) + return; + + // get frame + var frame = this.event_get_frame(e.target); + var self = this; + + // fade out + $(frame.id).fadeOut('fast', function() + { + // remove element + $(frame.id).remove(); + + // remove from dictionary + delete self.frame_list[frame.id]; + + // reduce frame counter + self.frame_counter--; + + // reload + self.panel_refresh(true); + + // refresh scroll state once all animations completed + self.panel_animation_complete(); + + // hide if no frames left + if (self.visible && self.frame_counter == 0) + self.panel_show_hide(); + }); + }, + + // drag start + event_frame_lock: function (e) + { + // check + if (this.event.type !== null) + return; + + // get frame + var frame = this.event_get_frame(e.target); + + // check + if (frame.grid_lock) + { + // unlock + frame.grid_lock = false; + + // remove class + $(frame.id).find('.f-pin').removeClass('f-toggle'); + $(frame.id).find('.f-header').removeClass('f-not-allowed'); + $(frame.id).find('.f-title').removeClass('f-not-allowed'); + $(frame.id).find('.f-resize').show(); + $(frame.id).find('.f-close').show(); + } else { + // lock + frame.grid_lock = true; + + // add class + $(frame.id).find('.f-pin').addClass('f-toggle'); + $(frame.id).find('.f-header').addClass('f-not-allowed'); + $(frame.id).find('.f-title').addClass('f-not-allowed'); + $(frame.id).find('.f-resize').hide(); + $(frame.id).find('.f-close').hide(); + } + }, + + // show/hide panel + event_panel_load: function () + { + // check + if (this.event.type !== null) + return; + + // load panel + this.panel_show_hide(); + }, + + // activate/disable panel + event_panel_active: function () + { + // check + if (this.event.type !== null) + return; + + // load panel + this.panel_active_disable(); + }, + + // scroll + event_panel_scroll: function(e) + { + // get wheel delta + var delta = e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3; + + // refresh panel + this.panel_scroll(delta); + }, + + // scroll up + event_panel_scroll_up: function() + { + this.panel_scroll(-this.options.scroll); + }, + + // scroll down + event_panel_scroll_down: function() + { + this.panel_scroll(this.options.scroll); + }, + + // identify + event_get_frame: function(target) + { + return this.frame_list['#' + $(target).closest('.galaxy-frame').attr('id')]; + }, + + /* + FRAME EVENTS START/STOP + */ + + // drag start + frame_drag_start : function (frame) + { + // set focus + this.frame_focus(frame, true); + + // get current dimensions + var p = this.frame_screen (frame); + + // initialize shadow + this.frame_resize(this.galaxy_frame_shadow, p); + this.frame_grid(this.galaxy_frame_shadow, frame.grid_location); + + // reset location + frame.grid_location = null; + + // show shadow + $(this.galaxy_frame_shadow.id).show(); + + // load frame cover + $('.f-cover').show(); + }, + + // drag stop + frame_drag_stop : function (frame) + { + // remove focus + this.frame_focus(frame, false); + + // get new dimensions + var p = this.frame_screen(this.galaxy_frame_shadow); + + // update frame + this.frame_resize(frame, p); + this.frame_grid(frame, this.galaxy_frame_shadow.grid_location, true); + + // reset location of shadow + this.galaxy_frame_shadow.grid_location = null; + + // hide shadow + $(this.galaxy_frame_shadow.id).hide(); + + // hide frame cover + $('.f-cover').hide(); + + // refresh scroll state once all animations completed + this.panel_animation_complete(); + }, + + /* + GRID/PIXEL CONVERTER + */ + + // converts a pixel coordinate to grids + to_grid_coord: function (type, px) + { + // determine sign + var sign = (type == 'width' || type == 'height') ? 1 : -1; + + if (type == 'top') px -= this.top; + + // return + return parseInt((px + sign * this.options.margin) / this.options.cell, 10); + }, + + // converts a grid coordinate to pixels + to_pixel_coord: function (type, g) + { + // determine sign + var sign = (type == 'width' || type == 'height') ? 1 : -1; + + // return + var px = (g * this.options.cell) - sign * this.options.margin; + + if (type == 'top') px += this.top; + + return px; + }, + + // get grid coordinates + to_grid: function (px) + { + // full set + return { + top : this.to_grid_coord('top', px.top), + left : this.to_grid_coord('left', px.left), + width : this.to_grid_coord('width', px.width), + height : this.to_grid_coord('height', px.height) + }; + }, + + // get pixel coordinates + to_pixel: function(g) + { + return { + top : this.to_pixel_coord('top', g.top), + left : this.to_pixel_coord('left', g.left), + width : this.to_pixel_coord('width', g.width), + height : this.to_pixel_coord('height', g.height) + }; + }, + + /* + COLLISION DETECTION + */ + + // check collision + is_collision: function(g) + { + // is collision pair + function is_collision_pair (a, b) + { + return !(a.left > b.left + b.width - 1 || a.left + a.width - 1 < b.left || + a.top > b.top + b.height - 1 || a.top + a.height - 1 < b.top); + } + + // search + for (var i in this.frame_list) + { + // get frame + var frame = this.frame_list[i]; + + // skip + if (frame.grid_location === null) + continue; + + // check if g collides with frame + if (is_collision_pair (g, frame.grid_location)) + return true; + } + + // return + return false; + }, + + // location/grid rank + location_rank: function(loc) + { + return (loc.top * this.cols) + loc.left; + }, + + /* + ONSCREEN MENU + */ + + // update frame counter + menu_refresh: function() + { + // update on screen counter + $(".galaxy-frame-load .number").text(this.frame_counter); + + // check + if(this.frame_counter == 0) + $(".galaxy-frame-load").hide(); + else + $(".galaxy-frame-load").show(); + + // scroll up possible? + if (this.top == this.options.top_min) + $(".galaxy-frame-scroll-up").hide(); + else + $(".galaxy-frame-scroll-up").show(); + + // scroll down possible? + if (this.top == this.top_max) + $(".galaxy-frame-scroll-down").hide(); + else + $(".galaxy-frame-scroll-down").show(); + }, + + /* + PANEL/WINDOW FUNCTIONS + */ + + // panel on animation complete / frames not moving + panel_animation_complete: function() + { + var self = this; + $(".galaxy-frame").promise().done(function() {self.panel_scroll(0, true)}); + }, + + // refresh panel + panel_refresh: function(animate) + { + // get current size + this.cols = parseInt($(window).width() / this.options.cell, 10) + 1; + + // recalculate frame positions + this.frame_insert(null, null, animate); + }, + + // update scroll + panel_scroll: function(delta, animate) + { + // new top value + var top_new = this.top - this.options.scroll * delta; + + // update top + top_new = Math.max(top_new, this.top_max); + top_new = Math.min(top_new, this.options.top_min); + + // update screen if necessary + if (this.top != top_new) + { + // update screen + for (var i in this.frame_list) + { + // get frame + var frame = this.frame_list[i]; + + // skip + if (frame.grid_location !