From febf037bb9fb268f861667f50ec0f29a3e52af2f Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 26 Mar 2012 10:12:37 -0400 Subject: [PATCH 001/250] Strip whitespace around separators in start_job_runners --- lib/galaxy/jobs/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index cbe636d04b0..c2be8c28825 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1183,7 +1183,7 @@ class DefaultJobDispatcher( object ): self.job_runners = {} start_job_runners = ["local"] if app.config.start_job_runners is not None: - start_job_runners.extend( app.config.start_job_runners.split(",") ) + start_job_runners.extend( [ x.strip() for x in util.listify( app.config.start_job_runners ) ] ) if app.config.use_tasked_jobs: start_job_runners.append("tasks") for name in start_job_runners: From c0c9232912e326c48575e10aae88c692d194a8ac Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Mon, 26 Mar 2012 10:16:39 -0400 Subject: [PATCH 002/250] Trackster: make show/hide content compatible with 8e9d2b492c4c. --- static/scripts/trackster.js | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js index b0cac0a2270..9d5c083c097 100644 --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -393,8 +393,8 @@ var DATA_ERROR = "There was an error in indexing this dataset. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", - DATA_PENDING = "Preparing data. This takes seconds for a small dataset but longer for a large dataset.
\ - You can save and close the visualization and preparation will continue.
", + DATA_PENDING = "Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. \ + If visualization is saved and closed, preparation will continue in the background.", DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ", DATA_LOADING = "Loading data...", DATA_OK = "Ready for display", @@ -3329,18 +3329,15 @@ extend(Track.prototype, Drawable.prototype, { * Hide any elements that are part of the tracks contents area. Should * remove as approprite, the track will be redrawn by show_contents. */ - hide_contents : function () { - // Clear contents by removing any elements that are contained in - // the tracks content_div - this.content_div.children().remove(); - // Hide the content div - this.content_div.hide(); - // And any y axis labels (common to several track types) + hide_contents: function () { + // Hide tiles. + this.tiles_div.hide(); + // Hide any y axis labels (common to several track types) this.container_div.find(".yaxislabel, .track-resize").hide() }, - show_contents : function() { + show_contents: function() { // Show the contents div and labels (if present) - this.content_div.show(); + this.tiles_div.show(); this.container_div.find(".yaxislabel, .track-resize").show() // Request a redraw of the content this.request_draw(); @@ -4282,7 +4279,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { } return new Tile(track, tile_index, resolution, canvas, seq); } - this.content_div.css("height", "0px"); + track.content_div.css("height", "0px"); }, /** * If there is a tile with sequence data, set content div so that data is visible. From eda1ac38bc0ff201c07531a9bfd1f928a3490bd2 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Mon, 26 Mar 2012 10:18:09 -0400 Subject: [PATCH 003/250] Add open ID config to .hgignore --- .hgignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.hgignore b/.hgignore index 59c2b3ce68b..ca04056f724 100644 --- a/.hgignore +++ b/.hgignore @@ -36,6 +36,7 @@ shed_tool_conf.xml tool_data_table_conf.xml tool_sheds_conf.xml integrated_tool_panel.xml +openid_conf.xml static/welcome.html.* static/welcome.html From a258a45b2f5110c7e299bb0f541741ce37b4e4cd Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Mon, 26 Mar 2012 10:50:31 -0400 Subject: [PATCH 004/250] Trackster: use show/hide framework to manage reference track. --- static/scripts/trackster.js | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js index 9d5c083c097..7ba8f2b8186 100644 --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4249,6 +4249,7 @@ var ReferenceTrack = function (view) { this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false); + this.hide_contents(); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { build_header_div: function() {}, @@ -4266,7 +4267,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { if (w_scale > this.view.canvas_manager.char_width_px) { if (seq.data === null) { - track.content_div.css("height", "0px"); + this.hide_contents(); return; } var canvas = ctx.canvas; @@ -4277,17 +4278,10 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { var c_start = Math.floor(c * w_scale); ctx.fillText(seq[c], c_start, 10); } + this.show_contents(); return new Tile(track, tile_index, resolution, canvas, seq); } - track.content_div.css("height", "0px"); - }, - /** - * If there is a tile with sequence data, set content div so that data is visible. - */ - after_show_tile: function(tile) { - if (tile) { - this.content_div.css("height", "12px"); - } + this.hide_contents(); } }); From 7114a48cb18baa84ca830b9dba5f4fe391541e80 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Mon, 26 Mar 2012 12:34:15 -0400 Subject: [PATCH 005/250] Refactor changeset 164eef0d7693 to use less templates. --- static/june_2007_style/blue/base.css | 4 ++-- static/june_2007_style/bootstrap/reset.less | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css index 6380a94d441..3c48550f946 100644 --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -9,12 +9,12 @@ sup{top:-0.5em;} sub{bottom:-0.25em;} img{max-width:100%;height:auto;border:0;-ms-interpolation-mode:bicubic;} button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} button,input{*overflow:visible;line-height:normal;} button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} -input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} textarea{overflow:auto;vertical-align:top;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} @@ -225,7 +225,7 @@ button.btn.small,input[type="submit"].btn.small{*padding-top:3px;*padding-bottom .navbar-form .radio,.navbar-form .checkbox{margin-top:5px;} .navbar-form input[type="image"],.navbar-form input[type="checkbox"],.navbar-form input[type="radio"]{margin-top:3px;} .navbar-search{position:relative;float:left;margin-top:6px;margin-bottom:0;}.navbar-search .search-query{padding:4px 9px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;color:#ffffff;color:rgba(255, 255, 255, 0.75);background:#666;background:rgba(255, 255, 255, 0.3);border:1px solid #111;-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;}.navbar-search .search-query :-moz-placeholder{color:#eeeeee;} -.navbar-search .search-query::-webkit-input-placeholder{color:#eeeeee;} +.navbar-search .search-query ::-webkit-input-placeholder{color:#eeeeee;} .navbar-search .search-query:hover{color:#ffffff;background-color:#999999;background-color:rgba(255, 255, 255, 0.5);} .navbar-search .search-query:focus,.navbar-search .search-query.focused{padding:5px 10px;color:#333333;text-shadow:0 1px 0 #ffffff;background-color:#ffffff;border:0;-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);outline:0;} .navbar-fixed-top{position:fixed;top:0;right:0;left:0;z-index:1030;} diff --git a/static/june_2007_style/bootstrap/reset.less b/static/june_2007_style/bootstrap/reset.less index 28d8eb60ca4..b60881c82c0 100644 --- a/static/june_2007_style/bootstrap/reset.less +++ b/static/june_2007_style/bootstrap/reset.less @@ -93,6 +93,11 @@ textarea { font-size: 100%; vertical-align: middle; } +// Use Webkit margins for checkboxs and radio buttons. +input[type="checkbox"],input[type="radio"] { + margin-left: 0.5ex; + margin-right: 0.5ex; +} button, input { *overflow: visible; // Inner spacing ie IE6/7 From 8a915c5e6652b539cddb8a5bc57cf3c39ed1af69 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Mon, 26 Mar 2012 13:27:17 -0400 Subject: [PATCH 006/250] Don't create the default path for installing tools from the tool shed until the time of installation, at which time the admin whll have over-ridden the default if they wanted to. --- lib/galaxy/config.