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commit/galaxy-central: greg: Handle exceptions when resetting all repository metadata in the tool shed.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e7420c93edfa/ changeset: e7420c93edfa user: greg date: 2012-04-03 20:15:53 summary: Handle exceptions when resetting all repository metadata in the tool shed. affected #: 1 file diff -r e380ade65ea1684025099e4b3543a77d07f3e3fe -r e7420c93edfab1766ec32a0002adee1dec8d30b3 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -464,9 +464,12 @@ count = 0 for repository in trans.sa_session.query( trans.model.Repository ) \ .filter( trans.model.Repository.table.c.deleted == False ): - reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) - log.debug( "Reset metadata on repository %s" % repository.name ) - count += 1 + try: + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) ) message = "Reset metadata on %d repositories" % count trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', 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: Include invalid tools in repository metadata, and enable the admin to reset all repository metadata.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e380ade65ea1/ changeset: e380ade65ea1 user: greg date: 2012-04-03 19:52:50 summary: Include invalid tools in repository metadata, and enable the admin to reset all repository metadata. affected #: 5 files diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -457,6 +457,24 @@ status=status ) ) @web.expose @web.require_admin + def reset_all_repository_metadata( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + count = 0 + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ): + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + message = "Reset metadata on %d repositories" % count + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + webapp='community', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -201,7 +201,7 @@ can_set_metadata = False correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to resolve this issue.<br/>" + correction_msg += "that includes the required entry to correct this error.<br/>" invalid_files.append( ( name, correction_msg ) ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. @@ -290,6 +290,7 @@ # repository tip, we handle things like .loc.sample files here. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -324,6 +325,7 @@ except Exception, e: valid = False invalid_files.append( ( name, str( e ) ) ) + invalid_tool_configs.append( name ) if valid and tool is not None: can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) if can_set_metadata: @@ -331,6 +333,8 @@ tool_config = os.path.join( root, name ) repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( name ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -344,11 +348,14 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ): # Browse repository files within a change set to generate metadata. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] tmp_datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -392,6 +399,7 @@ valid = True except Exception, e: invalid_files.append( ( filename, str( e ) ) ) + invalid_tool_configs.append( filename ) valid = False if valid and tool is not None: # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename @@ -403,6 +411,8 @@ # tip, we do not have to handle any .loc.sample files since they would have been handled previously. repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( filename ) try: os.unlink( tmp_filename ) except: @@ -417,6 +427,8 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata""" diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -770,15 +770,14 @@ """ If the received changeset_revision includes a file named readme (case ignored), return it's contents. """ - name = kwd[ 'name' ] - owner = kwd[ 'owner' ] + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) for root, dirs, files in os.walk( repo_dir ): for name in files: - if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt' ]: + if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt', '%s.txt' % repository_name ]: f = open( os.path.join( root, name ), 'r' ) text = f.read() f.close() @@ -1814,6 +1813,81 @@ changeset_revision=changeset_revision, message=message, status='error' ) ) + @web.expose + def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'error' ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository( trans, repository_id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + invalid_message = '' + if changeset_revision == repository.tip: + for root, dirs, files in os.walk( repo_dir ): + found = False + for name in files: + if name == tool_config: + tool_config_path = os.path.join( root, name ) + found = True + break + if found: + break + else: + for filename in ctx: + if filename == tool_config: + fctx = ctx[ filename ] + # Write the contents of datatypes_config.xml to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tool_config_path = fh.name + fh.close() + fh = open( tool_config_path, 'w' ) + fh.write( fctx.data() ) + fh.close() + break + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir ) + for invalid_file_tup in invalid_files: + invalid_tool_config, invalid_msg = invalid_file_tup + if tool_config == invalid_tool_config: + invalid_message = invalid_msg + break + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_path ) + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + if changeset_revision != repository.tip: + try: + os.unlink( tool_config_path ) + except: + pass + try: + if invalid_message: + message = invalid_message + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + changeset_revision=changeset_revision, + tool=tool, + tool_state=tool_state, + is_malicious=is_malicious, + webapp=webapp, + message=message, + status='error' ) + except Exception, e: + message = "This tool is invalid because: %s." % str( e ) + if webapp == 'galaxy': + return trans.response.send_redirect( web.url_for( controller='repository', + action='preview_tools_in_changeset', + repository_id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -55,6 +55,9 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div><div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_all_repository_metadata', webapp='community' )}">Reset all metadata</a> + </div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a></div></div> diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -95,7 +95,7 @@ <div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td> + <td><b>Valid tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td></tr></table></div> @@ -147,6 +147,31 @@ </div><div style="clear: both"></div> %endif + %if 'invalid_tools' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Invalid tools</b><i> - click the tool config file name to see why the tool is invalid</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% invalid_tool_configs = metadata[ 'invalid_tools' ] %> + <table class="grid"> + %for invalid_tool_config in invalid_tool_configs: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + ${invalid_tool_config} + </a> + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %if 'workflows' in metadata: ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: In the DistributedObjectStore, when update_from_file is called with create=True, call DistributedObjectStore.create().