== null) + { + var screen_location = { + top : frame.screen_location.top - (this.top - top_new), + left : frame.screen_location.left + } + this.frame_offset(frame, screen_location, animate); + } + } + + // update top value + this.top = top_new; + } + + // refresh + this.menu_refresh(); + }, + + // show or hide panel + panel_show_hide: function() + { + // check + if (this.visible) + { + // hide + this.visible = false; + + // hide + for (var i in this.frame_list) + $(this.frame_list[i].id).fadeOut('fast'); + + // add class + $(".galaxy-frame-load .icon").addClass("fa-icon-eye-close"); + $(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open"); + + // hide background + $(".galaxy-frame-background").hide(); + + // hide menu + $(".galaxy-frame-menu").hide(); + } else { + // show + this.visible = true; + + // show + for (var i in this.frame_list) + $(this.frame_list[i].id).fadeIn('fast'); + + // add class + $(".galaxy-frame-load .icon").addClass("fa-icon-eye-open"); + $(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close"); + + // hide shadow + $(this.galaxy_frame_shadow.id).hide(); + + // show background + $(".galaxy-frame-background").show(); + + // show menu + this.menu_refresh(); + } + }, + + // show or hide panel + panel_active_disable: function() + { + // check + if (this.active) + { + // disable + this.active = false; + + // untoggle + $(".galaxy-frame-active .icon").removeClass("f-toggle"); + + } else { + // activate + this.active = true; + + // toggle + $(".galaxy-frame-active .icon").addClass("f-toggle"); + } + }, + + /* + FRAME FUNCTIONS + */ + // adds and displays a new frame/window + frame_new: function(options) + { + // validate + if (!this.active) + { + // load frame in main window + if (options.center) + { + var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ); + galaxy_main.attr( 'src', options.content ); + } else + window.location = options.content; + + // stop + return; + } + + // generate frame identifier + var frame_id = '#galaxy-frame-' + (this.frame_counter_id++); + + // check if frame exists + if ($(frame_id).length === 0 && this.options.frame_max > this.frame_counter) + { + // reset top + this.top = this.options.top_min; + + // set dimensions + options.width = this.to_pixel_coord('width', this.options.frame.cols); + options.height = this.to_pixel_coord('height', this.options.frame.rows); + + // append + $(this.el).append(this.frame_template(frame_id.substring(1), options.title, options.type, options.content)); + + // construct a new frame + var frame = { + id : frame_id, + screen_location : {}, + grid_location : {}, + grid_rank : null, + grid_lock : false + }; + + // increase frame counter + this.frame_counter++; + + // add to frame list + this.frame_list[frame_id] = frame; + + // resize + this.frame_resize(frame, {width: options.width, height: options.height}); + + // place frame + this.frame_insert(frame, {top: 0, left: 0}, true); + + // show frames if hidden + if (!this.visible) + this.panel_show_hide(); + } else + alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ")."); + }, + + // frame insert at given location + frame_insert: function(frame, new_loc, animate) + { + // define + var place_list = []; + + // frame to place + if (frame) + { + // reset grid location + frame.grid_location = null; + + // set first one to be placed + place_list.push([frame, this.location_rank(new_loc)]); + } + + // search + var i = null; + for (i in this.frame_list) + { + // get frame + var f = this.frame_list[i]; + + // check + if (f.grid_location !== null && !f.grid_lock) + { + // reset grid location + f.grid_location = null; + + // set up for placement + place_list.push([f, f.grid_rank]); + } + } + + // sort place list by rank + place_list.sort(function(a, b) + { + var i = a[1]; + var j = b[1]; + return i < j ? -1 : (i > j ? 1 : 0); + }); + + // place + for (i = 0; i < place_list.length; i++) + this.frame_place(place_list[i][0], animate); + + // identify maximum viewport size + this.top_max = 0; + for (var i in this.frame_list) + { + // get frame + var frame = this.frame_list[i]; + + // skip + if (frame.grid_location !== null) + this.top_max = Math.max(this.top_max, frame.grid_location.top + frame.grid_location.height); + } + + // mesh maximum top with window size and margin + this.top_max = $(window).height() - this.top_max * this.options.cell - 2 * this.options.margin; + + // fix value + this.top_max = Math.min(this.top_max, this.options.top_min); + + // panel menu + this.menu_refresh(); + }, + + // naive frame place + frame_place: function(frame, animate) + { + // reset grid location + frame.grid_location = null; + + // grid coordinates of new frame + var g = this.to_grid(this.frame_screen(frame)); + + // try grid coordinates + var done = false; + for (var i = 0; i < this.options.rows; i++) + { + // ensure that the first grid column is checked despite limited window space + for (var j = 0; j < Math.max(1, this.cols - g.width); j++) + { + // coordinates + g.top = i; + g.left = j; + + // no collision + if (!this.is_collision(g)) + { + done = true; + break; + } + } + + // break + if (done) + break; + } + + // check if valid spot was found + if (done) + this.frame_grid(frame, g, animate); + else + console.log("Grid dimensions exceeded."); + }, + + // focus + frame_focus: function(frame, has_focus) + { + // get new z-value + var z = parseInt(css.get_attribute('galaxy-frame', 'z-index')) + (has_focus ? 1 : 0); + + // update + $(frame.id).css('z-index', z); + }, + + // new left/top position frame + frame_offset: function(frame, p, animate) + { + // update screen location + frame.screen_location.left = p.left; + frame.screen_location.top = p.top; + + // animate + if (animate) + { + // set focus on animated + this.frame_focus(frame, true); + + // prepare for callback + var self = this; + + // animate and remove focus + $(frame.id).animate({top: p.top, left: p.left}, 'fast', function() + { + // remove focus + self.frame_focus(frame, false); + }); + } else + // update css + $(frame.id).css({top: p.top, left: p.left}); + }, + + // resize frame + frame_resize: function(frame, p) + { + // update css + $(frame.id).css({width: p.width, height: p.height}); + + // update descriptor + frame.screen_location.width = p.width; + frame.screen_location.height = p.height; + }, + + // new grid location + frame_grid: function (frame, l, animate) + { + // update grid location + frame.grid_location = l; + + // place frame + this.frame_offset(frame, this.to_pixel(l), animate); + + // update grid rank + frame.grid_rank = this.location_rank(l); + }, + + // get frame dimensions + frame_screen: function(frame) + { + var p = frame.screen_location; + return {top: p.top, left: p.left, width: p.width, height: p.height}; + }, + + /* + HTML TEMPLATES + */ + + // fill regular frame template + frame_template: function(id, title, type, content) + { + // check title + if (!title) + title = ''; + + // identify content type + if (type == 'url') + content = '<iframe scrolling="auto" class="f-iframe" src="' + content + '"></iframe>'; + + // load template + return '<div id="' + id + '" class="galaxy-frame f-corner">' + + '<div class="f-header f-corner">' + + '<span class="f-title">' + title + '</span>' + + '<span class="f-icon f-pin fa-icon-pushpin"></span>' + + '<span class="f-icon f-close fa-icon-trash"></span>' + + '</div>' + + '<div class="f-content f-corner">' + content + + '<div class="f-cover"></div>' + + '</div>' + + '<span class="f-resize f-icon f-corner fa-icon-resize-full"></span>' + + '</div>'; + }, + + // fill shadow template + frame_template_shadow: function(id) + { + return '<div id="' + id + '" class="galaxy-frame-shadow f-corner"></div>'; + }, + + // fill background template in order to cover underlying iframes + frame_template_background: function() + { + return '<div class="galaxy-frame-background"></div>'; + }, + + // fill load button template + frame_template_load: function() + { + return '<div class="galaxy-frame-load f-corner">' + + '<div class="number f-corner">0</div>' + + '<div class="icon fa-icon-2x"></div>' + + '</div>'+ + '<div title="Enable/Disable Scratchbook Viewer" class="galaxy-frame-active f-corner">' + + '<div class="icon fa-icon-2x fa-icon-th"></div>' + + '</div>'; + }, + + // fill menu button template + frame_template_menu: function() + { + return '<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div>' + + '<div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'; + } +}); + +// return +return { + GalaxyFrameManager: GalaxyFrameManager +}; + +}); diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -367,13 +367,34 @@ $(parent.document).find('input[name=id]:checked').each(function() { var vis_id = $(this).val(); dataset_params.id = vis_id; - parent.location = vis_url + "/trackster?" + $.param(dataset_params); + + // add widget + parent.frame_manager.frame_new( + { + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); + + // hide + parent.hide_modal(); }); } }); }, "View in new visualization": function() { - parent.location = vis_url + "/trackster?" + $.param(dataset_params); + var url = vis_url + "/trackster?" + $.param(dataset_params); + + // add widget + parent.frame_manager.frame_new( + { + title : "Trackster", + type : "url", + content : url + }); + + // hide + parent.hide_modal(); } }); } diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -237,7 +237,7 @@ } else { displayBtnData.title = _l( 'View data' ); - displayBtnData.href = this.urls.display; + displayBtnData.href = "javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', center: true, content: '" + this.urls.display + "'});"; } this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -239,25 +239,8 @@ * @returns {jQuery} rendered DOM */ _render_visualizationsButton : function(){ - var visualizations = this.model.get( 'visualizations' ); - if( ( !this.model.hasData() ) - || ( _.isEmpty( visualizations ) ) ){ - this.visualizationsButton = null; - return null; - } - - //TODO: this is a bridge to allow the framework to be switched off - // remove this fn and use the other when fully integrated - if( _.isObject( visualizations[0] ) ){ - return this._render_visualizationsFrameworkButton( visualizations ); - } - - if( !this.urls.visualization ){ - this.visualizationsButton = null; - return null; - } - var dbkey = this.model.get( 'dbkey' ), + visualizations = this.model.get( 'visualizations' ), visualization_url = this.urls.visualization, popup_menu_dict = {}, params = { @@ -267,10 +250,17 @@ // Add dbkey to params if it exists. if( dbkey ){ params.dbkey = dbkey; } + if( !( this.model.hasData() ) + || !( visualizations && visualizations.length ) + || !( visualization_url ) ){ + this.visualizationsButton = null; + return null; + } + // render the icon from template this.visualizationsButton = new IconButtonView({ model : new IconButton({ title : _l( 'Visualize' ), - href : this.urls.visualization, + href : visualization_url, icon_class : 'chart_curve' })}); var $icon = this.visualizationsButton.render().$el; @@ -289,7 +279,14 @@ return create_scatterplot_action_fn( visualization_url, params ); default: return function(){ - window.parent.location = visualization_url + '/' + visualization + '?' + $.param( params ); }; + // add widget + parent.frame_manager.frame_new( + { + title : "Visualization", + type : "url", + content : visualization_url + '/' + visualization + '?' + $.param( params ) + }); + }; } } @@ -309,40 +306,6 @@ } return $icon; }, - - /** Render an icon-button or popupmenu of links based on the applicable visualizations - * @returns {jQuery} rendered DOM - */ - _render_visualizationsFrameworkButton : function( visualizations ){ - if( !( this.model.hasData() ) - || !( visualizations && !_.isEmpty( visualizations ) ) ){ - this.visualizationsButton = null; - return null; - } - - // render the icon from template - this.visualizationsButton = new IconButtonView({ model : new IconButton({ - title : _l( 'Visualize' ), - icon_class : 'chart_curve' - })}); - var $icon = this.visualizationsButton.render().$el; - $icon.addClass( 'visualize-icon' ); // needed? - - // No need for popup menu because there's a single visualization. - if( _.keys( visualizations ).length === 1 ) { - $icon.attr( 'title', _.keys( visualizations )[0] ); - $icon.attr( 'href', _.values( visualizations )[0] ); - - // >1: Populate menu dict with visualization fns, make the popupmenu - } else { - var popup_menu_options = []; - _.each( visualizations, function( linkData ) { - popup_menu_options.push( linkData ); - }); - var popup = new PopupMenu( $icon, popup_menu_options ); - } - return $icon; - }, // ......................................................................... secondary actions /** Render secondary actions: currently tagging and annotation (if user is allowed). @@ -604,9 +567,16 @@ //TODO: should be imported from scatterplot.js OR abstracted to 'load this in the galaxy_main frame' function create_scatterplot_action_fn( url, params ){ action = function() { - var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), - final_url = url + '/scatterplot?' + $.param(params); - galaxy_main.attr( 'src', final_url ); + + // add widget + parent.frame_manager.frame_new( + { + title : "Scatterplot", + type : "url", + content : url + '/scatterplot?' + $.param(params), + center : true + }); + //TODO: this needs to go away $( 'div.popmenu-wrapper' ).remove(); return false; @@ -650,13 +620,32 @@ $(parent.document).find('input[name=id]:checked').each(function() { var vis_id = $(this).val(); dataset_params.id = vis_id; - parent.location = vis_url + "/trackster?" + $.param(dataset_params); + + // hide modal + parent.hide_modal(); + + // add widget + parent.frame_manager.frame_new( + { + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); }); } }); }, "View in new visualization": function() { - parent.location = vis_url + "/trackster?" + $.param(dataset_params); + // hide modal + parent.hide_modal(); + + // add widget + parent.frame_manager.frame_new( + { + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); } }); } diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/scripts/utils/galaxy.css.js --- /dev/null +++ b/static/scripts/utils/galaxy.css.js @@ -0,0 +1,41 @@ +/** + * Galaxy CSS utilities +*/ + +// dependencies +define(["libs/underscore"], function(_) { + +// get css value +function get_attribute (classname, name) +{ + // place dummy element + var el = $('<div class="' + classname + '"></div>'); + + // required append + el.appendTo(':eq(0)'); + + // get value + var value = el.css(name).replace(/[^-\d\.]