January 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Pep-8 fixes for the base admin controller.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd6cd92888ed/ Changeset: fd6cd92888ed User: greg Date: 2014-01-22 22:52:18 Summary: Pep-8 fixes for the base admin controller. Affected #: 1 file diff -r fe2fdbbecd853aafbd0d5748c796d37399d98bd6 -r fd6cd92888edf53c86378e3ec36dae1e0cf54884 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -6,8 +6,8 @@ from galaxy.web.form_builder import CheckboxField from string import punctuation as PUNCTUATION +log = logging.getLogger( __name__ ) -log = logging.getLogger( __name__ ) class Admin( object ): # Override these @@ -38,6 +38,7 @@ return trans.fill_template( '/webapps/tool_shed/admin/index.mako', message=message, status=status ) + @web.expose @web.require_admin def center( self, trans, **kwd ): @@ -51,6 +52,7 @@ return trans.fill_template( '/webapps/tool_shed/admin/center.mako', message=message, status=status ) + @web.expose @web.require_admin def reload_tool( self, trans, **kwd ): @@ -67,13 +69,14 @@ toolbox=toolbox, message=message, status=status ) + @web.expose @web.require_admin def tool_versions( self, trans, **kwd ): if 'message' not in kwd or not kwd[ 'message' ]: kwd[ 'message' ] = 'Tool ids for tools that are currently loaded into the tool panel are highlighted in green (click to display).' return self.tool_version_list_grid( trans, **kwd ) - # Galaxy Role Stuff + @web.expose @web.require_admin def roles( self, trans, **kwargs ): @@ -95,6 +98,7 @@ return self.rename_role( trans, **kwargs ) # Render the list view return self.role_list_grid( trans, **kwargs ) + @web.expose @web.require_admin def create_role( self, trans, **kwd ): @@ -169,6 +173,7 @@ create_group_for_role_checked=create_group_for_role_checked, message=message, status=status ) + @web.expose @web.require_admin def rename_role( self, trans, **kwd ): @@ -210,6 +215,7 @@ role=role, message=message, status=status ) + @web.expose @web.require_admin def manage_users_and_groups_for_role( self, trans, **kwd ): @@ -302,6 +308,7 @@ library_dataset_actions=library_dataset_actions, message=message, status=status ) + @web.expose @web.require_admin def mark_role_deleted( self, trans, **kwd ): @@ -324,6 +331,7 @@ action='roles', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def undelete_role( self, trans, **kwd ): @@ -355,6 +363,7 @@ action='roles', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def purge_role( self, trans, **kwd ): @@ -408,7 +417,6 @@ message=util.sanitize_text( message ), status='done' ) ) - # Galaxy Group Stuff @web.expose @web.require_admin def groups( self, trans, **kwargs ): @@ -430,6 +438,7 @@ return self.rename_group( trans, **kwargs ) # Render the list view return self.group_list_grid( trans, **kwargs ) + @web.expose @web.require_admin def rename_group( self, trans, **kwd ): @@ -469,6 +478,7 @@ group=group, message=message, status=status ) + @web.expose @web.require_admin def manage_users_and_roles_for_group( self, trans, **kwd ): @@ -513,6 +523,7 @@ out_users=out_users, message=message, status=status ) + @web.expose @web.require_admin def create_group( self, trans, **kwd ): @@ -588,6 +599,7 @@ create_role_for_group_checked=create_role_for_group_checked, message=message, status=status ) + @web.expose @web.require_admin def mark_group_deleted( self, trans, **kwd ): @@ -611,6 +623,7 @@ action='groups', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def undelete_group( self, trans, **kwd ): @@ -642,6 +655,7 @@ action='groups', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def purge_group( self, trans, **kwd ): @@ -678,13 +692,13 @@ message=util.sanitize_text( message ), status='done' ) ) - # Galaxy User Stuff @web.expose @web.require_admin def create_new_user( self, trans, **kwd ): return trans.response.send_redirect( web.url_for( controller='user', action='create', cntrller='admin' ) ) + @web.expose @web.require_admin def reset_user_password( self, trans, **kwd ): @@ -730,6 +744,7 @@ users=users, password='', confirm='' ) + @web.expose @web.require_admin def mark_user_deleted( self, trans, **kwd ): @@ -752,6 +767,7 @@ action='users', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def undelete_user( self, trans, **kwd ): @@ -783,6 +799,7 @@ action='users', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def purge_user( self, trans, **kwd ): @@ -850,6 +867,7 @@ action='users', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def users( self, trans, **kwd ): @@ -888,6 +906,7 @@ self.user_list_grid.operations.append( self.purge_operation ) # Render the list view return self.user_list_grid( trans, **kwd ) + @web.expose @web.require_admin def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): @@ -896,6 +915,7 @@ for user in trans.sa_session.query( trans.app.model.User ).filter_by( deleted=False ).filter( func.lower( trans.app.model.User.email ).like( q.lower() + "%" ) ): ac_data = ac_data + user.email + "\n" return ac_data + @web.expose @web.require_admin def manage_roles_and_groups_for_user( self, trans, **kwd ): @@ -968,6 +988,7 @@ out_groups=out_groups, message=message, status=status ) + @web.expose @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): @@ -1089,12 +1110,14 @@ if not user: return trans.show_error_message( "User not found for id (%s)" % str( user_id ) ) return user + def get_user_by_username( trans, username ): """Get a user from the database by username""" # TODO: Add exception handling here. return trans.sa_session.query( trans.model.User ) \ .filter( trans.model.User.table.c.username == username ) \ .one() + def get_role( trans, id ): """Get a Role from the database by id.""" # Load user from database @@ -1103,6 +1126,7 @@ if not role: return trans.show_error_message( "Role not found for id (%s)" % str( id ) ) return role + def get_group( trans, id ): """Get a Group from the database by id.""" # Load user from database @@ -1111,6 +1135,7 @@ if not group: return trans.show_error_message( "Group not found for id (%s)" % str( id ) ) return group + def get_quota( trans, id ): """Get a Quota from the database by id.""" # Load user from database Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Use url_for with webhelpers + reinstate previous absolute path w/ slash.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe2fdbbecd85/ Changeset: fe2fdbbecd85 User: dannon Date: 2014-01-22 22:03:57 Summary: Use url_for with webhelpers + reinstate previous absolute path w/ slash. Affected #: 1 file diff -r 4f898ebb8a0fe36c762ed61f09847af8afcfbd79 -r fe2fdbbecd853aafbd0d5748c796d37399d98bd6 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -57,7 +57,7 @@ Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link( "static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ stylesheet_link( url_for( "/static/style/%s.css?v=%s" % (name, server_starttime) ) ) for name in args ] ) def js_helper( prefix, *args ): """ @@ -66,7 +66,7 @@ Cache-bust with time that server started running on """ - return "\n".join( [ javascript_link( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ javascript_link( url_for( "/%s%s.js?v=%s" % (prefix, name, server_starttime ) ) ) for name in args ] ) def js( *args ): """ 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 commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c893e34c0ef3/ Changeset: c893e34c0ef3 User: Galaxy Date: 2013-03-27 00:32:29 Summary: lower case external remote user - canonicalise email address Affected #: 1 file diff -r dfa5f6b881769995d4bb660e82b4c20256779bf3 -r c893e34c0ef3ca12ef8878944f70b11a92e1a43d lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -726,7 +726,7 @@ #If this is an api request, and they've passed a key, we let this go. assert self.app.config.remote_user_header in self.environ, \ "use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header - remote_user_email = self.environ[ self.app.config.remote_user_header ] + remote_user_email = self.environ[ self.app.config.remote_user_header ].lower() if galaxy_session: # An existing session, make sure correct association exists if galaxy_session.user is None: @@ -854,7 +854,7 @@ """ if not self.app.config.use_remote_user: return None - + remote_user_email = remote_user_email.lower() user = self.sa_session.query( self.app.model.User ) \ .filter( self.app.model.User.table.c.email==remote_user_email ) \ .first() https://bitbucket.org/galaxy/galaxy-central/commits/de7af0ce204e/ Changeset: de7af0ce204e User: jmchilton Date: 2014-01-17 08:10:58 Summary: Make normalizing remote user e-mail optional (off by default). I don't think we can make this change as is in case other institutions have configured their proxies to supply consistent e-mail addresses or other identifiers and these identifiers