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a0f64b544cc6/ changeset: a0f64b544cc6 user: natefoo date: 2012-04-03 17:55:56 summary: In the DistributedObjectStore, when update_from_file is called with create=True, call DistributedObjectStore.create(). affected #: 1 file diff -r 8a572a3e1685e58212533c6141714c323bc67159 -r a0f64b544cc6412516a62459808e0026d2897dc0 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -963,6 +963,9 @@ return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) def update_from_file(self, obj, **kwargs): + if kwargs.get('create', False): + self.create(obj, **kwargs) + kwargs['create'] = False return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) def get_object_url(self, obj, **kwargs): 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 02 Apr '12

02 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5fdeb38b1e65/ changeset: 5fdeb38b1e65 user: james_taylor date: 2012-04-03 08:25:52 summary: style: fixes for history state images affected #: 3 files diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1401,8 +1401,6 @@ padding: 0; } -@import "base_sprites"; - .tipsy { padding: 5px; font-size: 10px; @@ -1521,19 +1519,19 @@ div.historyItem-error { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_error.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_error.png; + // } } div.historyItem-empty { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_empty.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_empty.png; + // } } div.historyItem-running { @@ -1561,11 +1559,11 @@ } div.historyItem-queued { - // background: @history_queued_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_queued.png; - } + background: @history_queued_bg; + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_queued.png; + // } } div.historyItem-noPermission { @@ -1681,3 +1679,4 @@ font-weight: bold; } +@import "base_sprites"; diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -99,4 +99,20 @@ -sprite-group: fugue; -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; +} + + +div.historyItem-error .state-icon { + -sprite-group: history-states; + -sprite-image: data_error.png; +} + +div.historyItem-empty .state-icon { + -sprite-group: history-states; + -sprite-image: data_empty.png; +} + +div.historyItem-queued .state-icon { + -sprite-group: history-states; + -sprite-image: data_queued.png; } \ No newline at end of file diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -224,7 +224,7 @@ .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;} @@ -677,6 +677,45 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} +.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} +.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} +.tipsy-north{background-position:top center;} +.tipsy-south{background-position:bottom center;} +.tipsy-east{background-position:right center;} +.tipsy-west{background-position:left center;} +.editable-text{cursor:pointer;} +.editable-text:hover{cursor:text;border:dotted #999999 1px;} +.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} +body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} +div.historyLinks{margin:5px 5px;} +div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} +.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} +div.historyItem div.historyItem{margin-right:-11px;} +div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} +div.historyItem-error{background:#ffcccc;} +div.historyItem-empty{background:#ffcccc;} +div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} +div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} +div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} +div.historyItem-queued{background:#eeeeee;} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} +div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} +div.historyItemButtons{float:right;} +div.historyItemBody div{padding-top:2px;} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} +body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} +hr{border:none;height:0px;margin-top:0px;} +div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} +div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} +div.toolSectionTitle{font-weight:bold;} +div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} +div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} +div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} +div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} @@ -702,42 +741,6 @@ .icon-button.plus-button{background:url(fugue.png) no-repeat 0px -338px;} .icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -390px;} -.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} -.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} -.tipsy-north{background-position:top center;} -.tipsy-south{background-position:bottom center;} -.tipsy-east{background-position:right center;} -.tipsy-west{background-position:left center;} -.editable-text{cursor:pointer;} -.editable-text:hover{cursor:text;border:dotted #999999 1px;} -.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} -div.historyLinks{margin:5px 5px;} -div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} -div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} -.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} -div.historyItem div.historyItem{margin-right:-11px;} -div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} -div.historyItem-error{background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} -div.historyItem-empty{background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} -div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} -div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} -div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} -div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} -div.historyItemButtons{float:right;} -div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} -pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -hr{border:none;height:0px;margin-top:0px;} -div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} -div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} -div.toolSectionTitle{font-weight:bold;} -div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} -div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} +div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} +div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} +div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} https://bitbucket.org/galaxy/galaxy-central/changeset/8a572a3e1685/ changeset: 8a572a3e1685 user: james_taylor date: 2012-04-03 08:29:00 summary: merge affected #: 3 files diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1422,8 +1422,6 @@ padding: 0; } -@import "base_sprites"; - .tipsy { padding: 5px; font-size: 10px; @@ -1542,19 +1540,19 @@ div.historyItem-error { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_error.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_error.png; + // } } div.historyItem-empty { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_empty.