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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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commit/galaxy-central: dan: Remove print debug.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b27b1e42fc9/ changeset: 2b27b1e42fc9 user: dan date: 2012-03-24 01:50:32 summary: Remove print debug. affected #: 1 file diff -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 lib/galaxy/openid/providers.py --- a/lib/galaxy/openid/providers.py +++ b/lib/galaxy/openid/providers.py @@ -76,7 +76,6 @@ for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) - print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] else: raise Exception( 'Only sreg is currently supported.' ) trans.sa_session.add( trans.user ) 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: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b9e188c4ecba/ changeset: b9e188c4ecba user: dan date: 2012-03-23 18:41:01 summary: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed. affected #: 17 files diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -13,6 +13,7 @@ from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.tools.imp_exp import load_history_imp_exp_tools from galaxy.sample_tracking import external_service_types +from galaxy.openid.providers import OpenIDProviders class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -105,6 +106,9 @@ if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) + self.openid_providers = OpenIDProviders.from_file( self.config.openid_config ) + else: + self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -44,7 +44,9 @@ self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) + self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' ) self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/__init__.py --- /dev/null +++ b/lib/galaxy/openid/__init__.py @@ -0,0 +1,3 @@ +""" +OpenID functionality +""" \ No newline at end of file diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/providers.py --- /dev/null +++ b/lib/galaxy/openid/providers.py @@ -0,0 +1,118 @@ +""" +Contains OpenID provider functionality +""" + +import logging, os +from galaxy.util import parse_xml, string_as_bool +from galaxy.util.odict import odict + + +log = logging.getLogger( __name__ ) + +class OpenIDProvider( object ): + '''An OpenID Provider object.''' + @classmethod + def from_file( cls, filename ): + return cls.from_elem( parse_xml( filename ).getroot() ) + @classmethod + def from_elem( cls, xml_root ): + provider_elem = xml_root + provider_id = provider_elem.get( 'id', None ) + provider_name = provider_elem.get( 'name', provider_id ) + op_endpoint_url = provider_elem.find( 'op_endpoint_url' ) + if op_endpoint_url is not None: + op_endpoint_url = op_endpoint_url.text + assert (provider_id and provider_name and op_endpoint_url), Exception( "OpenID Provider improperly configured" ) + sreg_required = [] + sreg_optional = [] + use_for = {} + store_user_preference = {} + use_default_sreg = True + for elem in provider_elem.findall( 'sreg' ): + use_default_sreg = False + for field_elem in elem.findall( 'field' ): + sreg_name = field_elem.get( 'name' ) + assert sreg_name, Exception( 'A name is required for a sreg element' ) + if string_as_bool( field_elem.get( 'required' ) ): + sreg_required.append( sreg_name ) + else: + sreg_optional.append( sreg_name ) + for use_elem in field_elem.findall( 'use_for' ): + use_for[ use_elem.get( 'name' ) ] = sreg_name + for store_user_preference_elem in field_elem.findall( 'store_user_preference' ): + store_user_preference[ store_user_preference_elem.get( 'name' ) ] = sreg_name + if use_default_sreg: + sreg_required = None + sreg_optional = None + use_for = None + return cls( provider_id, provider_name, op_endpoint_url, sreg_required, sreg_optional, use_for, store_user_preference ) + def __init__( self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=None, use_for=None, store_user_preference=None ): + '''When sreg options are not specified, defaults are used.''' + self.id = id + self.name = name + self.op_endpoint_url = op_endpoint_url + if sreg_optional is None: + self.sreg_optional = [ 'nickname', 'email' ] + else: + self.sreg_optional = sreg_optional + if sreg_required: + self.sreg_required = sreg_required + else: + self.sreg_required = [] + if use_for is not None: + self.use_for = use_for + else: + self.use_for = {} + if 'nickname' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'username' ] = 'nickname' + if 'email' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'email' ] = 'email' + if store_user_preference: + self.store_user_preference = store_user_preference + else: + self.store_user_preference = {} + def post_authentication( self, trans, openid_manager, info ): + sreg_attributes = openid_manager.get_sreg( info ) + for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): + if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): + trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) + print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] + else: + raise Exception( 'Only sreg is currently supported.' ) + trans.sa_session.add( trans.user ) + trans.sa_session.flush() + +class OpenIDProviders( object ): + '''Collection of OpenID Providers''' + @classmethod + def from_file( cls, filename ): + try: + return cls.from_elem( parse_xml( filename ).getroot() ) + except Exception, e: + log.error( 'Failed to load OpenID Providers: %s' % ( e ) ) + return cls() + @classmethod + def from_elem( cls, xml_root ): + oid_elem = xml_root + providers = odict() + for elem in oid_elem.findall( 'provider' ): + try: + provider = OpenIDProvider.from_file( os.path.join( 'openid', elem.get( 'file' ) ) ) + providers[ provider.id ] = provider + log.debug( 'Loaded OpenID provider: %s (%s)' % ( provider.name, provider.id ) ) + except Exception, e: + log.error( 'Failed to add OpenID provider: %s' % ( e ) ) + return cls( providers ) + def __init__( self, providers=None ): + if providers: + self.providers = providers + else: + self.providers = odict() + def __iter__( self ): + for provider in self.providers.itervalues(): + yield provider + def get( self, name, default=None ): + if name in self.providers: + return self.providers[ name ] + else: + return default diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -11,6 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.web.framework.helpers import iff from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password +from galaxy.openid.providers import OpenIDProvider log = logging.getLogger( __name__ ) @@ -21,12 +22,6 @@ <p/> """ -OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', - 'Yahoo!' : 'http://yahoo.com', - 'AOL/AIM' : 'http://openid.aol.com', - 'Launchpad' : 'http://login.launchpad.net', - } - class UserOpenIDGrid( grids.Grid ): use_panels = False title = "OpenIDs linked to your account" @@ -68,19 +63,26 @@ if not referer: referer = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) - process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate ) - if not openid_url and openid_provider and openid_provider in OPENID_PROVIDERS: - openid_url = OPENID_PROVIDERS[openid_provider] - if openid_url: + openid_provider_obj = None + if not openid_url and openid_provider and trans.app.openid_providers.get( openid_provider ): + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + elif openid_url: + openid_provider_obj = OpenIDProvider( openid_url, openid_url, openid_url ) #for manually entered links use the link for id, name and url + elif openid_provider: + message = 'Invalid OpenID provider specified: %s' % ( openid_provider ) + else: + message = 'An OpenID provider was not specified' + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate, openid_provider=openid_provider ) + if openid_provider_obj is not None: request = None try: - request = consumer.begin( openid_url ) + request = consumer.begin( openid_provider_obj.op_endpoint_url ) if request is None: - message = 'No OpenID services are available at %s' % openid_url + message = 'No OpenID services are available at %s' % openid_provider_obj.op_endpoint_url except Exception, e: message = 'Failed to begin OpenID authentication: %s' % str( e ) if request is not None: - trans.app.openid_manager.add_sreg( trans, request, optional=[ 'nickname', 'email' ] ) + sreg_request = trans.app.openid_manager.add_sreg( trans, request, required=openid_provider_obj.sreg_required, optional=openid_provider_obj.sreg_optional ) if request.shouldSendRedirect(): redirect_url = request.redirectURL( trans.request.base, process_url ) @@ -114,6 +116,7 @@ info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() redirect_url = kwd.get( 'referer', url_for( '/' ) ) + openid_provider = kwd.get( 'openid_provider', '' ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) return trans.response.send_redirect( url_for( controller='user', @@ -125,6 +128,9 @@ if info.endpoint.canonicalID: display_identifier = info.endpoint.canonicalID user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + if not openid_provider_obj: + openid_provider_obj = OpenIDProvider( display_identifier, display_identifier, display_identifier ) if not user_openid: user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: @@ -132,6 +138,7 @@ elif user_openid.user and not auto_associate: trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( redirect_url ) return if auto_associate and trans.user: @@ -151,6 +158,7 @@ trans.log_event( "User associated OpenID: %s" % display_identifier ) message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) status = "done" + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -162,15 +170,18 @@ message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." sreg_resp = trans.app.openid_manager.get_sreg( info ) try: - username = sreg_resp.get( 'nickname', '' ) + sreg_username_name = openid_provider_obj.use_for.get( 'username' ) + username = sreg_resp.get( sreg_username_name, '' ) except