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 6fc42236775..1fb2921189c 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -238,16 +238,6 @@ class Configuration( object ): return default def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] - # Look for any tool shed configs and retrieve the tool_path attribute from the tag. - tool_configs = self.tool_configs - if self.migrated_tools_config not in tool_configs: - tool_configs.append( self.migrated_tools_config ) - for config_filename in tool_configs: - tree = parse_xml( config_filename ) - root = tree.getroot() - tool_path = root.get( 'tool_path' ) - if tool_path not in [ None, False ]: - paths_to_check.append( resolve_path( tool_path, self.root ) ) # Check that required directories exist for path in paths_to_check: if path not in [ None, False ] and not os.path.isdir( path ): From dd3f3e34773c9a1a6aa8a6ea03fe4f5f9abfbc50 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Mon, 26 Mar 2012 13:55:05 -0400 Subject: [PATCH 007/250] allow limiting the number of data lines used to determine column data types while still counting all data lines --- lib/galaxy/datatypes/tabular.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 73584ea2f27..43c6e24af26 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -26,7 +26,7 @@ class Tabular( data.Text ): def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, **kwd ): + def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, max_guess_type_data_lines = None, **kwd ): """ Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is @@ -116,13 +116,14 @@ class Tabular( data.Text ): comment_lines += 1 else: data_lines += 1 - fields = line.split( '\t' ) - for field_count, field in enumerate( fields ): - if field_count >= len( column_types ): #found a previously unknown column, we append None - column_types.append( None ) - column_type = guess_column_type( field ) - if type_overrules_type( column_type, column_types[field_count] ): - column_types[field_count] = column_type + if max_guess_type_data_lines is None or data_lines <= max_guess_type_data_lines: + fields = line.split( '\t' ) + for field_count, field in enumerate( fields ): + if field_count >= len( column_types ): #found a previously unknown column, we append None + column_types.append( None ) + column_type = guess_column_type( field ) + if type_overrules_type( column_type, column_types[field_count] ): + column_types[field_count] = column_type if i == 0 and requested_skip is None: # This is our first line, people seem to like to upload files that have a header line, but do not # start with '#' (i.e. all column types would then most likely be detected as str). We will assume From ae373b57edee8445168372c6f21be2f1e3582619 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Mon, 26 Mar 2012 15:43:27 -0400 Subject: [PATCH 008/250] Fix for ordering the options of the select list displaying change sets for a tool shed repository. --- lib/galaxy/webapps/community/controllers/common.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py index 813f0b9d91d..d7855757880 100644 --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1003,6 +1003,10 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non revision_label = get_revision_label( trans, repository, changeset_revision ) options.append( ( revision_label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) + # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time, + # screwing up the order. + sorted_options = sorted( options ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -1010,7 +1014,7 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: + for option_tup in sorted_options: selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field From 9f0e8a9bfb1ef41146f1043059f06ecef448a2d9 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Tue, 27 Mar 2012 08:49:44 -0400 Subject: [PATCH 009/250] Remove duplicate hr style; this reinstates dashed lines between sections in help text. --- static/june_2007_style/base.less | 7 ------- static/june_2007_style/blue/base.css | 1 - 2 files changed, 8 deletions(-) diff --git a/static/june_2007_style/base.less b/static/june_2007_style/base.less index a55e96193ae..0afbc63f928 100644 --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1616,13 +1616,6 @@ body.toolMenuPage margin-left: 10px; } -hr -{ - border: none; - height: 0px; - margin-top: 0px; -} - div.toolSectionPad { margin: 0; diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css index 3c48550f946..082e5aa09de 100644 --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -734,7 +734,6 @@ div.historyItemBody div{padding-top:2px;} pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -hr{border:none;height:0px;margin-top:0px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} div.toolSectionTitle{font-weight:bold;} From a429192b75e7ff3ffb8d0a97625e945bbdbfd04f Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Tue, 27 Mar 2012 09:45:18 -0400 Subject: [PATCH 010/250] Fixes for tool shed changeset revision select field generation. --- .../webapps/community/controllers/common.py | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py index d7855757880..5640243f4ed 100644 --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -997,16 +997,24 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non """ repo = hg.repository( get_configured_ui(), repository.repo_path ) options = [] + changeset_tups = [] refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - revision_label = get_revision_label( trans, repository, changeset_revision ) - options.append( ( revision_label, changeset_revision ) ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time, - # screwing up the order. - sorted_options = sorted( options ) + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. + for changeset_tup in sorted( changeset_tups ): + # Display the latest revision first. + options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -1014,7 +1022,7 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) - for option_tup in sorted_options: + for option_tup in options: selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field From bad271ec0d0ccbc1f8e1462122def62deb898861 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Tue, 27 Mar 2012 10:19:04 -0400 Subject: [PATCH 011/250] Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon. --- contrib/universe_merger.py | 71 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 contrib/universe_merger.py diff --git a/contrib/universe_merger.py b/contrib/universe_merger.py new file mode 100644 index 00000000000..a91c899565f --- /dev/null +++ b/contrib/universe_merger.py @@ -0,0 +1,71 @@ +#! /usr/bin/env python +''' +universe_merger.py + +Created by Anne Pajon on 31 Jan 2012 +Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. All rights reserved. + +Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample +''' +import ConfigParser +import sys +import optparse +import logging + +def main(): + # logging configuration + logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) + + # get the options + parser = optparse.OptionParser() + parser.add_option("-s", "--sample", dest="sample", action="store", help="the path to the Galaxy universe_wsgi.ini.sample file") + parser.add_option("-c", "--config", dest="config", action="store", help="the path to your own universe_wsgi.ini.cri file") + parser.add_option("-o", "--output", dest="output", action="store", help="the path to the new merged universe_wsgi.ini file") + (options, args) = parser.parse_args() + + for option in ['sample', 'config']: + if getattr(options, option) == None: + print "Please supply a --%s parameter.