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_empty.png; + // } } div.historyItem-running { @@ -1582,11 +1580,11 @@ } div.historyItem-queued { - // background: @history_queued_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_queued.png; - } + background: @history_queued_bg; + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_queued.png; + // } } div.historyItem-noPermission { @@ -1695,3 +1693,4 @@ font-weight: bold; } +@import "base_sprites"; diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -103,4 +103,20 @@ -sprite-group: fugue; -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; +} + + +div.historyItem-error .state-icon { + -sprite-group: history-states; + -sprite-image: data_error.png; +} + +div.historyItem-empty .state-icon { + -sprite-group: history-states; + -sprite-image: data_empty.png; +} + +div.historyItem-queued .state-icon { + -sprite-group: history-states; + -sprite-image: data_queued.png; } \ No newline at end of file diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -682,6 +682,44 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} +.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} +.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} +.tipsy-north{background-position:top center;} +.tipsy-south{background-position:bottom center;} +.tipsy-east{background-position:right center;} +.tipsy-west{background-position:left center;} +.editable-text{cursor:pointer;} +.editable-text:hover{cursor:text;border:dotted #999999 1px;} +.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} +body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} +div.historyLinks{margin:5px 5px;} +div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} +.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} +div.historyItem div.historyItem{margin-right:-11px;} +div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} +div.historyItem-error{background:#ffcccc;} +div.historyItem-empty{background:#ffcccc;} +div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} +div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} +div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} +div.historyItem-queued{background:#eeeeee;} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} +div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} +div.historyItemButtons{float:right;} +div.historyItemBody div{padding-top:2px;} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} +body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} +div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} +div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} +div.toolSectionTitle{font-weight:bold;} +div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} +div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} +div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} +div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} @@ -708,41 +746,6 @@ .icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} .icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -390px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;} -.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} -.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} -.tipsy-north{background-position:top center;} -.tipsy-south{background-position:bottom center;} -.tipsy-east{background-position:right center;} -.tipsy-west{background-position:left center;} -.editable-text{cursor:pointer;} -.editable-text:hover{cursor:text;border:dotted #999999 1px;} -.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} -div.historyLinks{margin:5px 5px;} -div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} -div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} -.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} -div.historyItem div.historyItem{margin-right:-11px;} -div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} -div.historyItem-error{background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} -div.historyItem-empty{background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} -div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} -div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} -div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} -div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} -div.historyItemButtons{float:right;} -div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} -pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} -div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} -div.toolSectionTitle{font-weight:bold;} -div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} -div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} +div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} +div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} +div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} 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.

1 0

commit/galaxy-central: dannon: Fix inflector for n == 0
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1200112cd51a/ changeset: 1200112cd51a user: dannon date: 2012-04-02 22:58:16 summary: Fix inflector for n == 0 affected #: 1 file diff -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 lib/galaxy/util/inflection.py --- a/lib/galaxy/util/inflection.py +++ b/lib/galaxy/util/inflection.py @@ -14,7 +14,7 @@ def cond_plural(self, number_of_records, word) : '''Returns the plural form of a word if first parameter is greater than 1''' - if number_of_records > 1 : + if number_of_records != 1: return self.pluralize(word) else : return word @@ -385,4 +385,4 @@ # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THIS SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THIS SOFTWARE. \ No newline at end of file +# THIS SOFTWARE. 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.

1 0

commit/galaxy-central: jgoecks: Fix variable name bug that occurred when rendering tool links outside a section.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f9b7d8a617d/ changeset: 3f9b7d8a617d user: jgoecks date: 2012-04-02 22:25:17 summary: Fix variable name bug that occurred when rendering tool links outside a section. affected #: 2 files diff -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -355,7 +355,7 @@ this_el.append(section_title_view.$el); } else if (panel_elt instanceof Tool) { - var tool_view = new ToolLinkView({model: elt, className: "toolTitleNoSection"}); + var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); tool_view.render(); this_el.append(tool_view.$el); } diff -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Make sure a valid tool has a guid.