AttributeError: username = '' try: - email = sreg_resp.get( 'email', '' ) + sreg_email_name = openid_provider_obj.use_for.get( 'email' ) + email = sreg_resp.get( sreg_email_name, '' ) except AttributeError: email = '' trans.response.send_redirect( url_for( controller='user', action='openid_associate', + openid_provider=openid_provider, use_panels=True, username=username, email=email, @@ -199,6 +210,8 @@ email = kwd.get( 'email', '' ) username = kwd.get( 'username', '' ) referer = kwd.get( 'referer', trans.request.referer ) + openid_provider = kwd.get( 'openid_provider', '' ) + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() openids = trans.galaxy_session.openids @@ -219,8 +232,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) - return + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -251,7 +265,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) else: message = error status = 'error' @@ -285,7 +301,8 @@ user_type_fd_id_select_field=user_type_fd_id_select_field, user_type_form_definition=user_type_form_definition, widgets=widgets, - openids=openids ) + openids=openids, + openid_provider=openid_provider ) @web.expose @web.require_login( 'manage OpenIDs' ) def openid_disassociate( self, trans, webapp='galaxy', **kwd ): @@ -340,7 +357,7 @@ use_panels=use_panels, id=kwd['id'] ) ) kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) - kwd['openid_providers'] = OPENID_PROVIDERS + kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): @@ -351,6 +368,7 @@ header = '' user = None email = kwd.get( 'email', '' ) + openid_provider = kwd.get( 'openid_provider', '' ) if kwd.get( 'login_button', False ): if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: @@ -385,7 +403,7 @@ refresh_frames=refresh_frames, message=message, status=status, - openid_providers=OPENID_PROVIDERS, + openid_providers=trans.app.openid_providers, active_view="user" ) def __validate_login( self, trans, webapp='galaxy', **kwd ): message = kwd.get( 'message', '' ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/framework/openid_manager.py --- a/lib/galaxy/web/framework/openid_manager.py +++ b/lib/galaxy/web/framework/openid_manager.py @@ -1,5 +1,5 @@ """ -Mange the OpenID consumer and related data stores. +Manage the OpenID consumer and related data stores. """ import os, pickle, logging diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/aol.xml --- /dev/null +++ b/openid/aol.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="aol" name="AOL/AIM"> + <op_endpoint_url>http://openid.aol.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/genomespace.xml --- /dev/null +++ b/openid/genomespace.xml @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<provider id="genomespace" name="GenomeSpace"> + <op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url> + <sreg> + <field name="nickname" required="True"> + <use_for name="username"/> + <store_user_preference name="genomespace_username"/> + </field> + <field name="email" required="False"> + <use_for name="email"/> + </field> + <field name="gender" required="True"> + <store_user_preference name="genomespace_token"/> + </field> + </sreg> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/google.xml --- /dev/null +++ b/openid/google.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="google" name="Google"> + <op_endpoint_url>https://www.google.com/accounts/o8/id</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/launchpad.xml --- /dev/null +++ b/openid/launchpad.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="launchpad" name="Launchpad"> + <op_endpoint_url>http://login.launchpad.net</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/yahoo.xml --- /dev/null +++ b/openid/yahoo.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="yahoo" name="Yahoo!"> + <op_endpoint_url>http://yahoo.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid_conf.xml.sample --- /dev/null +++ b/openid_conf.xml.sample @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<openid> + <provider file="google.xml" /> + <provider file="yahoo.xml" /> + <provider file="aol.xml" /> + <provider file="launchpad.xml" /> + <provider file="genomespace.xml" /> +</openid> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 run.sh --- a/run.sh +++ b/run.sh @@ -15,6 +15,7 @@ tool_conf.xml.sample tool_data_table_conf.xml.sample tool_sheds_conf.xml.sample + openid_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -59,7 +59,7 @@ </%def> -<%def name="render_login_form( form_action=None )"> +<%def name="render_login_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -77,6 +77,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> @@ -94,10 +95,9 @@ </%def><%def name="render_openid_form( referer, auto_associate, openid_providers )"> - <div class="toolForm"><div class="toolFormTitle">OpenID Login</div> - <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" > + <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" target="_parent" ><div