are not uniformly lower case. In such cases these changes (Pull Request 144) would break Galaxy's existing user management. Affected #: 2 files diff -r c893e34c0ef3ca12ef8878944f70b11a92e1a43d -r de7af0ce204e4e632ae28449f8de82e6ac440066 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -122,6 +122,7 @@ self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) + self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_header = kwargs.get( "remote_user_header", 'HTTP_REMOTE_USER' ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) diff -r c893e34c0ef3ca12ef8878944f70b11a92e1a43d -r de7af0ce204e4e632ae28449f8de82e6ac440066 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -726,7 +726,9 @@ #If this is an api request, and they've passed a key, we let this go. assert self.app.config.remote_user_header in self.environ, \ "use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header - remote_user_email = self.environ[ self.app.config.remote_user_header ].lower() + remote_user_email = self.environ[ self.app.config.remote_user_header ] + if getattr( self.app.config, "normalize_remote_user_email", False ): + remote_user_email = remote_user_email.lower() if galaxy_session: # An existing session, make sure correct association exists if galaxy_session.user is None: @@ -854,7 +856,8 @@ """ if not self.app.config.use_remote_user: return None - remote_user_email = remote_user_email.lower() + if getattr( self.app.config, "normalize_remote_user_email", False ): + remote_user_email = remote_user_email.lower() user = self.sa_session.query( self.app.model.User ) \ .filter( self.app.model.User.table.c.email==remote_user_email ) \ .first() https://bitbucket.org/galaxy/galaxy-central/commits/4f898ebb8a0f/ Changeset: 4f898ebb8a0f User: jmchilton Date: 2014-01-22 21:39:55 Summary: Document new normalize_remote_user_email option. Affected #: 1 file diff -r de7af0ce204e4e632ae28449f8de82e6ac440066 -r 4f898ebb8a0fe36c762ed61f09847af8afcfbd79 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -601,6 +601,11 @@ # users out. #remote_user_logout_href = None +# If your proxy and/or authentication source does not normalize e-mail +# addresses or user names being passed to Galaxy - enable the following option +# to force these to lower case. +#normalize_remote_user_email = True + # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, 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: jeremy goecks: Fix for 9bc3fa1 to allow path rewrites; old Webhelper functions stripped preceding '/' but current functions do not.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dfa5f6b88176/ Changeset: dfa5f6b88176 User: jeremy goecks Date: 2014-01-22 20:09:09 Summary: Fix for 9bc3fa1 to allow path rewrites; old Webhelper functions stripped preceding '/' but current functions do not. Affected #: 1 file diff -r 5217c8c788a31716758d943204b20ad4a4850c37 -r dfa5f6b881769995d4bb660e82b4c20256779bf3 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -57,7 +57,7 @@ Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ stylesheet_link( "static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) def js_helper( prefix, *args ): """ @@ -73,14 +73,14 @@ Take a prefix and list of javascript names and return appropriate string of script tags. """ - return js_helper( '/static/scripts/', *args ) + return js_helper( 'static/scripts/', *args ) def templates( *args ): """ Take a list of template names (no extension) and return appropriate string of script tags. """ - return js_helper( '/static/scripts/templates/compiled/', *args ) + return js_helper( 'static/scripts/templates/compiled/', *args ) # Hashes 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: jmchilton: Document recently introduced reset_password_length option.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5217c8c788a3/ Changeset: 5217c8c788a3 User: jmchilton Date: 2014-01-22 18:37:15 Summary: Document recently introduced reset_password_length option. Affected #: 1 file diff -r 8c1cc5febdaf099ed9175bcfd5b00183ecc0f1fb -r 5217c8c788a31716758d943204b20ad4a4850c37 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -290,6 +290,10 @@ # If no message specified the warning box will not be shown. #registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + # -- Account activation 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: 2 new changesets
