[galaxy-commits] commit/galaxy-central: greg: Rename community template path to tool_shed.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b985587c3392/ changeset: b985587c3392 user: greg date: 2013-02-26 23:12:52 summary: Rename community template path to tool_shed. affected #: 101 files diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -36,7 +36,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/index.mako', + return trans.fill_template( '/webapps/tool_shed/admin/index.mako', message=message, status=status ) @web.expose @@ -49,7 +49,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/center.mako', + return trans.fill_template( '/webapps/tool_shed/admin/center.mako', message=message, status=status ) @web.expose diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -454,7 +454,7 @@ """ Column that displays community ratings for an item. """ def get_value( self, trans, grid, item ): ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, item, webapp_model=trans.model ) - return trans.fill_template( "community_rating.mako", + return trans.fill_template( "tool_shed_rating.mako", ave_item_rating=ave_item_rating, num_ratings=num_ratings, item_id=trans.security.encode_id( item.id ) ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -403,7 +403,7 @@ # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ IdColumn( "Id", @@ -567,7 +567,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/create_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/create_category.mako', name=name, description=description, message=message, @@ -667,7 +667,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/edit_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/edit_category.mako', category=category, message=message, status=status ) @@ -677,7 +677,7 @@ if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. # What we've done is rendered the search box for the RepositoryGrid on the grid.mako - # template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. + # template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). return trans.response.send_redirect( web.url_for( controller='admin', action='browse_repositories', @@ -714,7 +714,7 @@ if 'regenerate_statistics_button' in kwd: trans.app.shed_counter.generate_statistics() message = "Successfully regenerated statistics" - return trans.fill_template( '/webapps/community/admin/statistics.mako', + return trans.fill_template( '/webapps/tool_shed/admin/statistics.mako', message=message, status=status ) @web.expose @@ -726,7 +726,7 @@ message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repositories_select_field = suc.build_repository_ids_select_field( trans ) - return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako', + return trans.fill_template( '/webapps/tool_shed/admin/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, status=status ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -46,7 +46,7 @@ return 0 title = "Categories" model_class = model.Category - template='/webapps/community/category/grid.mako' + template='/webapps/tool_shed/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -82,7 +82,7 @@ return 0 title = "Categories of valid repositories" model_class = model.Category - template='/webapps/community/category/valid_grid.mako' + template='/webapps/tool_shed/category/valid_grid.mako' default_sort_key = "name" columns = [ CategoryGrid.NameColumn( "Name", @@ -172,7 +172,7 @@ # Grid definition title = "Repositories" model_class = model.Repository - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -503,7 +503,7 @@ # Grid definition title = "Matching repositories" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", @@ -571,7 +571,7 @@ # The request came from the tool shed. if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. What we've done is rendered the search box for the - # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we + # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. Since we # are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository @@ -629,7 +629,7 @@ repository.name, repository.user.username, downloadable_revision.changeset_revision ) - return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, message=message, @@ -747,7 +747,7 @@ suc.update_repository( repo ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, metadata=metadata, commit_message=commit_message, @@ -937,7 +937,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: - return trans.fill_template( "/webapps/community/repository/contact_owner.mako", + return trans.fill_template( "/webapps/tool_shed/repository/contact_owner.mako", repository=repository, metadata=metadata, message=message, @@ -1032,7 +1032,7 @@ action='view_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - return trans.fill_template( '/webapps/community/repository/create_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, description=description, long_description=long_description, @@ -1073,7 +1073,7 @@ is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, metadata=metadata, changeset_revision=changeset_revision, @@ -1197,7 +1197,7 @@ message = "No search performed - each field must contain the same number of comma-separated items." status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_tools.mako', tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1286,7 +1286,7 @@ exact_matches_checked = False workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_workflows.mako', workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1690,7 +1690,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) + return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -1762,7 +1762,7 @@ user_id = params.get( 'user_id', None ) repository_id = params.get( 'repository_id', None ) changeset_revision = params.get( 'changeset_revision', None ) - return