February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Fix styles related to ratings and reviews when managing or viewing a repository in the tool shed.
by Bitbucket 07 Feb '13

07 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd82f2ff9533/ changeset: fd82f2ff9533 user: greg date: 2013-02-07 19:26:42 summary: Fix styles related to ratings and reviews when managing or viewing a repository in the tool shed. affected #: 4 files diff -r feb05b2ef24c665e9245e554af40104a812f03a9 -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ b/templates/webapps/community/common/common.mako @@ -66,3 +66,19 @@ <div style="clear: both"></div></div></%def> + +<%def name="render_review_comment( comment_text )"> + <style type="text/css"> + #reviews_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> + <table id="reviews_table"> + <tr><td>${comment_text}</td></tr> + </table> +</%def> diff -r feb05b2ef24c665e9245e554af40104a812f03a9 -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -48,7 +48,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "library" )} + ${h.css('base','library','panel_layout','jquery.rating')} </%def><%def name="javascripts()"> @@ -322,33 +322,38 @@ <div class="form-row"><a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div> - <table class="grid"> - <thead> - <tr> - <th>Rating</th> - <th>Comments</th> - <th>Reviewed</th> - <th>User</th> - </tr> - </thead> - <% count = 0 %> - %for review in repository.ratings: - <% - count += 1 - name = 'rating%d' % count - %> - <tr> - <td>${render_star_rating( name, review.rating, disabled=True )}</td> - <td><pre>${review.comment | h}</pre></td> - <td>${time_ago( review.update_time )}</td> - <td>${review.user.username | h}</td> - </tr> - %endfor - </table> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <thead> + <tr> + <th>Rating</th> + <th>Comments</th> + <th>Reviewed</th> + <th>User</th> + </tr> + </thead> + <% count = 0 %> + %for review in repository.ratings: + <% + count += 1 + name = 'rating%d' % count + %> + <tr> + <td>${render_star_rating( name, review.rating, disabled=True )}</td> + <td>${render_review_comment( to_safe_string( review.comment, to_html=True ) )}</td> + <td>${time_ago( review.update_time )}</td> + <td>${review.user.username | h}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> %else: <div class="form-row"><a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> + <div style="clear: both"></div> %endif </div></div> diff -r feb05b2ef24c665e9245e554af40104a812f03a9 -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -33,31 +33,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "jquery.rating" )} - <style type="text/css"> - ul.fileBrowser, - ul.toolFile { - margin-left: 0; - padding-left: 0; - list-style: none; - } - ul.fileBrowser { - margin-left: 20px; - } - .fileBrowser li, - .toolFile li { - padding-left: 20px; - background-repeat: no-repeat; - background-position: 0; - min-height: 20px; - } - .toolFile li { - background-image: url( ${h.url_for( '/static/images/silk/page_white_compressed.png' )} ); - } - .fileBrowser li { - background-image: url( ${h.url_for( '/static/images/silk/page_white.png' )} ); - } - </style> + ${h.css('base','panel_layout','jquery.rating')} </%def><%def name="javascripts()"> diff -r feb05b2ef24c665e9245e554af40104a812f03a9 -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -39,7 +39,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "library" )} + ${h.css('base','library','panel_layout','jquery.rating')} </%def><%def name="javascripts()"> @@ -251,33 +251,38 @@ <div class="form-row"><a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div> - <table class="grid"> - <thead> - <tr> - <th>Rating</th> - <th>Comments</th> - <th>Reviewed</th> - <th>User</th> - </tr> - </thead> - <% count = 0 %> - %for review in repository.ratings: - <% - count += 1 - name = 'rating%d' % count - %> - <tr> - <td>${render_star_rating( name, review.rating, disabled=True )}</td> - <td><pre>${review.comment}</pre></td> - <td>${time_ago( review.update_time )}</td> - <td>${review.user.username}</td> - </tr> - %endfor - </table> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <thead> + <tr> + <th>Rating</th> + <th>Comments</th> + <th>Reviewed</th> + <th>User</th> + </tr> + </thead> + <% count = 0 %> + %for review in repository.ratings: + <% + count += 1 + name = 'rating%d' % count + %> + <tr> + <td>${render_star_rating( name, review.rating, disabled=True )}</td> + <td>${render_review_comment( to_safe_string( review.comment, to_html=True ) )}</td> + <td>${time_ago( review.update_time )}</td> + <td>${review.user.username}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> %else: <div class="form-row"><a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> + <div style="clear: both"></div> %endif </div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add get() method to ToolDataTableManager.