/g, ''); + + // remove element + el.remove(); + + // return css value + return value; +} + +// load css +function load_file (url) +{ + // check if css is already available + if (!$('link[href="' + url + '"]').length) + $('<link href="' + url + '" rel="stylesheet">').appendTo('head'); +}; + +// return +return { + load_file : load_file, + get_attribute : get_attribute +}; + +}); diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/style/blue/galaxy.frame.css --- /dev/null +++ b/static/style/blue/galaxy.frame.css @@ -0,0 +1,214 @@ +body {background: #000000} +.f-corner +{ + -moz-border-radius: 4px; + border-radius: 4px; +} + +.f-toggle +{ + color: #BCC800; +} + +/* + galaxy-frames +*/ + +.galaxy-frame-background +{ + z-index : 14000; + position : absolute; + display : none; + top : 0px; + left : 0px; + height : 100%; + width : 100%; + opacity : 0.6; + background : #11131A; + overflow : auto; +} + +.galaxy-frame-shadow +{ + z-index : 14001; + position : absolute; + display : none; + top : 0px; + left : 0px; + opacity : 0.5; + background : #2C3143; + border : 1px solid #EEEEEE; +} + +.galaxy-frame +{ + z-index : 14002; + overflow : hidden; + position : absolute; + top : 0px; + left : 0px; + height : 100%; + width : 100%; + opacity : 1.0; + background : #FFFFFF; + border : 1px solid #D0D0D0; + -webkit-box-shadow: 0 0 5px rgba(0,0,0,0.3); +} +/* + panel menu button +*/ +.galaxy-frame-menu +{ + z-index : 14003; + position : absolute; + cursor : pointer; + color : #BCC800; + right : 10px; +} + +.galaxy-frame-scroll-up +{ + top : 50px; +} + +.galaxy-frame-scroll-down +{ + bottom : 20px; +} + +/* + panel active button +*/ +.galaxy-frame-active +{ + z-index : 34010; + position : absolute; + top : 8px; + right : 120px; + padding : 0px 0px 0px 0px; + cursor : pointer; + color : #D0D0D0; +} + +/* + panel load button +*/ +.galaxy-frame-load +{ + z-index : 34010; + position : absolute; + top : 6px; + right : 165px; + padding : 0px 0px 0px 0px; + cursor : pointer; + color : #BCC800; +} + +.galaxy-frame-load .number +{ + position : absolute; + font-weight : bold; + font-size : 12px; + font-family : Verdana, Arial; + top : 8px; + left : 26px; +} + +/* + frame components +*/ +.galaxy-frame .f-content +{ + position : absolute; + overflow : hidden; + background : #FFFFFF; + border : none; + top : 24px; + bottom : 3px; + left : 3px; + right : 3px; +} + +.galaxy-frame .f-cover +{ + position : absolute; + display : none; + top : 0px; + left : 0px; + height : 100%; + width : 100%; + opacity : 0.0; + background : #FFFFFF; +} + +.galaxy-frame .f-iframe +{ + border : none; + width : 100%; + height : 100%; +} + +.galaxy-frame .f-header +{ + height : 17px; + margin : 2px; + cursor : pointer; + border : 1px solid #000000; + background : #2C3143; + color : #FFFFFF; + font-weight : bold; +} + +.galaxy-frame .f-title +{ + position : absolute; + top : 4px; + left : 16px; + right : 16px; + font-size : 12px; + font-family : Verdana, Arial; + text-align : center; +} + +/* + frame icons +*/ + +.galaxy-frame .f-icon +{ + position : absolute; + cursor : pointer; + font-style : normal; +} + +.galaxy-frame .f-not-allowed +{ + cursor : not-allowed; +} + +.galaxy-frame .f-close +{ + right : 5px; + top : 4px; +} + +.galaxy-frame .f-pin +{ + left : 6px; + top : 4px; +} + +.galaxy-frame .f-resize +{ + right : 0px; + bottom : 0px; + background : #FFFFFF; + width : 16px; + height : 16px; + color : #2C3143; + right : 0px; + bottom : 0px; + text-align : center; + line-height : 16px; + border : 0px solid #2C3143; +} \ No newline at end of file diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 static/style/blue/galaxy.frame.masthead.css --- /dev/null +++ b/static/style/blue/galaxy.frame.masthead.css @@ -0,0 +1,19 @@ +#masthead +{ + display: none; +} + +#messagebox +{ + display: none; +} + +#center +{ + top: 0 !important; +} + +#right +{ + top: 0 !important; +} \ No newline at end of file diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -59,7 +59,8 @@ 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', - 'galaxy.base' + 'galaxy.base', + 'libs/require' )} ${h.templates( @@ -71,6 +72,28 @@ )} <script type="text/javascript"> + ## check if its in a galaxy iframe + function is_in_galaxy_frame() + { + var iframes = parent.document.getElementsByTagName("iframe"); + for (var i=0, len=iframes.length; i < len; ++i) + if (document == iframes[i].contentDocument || self == iframes[i].contentWindow) + return $(iframes[i]).hasClass('f-iframe'); + return false; + }; + + ## load css + function load_css (url) + { + ## check if css is already available + if (!$('link[href="' + url + '"]').length) + $('<link href="' + url + '" rel="stylesheet">').appendTo('head'); + }; + + ## load additional style sheet + if (is_in_galaxy_frame()) + load_css('/static/style/galaxy.frame.masthead.css'); + // console protection window.console = window.console || { log : function(){}, @@ -93,6 +116,20 @@ sweepster_url: '${h.url_for( controller="/visualization", action="sweepster" )}', visualization_url: '${h.url_for( controller="/visualization", action="save" )}', }); + + ## configure require + require.config({ + baseUrl: "${h.url_for('/static/scripts') }", + shim: { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); + + ## frame manager + var frame_manager = null; + require(['galaxy.frame'], function(frame) { this.frame_manager = new frame.GalaxyFrameManager(); }); </script></%def> @@ -276,7 +313,7 @@ </div></noscript> %endif - <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"> ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -142,13 +142,15 @@ tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) %> + + ## Visualization menu. <% menu_options = [ - [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' ) ], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] + [_('New Track Browser'), "javascript:frame_manager.frame_new({title: 'Trackster', type: 'url', content: '/visualization/trackster'});"], + [_('Saved Visualizations'), "javascript:frame_manager.frame_new({ type: 'url', content : '/visualization/list'});" ] ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + tab( "visualization", _("Visualization"), "javascript:frame_manager.frame_new({title: 'Trackster', type: 'url', content: '/visualization/trackster'});", menu_options=menu_options ) %> ## Cloud menu. diff -r 7538c4cb86dcb9383ece63152f623d3c5e517256 -r a27c1c3a628bc0167981865b82442fc790bd8406 templates/webapps/galaxy/tracks/browser.mako --- a/templates/webapps/galaxy/tracks/browser.mako +++ b/templates/webapps/galaxy/tracks/browser.mako @@ -64,7 +64,7 @@ $("#center .unified-panel-header-inner").append(ui.buttonMenu.