\n" % (option) + parser.print_help() + sys.exit() + + config_sample = ConfigParser.RawConfigParser() + config_sample.read(options.sample) + config_sample_content = open(options.sample, 'r').read() + + config = ConfigParser.RawConfigParser() + config.read(options.config) + + logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) + logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") + for section in config.sections(): + if not config_sample.has_section(section): + logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) + else: + for (name, value) in config.items(section): + if not config_sample.has_option(section, name): + if not "#%s" % name in config_sample_content: + logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) + else: + logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) + config_sample.set(section, name, value) + else: + if not config_sample.get(section, name) == value: + logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) + config_sample.set(section, name, value) + logging.info("---------- DIFFERENCE ANALYSIS END ----------") + + if options.output: + outputfile = open(options.output, 'w') + config_sample.write(outputfile) + outputfile.close() + else: + #print "----------" + #config_sample.write(sys.stdout) + #print "----------" + logging.info("use -o OUTPUT to write the merged configuration into a file.") + + logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") + +if __name__ == '__main__': + main() From 3d5ba971ce79310ed6ffffa56615e62faba9420f Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Tue, 27 Mar 2012 10:53:45 -0400 Subject: [PATCH 012/250] Missed the copyright - removed from the distribution. --- contrib/universe_merger.py | 71 -------------------------------------- 1 file changed, 71 deletions(-) delete mode 100644 contrib/universe_merger.py diff --git a/contrib/universe_merger.py b/contrib/universe_merger.py deleted file mode 100644 index a91c899565f..00000000000 --- a/contrib/universe_merger.py +++ /dev/null @@ -1,71 +0,0 @@ -#! /usr/bin/env python -''' -universe_merger.py - -Created by Anne Pajon on 31 Jan 2012 -Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. All rights reserved. - -Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample -''' -import ConfigParser -import sys -import optparse -import logging - -def main(): - # logging configuration - logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) - - # get the options - parser = optparse.OptionParser() - parser.add_option("-s", "--sample", dest="sample", action="store", help="the path to the Galaxy universe_wsgi.ini.sample file") - parser.add_option("-c", "--config", dest="config", action="store", help="the path to your own universe_wsgi.ini.cri file") - parser.add_option("-o", "--output", dest="output", action="store", help="the path to the new merged universe_wsgi.ini file") - (options, args) = parser.parse_args() - - for option in ['sample', 'config']: - if getattr(options, option) == None: - print "Please supply a --%s parameter.\n" % (option) - parser.print_help() - sys.exit() - - config_sample = ConfigParser.RawConfigParser() - config_sample.read(options.sample) - config_sample_content = open(options.sample, 'r').read() - - config = ConfigParser.RawConfigParser() - config.read(options.config) - - logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) - logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") - for section in config.sections(): - if not config_sample.has_section(section): - logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) - else: - for (name, value) in config.items(section): - if not config_sample.has_option(section, name): - if not "#%s" % name in config_sample_content: - logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) - else: - logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) - config_sample.set(section, name, value) - else: - if not config_sample.get(section, name) == value: - logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) - config_sample.set(section, name, value) - logging.info("---------- DIFFERENCE ANALYSIS END ----------") - - if options.output: - outputfile = open(options.output, 'w') - config_sample.write(outputfile) - outputfile.close() - else: - #print "----------" - #config_sample.write(sys.stdout) - #print "----------" - logging.info("use -o OUTPUT to write the merged configuration into a file.") - - logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") - -if __name__ == '__main__': - main() From 6b2244941952570bbfdf803135409a279329a371 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Tue, 27 Mar 2012 10:59:31 -0400 Subject: [PATCH 013/250] Add backbone.js, underscore.js, and handlebars.js libraries in a new /libs directory and modify pack scripts accordingly. --- static/scripts/libs/backbone.js | 1431 +++++++++++++++ .../scripts/libs/handlebars-1.0.0.beta.6.js | 1550 +++++++++++++++++ static/scripts/libs/underscore.js | 999 +++++++++++ static/scripts/pack_scripts.py | 1 + static/scripts/packed/libs/backbone.js | 1 + .../packed/libs/handlebars-1.0.0.beta.6.js | 1 + static/scripts/packed/libs/underscore.js | 1 + static/scripts/packed/trackster.js | 2 +- 8 files changed, 3985 insertions(+), 1 deletion(-) create mode 100644 static/scripts/libs/backbone.js create mode 100644 static/scripts/libs/handlebars-1.0.0.beta.6.js create mode 100644 static/scripts/libs/underscore.js create mode 100644 static/scripts/packed/libs/backbone.js create mode 100644 static/scripts/packed/libs/handlebars-1.0.0.beta.6.js create mode 100644 static/scripts/packed/libs/underscore.js diff --git a/static/scripts/libs/backbone.js b/static/scripts/libs/backbone.js new file mode 100644 index 00000000000..3373c952bfa --- /dev/null +++ b/static/scripts/libs/backbone.js @@ -0,0 +1,1431 @@ +// Backbone.js 0.9.2 + +// (c) 2010-2012 Jeremy Ashkenas, DocumentCloud Inc. +// Backbone may be freely distributed under the MIT license. +// For all details and documentation: +// http://backbonejs.org + +(function(){ + + // Initial Setup + // ------------- + + // Save a reference to the global object (`window` in the browser, `global` + // on the server). + var root = this; + + // Save the previous value of the `Backbone` variable, so that it can be + // restored later on, if `noConflict` is used. + var previousBackbone = root.Backbone; + + // Create a local reference to slice/splice. + var slice = Array.prototype.slice; + var splice = Array.prototype.splice; + + // The top-level namespace. All public Backbone classes and modules will + // be attached to this. Exported for both CommonJS and the browser. + var Backbone; + if (typeof exports !== 'undefined') { + Backbone = exports; + } else { + Backbone = root.Backbone = {}; + } + + // Current version of the library. Keep in sync with `package.json`. + Backbone.VERSION = '0.9.2'; + + // Require Underscore, if we're on the server, and it's not already present. + var _ = root._; + if (!_ && (typeof require !== 'undefined')) _ = require('underscore'); + + // For Backbone's purposes, jQuery, Zepto, or Ender owns the `$` variable. + var $ = root.jQuery || root.Zepto || root.ender; + + // Set the JavaScript library that will be used for DOM manipulation and + // Ajax calls (a.k.a. the `$` variable). By default Backbone will use: jQuery, + // Zepto, or Ender; but the `setDomLibrary()` method lets you inject an + // alternate JavaScript library (or a mock library for testing your views + // outside of a browser). + Backbone.setDomLibrary = function(lib) { + $ = lib; + }; + + // Runs Backbone.js in *noConflict* mode, returning the `Backbone` variable + // to its previous owner. Returns a reference to this Backbone object. + Backbone.noConflict = function() { + root.Backbone = previousBackbone; + return this; + }; + + // Turn on `emulateHTTP` to support legacy HTTP servers. Setting this option + // will fake `"PUT"` and `"DELETE"` requests via the `_method` parameter and + // set a `X-Http-Method-Override` header. + Backbone.emulateHTTP = false; + + // Turn on `emulateJSON` to support legacy servers that can't deal with direct + // `application/json` requests ... will encode the body as + // `application/x-www-form-urlencoded` instead and will send the model in a + // form param named `model`. + Backbone.emulateJSON = false; + + // Backbone.Events + // ----------------- + + // Regular expression used to split event strings + var eventSplitter = /\s+/; + + // A module that can be mixed in to *any object* in order to provide it with + // custom events. You may bind with `on` or remove with `off` callback functions + // to an event; trigger`-ing an event fires all callbacks in succession. + // + // var