by Bitbucket 07 Feb '13

07 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/feb05b2ef24c/ changeset: feb05b2ef24c user: dan date: 2013-02-07 19:16:41 summary: Add get() method to ToolDataTableManager. affected #: 1 file diff -r bc309f6d4ce5e18c9d2c8eac6a50eeac06664554 -r feb05b2ef24c665e9245e554af40104a812f03a9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -28,6 +28,11 @@ return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) + def get( self, name, default=None ): + try: + return self[ name ] + except KeyError: + return default def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: 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: Add function to query tool data tables by attribute-value pairs and expose this functionality to tool wrappers. This is needed for tool wrappers that use data tables but do not use dynamic options.
by Bitbucket 07 Feb '13

07 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc309f6d4ce5/ changeset: bc309f6d4ce5 user: jgoecks date: 2013-02-07 18:57:30 summary: Add function to query tool data tables by attribute-value pairs and expose this functionality to tool wrappers. This is needed for tool wrappers that use data tables but do not use dynamic options. affected #: 2 files diff -r 57bd06b6e9fa4cb1b6591216b6f4d3010b21f060 -r bc309f6d4ce5e18c9d2c8eac6a50eeac06664554 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2267,10 +2267,14 @@ `to_param_dict_string` method of the associated input. """ param_dict = dict() + # All parameters go into the param_dict param_dict.update( incoming ) - # Wrap parameters as neccesary + def wrap_values( inputs, input_values ): + """ + Wraps parameters as neccesary. + """ for input in inputs.itervalues(): if isinstance( input, Repeat ): for d in input_values[ input.name ]: @@ -2333,11 +2337,13 @@ else: input_values[ input.name ] = InputValueWrapper( input, input_values[ input.name ], param_dict ) + # HACK: only wrap if check_values is not false, this deals with external # tools where the inputs don't even get passed through. These # tools (e.g. UCSC) should really be handled in a special way. if self.check_values: wrap_values( self.inputs, param_dict ) + ## FIXME: when self.check_values==True, input datasets are being wrapped ## twice (above and below, creating 2 separate ## DatasetFilenameWrapper objects - first is overwritten by @@ -2390,6 +2396,20 @@ # failed to pass; for tool writing convienence, provide a # NoneDataset param_dict[ out_name ] = NoneDataset( datatypes_registry = self.app.datatypes_registry, ext = output.format ) + + # -- Add useful attributes/functions for use in creating command line. + + # Function for querying a data table. + def get_data_table_entry(table_name, query_attr, query_val, return_attr): + """ + Queries and returns an entry in a data table. + """ + + if table_name in self.app.tool_data_tables: + return self.app.tool_data_tables[ table_name ].get_entry( query_attr, query_val, return_attr ) + + param_dict['__get_data_table_entry__'] = get_data_table_entry + # We add access to app here, this allows access to app.config, etc param_dict['__app__'] = RawObjectWrapper( self.app ) # More convienent access to app.config.new_file_path; we don't need to diff -r 57bd06b6e9fa4cb1b6591216b6f4d3010b21f060 -r bc309f6d4ce5e18c9d2c8eac6a50eeac06664554 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -240,7 +240,26 @@ fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) - return rval + return rval + + def get_entry( self, query_attr, query_val, return_attr ): + """ + Returns table entry associated with a col/val pair. + """ + query_col = self.columns.get( query_attr, None ) + if not query_col: + return None + return_col = self.columns.get( return_attr, None ) + if not return_col: + return None + + # Look for table entry. + for fields in self.data: + if fields[ query_col ] == query_val: + rval = fields[ return_col ] + break + + return rval # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) 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 Bitbucket 07 Feb '13

07 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8ead26aaf2b/ changeset: b8ead26aaf2b user: joachimjacob date: 2013-01-23 11:08:03 summary: Adjusted subtract_query.py to accomodate for empty fields at end of lines. affected #: 1 file diff -r 3c752f2d4d958f34f085f2cc707c503693b4680d -r b8ead26aaf2b3e82334a2b071ad5221b54316e8d tools/new_operations/subtract_query.py --- a/tools/new_operations/subtract_query.py +++ b/tools/new_operations/subtract_query.py @@ -29,9 +29,12 @@ try: line = line.split('\t') line = '\t'.join([line[j] for j in range(begin_col-1, end_col)]) + # removing empty fields, we do not compare empty fields at the end of a line. + line = line.rstrip() lines.add( line ) except: pass else: + line = line.rstrip() lines.add( line ) if i: return (i+1, lines) else: return (i, lines) https://bitbucket.org/galaxy/galaxy-central/commits/57bd06b6e9fa/ changeset: 57bd06b6e9fa user: jgoecks date: 2013-02-07 15:38:56 summary: Merged in joachimjacob/galaxy-central-subtract_query_change (pull request #111) Adjusted subtract_query.py to accomodate for empty fields at end of lines. affected #: 1 file diff -r 14733d29e6dda03a49e5fe67e222480235f1901c -r 57bd06b6e9fa4cb1b6591216b6f4d3010b21f060 tools/new_operations/subtract_query.py --- a/tools/new_operations/subtract_query.py +++ b/tools/new_operations/subtract_query.py @@ -29,9 +29,12 @@ try: line = line.split('\t') line = '\t'.join([line[j] for j in range(begin_col-1, end_col)]) + # removing empty fields, we do not compare empty fields at the end of a line. + line = line.rstrip() lines.add( line ) except: pass else: + line = line.rstrip() lines.add( line ) if i: return (i+1, lines) else: return (i, lines) 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: Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14733d29e6dd/ changeset: 14733d29e6dd user: dan date: 2013-02-06 23:34:36 summary: Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko(a)jax.org) affected #: 3 files diff -r 8ada40b184144447c5949bbbac3e2ec65cfaac58 -r 14733d29e6dda03a49e5fe67e222480235f1901c tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -11,6 +11,7 @@ <tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" /><tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /><tool file="data_source/ratmine.xml" /><tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /> diff -r 8ada40b184144447c5949bbbac3e2ec65cfaac58 -r 14733d29e6dda03a49e5fe67e222480235f1901c tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -16,6 +16,7 @@ <tool file="data_source/flymine.xml" /><tool file="data_source/flymine_test.xml" /><tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /><tool file="data_source/ratmine.xml" /><tool file="data_source/yeastmine.xml" /><tool file="data_source/metabolicmine.xml" /> diff -r 8ada40b184144447c5949bbbac3e2ec65cfaac58 -r 14733d29e6dda03a49e5fe67e222480235f1901c tools/data_source/mousemine.xml --- /dev/null +++ b/tools/data_source/mousemine.xml @@ -0,0 +1,35 @@ +<?xml version="1.0"?> + +<tool name="MouseMine" id="mousemine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get"> + <display>go to MouseMine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="MouseMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + 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: Add a confirm dialog when deprecating repositories in the Tool Shed.
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ada40b18414/ changeset: 8ada40b18414 user: dan date: 2013-02-06 20:59:46 summary: Add a confirm dialog when deprecating repositories in the Tool Shed. affected #: 2 files diff -r b3a7c8da804caa2330b393ddb2a1fcfefad4e41e -r 8ada40b184144447c5949bbbac3e2ec65cfaac58 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -248,7 +248,8 @@ operations = [ grids.GridOperation( "Mark as deprecated", allow_multiple=False, condition=( lambda item: not item.deleted and not item.deprecated ), - async_compatible=False ), + async_compatible=False, + confirm="Are you sure that you want to deprecate this repository?" ), grids.GridOperation( "Mark as not deprecated", allow_multiple=False, condition=( lambda item: not item.deleted and item.deprecated ), diff -r b3a7c8da804caa2330b393ddb2a1fcfefad4e41e -r 8ada40b184144447c5949bbbac3e2ec65cfaac58 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -97,7 +97,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ) )}">Reset all repository metadata</a> %endif %if can_deprecate: - <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=True )}">Mark repository as deprecated</a> + <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=True )}" confirm="Are you sure that you want to deprecate this repository?">Mark repository as deprecated</a> %endif %if can_undeprecate: <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel: fix to hda update logging typo
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3a7c8da804c/ changeset: b3a7c8da804c user: carlfeberhard date: 2013-02-06 18:05:56 summary: history panel: fix to hda update logging typo affected #: 1 file diff -r ae446180fd11e74cfdcb25bf26d23b05889ab798 -r b3a7c8da804caa2330b393ddb2a1fcfefad4e41e static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -230,7 +230,7 @@ } else { var msg = _l( 'ERROR updating hdas from api history contents' ) + ': '; - history.log( msg, hdaIds, xhr, status, error, errorJSON ); + history.log( msg, hdaIds, xhr, status, error, errorJson ); alert( msg + hdaIds.join(',') ); } }, 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: Fix MarkupSafe import issue introduced in 7461:5f2db4a18d3d.