$el); // Hide bookmarks by default right now. - parent.force_right_panel("hide"); + force_right_panel("hide"); // Resize view when showing/hiding right panel (bookmarks for now). $("#right-border").click(function() { view.resize_window(); }); @@ -118,6 +118,7 @@ function init_editor() { $("#title").text(view.name + " (" + view.dbkey + ")"); + if (!is_in_galaxy_frame()) window.onbeforeunload = function() { if (view.has_changes) { return "There are unsaved changes to your visualization which will be lost."; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff8ac1441d90/ Changeset: ff8ac1441d90 User: nsoranzo Date: 2013-06-24 14:15:46 Summary: Use sam_fa_indexes tool data table instead of searching the dbkey in sam_fa_indices.loc Also remove some unused imports. Affected #: 5 files diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py +++ b/tools/samtools/sam_pileup.py @@ -8,8 +8,7 @@ -o, --output1=o: Output pileup -R, --ref=R: Reference file type -n, --ownFile=n: User-supplied fasta reference file - -d, --dbkey=d: dbkey of user-supplied file - -x, --indexDir=x: Index directory + -g, --index=g: Path of the indexed reference genome -b, --bamIndex=b: BAM index file -s, --lastCol=s: Print the mapping quality as the last column -i, --indels=i: Only output lines containing indels @@ -31,24 +30,9 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): - seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR - seqPath = '' - for line in open( seqFile ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seqPath = fields[2].strip() - break - return seqPath - def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) - seqPath = check_seq_file( options.dbkey, options.indexDir ) # output version # of tool try: tmp = tempfile.NamedTemporaryFile().name @@ -77,7 +61,6 @@ tmpf1 = tempfile.NamedTemporaryFile( dir=tmpDir ) tmpf1_name = tmpf1.name tmpf1.close() - tmpf1fai_name = '%s.fai' % tmpf1_name #link bam and bam index to working directory (can't move because need to leave original) os.symlink( options.input1, tmpf0bam_name ) os.symlink( options.bamIndex, tmpf0bambai_name ) @@ -100,9 +83,9 @@ try: #index reference if necessary and prepare pileup command if options.ref == 'indexed': - if not os.path.exists( "%s.fai" % seqPath ): - raise Exception, "No sequences are available for '%s', request them by reporting this error." % options.dbkey - cmd = cmd % ( opts, seqPath, tmpf0bam_name, options.output1 ) + if not os.path.exists( "%s.fai" % options.index ): + raise Exception, "Indexed genome %s not present, request it by reporting this error." % options.index + cmd = cmd % ( opts, options.index, tmpf0bam_name, options.output1 ) elif options.ref == 'history': os.symlink( options.ownFile, tmpf1_name ) cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -1,4 +1,4 @@ -<tool id="sam_pileup" name="Generate pileup" version="1.1.1"> +<tool id="sam_pileup" name="Generate pileup" version="1.1.2"><description>from BAM dataset</description><requirements><requirement type="package" version="0.1.16">samtools</requirement> @@ -11,10 +11,8 @@ #if $refOrHistory.reference == "history": --ownFile=$refOrHistory.ownFile #else: - --ownFile="None" + --index=${refOrHistory.index.fields.path} #end if - --dbkey=${input1.metadata.dbkey} - --indexDir=${GALAXY_DATA_INDEX_DIR} --bamIndex=${input1.metadata.bam_index} --lastCol=$lastCol --indels=$indels @@ -41,7 +39,13 @@ <when value="indexed"><param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options></param></when><when value="history"> @@ -100,6 +104,7 @@ --><param name="reference" value="indexed" /><param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> + <param name="index" value="chr_m" /><param name="lastCol" value="no" /><param name="indels" value="no" /><param name="mapCap" value="60" /> diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py +++ b/tools/samtools/sam_to_bam.py @@ -3,43 +3,24 @@ Converts SAM data to sorted BAM data. usage: sam_to_bam.py [options] --input1: SAM file to be converted - --dbkey: dbkey value + --index: path of the indexed reference genome --ref_file: Reference file if choosing from history --output1: output dataset in bam format - --index_dir: GALAXY_DATA_INDEX_DIR """ -import optparse, os, sys, subprocess, tempfile, shutil, gzip -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.cookbook import doc_optparse -from galaxy import util +import optparse, os, sys, subprocess, tempfile, shutil def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) + parser.add_option( '', '--index', dest='index', help='The path of the indexed reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -61,24 +42,17 @@ except: sys.stdout.write( 'Could not determine Samtools version\n' ) - cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai - fai_index_file_base = seq_path - fai_index_file_path = '%s.fai' % seq_path + fai_index_file_path = '%s.fai' % options.index if not os.path.exists( fai_index_file_path ): #clean up temp files if os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) - stop_err( 'No sequences are available for build (%s), request them by reporting this error.' % options.dbkey ) + stop_err( 'Indexed genome %s not present, request it by reporting this error.' % options.index ) else: try: # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will: diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3"><description>converts SAM format to BAM format</description><requirements><requirement type="package">samtools</requirement> @@ -7,13 +7,11 @@ sam_to_bam.py --input1=$source.input1 #if $source.index_source == "history": - --dbkey=${ref_file.metadata.dbkey} --ref_file=$source.ref_file #else - --dbkey=${input1.metadata.dbkey} + --index=${source.index.fields.path} #end if --output1=$output1 - --index_dir=${GALAXY_DATA_INDEX_DIR} </command><inputs><conditional name="source"> @@ -22,13 +20,19 @@ <option value="history">History</option></param><when value="cached"> - <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> + <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options></param></when><when value="history"> - <param name="input1" type="data" format="sam" label="Convert SAM file" /> + <param name="input1" type="data" format="sam" label="SAM file to convert" /><param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /></when></conditional> @@ -76,6 +80,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> + <param name="index" value="chr_m" /><output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /></test></tests> diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 tools/samtools/samtools_mpileup.xml --- a/tools/samtools/samtools_mpileup.xml +++ b/tools/samtools/samtools_mpileup.xml @@ -1,4 +1,4 @@ -<tool id="samtools_mpileup" name="MPileup" version="0.0.1"> +<tool id="samtools_mpileup" name="MPileup" version="0.0.2"><description>SNP and indel caller</description><requirements><requirement type="package">samtools</requirement> @@ -59,22 +59,22 @@ </param><when value="cached"><repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> - </param> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param></repeat><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="sam_fa_indexes"> -  + </options></param></when><when value="history"><repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - </param> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." /> + </param></repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> https://bitbucket.org/galaxy/galaxy-central/commits/6769c6ef2ae1/ Changeset: 6769c6ef2ae1 User: nsoranzo Date: 2013-06-24 14:17:42 Summary: Use sam_fa_indexes tool data table instead of searching the dbkey in sam_fa_indices.loc also in Cufflinks wrappers Affected #: 8 files diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -8,20 +8,6 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -30,8 +16,7 @@ parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') # Wrapper / Galaxy options. - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -60,21 +45,16 @@ # Set/link to sequence file. if options.use_seq_data: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> +<tool id="cuffcompare" name="Cuffcompare" version="0.0.6"><description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements> @@ -17,14 +17,12 @@ ## Use sequence data? #if $seq_data.use_seq_data == "Yes": - -s + -s #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${seq_data.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -66,7 +64,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -35,20 +35,6 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -83,8 +69,7 @@ # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -123,21 +108,16 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.0.5"> +<tool id="cuffdiff" name="Cuffdiff" version="0.0.6"><description>find significant changes in transcript expression, splicing, and promoter use</description><requirements> @@ -42,14 +42,12 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${gtf_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Inputs. @@ -131,7 +129,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -10,20 +10,6 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -52,8 +38,7 @@ # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Global model. @@ -82,21 +67,16 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.5"> +<tool id="cufflinks" name="Cufflinks" version="0.0.6"><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements> @@ -28,14 +28,12 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Multi-read correct? @@ -66,15 +64,15 @@ <when value="No"></when><when value="Use reference annotation"><param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> - <when value="Use reference annotation guide"> + </when> + <when value="Use reference annotation guide"><param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> + </when></conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."><option value="No" selected="true">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source"> @@ -82,7 +80,14 @@ <option value="cached" selected="true">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -8,20 +8,6 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -31,8 +17,7 @@ # Wrapper / Galaxy options. - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -61,21 +46,16 @@ # Set/link to sequence file. if options.use_seq_data: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r ff8ac1441d909237bcac94f18aa7db3df61e6be9 -r 6769c6ef2ae18b120b208c63474f8877865128c6 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> +<tool id="cuffmerge" name="Cuffmerge" version="0.0.6"><description>merge together several Cufflinks assemblies</description><requirements> @@ -16,14 +16,12 @@ ## Use sequence data? #if $seq_data.use_seq_data == "Yes": - -s + -s #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${seq_data.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -64,7 +62,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> https://bitbucket.org/galaxy/galaxy-central/commits/af20b15f7eda/ Changeset: af20b15f7eda User: nsoranzo Date: 2013-04-18 19:25:55 Summary: Add new loc file for SAMtools indexes to support genome variants Affected #: 2 files diff -r 6769c6ef2ae18b120b208c63474f8877865128c6 -r af20b15f7eda2332313933055c87056ef9af252a tool-data/sam_fa_new_indices.loc.sample --- /dev/null +++ b/tool-data/sam_fa_new_indices.loc.sample @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_new_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_new_indices.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id><dbkey><display_name><file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the sam_fa_new_indices.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your sam_fa_new_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa + diff -r 6769c6ef2ae18b120b208c63474f8877865128c6 -r af20b15f7eda2332313933055c87056ef9af252a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -55,10 +55,26 @@ <columns>value, name, path</columns><file path="tool-data/perm_color_index.loc" /></table> -  - <table name="sam_fa_indexes" comment_char="#"> +  + <table name="sam_fa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/sam_fa_new_indices.loc" /></table><table name="picard_indexes" comment_char="#"> https://bitbucket.org/galaxy/galaxy-central/commits/7538c4cb86dc/ Changeset: 7538c4cb86dc User: jgoecks Date: 2013-06-24 16:37:12 Summary: Merged in nsoranzo/galaxy-central (pull request #188) New loc file for SAMtools indexes to support genome variants (backward compatible) Affected #: 15 files diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tool-data/sam_fa_new_indices.loc.sample --- /dev/null +++ b/tool-data/sam_fa_new_indices.loc.sample @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_new_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_new_indices.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id><dbkey><display_name><file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the sam_fa_new_indices.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your sam_fa_new_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa + diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -55,10 +55,26 @@ <columns>value, name, path</columns><file path="tool-data/perm_color_index.loc" /></table> -  - <table name="sam_fa_indexes" comment_char="#"> +  + <table name="sam_fa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/sam_fa_new_indices.loc" /></table><table name="picard_indexes" comment_char="#"> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -8,20 +8,6 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -30,8 +16,7 @@ parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') # Wrapper / Galaxy options. - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -60,21 +45,16 @@ # Set/link to sequence file. if options.use_seq_data: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> +<tool id="cuffcompare" name="Cuffcompare" version="0.0.6"><description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements> @@ -17,14 +17,12 @@ ## Use sequence data? #if $seq_data.use_seq_data == "Yes": - -s + -s #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${seq_data.