object = {}; + // _.extend(object, Backbone.Events); + // object.on('expand', function(){ alert('expanded'); }); + // object.trigger('expand'); + // + var Events = Backbone.Events = { + + // Bind one or more space separated events, `events`, to a `callback` + // function. Passing `"all"` will bind the callback to all events fired. + on: function(events, callback, context) { + + var calls, event, node, tail, list; + if (!callback) return this; + events = events.split(eventSplitter); + calls = this._callbacks || (this._callbacks = {}); + + // Create an immutable callback list, allowing traversal during + // modification. The tail is an empty object that will always be used + // as the next node. + while (event = events.shift()) { + list = calls[event]; + node = list ? list.tail : {}; + node.next = tail = {}; + node.context = context; + node.callback = callback; + calls[event] = {tail: tail, next: list ? list.next : node}; + } + + return this; + }, + + // Remove one or many callbacks. If `context` is null, removes all callbacks + // with that function. If `callback` is null, removes all callbacks for the + // event. If `events` is null, removes all bound callbacks for all events. + off: function(events, callback, context) { + var event, calls, node, tail, cb, ctx; + + // No events, or removing *all* events. + if (!(calls = this._callbacks)) return; + if (!(events || callback || context)) { + delete this._callbacks; + return this; + } + + // Loop through the listed events and contexts, splicing them out of the + // linked list of callbacks if appropriate. + events = events ? events.split(eventSplitter) : _.keys(calls); + while (event = events.shift()) { + node = calls[event]; + delete calls[event]; + if (!node || !(callback || context)) continue; + // Create a new list, omitting the indicated callbacks. + tail = node.tail; + while ((node = node.next) !== tail) { + cb = node.callback; + ctx = node.context; + if ((callback && cb !== callback) || (context && ctx !== context)) { + this.on(event, cb, ctx); + } + } + } + + return this; + }, + + // Trigger one or many events, firing all bound callbacks. Callbacks are + // passed the same arguments as `trigger` is, apart from the event name + // (unless you're listening on `"all"`, which will cause your callback to + // receive the true name of the event as the first argument). + trigger: function(events) { + var event, node, calls, tail, args, all, rest; + if (!(calls = this._callbacks)) return this; + all = calls.all; + events = events.split(eventSplitter); + rest = slice.call(arguments, 1); + + // For each event, walk through the linked list of callbacks twice, + // first to trigger the event, then to trigger any `"all"` callbacks. + while (event = events.shift()) { + if (node = calls[event]) { + tail = node.tail; + while ((node = node.next) !== tail) { + node.callback.apply(node.context || this, rest); + } + } + if (node = all) { + tail = node.tail; + args = [event].concat(rest); + while ((node = node.next) !== tail) { + node.callback.apply(node.context || this, args); + } + } + } + + return this; + } + + }; + + // Aliases for backwards compatibility. + Events.bind = Events.on; + Events.unbind = Events.off; + + // Backbone.Model + // -------------- + + // Create a new model, with defined attributes. A client id (`cid`) + // is automatically generated and assigned for you. + var Model = Backbone.Model = function(attributes, options) { + var defaults; + attributes || (attributes = {}); + if (options && options.parse) attributes = this.parse(attributes); + if (defaults = getValue(this, 'defaults')) { + attributes = _.extend({}, defaults, attributes); + } + if (options && options.collection) this.collection = options.collection; + this.attributes = {}; + this._escapedAttributes = {}; + this.cid = _.uniqueId('c'); + this.changed = {}; + this._silent = {}; + this._pending = {}; + this.set(attributes, {silent: true}); + // Reset change tracking. + this.changed = {}; + this._silent = {}; + this._pending = {}; + this._previousAttributes = _.clone(this.attributes); + this.initialize.apply(this, arguments); + }; + + // Attach all inheritable methods to the Model prototype. + _.extend(Model.prototype, Events, { + + // A hash of attributes whose current and previous value differ. + changed: null, + + // A hash of attributes that have silently changed since the last time + // `change` was called. Will become pending attributes on the next call. + _silent: null, + + // A hash of attributes that have changed since the last `'change'` event + // began. + _pending: null, + + // The default name for the JSON `id` attribute is `"id"`. MongoDB and + // CouchDB users may want to set this to `"_id"`. + idAttribute: 'id', + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // Return a copy of the model's `attributes` object. + toJSON: function(options) { + return _.clone(this.attributes); + }, + + // Get the value of an attribute. + get: function(attr) { + return this.attributes[attr]; + }, + + // Get the HTML-escaped value of an attribute. + escape: function(attr) { + var html; + if (html = this._escapedAttributes[attr]) return html; + var val = this.get(attr); + return this._escapedAttributes[attr] = _.escape(val == null ? '' : '' + val); + }, + + // Returns `true` if the attribute contains a value that is not null + // or undefined. + has: function(attr) { + return this.get(attr) != null; + }, + + // Set a hash of model attributes on the object, firing `"change"` unless + // you choose to silence it. + set: function(key, value, options) { + var attrs, attr, val; + + // Handle both `"key", value` and `{key: value}` -style arguments. + if (_.isObject(key) || key == null) { + attrs = key; + options = value; + } else { + attrs = {}; + attrs[key] = value; + } + + // Extract attributes and options. + options || (options = {}); + if (!attrs) return this; + if (attrs instanceof Model) attrs = attrs.attributes; + if (options.unset) for (attr in attrs) attrs[attr] = void 0; + + // Run validation. + if (!this._validate(attrs, options)) return false; + + // Check for changes of `id`. + if (this.idAttribute in attrs) this.id = attrs[this.idAttribute]; + + var changes = options.changes = {}; + var now = this.attributes; + var escaped = this._escapedAttributes; + var prev = this._previousAttributes || {}; + + // For each `set` attribute... + for (attr in attrs) { + val = attrs[attr]; + + // If the new and current value differ, record the change. + if (!_.isEqual(now[attr], val) || (options.unset && _.has(now, attr))) { + delete escaped[attr]; + (options.silent ? this._silent : changes)[attr] = true; + } + + // Update or delete the current value. + options.unset ? delete now[attr] : now[attr] = val; + + // If the new and previous value differ, record the change. If not, + // then remove changes for this attribute. + if (!_.isEqual(prev[attr], val) || (_.has(now, attr) != _.has(prev, attr))) { + this.changed[attr] = val; + if (!options.silent) this._pending[attr] = true; + } else { + delete this.changed[attr]; + delete this._pending[attr]; + } + } + + // Fire the `"change"` events. + if (!options.silent) this.change(options); + return this; + }, + + // Remove an attribute from the model, firing `"change"` unless you choose + // to silence it. `unset` is a noop if the attribute doesn't exist. + unset: function(attr, options) { + (options || (options = {})).unset = true; + return this.set(attr, null, options); + }, + + // Clear all attributes on the model, firing `"change"` unless you choose + // to silence it. + clear: function(options) { + (options || (options = {})).unset = true; + return this.set(_.clone(this.attributes), options); + }, + + // Fetch the model from the server. If the server's representation of the + // model differs from its current attributes, they will be overriden, + // triggering a `"change"` event. + fetch: function(options) { + options = options ? _.clone(options) : {}; + var model = this; + var success = options.success; + options.success = function(resp, status, xhr) { + if (!model.set(model.parse(resp, xhr), options)) return