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commit/galaxy-central: greg: Fix the operation handling in the rols and groups methos of the Admin controller.
by Bitbucket 07 Feb '13

07 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e8ad17c1786/ changeset: 2e8ad17c1786 user: greg date: 2013-02-07 22:36:53 summary: Fix the operation handling in the rols and groups methos of the Admin controller. affected #: 1 file diff -r ce9789a35356da2b2ee4ae723506d5af57a0ce69 -r 2e8ad17c1786b73ca6a5b9d60dcdf69ef7e50f4d lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1,3 +1,4 @@ +import logging from datetime import datetime, timedelta from string import punctuation as PUNCTUATION @@ -7,6 +8,8 @@ from galaxy.util import inflector from galaxy.web.form_builder import CheckboxField +log = logging.getLogger( __name__ ) + class Admin( object ): # Override these user_list_grid = None @@ -76,7 +79,7 @@ @web.require_admin def roles( self, trans, **kwargs ): if 'operation' in kwargs: - operation = kwargs['operation'].lower() + operation = kwargs[ 'operation' ].lower().replace( '+', ' ' ) if operation == "roles": return self.role( trans, **kwargs ) if operation == "create": @@ -411,7 +414,7 @@ @web.require_admin def groups( self, trans, **kwargs ): if 'operation' in kwargs: - operation = kwargs['operation'].lower() + operation = kwargs[ 'operation' ].lower().replace( '+', ' ' ) if operation == "groups": return self.group( trans, **kwargs ) if operation == "create": 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: Subtract query tool: make ignoring empty end columns and whitespace optional.
by Bitbucket 07 Feb '13

07 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce9789a35356/ changeset: ce9789a35356 user: jgoecks date: 2013-02-07 20:46:49 summary: Subtract query tool: make ignoring empty end columns and whitespace optional. affected #: 3 files diff -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 -r ce9789a35356da2b2ee4ae723506d5af57a0ce69 test-data/eq-showbeginning_e.dat --- /dev/null +++ b/test-data/eq-showbeginning_e.dat @@ -0,0 +1,10 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - diff -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 -r ce9789a35356da2b2ee4ae723506d5af57a0ce69 tools/new_operations/subtract_query.py --- a/tools/new_operations/subtract_query.py +++ b/tools/new_operations/subtract_query.py @@ -3,7 +3,8 @@ """ Subtract an entire query from another query -usage: %prog in_file_1 in_file_2 begin_col end_col output +usage: %prog in_file_1 in_file_2 begin_col end_col output + --ignore-empty-end-cols: ignore empty end columns when subtracting """ import sys, re from galaxy import eggs @@ -18,7 +19,7 @@ assert sys.version_info[:2] >= ( 2, 4 ) -def get_lines(fname, begin_col='', end_col=''): +def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False): lines = set([]) i = 0 for i, line in enumerate(file(fname)): @@ -29,12 +30,15 @@ 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() + if ignore_empty_end_cols: + # 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() + if ignore_empty_end_cols: + # removing empty fields, we do not compare empty fields at the end of a line. + line = line.rstrip() lines.add( line ) if i: return (i+1, lines) else: return (i, lines) @@ -83,9 +87,9 @@ lines1 is the set of unique lines in inp1_file diff1 is the number of duplicate lines removed from inp1_file """ - len1, lines1 = get_lines(inp1_file, begin_col, end_col) + len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols) diff1 = len1 - len(lines1) - len2, lines2 = get_lines(inp2_file, begin_col, end_col) + len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols) lines1.difference_update(lines2) """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file""" diff -r fd82f2ff9533fb5e4ef37c0404ede7c58d9234c5 -r ce9789a35356da2b2ee4ae723506d5af57a0ce69 tools/new_operations/subtract_query.xml --- a/tools/new_operations/subtract_query.xml +++ b/tools/new_operations/subtract_query.xml @@ -1,11 +1,18 @@ -<tool id="subtract_query1" name="Subtract Whole Dataset"> +<tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1"><description>from another dataset</description> - <command interpreter="python">subtract_query.py $input1 $input2 $begin_col $end_col $output</command> + <command interpreter="python"> + subtract_query.py $input1 $input2 $begin_col $end_col $output + #if str($ignore_empty_end_cols) == 'true': + --ignore-empty-end-cols + #end if + + </command><inputs><param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" /><param format="txt" name="input1" type="data" label="from" help="First dataset" /><param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" /><param name="end_col" type="data_column" data_ref="input1" force_select="False" label="and 'end column'" help="Specifying columns for restricting subtraction is available only for tabular formatted datasets" /> + <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/></inputs><outputs><data format="input" name="output" metadata_source="input1" /> @@ -45,6 +52,15 @@ <param name="end_col" value="None" /><output name="output" file="subtract-query-4.dat" /></test> +  + <test> + <param name="input1" value="eq-showbeginning_e.dat" /> + <param name="input2" value="eq-showtail.dat" /> + <param name="begin_col" value="None" /> + <param name="end_col" value="None" /> + <param name="ignore_empty_end_cols" value="true" /> + <output name="output" file="subtract-query-2.dat" /> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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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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