trans.fill_template( '/webapps/community/index.mako', + return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, has_reviewed_repositories=has_reviewed_repositories, has_deprecated_repositories=has_deprecated_repositories, @@ -1813,7 +1813,7 @@ elif error_message: message = error_message try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, tool=tool, @@ -1872,7 +1872,7 @@ .order_by( trans.model.Repository.table.c.name ): if user.email in repository.email_alerts: email_alert_repositories.append( repository ) - return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + return trans.fill_template( "/webapps/tool_shed/user/manage_email_alerts.mako", new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -2056,7 +2056,7 @@ review_id = None can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/manage_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, long_description=long_description, @@ -2163,7 +2163,7 @@ add_id_to_name=False, downloadable=False ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, repository_metadata_id=repository_metadata_id, @@ -2230,7 +2230,7 @@ rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/rate_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, avg_rating=avg_rating, @@ -2242,7 +2242,7 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template. + # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. # It resets all metadata on the complete changelog for a single repository in the tool shed. invalid_file_tups, metadata_dict = suc.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: @@ -2405,7 +2405,7 @@ message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, @@ -2672,7 +2672,7 @@ changesets.insert( 0, change_dict ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/view_changelog.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changelog.mako', repository=repository, metadata=metadata, changesets=changesets, @@ -2703,7 +2703,7 @@ diffs.append( suc.to_safe_string( diff, to_html=True ) ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, ctx_str ) - return trans.fill_template( '/webapps/community/repository/view_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', repository=repository, metadata=metadata, ctx=ctx, @@ -2810,7 +2810,7 @@ review_id = None containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) - return trans.fill_template( '/webapps/community/repository/view_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, repository_metadata_id=repository_metadata_id, @@ -2893,7 +2893,7 @@ review_id = trans.security.encode_id( review.id ) else: review_id = None - return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_tool_metadata.mako", repository=repository, metadata=metadata, tool=tool, @@ -2919,7 +2919,7 @@ repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata - return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_workflow.mako", repository=repository, changeset_revision=changeset_revision, repository_metadata_id=repository_metadata_id, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -27,7 +27,7 @@ return component.description title = "Repository review components" model_class = model.Component - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -89,7 +89,7 @@ return rval title = "All reviewed repositories" model_class = model.Repository - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "Repository.name" columns = [ RepositoryGrid.NameColumn( "Repository name", @@ -196,7 +196,7 @@ return '' title = "Reviews by user" model_class = model.RepositoryReview - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = 'repository_id' columns = [ RepositoryNameColumn( "Repository Name", @@ -316,7 +316,7 @@ repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/browse_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, review=review, @@ -361,7 +361,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/create_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/create_component.mako', name=name, description=description, message=message, @@ -456,7 +456,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/edit_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_component.mako', component=component, message=message, status=status ) @@ -576,7 +576,7 @@ selected_value=selected_value, for_component=False ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/edit_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, changeset_revision_label=changeset_revision_label, @@ -688,7 +688,7 @@ installable=installable, can_add_review=can_add_review ) reviews_dict[ changeset_revision ] = revision_dict - return trans.fill_template( '/webapps/community/repository_review/reviews_of_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_repository.mako', repository=repository, reviews_dict=reviews_dict, mine=mine, @@ -709,7 +709,7 @@ installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/reviews_of_changeset_revision.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, @@ -773,7 +773,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = suc.get_previous_repository_reviews( trans, repository, changeset_revision ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -204,7 +204,7 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - return trans.fill_template( '/webapps/community/repository/upload.mako', + return trans.fill_template( '/webapps/tool_shed/repository/upload.mako', repository=repository, url=url, commit_message=commit_message, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -733,7 +733,7 @@ status = util.restore_text( kwd.get( 'status', 'done' ) ) migration_stages_dict = odict() migration_modules = [] - migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'migrate', 'versions' ) ) + migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions' ) ) migration_scripts_dir_contents = os.listdir( migration_scripts_dir ) for item in migration_scripts_dir_contents: if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ): diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -735,7 +735,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/user/manage_info.mako', + return trans.fill_template( '/webapps/tool_shed/user/manage_info.mako', cntrller=cntrller, user=user, email=email, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -1,4 +1,4 @@ -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="browse_files(title_text, directory_path)"><script type="text/javascript"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%namespace file="/admin/tool_shed_repository/common.mako" import="*" /><%def name="stylesheets()"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()"> ${parent.javascripts()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/view_workflow.mako --- a/templates/admin/tool_shed_repository/view_workflow.mako +++ b/templates/admin/tool_shed_repository/view_workflow.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><% from galaxy.web.framework.helpers import time_ago @@ -11,7 +11,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/webapps/community/base_panels.mako' + return '/webapps/tool_shed/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/community_rating.mako --- a/templates/community_rating.mako +++ /dev/null @@ -1,33 +0,0 @@ -<% - label = "ratings" - if num_ratings == 1: - label = "rating" -%> -<div> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" - %if ave_item_rating > 0 and ave_item_rating <= 1.5: - checked="checked" - %endif - - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" - %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" - %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" - %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" - %if ave_item_rating > 4.5: - checked="checked" - %endif - /> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/tool_shed_rating.mako --- /dev/null +++ b/templates/tool_shed_rating.mako @@ -0,0 +1,33 @@ +<% + label = "ratings" + if num_ratings == 1: + label = "rating" +%> +<div> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" + %if ave_item_rating > 0 and ave_item_rating <= 1.5: + checked="checked" + %endif + + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" + %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" + %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" + %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" + %if ave_item_rating > 4.5: + checked="checked" + %endif + /> +</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/logout.mako --- a/templates/user/logout.mako +++ b/templates/user/logout.mako @@ -1,4 +1,4 @@ -<%inherit file="/base_panels.mako"/> +<%inherit file="/webapps/galaxy/base_panels.mako"/><%namespace file="/message.mako" import="render_msg" /> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/center.mako --- a/templates/webapps/community/admin/center.mako +++ /dev/null @@ -1,50 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - - -<%def name="title()">Galaxy Administration</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>Administration</h2> - -<p>The menu on the left provides the following features</p> -<ul> - <li> - <strong>Categories</strong> - <p/> - <ul> - <li> - <strong>Manage categories</strong> - </li> - <p/> - </ul> - </li> - <li> - <strong>Security</strong> - <p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> - <p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> - <p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> - <p/> -</ul> -<br/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ /dev/null @@ -1,139 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Administration</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - <div class="toolSectionTitle"> - Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}">Reset selected metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a> - </div> - </div> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Categories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Security - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Statistics - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a> - </div> - </div> - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - center_url = h.url_for(controller='admin', action='center' ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ /dev/null @@ -1,40 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_misc_javascripts()} -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="warningmessage"> - Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. - Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful. Watch - the tool shed paster log to pass the time if necessary. -</div> - -<div class="toolForm"> - <div class="toolFormTitle">Reset all metadata on each selected repository</div> - <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}" method="post" > - <div class="form-row"> - Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b> - </div> - <div style="clear: both"></div> - <div class="form-row"> - ${repositories_select_field.get_html()} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ /dev/null @@ -1,56 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" > - <div class="form-row"> - <table class="grid"> - <tr> - <th>Item</th> - <th>Count</th> - </tr> - <tr> - <td>Total repositories</td> - <td>${trans.app.shed_counter.repositories | h}</td> - </tr> - ##<tr> - ## <td>Empty repositories</td> - ## <td>${trans.app.shed_counter.new_repositories | h}</td> - ##</tr> - <tr> - <td>Deleted repositories</td> - <td>${trans.app.shed_counter.deleted_repositories | h}</td> - </tr> - <tr> - <td>Valid tools</td> - <td>${trans.app.shed_counter.valid_tools | h}</td> - </tr> - <tr> - <td>Invalid