class="form-row"><label>OpenID URL:</label><input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> @@ -107,8 +107,8 @@ </div><div class="form-row"> Or, authenticate with your <select name="openid_provider"> - %for provider in openid_providers.keys(): - <option>${provider}</option> + %for provider in openid_providers: + <option value="${provider.id}">${provider.name}</option> %endfor </select> account. </div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -65,11 +65,11 @@ <% form_action = h.url_for( cntrller=cntrller, use_panels=use_panels ) %> - ${render_login_form( form_action=form_action )} + ${render_login_form( form_action=form_action, openid_provider=openid_provider )} <br/> - ${render_registration_form( form_action=form_action )} + ${render_registration_form( form_action=form_action, openid_provider=openid_provider )} </div></div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -21,7 +21,7 @@ ${render_registration_form()} %endif -<%def name="render_registration_form( form_action=None )"> +<%def name="render_registration_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -38,6 +38,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -495,6 +495,7 @@ # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. #enable_openid = False +#openid_config_file = openid_conf.xml # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Convert loc file examples to use tabs instead of spaces.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/463fc935b97c/ changeset: 463fc935b97c user: dannon date: 2012-03-23 13:59:34 summary: Convert loc file examples to use tabs instead of spaces. affected #: 22 files diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/all_fasta.loc.sample --- a/tool-data/all_fasta.loc.sample +++ b/tool-data/all_fasta.loc.sample @@ -4,13 +4,13 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb.loc.sample --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -2,7 +2,7 @@ #list of nucleotide BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -25,9 +25,9 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -2,25 +2,25 @@ #list of protein BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, #and that the first tab that appears in the line is right before the path. # -#So, for example, if your database is NR and the path to your base name +#So, for example, if your database is NR and the path to your base name #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#nr NCBI NR (non redundant) /data/blastdb/nr +#nr NCBI NR (non redundant) /data/blastdb/nr # #and your /data/blastdb directory would contain all of the files associated #with the database, /data/blastdb/nr.*. # -#Your blastdb_p.loc file should include an entry per line for each "base name" +#Your blastdb_p.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr #...etc... # #See also blastdb.loc which is for any nucleotide BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bowtie_indices_color.loc.sample --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bowtie_indices.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index_color.loc.sample --- a/tool-data/bwa_index_color.loc.sample +++ b/tool-data/bwa_index_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bwa_index_color.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/color/, @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/faseq.loc.sample --- a/tool-data/faseq.loc.sample +++ b/tool-data/faseq.loc.sample @@ -20,7 +20,7 @@ #Your faseq.loc file should include an entry per line for each set of fasta #sequence files you have stored. For example: # -#hg18 /depot/data2/galaxy/faseq/hg18 -#mm9 /depot/data2/galaxy/faseq/mm9 -#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis +#hg18 /depot/data2/galaxy/faseq/hg18 +#mm9 /depot/data2/galaxy/faseq/mm9 +#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gatk_sorted_picard_index.loc.sample --- a/tool-data/gatk_sorted_picard_index.loc.sample +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in -#/depot/data2/galaxy/srma/hg18/, +#/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ b/tool-data/gd.chrlens.loc.sample @@ -6,17 +6,17 @@ # file has the following format (white space characters are TAB # characters): # -#<species><reference_species_file_path> +#<species><reference_species_file_path> # # So, for example, if you used Monodelphis domestica as the reference # species for a collection of Sarcophilus harrisii SNPs, then the # gd.chrlens.loc entry would look like this: # -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt # # Your gd.chrlens.loc file should include an entry for each pair of # species SNPs and reference species. For example: # -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ b/tool-data/gd.primers.loc.sample @@ -5,18 +5,18 @@ # primers files are stored. The gd.primers.loc file has the following # format (white space characters are TAB characters): # -#<species><primers_file_path> +#<species><primers_file_path> # # So, for example, if you