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f551163787b/ Changeset: 2f551163787b User: jmchilton Date: 2014-01-22 18:06:26 Summary: Allow adjusting the reset password length in unvierse_wsgi.ini. Purposely not annotated in universe_wsgi.ini.sample - though could be persuaded to add it. Affected #: 2 files diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2f551163787b54983b62d3ea052e7d1039844e52 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -151,6 +151,7 @@ h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ] self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) + self.reset_password_length = int( kwargs.get('reset_password_length', '15') ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2f551163787b54983b62d3ea052e7d1039844e52 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1083,7 +1083,8 @@ else: chars = string.letters + string.digits new_pass = "" - for i in range(15): + reset_password_length = getattr( trans.app.config, "reset_password_length", 15 ) + for i in range(reset_password_length): new_pass = new_pass + random.choice(chars) host = trans.request.host.split(':')[0] if host == 'localhost': https://bitbucket.org/galaxy/galaxy-central/commits/8c1cc5febdaf/ Changeset: 8c1cc5febdaf User: jmchilton Date: 2014-01-22 18:17:26 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #307) Allow adjusting the reset password length in unvierse_wsgi.ini. Affected #: 2 files diff -r 2703795990b091a98398b19e042f88584533704d -r 8c1cc5febdaf099ed9175bcfd5b00183ecc0f1fb lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -151,6 +151,7 @@ h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ] self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) + self.reset_password_length = int( kwargs.get('reset_password_length', '15') ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) diff -r 2703795990b091a98398b19e042f88584533704d -r 8c1cc5febdaf099ed9175bcfd5b00183ecc0f1fb lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1083,7 +1083,8 @@ else: chars = string.letters + string.digits new_pass = "" - for i in range(15): + reset_password_length = getattr( trans.app.config, "reset_password_length", 15 ) + for i in range(reset_password_length): new_pass = new_pass + random.choice(chars) host = trans.request.host.split(':')[0] if host == 'localhost': 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: jeremy goecks: Circster: (a) add style sheet and (b) update styles to use smaller labels.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2703795990b0/ Changeset: 2703795990b0 User: jeremy goecks Date: 2014-01-22 18:06:59 Summary: Circster: (a) add style sheet and (b) update styles to use smaller labels. Affected #: 4 files diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2703795990b091a98398b19e042f88584533704d static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,4 +1,7 @@ -define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { +define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization"], function(utils, _, d3, visualization) { + +// Load needed CSS. +utils.cssLoadFile("static/style/circster.css"); /** * Utility class for working with SVG. @@ -652,7 +655,7 @@ this.bg_fill = 'fff'; // Minimum arc distance for labels to be applied. - this.min_arc_len = 0.08; + this.min_arc_len = 0.05; }, /** @@ -673,9 +676,9 @@ }) .attr('text-anchor', 'middle') .append("svg:textPath") + .attr("class", "chrom-label") .attr("xlink:href", function(d) { return "#label-" + d.data.chrom; }) .attr('startOffset', '25%') - .attr('font-weight', 'bold') .text(function(d) { return d.data.chrom; }); @@ -791,11 +794,16 @@ return "rotate(90)"; }; + // Draw min, max on first chrom only. + this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true); + + /* // Filter for visible chroms, then for every third chrom so that labels attached to only every // third chrom. var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }), labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }); this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true); + */ }, /** @@ -868,7 +876,8 @@ if (d) { // Each data point has the form [position, value], so return all values. return _.map(d.data, function(p) { - return p[1]; + // Null is used for a lack of data; resolve null to 0 for comparison. + return parseInt(p[1], 10) || 0; }); } else { @@ -876,7 +885,9 @@ } }) ); - return [ _.min(values), this._quantile(values, 