tools</td> - <td>${trans.app.shed_counter.invalid_tools | h}</td> - </tr> - <tr> - <td>Workflows</td> - <td>${trans.app.shed_counter.workflows | h}</td> - </tr> - <tr> - <td>Proprietary datatypes</td> - <td>${trans.app.shed_counter.proprietary_datatypes | h}</td> - </tr> - <tr> - <td>Total clones</td> - <td>${trans.app.shed_counter.total_clones | h}</td> - </tr> - </table> - </div> - <div class="form-row"> - <input type="submit" name="regenerate_statistics_button" value="Regenerate statistics"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ /dev/null @@ -1,133 +0,0 @@ -<%inherit file="/base/base_panels.mako"/> - -## Default title -<%def name="title()">Galaxy Tool Shed</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -## Masthead -<%def name="masthead()"> - - ## Tab area, fills entire width - <div style="position: relative; right: -50%; float: left;"> - <div style="display: block; position: relative; right: 50%;"> - - <ul class="nav" border="0" cellspacing="0"> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> - <% - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - %> - <li class="${cls}" style="${style}"> - %if href: - <a class="${a_cls}" data-toggle="dropdown" target="${target}" href="${href}">${display}${extra}</a> - %else: - <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> - %endif - %if menu_options: - <ul class="dropdown-menu"> - %for menu_item in menu_options: - %if not menu_item: - <li class="divider"></li> - %else: - <li> - %if len ( menu_item ) == 1: - ${menu_item[0]} - %elif len ( menu_item ) == 2: - <% name, link = menu_item %> - <a href="${link}">${name | h}</a> - %else: - <% name, link, target = menu_item %> - <a target="${target}" href="${link}">${name | h}</a> - %endif - </li> - %endif - %endfor - </ul> - %endif - </li> - </%def> - - ## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )} - - ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - ## Help tab. - <% - menu_options = [] - qa_url = app.config.get( "qa_url", None ) - if qa_url: - menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ] - menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] ) - tab( "help", _("Help"), None, menu_options=menu_options ) - %> - - ## User tabs. - <% - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - %> - </ul> - </div> - </div> - - ## Logo, layered over tabs to be clickable - <div class="title"> - <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> - Galaxy Tool Shed - %if app.config.brand: - <span>/ ${app.config.brand}</span> - %endif - </a> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/create_category.mako --- a/templates/webapps/community/category/create_category.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Category</div> - <div class="toolFormBody"> - <form name="create_category_form" id="create_category_form" action="${h.url_for(controller='admin', action='create_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <input name="name" type="textfield" value="${name | h}" size=40"/> - </div> - <div class="form-row"> - <label>Description:</label> - <input name="description" type="textfield" value="${description | h}" size=40"/> - </div> - <div class="form-row"> - <input type="submit" name="create_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/edit_category.mako --- a/templates/webapps/community/category/edit_category.mako +++ /dev/null @@ -1,43 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="edit_category" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name | h}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description | h}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="edit_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/grid.mako --- a/templates/webapps/community/category/grid.mako +++ /dev/null @@ -1,64 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -## TODO: This is very similar to this directory's valid_grid.mako, so see if we can re-use this code in a better way. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import RepositoryGrid - repo_grid = RepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/valid_grid.mako --- a/templates/webapps/community/category/valid_grid.mako +++ /dev/null @@ -1,63 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import ValidRepositoryGrid - repo_grid = ValidRepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ /dev/null @@ -1,84 +0,0 @@ -<%def name="common_misc_javascripts()"> - <script type="text/javascript"> - function checkAllFields( name ) - { - var chkAll = document.getElementById( 'checkAll' ); - var checks = document.getElementsByTagName( 'input' ); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = false - } - } - } - } - </script> -</%def> - -<%def name="render_star_rating( name, rating, disabled=False )"> - <% - if disabled: - disabled_str = ' disabled="disabled"' - else: - disabled_str = '' - html = '' - for index in range( 1, 6 ): - html += '<input name="%s" type="radio" class="star" value="%s" %s' % ( str( name ), str( index ), disabled_str ) - if rating > ( index - 0.5 ) and rating < ( index + 0.5 ): - html += ' checked="checked"' - html += '/>' - %> - ${html} -</%def> - -<%def name="render_long_description( description_text )"> - <style type="text/css"> - #description_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> - <div class="form-row"> - <label>Detailed description:</label> - <table id="description_table"> - <tr><td>${description_text}</td></tr> - </table> - <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 ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ /dev/null @@ -1,165 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - %if user_id or repository_id: - ## The route in was a sharable url, and may have included a changeset_revision, although we don't check for it. - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a