false; + if (success) success(model, resp); + }; + options.error = Backbone.wrapError(options.error, model, options); + return (this.sync || Backbone.sync).call(this, 'read', this, options); + }, + + // Set a hash of model attributes, and sync the model to the server. + // If the server returns an attributes hash that differs, the model's + // state will be `set` again. + save: function(key, value, options) { + var attrs, current; + + // Handle both `("key", value)` and `({key: value})` -style calls. + if (_.isObject(key) || key == null) { + attrs = key; + options = value; + } else { + attrs = {}; + attrs[key] = value; + } + options = options ? _.clone(options) : {}; + + // If we're "wait"-ing to set changed attributes, validate early. + if (options.wait) { + if (!this._validate(attrs, options)) return false; + current = _.clone(this.attributes); + } + + // Regular saves `set` attributes before persisting to the server. + var silentOptions = _.extend({}, options, {silent: true}); + if (attrs && !this.set(attrs, options.wait ? silentOptions : options)) { + return false; + } + + // After a successful server-side save, the client is (optionally) + // updated with the server-side state. + var model = this; + var success = options.success; + options.success = function(resp, status, xhr) { + var serverAttrs = model.parse(resp, xhr); + if (options.wait) { + delete options.wait; + serverAttrs = _.extend(attrs || {}, serverAttrs); + } + if (!model.set(serverAttrs, options)) return false; + if (success) { + success(model, resp); + } else { + model.trigger('sync', model, resp, options); + } + }; + + // Finish configuring and sending the Ajax request. + options.error = Backbone.wrapError(options.error, model, options); + var method = this.isNew() ? 'create' : 'update'; + var xhr = (this.sync || Backbone.sync).call(this, method, this, options); + if (options.wait) this.set(current, silentOptions); + return xhr; + }, + + // Destroy this model on the server if it was already persisted. + // Optimistically removes the model from its collection, if it has one. + // If `wait: true` is passed, waits for the server to respond before removal. + destroy: function(options) { + options = options ? _.clone(options) : {}; + var model = this; + var success = options.success; + + var triggerDestroy = function() { + model.trigger('destroy', model, model.collection, options); + }; + + if (this.isNew()) { + triggerDestroy(); + return false; + } + + options.success = function(resp) { + if (options.wait) triggerDestroy(); + if (success) { + success(model, resp); + } else { + model.trigger('sync', model, resp, options); + } + }; + + options.error = Backbone.wrapError(options.error, model, options); + var xhr = (this.sync || Backbone.sync).call(this, 'delete', this, options); + if (!options.wait) triggerDestroy(); + return xhr; + }, + + // Default URL for the model's representation on the server -- if you're + // using Backbone's restful methods, override this to change the endpoint + // that will be called. + url: function() { + var base = getValue(this, 'urlRoot') || getValue(this.collection, 'url') || urlError(); + if (this.isNew()) return base; + return base + (base.charAt(base.length - 1) == '/' ? '' : '/') + encodeURIComponent(this.id); + }, + + // **parse** converts a response into the hash of attributes to be `set` on + // the model. The default implementation is just to pass the response along. + parse: function(resp, xhr) { + return resp; + }, + + // Create a new model with identical attributes to this one. + clone: function() { + return new this.constructor(this.attributes); + }, + + // A model is new if it has never been saved to the server, and lacks an id. + isNew: function() { + return this.id == null; + }, + + // Call this method to manually fire a `"change"` event for this model and + // a `"change:attribute"` event for each changed attribute. + // Calling this will cause all objects observing the model to update. + change: function(options) { + options || (options = {}); + var changing = this._changing; + this._changing = true; + + // Silent changes become pending changes. + for (var attr in this._silent) this._pending[attr] = true; + + // Silent changes are triggered. + var changes = _.extend({}, options.changes, this._silent); + this._silent = {}; + for (var attr in changes) { + this.trigger('change:' + attr, this, this.get(attr), options); + } + if (changing) return this; + + // Continue firing `"change"` events while there are pending changes. + while (!_.isEmpty(this._pending)) { + this._pending = {}; + this.trigger('change', this, options); + // Pending and silent changes still remain. + for (var attr in this.changed) { + if (this._pending[attr] || this._silent[attr]) continue; + delete this.changed[attr]; + } + this._previousAttributes = _.clone(this.attributes); + } + + this._changing = false; + return this; + }, + + // Determine if the model has changed since the last `"change"` event. + // If you specify an attribute name, determine if that attribute has changed. + hasChanged: function(attr) { + if (!arguments.length) return !_.isEmpty(this.changed); + return _.has(this.changed, attr); + }, + + // Return an object containing all the attributes that have changed, or + // false if there are no changed attributes. Useful for determining what + // parts of a view need to be updated and/or what attributes need to be + // persisted to the server. Unset attributes will be set to undefined. + // You can also pass an attributes object to diff against the model, + // determining if there *would be* a change. + changedAttributes: function(diff) { + if (!diff) return this.hasChanged() ? _.clone(this.changed) : false; + var val, changed = false, old = this._previousAttributes; + for (var attr in diff) { + if (_.isEqual(old[attr], (val = diff[attr]))) continue; + (changed || (changed = {}))[attr] = val; + } + return changed; + }, + + // Get the previous value of an attribute, recorded at the time the last + // `"change"` event was fired. + previous: function(attr) { + if (!arguments.length || !this._previousAttributes) return null; + return this._previousAttributes[attr]; + }, + + // Get all of the attributes of the model at the time of the previous + // `"change"` event. + previousAttributes: function() { + return _.clone(this._previousAttributes); + }, + + // Check if the model is currently in a valid state. It's only possible to + // get into an *invalid* state if you're using silent changes. + isValid: function() { + return !this.validate(this.attributes); + }, + + // Run validation against the next complete set of model attributes, + // returning `true` if all is well. If a specific `error` callback has + // been passed, call that instead of firing the general `"error"` event. + _validate: function(attrs, options) { + if (options.silent || !this.validate) return true; + attrs = _.extend({}, this.attributes, attrs); + var error = this.validate(attrs, options); + if (!error) return true; + if (options && options.error) { + options.error(this, error, options); + } else { + this.trigger('error', this, error, options); + } + return false; + } + + }); + + // Backbone.Collection + // ------------------- + + // Provides a standard collection class for our sets of models, ordered + // or unordered. If a `comparator` is specified, the Collection will maintain + // its models in sort order, as they're added and removed. + var Collection = Backbone.Collection = function(models, options) { + options || (options = {}); + if (options.model) this.model = options.model; + if (options.comparator) this.comparator = options.comparator; + this._reset(); + this.initialize.apply(this, arguments); + if (models) this.reset(models, {silent: true, parse: options.parse}); + }; + + // Define the Collection's inheritable methods. + _.extend(Collection.prototype, Events, { + + // The default model for a collection is just a **Backbone.Model**. + // This should be overridden in most cases. + model: Model, + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // The JSON representation of a Collection is an array of the + // models' attributes. + toJSON: function(options) { + return this.map(function(model){ return model.toJSON(options); }); + }, + + // Add a model, or list of models to the set. Pass **silent** to avoid + // firing the `add` event for every new model. + add: function(models, options) { + var i, index, length, model, cid, id, cids = {}, ids = {}, dups = []; + options || (options = {}); + models = _.isArray(models) ? models.slice() : [models]; + + // Begin by turning bare objects into model references, and preventing + // invalid models or duplicate models from being added. + for (i = 0, length = models.length; i < length; i++) { + if (!