0.98) ]; + // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 + // for sparsely populated data, so use max in that case. + return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ]; } }); @@ -967,7 +978,7 @@ el : $('#center .unified-panel-body'), // gaps are difficult to set because it very dependent on chromosome size and organization. - total_gap : 2 * Math.PI * 0.1, + total_gap : 2 * Math.PI * 0.4, genome : genome, model : vis, dataset_arc_height : 25 diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2703795990b091a98398b19e042f88584533704d static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -5,11 +5,11 @@ var theme = grunt.option( 'theme', 'blue' ); - var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; + var out = 'blue'; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster', 'circster' ]; - var _ = grunt.util._; - var fmt = _.sprintf; + var _ = grunt.util._; + var fmt = _.sprintf; // Project configuration. grunt.initConfig({ diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2703795990b091a98398b19e042f88584533704d static/style/blue/circster.css --- /dev/null +++ b/static/style/blue/circster.css @@ -0,0 +1,2 @@ +.chrom-label{font-size:80%} +.tick{font-size:80%} diff -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f -r 2703795990b091a98398b19e042f88584533704d static/style/src/less/circster.less --- /dev/null +++ b/static/style/src/less/circster.less @@ -0,0 +1,7 @@ +.chrom-label { + font-size: 80%; +} + +.tick { + font-size: 80%; +} \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix tool shed functional test broken when the pull request resulting in changeset 329f9ac was accepted.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aae0e414a2fa/ Changeset: aae0e414a2fa User: greg Date: 2014-01-22 17:48:12 Summary: Fix tool shed functional test broken when the pull request resulting in changeset 329f9ac was accepted. Affected #: 1 file diff -r 28cd6a86d99dc6aaab95ee69ca706899be5b535b -r aae0e414a2fa595ee83cf576e36dc5bd25772a9f test/tool_shed/functional/test_1140_tool_help_images.py --- a/test/tool_shed/functional/test_1140_tool_help_images.py +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -109,10 +109,10 @@ In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: - src="/admin_toolshed/static/images/<id>/count_modes.png" + src="admin_toolshed/static/images/<id>/count_modes.png" ''' repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - image_path = 'src="/admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + image_path = 'src="admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. repository_metadata = repository.metadata tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] 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: jmchilton: Adjust logic related to_posix_lines to make optionally specified.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/28cd6a86d99d/ Changeset: 28cd6a86d99d User: jmchilton Date: 2014-01-22 17:35:31 Summary: Adjust logic related to_posix_lines to make optionally specified. Fixes library uploads and restores backward-compatiblity to create_paramfile interface to rest of Galaxy. This is an alternative to pull request #305. Affected #: 1 file diff -r edfc4baf2d0747f4bdc7d255bdef396b7dcf3599 -r 28cd6a86d99dc6aaab95ee69ca706899be5b535b lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -332,7 +332,7 @@ is_binary=is_binary, link_data_only=link_data_only, uuid=uuid_str, - to_posix_lines=uploaded_dataset.to_posix_lines, + to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True), space_to_tab=uploaded_dataset.space_to_tab, in_place=trans.app.config.external_chown_script is None, path=uploaded_dataset.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: greg: Tool Shed install and test framework fixes.
by commits-noreply＠bitbucket.org 22 Jan '14