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -66,7 +64,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -35,20 +35,6 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -83,8 +69,7 @@ # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -123,21 +108,16 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.0.5"> +<tool id="cuffdiff" name="Cuffdiff" version="0.0.6"><description>find significant changes in transcript expression, splicing, and promoter use</description><requirements> @@ -42,14 +42,12 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${gtf_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Inputs. @@ -131,7 +129,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -10,20 +10,6 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -52,8 +38,7 @@ # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Global model. @@ -82,21 +67,16 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.5"> +<tool id="cufflinks" name="Cufflinks" version="0.0.6"><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements> @@ -28,14 +28,12 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Multi-read correct? @@ -66,15 +64,15 @@ <when value="No"></when><when value="Use reference annotation"><param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> - <when value="Use reference annotation guide"> + </when> + <when value="Use reference annotation guide"><param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> + </when></conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."><option value="No" selected="true">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source"> @@ -82,7 +80,14 @@ <option value="cached" selected="true">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -8,20 +8,6 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -31,8 +17,7 @@ # Wrapper / Galaxy options. - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Outputs. @@ -61,21 +46,16 @@ # Set/link to sequence file. if options.use_seq_data: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index # Build command. diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> +<tool id="cuffmerge" name="Cuffmerge" version="0.0.6"><description>merge together several Cufflinks assemblies</description><requirements> @@ -16,14 +16,12 @@ ## Use sequence data? #if $seq_data.use_seq_data == "Yes": - -s + -s #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${seq_data.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -64,7 +62,14 @@ <option value="cached">Locally cached</option><option value="history">History</option></param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when><when value="history"><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py +++ b/tools/samtools/sam_pileup.py @@ -8,8 +8,7 @@ -o, --output1=o: Output pileup -R, --ref=R: Reference file type -n, --ownFile=n: User-supplied fasta reference file - -d, --dbkey=d: dbkey of user-supplied file - -x, --indexDir=x: Index directory + -g, --index=g: Path of the indexed reference genome -b, --bamIndex=b: BAM index file -s, --lastCol=s: Print the mapping quality as the last column -i, --indels=i: Only output lines containing indels @@ -31,24 +30,9 @@ sys.stderr.write( '%s\n' % msg ) sys.exit() -def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): - seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR - seqPath = '' - for line in open( seqFile ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seqPath = fields[2].strip() - break - return seqPath - def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) - seqPath = check_seq_file( options.dbkey, options.indexDir ) # output version # of tool try: tmp = tempfile.NamedTemporaryFile().name @@ -77,7 +61,6 @@ tmpf1 = tempfile.NamedTemporaryFile( dir=tmpDir ) tmpf1_name = tmpf1.name tmpf1.close() - tmpf1fai_name = '%s.fai' % tmpf1_name #link bam and bam index to working directory (can't move because need to leave original) os.symlink( options.input1, tmpf0bam_name ) os.symlink( options.bamIndex, tmpf0bambai_name ) @@ -100,9 +83,9 @@ try: #index reference if necessary and prepare pileup command if options.ref == 'indexed': - if not os.path.exists( "%s.fai" % seqPath ): - raise Exception, "No sequences are available for '%s', request them by reporting this error." % options.dbkey - cmd = cmd % ( opts, seqPath, tmpf0bam_name, options.output1 ) + if not os.path.exists( "%s.fai" % options.index ): + raise Exception, "Indexed genome %s not present, request it by reporting this error." % options.index + cmd = cmd % ( opts, options.index, tmpf0bam_name, options.output1 ) elif options.ref == 'history': os.symlink( options.ownFile, tmpf1_name ) cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -1,4 +1,4 @@ -<tool id="sam_pileup" name="Generate pileup" version="1.1.1"> +<tool id="sam_pileup" name="Generate pileup" version="1.1.2"><description>from BAM dataset</description><requirements><requirement type="package" version="0.1.16">samtools</requirement> @@ -11,10 +11,8 @@ #if $refOrHistory.reference == "history": --ownFile=$refOrHistory.ownFile #else: - --ownFile="None" + --index=${refOrHistory.index.fields.path} #end if - --dbkey=${input1.metadata.dbkey} - --indexDir=${GALAXY_DATA_INDEX_DIR} --bamIndex=${input1.metadata.bam_index} --lastCol=$lastCol --indels=$indels @@ -41,7 +39,13 @@ <when value="indexed"><param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"><validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options></param></when><when value="history"> @@ -100,6 +104,7 @@ --><param name="reference" value="indexed" /><param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> + <param name="index" value="chr_m" /><param name="lastCol" value="no" /><param name="indels" value="no" /><param name="mapCap" value="60" /> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py +++ b/tools/samtools/sam_to_bam.py @@ -3,43 +3,24 @@ Converts SAM data to sorted BAM data. usage: sam_to_bam.py [options] --input1: SAM file to be converted - --dbkey: dbkey value + --index: path of the indexed reference genome --ref_file: Reference file if choosing from history --output1: output dataset in bam format - --index_dir: GALAXY_DATA_INDEX_DIR """ -import optparse, os, sys, subprocess, tempfile, shutil, gzip -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.cookbook import doc_optparse -from galaxy import util +import optparse, os, sys, subprocess, tempfile, shutil