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae446180fd11/ changeset: ae446180fd11 user: dannon date: 2013-02-06 16:57:11 summary: Fix MarkupSafe import issue introduced in 7461:5f2db4a18d3d. affected #: 1 file diff -r a9913124b727dff41801c83fd74f06c6721a4f57 -r ae446180fd11e74cfdcb25bf26d23b05889ab798 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -4,6 +4,7 @@ import pkg_resources pkg_resources.require( "simplejson" ) +pkg_resources.require( "MarkupSafe" ) #MarkupSafe must load before mako pkg_resources.require( "Mako" ) import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Remove 'error' language from debug statement in GalaxyWebTransaction, get_history
by Bitbucket 06 Feb '13

06 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a9913124b727/ changeset: a9913124b727 user: carlfeberhard date: 2013-02-06 16:51:18 summary: Remove 'error' language from debug statement in GalaxyWebTransaction, get_history affected #: 1 file diff -r 3a0e3ef5414a06bc7ada75c3acb28affab7c916c -r a9913124b727dff41801c83fd74f06c6721a4f57 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -729,7 +729,7 @@ history = self.new_history() else: # Perhaps a bot is running a tool without having logged in to get a history - log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url ) + log.debug( "This request returned None from get_history(): %s" % self.request.browser_url ) return None return history def set_history( self, history ): 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: More url_for changes from base controllers.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a0e3ef5414a/ changeset: 3a0e3ef5414a user: dannon date: 2013-02-06 03:58:24 summary: More url_for changes from base controllers. affected #: 2 files diff -r cdd8b8a66a980d1761e47f9202114fbcfd218cf7 -r 3a0e3ef5414a06bc7ada75c3acb28affab7c916c lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -406,7 +406,7 @@ session.add( vis_rev ) session.flush() encoded_id = trans.security.encode_id( vis.id ) - return { "vis_id": encoded_id, "url": url_for( action=vis.type, id=encoded_id ) } + return { "vis_id": encoded_id, "url": url_for( controller='visualization', action=vis.type, id=encoded_id ) } def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ diff -r cdd8b8a66a980d1761e47f9202114fbcfd218cf7 -r 3a0e3ef5414a06bc7ada75c3acb28affab7c916c lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -987,18 +987,18 @@ sorts.append( 'None' ) elif new_sort is not None: sorts[-1] = new_sort - breadcrumb = "<a href='%s' class='breadcrumb'>heap</a>" % web.url_for() + breadcrumb = "<a href='%s' class='breadcrumb'>heap</a>" % web.url_for(controller='admin', action='memdump') # new lists so we can assemble breadcrumb links new_ids = [] new_sorts = [] for id, sort in zip( ids, sorts ): new_ids.append( id ) if id != 'None': - breadcrumb += "<a href='%s' class='breadcrumb'>[%s]</a>" % ( web.url_for( ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), id ) + breadcrumb += "<a href='%s' class='breadcrumb'>[%s]</a>" % ( web.url_for(controller='admin', action='memdump', ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), id ) heap = heap[int(id)] new_sorts.append( sort ) if sort != 'None': - breadcrumb += "<a href='%s' class='breadcrumb'>.by('%s')</a>" % ( web.url_for( ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), sort ) + breadcrumb += "<a href='%s' class='breadcrumb'>.by('%s')</a>" % ( web.url_for(controller='admin', action='memdump', ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), sort ) heap = heap.by( sort ) ids = ','.join( new_ids ) sorts = ','.join( new_sorts ) 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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