(model = models[i] = this._prepareModel(models[i], options))) { + throw new Error("Can't add an invalid model to a collection"); + } + cid = model.cid; + id = model.id; + if (cids[cid] || this._byCid[cid] || ((id != null) && (ids[id] || this._byId[id]))) { + dups.push(i); + continue; + } + cids[cid] = ids[id] = model; + } + + // Remove duplicates. + i = dups.length; + while (i--) { + models.splice(dups[i], 1); + } + + // Listen to added models' events, and index models for lookup by + // `id` and by `cid`. + for (i = 0, length = models.length; i < length; i++) { + (model = models[i]).on('all', this._onModelEvent, this); + this._byCid[model.cid] = model; + if (model.id != null) this._byId[model.id] = model; + } + + // Insert models into the collection, re-sorting if needed, and triggering + // `add` events unless silenced. + this.length += length; + index = options.at != null ? options.at : this.models.length; + splice.apply(this.models, [index, 0].concat(models)); + if (this.comparator) this.sort({silent: true}); + if (options.silent) return this; + for (i = 0, length = this.models.length; i < length; i++) { + if (!cids[(model = this.models[i]).cid]) continue; + options.index = i; + model.trigger('add', model, this, options); + } + return this; + }, + + // Remove a model, or a list of models from the set. Pass silent to avoid + // firing the `remove` event for every model removed. + remove: function(models, options) { + var i, l, index, model; + options || (options = {}); + models = _.isArray(models) ? models.slice() : [models]; + for (i = 0, l = models.length; i < l; i++) { + model = this.getByCid(models[i]) || this.get(models[i]); + if (!model) continue; + delete this._byId[model.id]; + delete this._byCid[model.cid]; + index = this.indexOf(model); + this.models.splice(index, 1); + this.length--; + if (!options.silent) { + options.index = index; + model.trigger('remove', model, this, options); + } + this._removeReference(model); + } + return this; + }, + + // Add a model to the end of the collection. + push: function(model, options) { + model = this._prepareModel(model, options); + this.add(model, options); + return model; + }, + + // Remove a model from the end of the collection. + pop: function(options) { + var model = this.at(this.length - 1); + this.remove(model, options); + return model; + }, + + // Add a model to the beginning of the collection. + unshift: function(model, options) { + model = this._prepareModel(model, options); + this.add(model, _.extend({at: 0}, options)); + return model; + }, + + // Remove a model from the beginning of the collection. + shift: function(options) { + var model = this.at(0); + this.remove(model, options); + return model; + }, + + // Get a model from the set by id. + get: function(id) { + if (id == null) return void 0; + return this._byId[id.id != null ? id.id : id]; + }, + + // Get a model from the set by client id. + getByCid: function(cid) { + return cid && this._byCid[cid.cid || cid]; + }, + + // Get the model at the given index. + at: function(index) { + return this.models[index]; + }, + + // Return models with matching attributes. Useful for simple cases of `filter`. + where: function(attrs) { + if (_.isEmpty(attrs)) return []; + return this.filter(function(model) { + for (var key in attrs) { + if (attrs[key] !== model.get(key)) return false; + } + return true; + }); + }, + + // Force the collection to re-sort itself. You don't need to call this under + // normal circumstances, as the set will maintain sort order as each item + // is added. + sort: function(options) { + options || (options = {}); + if (!this.comparator) throw new Error('Cannot sort a set without a comparator'); + var boundComparator = _.bind(this.comparator, this); + if (this.comparator.length == 1) { + this.models = this.sortBy(boundComparator); + } else { + this.models.sort(boundComparator); + } + if (!options.silent) this.trigger('reset', this, options); + return this; + }, + + // Pluck an attribute from each model in the collection. + pluck: function(attr) { + return _.map(this.models, function(model){ return model.get(attr); }); + }, + + // When you have more items than you want to add or remove individually, + // you can reset the entire set with a new list of models, without firing + // any `add` or `remove` events. Fires `reset` when finished. + reset: function(models, options) { + models || (models = []); + options || (options = {}); + for (var i = 0, l = this.models.length; i < l; i++) { + this._removeReference(this.models[i]); + } + this._reset(); + this.add(models, _.extend({silent: true}, options)); + if (!options.silent) this.trigger('reset', this, options); + return this; + }, + + // Fetch the default set of models for this collection, resetting the + // collection when they arrive. If `add: true` is passed, appends the + // models to the collection instead of resetting. + fetch: function(options) { + options = options ? _.clone(options) : {}; + if (options.parse === undefined) options.parse = true; + var collection = this; + var success = options.success; + options.success = function(resp, status, xhr) { + collection[options.add ? 'add' : 'reset'](collection.parse(resp, xhr), options); + if (success) success(collection, resp); + }; + options.error = Backbone.wrapError(options.error, collection, options); + return (this.sync || Backbone.sync).call(this, 'read', this, options); + }, + + // Create a new instance of a model in this collection. Add the model to the + // collection immediately, unless `wait: true` is passed, in which case we + // wait for the server to agree. + create: function(model, options) { + var coll = this; + options = options ? _.clone(options) : {}; + model = this._prepareModel(model, options); + if (!model) return false; + if (!options.wait) coll.add(model, options); + var success = options.success; + options.success = function(nextModel, resp, xhr) { + if (options.wait) coll.add(nextModel, options); + if (success) { + success(nextModel, resp); + } else { + nextModel.trigger('sync', model, resp, options); + } + }; + model.save(null, options); + return model; + }, + + // **parse** converts a response into a list of models to be added to the + // collection. The default implementation is just to pass it through. + parse: function(resp, xhr) { + return resp; + }, + + // Proxy to _'s chain. Can't be proxied the same way the rest of the + // underscore methods are proxied because it relies on the underscore + // constructor. + chain: function () { + return _(this.models).chain(); + }, + + // Reset all internal state. Called when the collection is reset. + _reset: function(options) { + this.length = 0; + this.models = []; + this._byId = {}; + this._byCid = {}; + }, + + // Prepare a model or hash of attributes to be added to this collection. + _prepareModel: function(model, options) { + options || (options = {}); + if (!