href="${h.url_for( controller='repository', action='index' )}">Browse by category</a> - </div> - %else: - %if repository_metadata: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Search - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - %if trans.user: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - My Repositories and Tools - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a> - </div> - %if has_reviewed_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='reviewed_repositories_i_own' )}">Reviewed repositories I own</a> - </div> - %endif - %if has_deprecated_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='deprecated_repositories_i_own' )}">Deprecated repositories I own</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_writable_repositories' )}">My writable repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - %else: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a> - </div> - %endif - %endif - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status ) - elif repository_id and changeset_revision: - # Route in was a sharable url: /view/{owner}/{name}/{changeset_revision}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, changeset_revision=changeset_revision, message=message, status=status ) - elif repository_id: - # Route in was a sharable url: /view/{owner}/{name}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, message=message, status=status ) - elif user_id: - # Route in was a sharable url: /view/{owner}. - center_url = h.url_for( controller='repository', action='browse_repositories', operation="repositories_by_user", user_id=user_id, message=message, status=status ) - else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/message.mako --- a/templates/webapps/community/message.mako +++ /dev/null @@ -1,1 +0,0 @@ -<%inherit file="../../message.mako"/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ /dev/null @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - %if invalid_tools_dict: - <div class="toolFormTitle">Invalid tools<i> - click the tool config file name to see why the tool is invalid</i></div> - <div class="form-row"> - <table class="grid"> - <tr> - <th>Tool config</th> - <th>Repository name</th> - <th>Repository owner</th> - <th>Changeset revision</th> - </tr> - %for invalid_tool_config, repository_tup in invalid_tools_dict.items(): - <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %> - <tr> - <td> - <a class="view-info" href="${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 )}"> - ${invalid_tool_config} - </a> - </td> - <td>${repository_name | h}</td> - <td>${repository_owner | h}</td> - <td>${changeset_revision | h}</td> - </tr> - %endfor - </table> - </div> - </div> - %else: - <div class="form-row"> - %if cntrller == 'admin' and trans.user_is_admin(): - No repositories in this tool shed contain invalid tools. - %else: - None of your repositories contain invalid tools. - %endif - </div> - %endif -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ /dev/null @@ -1,156 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> - -<% - from galaxy.web.framework.helpers import time_ago - is_admin = trans.user_is_admin() - is_new = repository.is_new( trans.app ) - can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) - can_upload = can_push and ( not repository.deprecated ) - can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = not is_new - can_rate = trans.user and repository.user != trans.user - can_manage = is_admin or repository.user == trans.user - can_view_change_log = not is_new - has_readme = metadata and 'readme' in metadata -%> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "jquery.rating", "dynatree_skin/ui.dynatree" )} - <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> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} - ${common_javascripts(repository)} -</%def> - -<br/><br/> -<ul class="manage-table-actions"> - %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %else: - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> - <div popupmenu="repository-${repository.id}-popup"> - %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> - %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> - %endif - %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %endif - %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> - %endif - %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> - %endif - %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> - %endif - </div> - %endif -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -%if can_browse_contents: - <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name | h} revision ${repository.tip( trans.app ) | h} (repository tip)</div> - %if can_download: - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} - </div> - %endif - %if can_push: - <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" > - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - <div class="toolParamHelp" style="clear: both;"> - Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. - </div> - <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/> - </div> - <div class="form-row"> - <label>Message:</label> - <div class="form-row-input"> - %if commit_message: - <textarea name="commit_message" rows="3" cols="35">${commit_message | h}</textarea> - %else: - <textarea name="commit_message" rows="3" cols="35"></textarea> - %endif - </div> - <div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created if you delete selected files. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </form> - %else: - <div class="toolFormBody"> - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </div> - %endif - </div> - <p/> -%endif This diff is so big that we needed to truncate the remainder. 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.