had a primers file located at # /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of # Ovis canadensis SNPs, then the gd.primers.loc entry would look like # this: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt # # Your gd.primers.loc file should include an entry for each pair of # species SNPs and primers file. For example: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ b/tool-data/gd.snps.loc.sample @@ -5,17 +5,17 @@ # SNP call files are stored. The gd.snps.loc file has the following # format (white space characters are TAB characters): # -#<species><SNP_call_file_path> +#<species><SNP_call_file_path> # # So, for example, if you had a SNP call file located at # /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of # Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt # # Your gd.snps.loc file should include an entry for each pair of species # SNPs and SNP call file. For example: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/lastz_seqs.loc.sample --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><display_name><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/liftOver.loc.sample --- a/tool-data/liftOver.loc.sample +++ b/tool-data/liftOver.loc.sample @@ -8,7 +8,7 @@ #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, #then the liftOver.loc entry would look like this: # -#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain # #and your /depot/data2/galaxy/anoCar1/liftOver directory would #contain all of your "chain" files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/mosaik_index.loc.sample --- a/tool-data/mosaik_index.loc.sample +++ b/tool-data/mosaik_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The mosaik_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/mosaik/hg18/ #then the mosaik_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa # #and your /depot/data2/galaxy/mosaik/hg18/ directory #would contain the following files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/ngs_sim_fasta.loc.sample --- a/tool-data/ngs_sim_fasta.loc.sample +++ b/tool-data/ngs_sim_fasta.loc.sample @@ -4,17 +4,17 @@ #in this directory) that points to the locations of those files. The ngs_sim.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18chrM.fa in #/data/path/hg18/seq/, #then the ngs_sim.loc entry would look like this: # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa # #Your ngs_sim.loc file should include an entry per line for each FASTA file you #have stored. # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa -#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa -#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa +#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_base_index.loc.sample --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_base_index.loc #file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_color_index.loc.sample --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/picard_index.loc.sample --- a/tool-data/picard_index.loc.sample +++ b/tool-data/picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/quality_scores.loc.sample --- a/tool-data/quality_scores.loc.sample +++ b/tool-data/quality_scores.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry #would look like this: # -#panTro2 /depot/data2/galaxy/panTro2/quality_scores +#panTro2 /depot/data2/galaxy/panTro2/quality_scores # #and your /depot/data2/galaxy/panTro2/quality_scores directory would #contain all of your quality score files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/regions.loc.sample --- a/tool-data/regions.loc.sample +++ b/tool-data/regions.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the #regions.loc entry would look like this: # -#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed +#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed # #and your /depot/data2/galaxy/regions/ directory would #contain all of your regions files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/srma_index.loc.sample --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -8,13 +8,13 @@ #the directories in which those files are stored. The srma_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/twobit.loc.sample --- a/tool-data/twobit.loc.sample +++ b/tool-data/twobit.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/droPer1/, then the twobit.loc entry #would look like this: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit # #and your /depot/data2/galaxy/droPer1/ directory would #contain all of your twobit files (e.g.): @@ -19,8 +19,8 @@ #Your twobit.loc file should include an entry per line for each twobit #file you have stored. For example: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit -#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit -#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit -#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit #...etc... 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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