galaxy-commits March 2012

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commit/galaxy-central: greg: Fixes for tool shed changeset revision select field generation.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7dc0e48e9105/ changeset: 7dc0e48e9105 user: greg date: 2012-03-27 15:45:18 summary: Fixes for tool shed changeset revision select field generation. affected #: 1 file diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 7dc0e48e9105f19a564263c54684d51bee8ac16e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -997,16 +997,24 @@ """ 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 @@ 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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove duplicate hr style; this reinstates dashed lines between sections in help text.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cb5ff5b1bd67/ changeset: cb5ff5b1bd67 user: jgoecks date: 2012-03-27 14:49:44 summary: Remove duplicate hr style; this reinstates dashed lines between sections in help text. affected #: 2 files diff -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1616,13 +1616,6 @@ margin-left: 10px; } -hr -{ - border: none; - height: 0px; - margin-top: 0px; -} - div.toolSectionPad { margin: 0; diff -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -734,7 +734,6 @@ 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;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for ordering the options of the select list displaying change sets for a tool shed repository.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8aa5dfcbbb08/ changeset: 8aa5dfcbbb08 user: greg date: 2012-03-26 21:43:27 summary: Fix for ordering the options of the select list displaying change sets for a tool shed repository. affected #: 1 file diff -r 29f8601357203ad282f3848b2fa2c144ef6980f2 -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1003,6 +1003,10 @@ 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 @@ 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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: allow limiting the number of data lines used to determine column data types while still counting all data lines
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29f860135720/ changeset: 29f860135720 user: richard_burhans date: 2012-03-26 19:55:05 summary: allow limiting the number of data lines used to determine column data types while still counting all data lines affected #: 1 file diff -r 6b8535e5b03001cc25e55f05b391fafacbf56b8e -r 29f8601357203ad282f3848b2fa2c144ef6980f2 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -26,7 +26,7 @@ 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 @@ 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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: 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.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6b8535e5b030/ changeset: 6b8535e5b030 user: greg date: 2012-03-26 19:27:17 summary: 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. affected #: 1 file diff -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 -r 6b8535e5b03001cc25e55f05b391fafacbf56b8e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -238,16 +238,6 @@ 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 <toolbox> 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 ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Refactor changeset 164eef0d7693 to use less templates.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba51ed3cf084/ changeset: ba51ed3cf084 user: jgoecks date: 2012-03-26 18:34:15 summary: Refactor changeset 164eef0d7693 to use less templates. affected #: 2 files diff -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -9,12 +9,12 @@ 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 @@ .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 -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 static/june_2007_style/bootstrap/reset.less --- a/static/june_2007_style/bootstrap/reset.less +++ b/static/june_2007_style/bootstrap/reset.less @@ -93,6 +93,11 @@ 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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use show/hide framework to manage reference track.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c401bfbbdcc7/ changeset: c401bfbbdcc7 user: jgoecks date: 2012-03-26 16:50:31 summary: Trackster: use show/hide framework to manage reference track. affected #: 1 file diff -r b17faef8f1f36dda41f44206805b35896ce57cdc -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4249,6 +4249,7 @@ 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 @@ 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 @@ 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(); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 26 Mar '12

26 Mar '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e5a58a1d3d90/ changeset: e5a58a1d3d90 user: jgoecks date: 2012-03-26 16:16:39 summary: Trackster: make show/hide content compatible with 8e9d2b492c4c. affected #: 1 file diff -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 -r e5a58a1d3d900105cdedd6ee9249d958834f60c3 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -393,8 +393,8 @@ 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.<br/>\ - You can save and close the visualization and preparation will continue.<br/>", + 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 @@ * 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 @@ } 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. https://bitbucket.org/galaxy/galaxy-central/changeset/3b396a26aaf6/ changeset: 3b396a26aaf6 user: jgoecks date: 2012-03-26 16:17:22 summary: Merge. affected #: 1 file diff -r e5a58a1d3d900105cdedd6ee9249d958834f60c3 -r 3b396a26aaf6d78480750e0a8d038a034153f887 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1183,7 +1183,7 @@ 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: https://bitbucket.org/galaxy/galaxy-central/changeset/b17faef8f1f3/ changeset: b17faef8f1f3 user: jgoecks date: 2012-03-26 16:18:09 summary: Add open ID config to .hgignore affected #: 1 file diff -r 3b396a26aaf6d78480750e0a8d038a034153f887 -r b17faef8f1f36dda41f44206805b35896ce57cdc .hgignore --- a/.hgignore +++ b/.hgignore @@ -36,6 +36,7 @@ tool_data_table_conf.xml tool_sheds_conf.xml integrated_tool_panel.xml +openid_conf.xml static/welcome.html.* static/welcome.html Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Strip whitespace around separators in start_job_runners
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fb39b478590/ changeset: 3fb39b478590 user: natefoo date: 2012-03-26 16:12:37 summary: Strip whitespace around separators in start_job_runners affected #: 1 file diff -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 -r 3fb39b478590de7f4547766bbd60f3c6f686ab60 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1183,7 +1183,7 @@ 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: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for bug introduced into Tool Shed with last OpenID commit.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a23e38b7a12/ changeset: 4a23e38b7a12 user: dan date: 2012-03-24 02:47:14 summary: Fix for bug introduced into Tool Shed with last OpenID commit. affected #: 1 file diff -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -3,6 +3,7 @@ import galaxy.quota import galaxy.datatypes.registry import galaxy.webapps.community.model +from galaxy.openid.providers import OpenIDProviders from galaxy.web import security from galaxy.tags.tag_handler import CommunityTagHandler @@ -42,5 +43,6 @@ # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) + self.openid_providers = OpenIDProviders() #TODO: Add OpenID support def shutdown( self ): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits March 2012