(model instanceof Model)) { + var attrs = model; + options.collection = this; + model = new this.model(attrs, options); + if (!model._validate(model.attributes, options)) model = false; + } else if (!model.collection) { + model.collection = this; + } + return model; + }, + + // Internal method to remove a model's ties to a collection. + _removeReference: function(model) { + if (this == model.collection) { + delete model.collection; + } + model.off('all', this._onModelEvent, this); + }, + + // Internal method called every time a model in the set fires an event. + // Sets need to update their indexes when models change ids. All other + // events simply proxy through. "add" and "remove" events that originate + // in other collections are ignored. + _onModelEvent: function(event, model, collection, options) { + if ((event == 'add' || event == 'remove') && collection != this) return; + if (event == 'destroy') { + this.remove(model, options); + } + if (model && event === 'change:' + model.idAttribute) { + delete this._byId[model.previous(model.idAttribute)]; + this._byId[model.id] = model; + } + this.trigger.apply(this, arguments); + } + + }); + + // Underscore methods that we want to implement on the Collection. + var methods = ['forEach', 'each', 'map', 'reduce', 'reduceRight', 'find', + 'detect', 'filter', 'select', 'reject', 'every', 'all', 'some', 'any', + 'include', 'contains', 'invoke', 'max', 'min', 'sortBy', 'sortedIndex', + 'toArray', 'size', 'first', 'initial', 'rest', 'last', 'without', 'indexOf', + 'shuffle', 'lastIndexOf', 'isEmpty', 'groupBy']; + + // Mix in each Underscore method as a proxy to `Collection#models`. + _.each(methods, function(method) { + Collection.prototype[method] = function() { + return _[method].apply(_, [this.models].concat(_.toArray(arguments))); + }; + }); + + // Backbone.Router + // ------------------- + + // Routers map faux-URLs to actions, and fire events when routes are + // matched. Creating a new one sets its `routes` hash, if not set statically. + var Router = Backbone.Router = function(options) { + options || (options = {}); + if (options.routes) this.routes = options.routes; + this._bindRoutes(); + this.initialize.apply(this, arguments); + }; + + // Cached regular expressions for matching named param parts and splatted + // parts of route strings. + var namedParam = /:\w+/g; + var splatParam = /\*\w+/g; + var escapeRegExp = /[-[\]{}()+?.,\\^$|#\s]/g; + + // Set up all inheritable **Backbone.Router** properties and methods. + _.extend(Router.prototype, Events, { + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // Manually bind a single named route to a callback. For example: + // + // this.route('search/:query/p:num', 'search', function(query, num) { + // ... + // }); + // + route: function(route, name, callback) { + Backbone.history || (Backbone.history = new History); + if (!_.isRegExp(route)) route = this._routeToRegExp(route); + if (!callback) callback = this[name]; + Backbone.history.route(route, _.bind(function(fragment) { + var args = this._extractParameters(route, fragment); + callback && callback.apply(this, args); + this.trigger.apply(this, ['route:' + name].concat(args)); + Backbone.history.trigger('route', this, name, args); + }, this)); + return this; + }, + + // Simple proxy to `Backbone.history` to save a fragment into the history. + navigate: function(fragment, options) { + Backbone.history.navigate(fragment, options); + }, + + // Bind all defined routes to `Backbone.history`. We have to reverse the + // order of the routes here to support behavior where the most general + // routes can be defined at the bottom of the route map. + _bindRoutes: function() { + if (!this.routes) return; + var routes = []; + for (var route in this.routes) { + routes.unshift([route, this.routes[route]]); + } + for (var i = 0, l = routes.length; i < l; i++) { + this.route(routes[i][0], routes[i][1], this[routes[i][1]]); + } + }, + + // Convert a route string into a regular expression, suitable for matching + // against the current location hash. + _routeToRegExp: function(route) { + route = route.replace(escapeRegExp, '\\$&') + .replace(namedParam, '([^\/]+)') + .replace(splatParam, '(.*?)'); + return new RegExp('^' + route + '$'); + }, + + // Given a route, and a URL fragment that it matches, return the array of + // extracted parameters. + _extractParameters: function(route, fragment) { + return route.exec(fragment).slice(1); + } + + }); + + // Backbone.History + // ---------------- + + // Handles cross-browser history management, based on URL fragments. If the + // browser does not support `onhashchange`, falls back to polling. + var History = Backbone.History = function() { + this.handlers = []; + _.bindAll(this, 'checkUrl'); + }; + + // Cached regex for cleaning leading hashes and slashes . + var routeStripper = /^[#\/]/; + + // Cached regex for detecting MSIE. + var isExplorer = /msie [\w.]+/; + + // Has the history handling already been started? + History.started = false; + + // Set up all inheritable **Backbone.History** properties and methods. + _.extend(History.prototype, Events, { + + // The default interval to poll for hash changes, if necessary, is + // twenty times a second. + interval: 50, + + // Gets the true hash value. Cannot use location.hash directly due to bug + // in Firefox where location.hash will always be decoded. + getHash: function(windowOverride) { + var loc = windowOverride ? windowOverride.location : window.location; + var match = loc.href.match(/#(.*)$/); + return match ? match[1] : ''; + }, + + // Get the cross-browser normalized URL fragment, either from the URL, + // the hash, or the override. + getFragment: function(fragment, forcePushState) { + if (fragment == null) { + if (this._hasPushState || forcePushState) { + fragment = window.location.pathname; + var search = window.location.search; + if (search) fragment += search; + } else { + fragment = this.getHash(); + } + } + if (!fragment.indexOf(this.options.root)) fragment = fragment.substr(this.options.root.length); + return fragment.replace(routeStripper, ''); + }, + + // Start the hash change handling, returning `true` if the current URL matches + // an existing route, and `false` otherwise. + start: function(options) { + if (History.started) throw new Error("Backbone.history has already been started"); + History.started = true; + + // Figure out the initial configuration. Do we need an iframe? + // Is pushState desired ... is it available? + this.options = _.extend({}, {root: '/'}, this.options, options); + this._wantsHashChange = this.options.hashChange !== false; + this._wantsPushState = !!this.options.pushState; + this._hasPushState = !!(this.options.pushState && window.history && window.history.pushState); + var fragment = this.getFragment(); + var docMode = document.documentMode; + var oldIE = (isExplorer.exec(navigator.userAgent.toLowerCase()) && (!docMode || docMode <= 7)); + + if (oldIE) { + this.iframe = $('" ) ); + show_modal( null, $( "
" ) ); $("#close_button").bind( "click", function() { hide_modal(); } ); } diff --git a/static/scripts/galaxy.workflow_editor.canvas.js b/static/scripts/galaxy.workflow_editor.canvas.js index ea60b600c03..45113cbb77b 100644 --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -188,7 +188,7 @@ $.extend( Node.prototype, { .appendTo( "body" ) .append( $("
").append( - $("").attr("src", image_path + '/delete_icon.png').click( function() { + $("").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function() { $.each( terminal.connectors, function( _, x ) { x.destroy(); }); @@ -335,13 +335,13 @@ $.extend( Node.prototype, { .css( { display: 'none' } ) .append( $("
").append( - $("").attr('src', image_path + '/fugue/asterisk-small-outline.png').click( function() { + $("").attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png').click( function() { if ($.inArray(output.name, node.workflow_outputs) != -1){ node.workflow_outputs.splice($.inArray(output.name, node.workflow_outputs), 1); - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ node.workflow_outputs.push(output.name); - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } workflow.has_changes = true; canvas_manager.draw_overview(); @@ -355,19 +355,19 @@ $.extend( Node.prototype, { callout.show(); r.append(callout); if ($.inArray(output.name, node.workflow_outputs) === -1){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } r.hover( function(){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-yellow.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-yellow.png'); }, function(){ if ($.inArray(output.name, node.workflow_outputs) === -1){ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small-outline.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png'); }else{ - callout.find('img').attr('src', image_path + '/fugue/asterisk-small.png'); + callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png'); } }); } @@ -793,18 +793,18 @@ function prebuild_node( type, title_text, tool_id ) { f.append( title ); f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 ); var b = $("