def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) + parser.add_option( '', '--index', dest='index', help='The path of the indexed reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -61,24 +42,17 @@ except: sys.stdout.write( 'Could not determine Samtools version\n' ) - cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai - fai_index_file_base = seq_path - fai_index_file_path = '%s.fai' % seq_path + fai_index_file_path = '%s.fai' % options.index if not os.path.exists( fai_index_file_path ): #clean up temp files if os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) - stop_err( 'No sequences are available for build (%s), request them by reporting this error.' % options.dbkey ) + stop_err( 'Indexed genome %s not present, request it by reporting this error.' % options.index ) else: try: # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will: diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3"><description>converts SAM format to BAM format</description><requirements><requirement type="package">samtools</requirement> @@ -7,13 +7,11 @@ sam_to_bam.py --input1=$source.input1 #if $source.index_source == "history": - --dbkey=${ref_file.metadata.dbkey} --ref_file=$source.ref_file #else - --dbkey=${input1.metadata.dbkey} + --index=${source.index.fields.path} #end if --output1=$output1 - --index_dir=${GALAXY_DATA_INDEX_DIR} </command><inputs><conditional name="source"> @@ -22,13 +20,19 @@ <option value="history">History</option></param><when value="cached"> - <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> + <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options></param></when><when value="history"> - <param name="input1" type="data" format="sam" label="Convert SAM file" /> + <param name="input1" type="data" format="sam" label="SAM file to convert" /><param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /></when></conditional> @@ -76,6 +80,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> + <param name="index" value="chr_m" /><output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /></test></tests> diff -r fc9b51ce979861604abaa9da6b15977f1238957d -r 7538c4cb86dcb9383ece63152f623d3c5e517256 tools/samtools/samtools_mpileup.xml --- a/tools/samtools/samtools_mpileup.xml +++ b/tools/samtools/samtools_mpileup.xml @@ -1,4 +1,4 @@ -<tool id="samtools_mpileup" name="MPileup" version="0.0.1"> +<tool id="samtools_mpileup" name="MPileup" version="0.0.2"><description>SNP and indel caller</description><requirements><requirement type="package">samtools</requirement> @@ -59,22 +59,22 @@ </param><when value="cached"><repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> - </param> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param></repeat><param name="ref_file" type="select" label="Using reference genome"><options from_data_table="sam_fa_indexes"> -  + </options></param></when><when value="history"><repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - </param> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." /> + </param></repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for managing tool dependencies for an installed tool shed repository.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc9b51ce9798/ Changeset: fc9b51ce9798 User: greg Date: 2013-06-24 16:36:01 Summary: Fix for managing tool dependencies for an installed tool shed repository. Affected #: 1 file diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r fc9b51ce979861604abaa9da6b15977f1238957d templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -35,7 +35,7 @@ else: error_message = '' if not can_install: - if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.INSTALLED ]: + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: can_install = True if not can_uninstall: if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: 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: greg: Enhance the Galaxy API for installing tool shed repositories to make sure the tool_dependency_dir setting is defined in the Galaxy configuration file if installing tool dependencies along with repositories.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc6e0347edff/ Changeset: dc6e0347edff User: greg Date: 2013-06-24 15:47:46 Summary: Enhance the Galaxy API for installing tool shed repositories to make sure the tool_dependency_dir setting is defined in the Galaxy configuration file if installing tool dependencies along with repositories. Affected #: 1 file diff -r acc4a2270e6a45ec03976fd53fb7b55da7b3fabc -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -179,6 +179,11 @@ # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information. install_repository_dependencies = payload.get( 'install_repository_dependencies', False ) install_tool_dependencies = payload.get( 'install_tool_dependencies', False ) + if install_tool_dependencies: + if trans.app.config.tool_dependency_dir is None: + no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set the value of your 'tool_dependency_dir' " + no_tool_dependency_dir_message += "setting in your Galaxy configuration file (universe_wsgi.ini) and restart your Galaxy server." + raise HTTPBadRequest( detail=no_tool_dependency_dir_message ) new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = payload.get( 'shed_tool_conf', None ) if shed_tool_conf: 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: greg: Add the threadpool_kill_thread_limit setting to the tool shed's sample configuration file.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/acc4a2270e6a/ Changeset: acc4a2270e6a User: greg Date: 2013-06-24 15:44:58 Summary: Add the threadpool_kill_thread_limit setting to the tool shed's sample configuration file. Affected #: 1 file diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r acc4a2270e6a45ec03976fd53fb7b55da7b3fabc tool_shed_wsgi.ini.sample --- a/tool_shed_wsgi.ini.sample +++ b/tool_shed_wsgi.ini.sample @@ -12,6 +12,8 @@ use_threadpool = true threadpool_workers = 10 +# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +threadpool_kill_thread_limit = 10800 # ---- Galaxy Webapps Community Interface ------------------------------------------------- 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: Add more package requirements for datatype converters
by commits-noreply＠bitbucket.org 22 Jun '13

22 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f7b7e4ca213/ Changeset: 4f7b7e4ca213 User: dannon Date: 2013-06-21 20:55:12 Summary: Add more package requirements for datatype converters Affected #: 3 files diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -1,5 +1,9 @@ <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. grep -v '^#' $input | sort -k1,1 | diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -1,6 +1,10 @@ <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -1,4 +1,9 @@ <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo 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 June 2013