22 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/edfc4baf2d07/ Changeset: edfc4baf2d07 User: greg Date: 2014-01-22 17:30:32 Summary: Tool Shed install and test framework fixes. Affected #: 1 file diff -r 8df0e01949818bb3a32a888f87fe261c8c30e877 -r edfc4baf2d0747f4bdc7d255bdef396b7dcf3599 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -753,7 +753,9 @@ owner = str( missing_repository_dependency.owner ) changeset_revision = str( missing_repository_dependency.changeset_revision ) error_message = unicodify( missing_repository_dependency.error_message ) - print 'Revision %s of repository %s owned by %s:\n%s' % ( changeset_revision, name, owner, error_message ) + print 'Revision %s of repository %s owned by %s has the following installation error:' % ( changeset_revision, name, owner ) + # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. + log.debug( '%s' % error_message ) missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, name=name, owner=owner, @@ -774,7 +776,9 @@ type = str( missing_tool_dependency.type ) version = str( missing_tool_dependency.version ) error_message = unicodify( missing_tool_dependency.error_message ) - print 'Version %s of tool dependency %s %s:\n%s' % ( version, type, name, error_message ) + print 'Version %s of tool dependency %s %s has the following installation error:' % ( version, type, name ) + # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. + log.debug( '%s' % error_message ) missing_tool_dependency_info_dict = dict( type=type, name=name, version=version, @@ -870,25 +874,38 @@ ( changeset_revision, name, owner ) print 'due to the following error getting tool_test_results:\n%s' % str( error_message ) else: - # Check the required repository's time_last_tested value to see if its tool_test_results column - # has been updated within the past 12 hours. The RepositoryMetadata class's to_dict() method - # returns the value of time_last_tested in datetime.isoformat(). - twenty_hours_ago = ( datetime.utcnow() - timedelta( hours=20 ) ).isoformat() + # The assumption is that the Tool SHed's install and test framework is executed no more than once per 24 hour + # period, so check the required repository's time_last_tested value to see if its tool_test_results column + # has been updated within the past 24 hours. The RepositoryMetadata class's to_dict() method returns the value + # of time_last_tested in datetime.isoformat(). time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, required_repository_metadata_id ) - if time_last_tested is not None and time_last_tested < twenty_hours_ago: - print 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ - ( changeset_revision, name, owner ) - print 'populated within the past 20 hours (likely in this test run), so skipping this check.' - continue - elif time_last_tested is None: + print 'Value of time_last_tested: %s' % str( time_last_tested ) + if time_last_tested is None: print 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ ( changeset_revision, name, owner ) - elif time_last_tested < twenty_hours_ago: - print 'Version %s of repository dependency %s owned by %s was last tested less than 20 hours ago.' % \ - ( changeset_revision, name, owner ) else: - print 'Version %s of repository dependency %s owned by %s was last tested more than 20 hours ago.' % \ - ( changeset_revision, name, owner ) + twenty_four_hours_ago = ( datetime.utcnow() - timedelta( hours=24 ) ).isoformat() + print 'Value of twenty_four_hours_ago: %s' % str( twenty_four_hours_ago ) + # This is counter intuitive because the following check is on strings like this: '2014-01-21T19:46:06.953741', + # so if "time_last_tested > twenty_four_hours_ago" is True, then it implies that the time_last_tested column + # was actually updated less than 24 hours ago, and should not be updated again because we're likely processing + # another dependent repository, many of which can have the same repository dependency. + try: + # Be very conservative here. Our default behavior will be to assume containers have not been populated + # during the current test run. + already_populated = time_last_tested > twenty_four_hours_ago + except Exception, e: + log.exception( 'Error attempting to set already_populated: %s' % str( e ) ) + already_populated = False + print 'Value of already_populated: %s' % str( already_populated ) + if already_populated: + print 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ + ( changeset_revision, name, owner ) + print 'populated within the past 24 hours (likely in this test run), so skipping this check.' + continue + else: + print 'Version %s of repository dependency %s owned by %s was last tested more than 24 hours ago.' % \ + ( changeset_revision, name, owner ) # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: tool_test_results_dict = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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