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2ec5e00abdc5/ changeset: 2ec5e00abdc5 user: greg date: 2012-04-02 22:16:37 summary: Make sure a valid tool has a guid. affected #: 1 file diff -r 080242921d9fb538b280a31260c687a0053a3eb7 -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -45,10 +45,11 @@ if 'tools' in metadata: tool_dicts = metadata[ 'tools' ] for tool_dict in tool_dicts: - guid = tool_dict[ 'guid' ] - if guid not in processed_guids: - valid_tools += 1 - processed_guids.append( guid ) + if 'guid' in tool_dict: + guid = tool_dict[ 'guid' ] + if guid not in processed_guids: + valid_tools += 1 + processed_guids.append( guid ) processed_repository_ids.append( repository.id ) return valid_tools 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: Add a counter utility to the tool shed.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/080242921d9f/ changeset: 080242921d9f user: greg date: 2012-04-02 22:13:08 summary: Add a counter utility to the tool shed. affected #: 7 files diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,6 +1,6 @@ import os, tempfile, shutil, subprocess, logging, string from datetime import date, datetime, timedelta -from time import strftime +from time import strftime, gmtime from galaxy import util from galaxy.datatypes.checkers import * from galaxy.util.json import * @@ -21,6 +21,37 @@ '\'' : ''' } VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +class ShedCounter( object ): + def __init__( self, model ): + self.model = model + self.count_time = strftime( "%b %d, %Y", gmtime() ) + self.valid_tools = self.count_valid_tools() + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.model.context + def count_valid_tools( self ): + valid_tools = 0 + processed_repository_ids = [] + for repository_metadata in self.sa_session.query( self.model.RepositoryMetadata ) \ + .filter( and_( self.model.RepositoryMetadata.table.c.malicious == False, + self.model.RepositoryMetadata.table.c.metadata is not None, + self.model.RepositoryMetadata.table.c.tool_versions is not None ) ): + processed_guids = [] + repository = repository_metadata.repository + if repository.id not in processed_repository_ids: + for revision_metadata in repository.downloadable_revisions: + metadata = revision_metadata.metadata + if 'tools' in metadata: + tool_dicts = metadata[ 'tools' ] + for tool_dict in tool_dicts: + guid = tool_dict[ 'guid' ] + if guid not in processed_guids: + valid_tools += 1 + processed_guids.append( guid ) + processed_repository_ids.append( repository.id ) + return valid_tools + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -43,6 +43,8 @@ # 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 + # TODO: Add OpenID support + self.openid_providers = OpenIDProviders() + self.shed_counter = self.model.shed_counter def shutdown( self ): pass diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -321,7 +321,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, repository_metadata.changeset_revision ) + ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -140,7 +140,7 @@ changeset rev and the changeset revision string. """ repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) else: @@ -425,7 +425,7 @@ repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) metadata_dict = {} invalid_files = [] if ctx is not None: @@ -514,7 +514,7 @@ ancestor_metadata_dict = None for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) + ctx = get_changectx_for_changeset( repo, current_changeset_revision ) if current_changeset_revision == repository.tip: current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) else: @@ -740,7 +740,7 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): +def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -963,7 +963,7 @@ # Get the tool config file name from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) fctx = None for filename in ctx: filename_head, filename_tail = os.path.split( filename ) @@ -1001,7 +1001,7 @@ refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -854,7 +854,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # Load each tool in the repository's changeset_revision to generate a list of # tool guids, since guids differentiate tools by id and version. - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx is not None: tool_guids = [] for filename in ctx: @@ -1579,7 +1579,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, ctx_str ) + ctx = get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -13,6 +13,7 @@ from galaxy.model.orm.ext.assignmapper import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch +from galaxy.util.shed_util import ShedCounter from galaxy.webapps.community.security import CommunityRBACAgent metadata = MetaData() @@ -247,4 +248,5 @@ result.create_tables = create_tables #load local galaxy security policy result.security_agent = CommunityRBACAgent( result ) + result.shed_counter = ShedCounter( result ) return result diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -39,7 +39,7 @@ <%def name="left_panel()"><div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Galaxy Tool Shed</div> + <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.count_time}</div></div><div class="page-container" style="padding: 10px;"><div class="toolMenu"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: I missed a call to a renamed method in the job manager.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/babda116a4c0/ changeset: babda116a4c0 user: natefoo date: 2012-04-02 21:38:02 summary: I missed a call to a renamed method in the job manager. affected #: 1 file diff -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 -r babda116a4c0193c2ee4941d09ac78940098fece lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -89,7 +89,7 @@ log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) else: - job.handler = self.__select_handler( job ) # handler's recovery method will take it from here + job.handler = self.__get_handler( job ) # handler's recovery method will take it from here log.info( "(%d) Job in '%s' state had no handler at job manager startup, assigned '%s' handler" % ( job.id, job.state, job.handler ) ) if self.sa_session.dirty: self.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: changes to aaChanges interface
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/07eb5affb4c0/ changeset: 07eb5affb4c0 user: richard_burhans date: 2012-04-02 20:28:08 summary: changes to aaChanges interface affected #: 1 file diff -r 758f425498670dbe992701df81d277dbc7cd6de7 -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > $out_file1 </command><inputs> @@ -17,6 +17,10 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <param name="uniqpos" type="select" label="Only report each SNP position once"> + <option value="1" selected="true">Yes</option> + <option value="0">No</option> + </param><conditional name="strand_source"><param name="strand_choice" type="select" label="Strand info"><option value="data_column">a column in the dataset</option> @@ -54,6 +58,7 @@ <param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output1.interval" /></test><test> @@ -62,6 +67,7 @@ <param name="col1" value="4" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output2.interval" /></test><test> 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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