"); - var tmp = "
loading tool info...
"; + var tmp = "
loading tool info...
"; b.append( tmp ); node.form_html = tmp; f.append( b ); // Fix width to computed width // Now add floats var buttons = $("
"); - buttons.append( $("").attr("src", image_path + '/delete_icon.png').click( function( e ) { + buttons.append( $("").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function( e ) { node.destroy(); } ).hover( - function() { $(this).attr( "src", image_path + "/delete_icon_dark.png" ); }, - function() { $(this).attr( "src", image_path + "/delete_icon.png" ); } + function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon_dark.png" ); }, + function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon.png" ); } ) ); // Place inside container f.appendTo( "#canvas-container" ); diff --git a/static/scripts/packed/backbone/ui.js b/static/scripts/packed/backbone/ui.js index 49bbafe2528..f3140ca7d17 100644 --- a/static/scripts/packed/backbone/ui.js +++ b/static/scripts/packed/backbone/ui.js @@ -1 +1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonView=Backbone.View.extend({tagName:"a",className:"icon-button menu-button",events:{click:"on_click"},render:function(){this.$el.attr("href","javascript:void(0)").attr("title",this.model.attributes.title).addClass(this.model.attributes.icon_class);return this},on_click:function(){this.model.attributes.on_click()}});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(c){var b=new IconButtonView({model:c});b.render();a.$el.append(b.$el)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file +var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.panels.js b/static/scripts/packed/galaxy.panels.js index 91d8692d43a..09dabfd8f9f 100644 --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1 +1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("
").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("
")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("
"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("
").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("
")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("
"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.workflow_editor.canvas.js b/static/scripts/packed/galaxy.workflow_editor.canvas.js index f5fd235a17e..14531559790 100644 --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1 +1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("
").css({display:"none"}).appendTo("body").append($("
").append($("").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('
').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("
").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("
");d.enable_input_terminal(j,f.name,f.extensions);var b=$("
"+f.label+"
");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("
"))}$.each(h.data_outputs,function(k,b){var j=$("
");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("
"+f+"
");if(d.type=="tool"){var l=$("
").css({display:"none"}).append($("
").append($("").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("
");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("
");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("
"+j.label+"
").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="
"+d+"
";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("
No node selected
")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("
");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("
"+j+"
");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("
");var h="
loading tool info...
";m.append(h);g.form_html=h;i.append(m);var k=$("
");k.append($("").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-qA){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-qu){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("
").css({display:"none"}).appendTo("body").append($("
").append($("").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('
').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("
").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("
");d.enable_input_terminal(j,f.name,f.extensions);var b=$("
"+f.label+"
");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("
"))}$.each(h.data_outputs,function(k,b){var j=$("
");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("
"+f+"
");if(d.type=="tool"){var l=$("
").css({display:"none"}).append($("
").append($("").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("
");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("
");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("
"+j.label+"
").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="
"+d+"
";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("
No node selected
")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("
");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("
"+j+"
");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("
");var h="
loading tool info...
";m.append(h);g.form_html=h;i.append(m);var k=$("
");k.append($("").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-qA){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-qu){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js index 88f834ff579..f59b23ecbbe 100644 --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1 +1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;ec){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetYah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al=aq&&ap.offsetY<=ah){if(ap.offsetY-aq0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. If visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("
").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("
"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("
").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("
").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("
").addClass("track-header");ac.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac0){this.saved_filters_managers=[];for(var ac=0;ac").addClass("top-container").appendTo(ae);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("
").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container).hide();var af=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("
").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='';for(var ai=0,af=ac.chrom_data.length;ai'+ah+""}if(ag.prev_chroms){aj+='"}if(ag.next_chroms){aj+='"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;agac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ahthis.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("
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").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("
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").addClass("param-row").appendTo(this.parent_div);var ai=$("").attr("value","Run on complete dataset").appendTo(at);var ac=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA").addClass("filter-row slider-row");var ac=$("
").addClass("elt-label").appendTo(ad.parent_div),aj=$("").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("").text(this.low+"-"+this.high),af=$("").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("
").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("
").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("
").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("
").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;acthis.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.minac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("
").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai").addClass("param-row").appendTo(this.parent_div);var aj=$("").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("
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