August 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: A couple of fixes in the manage_repository.mako template.
by Bitbucket 02 Aug '11

02 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/58ace2b0883a/ changeset: 58ace2b0883a user: greg date: 2011-08-02 20:35:24 summary: A couple of fixes in the manage_repository.mako template. affected #: 1 file (72 bytes) --- a/templates/webapps/community/repository/manage_repository.mako Tue Aug 02 14:19:38 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Aug 02 14:35:24 2011 -0400 @@ -5,6 +5,7 @@ <% from galaxy.web.framework.helpers import time_ago + is_admin = trans.user_is_admin() is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push @@ -17,6 +18,7 @@ browse_label = 'Browse or delete repository files' else: browse_label = 'Browse repository files' + can_set_malicious = metadata and can_set_metadata and is_admin %><%! @@ -140,7 +142,7 @@ <label>Times downloaded:</label> ${repository.times_downloaded} </div> - %if trans.user_is_admin(): + %if is_admin: <div class="form-row"><label>Location:</label> ${repository.repo_path} @@ -399,7 +401,7 @@ </div> %endif <p/> -%if not is_new and trans.user_is_admin(): +%if can_set_malicious: <p/><div class="toolForm"><div class="toolFormTitle">Malicious repository tip</div> 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 malicious flag to the tool shed's repository metadata - if true, downloading is restricted to only those users that can write to the repository. Fix a bug in determining if a user can write to a repository, and a bit of miscellaneous cleanup.
by Bitbucket 02 Aug '11

02 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2b954f70db10/ changeset: 2b954f70db10 user: greg date: 2011-08-02 20:19:38 summary: Add a malicious flag to the tool shed's repository metadata - if true, downloading is restricted to only those users that can write to the repository. Fix a bug in determining if a user can write to a repository, and a bit of miscellaneous cleanup. affected #: 15 files (9.6 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Tue Aug 02 13:52:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Aug 02 14:19:38 2011 -0400 @@ -33,6 +33,9 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +malicious_error = " This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content." +malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." + class ItemRatings( UsesItemRatings ): """Overrides rate_item method since we also allow for comments""" def rate_item( self, trans, user, item, rating, comment='' ): @@ -263,6 +266,12 @@ if str( ctx ) == change_set_revision: return ctx return None +def change_set_is_malicious( trans, id, change_set_revision, **kwd ): + """Check the malicious flag in repository metadata for a specified change set""" + repository_metadata = get_repository_metadata( trans, id, change_set_revision ) + if repository_metadata: + return repository_metadata.malicious + return False def copy_sample_loc_file( trans, filename ): """Copy xxx.loc.sample to ~/tool-data/xxx.loc""" sample_loc_file = os.path.split( filename )[1] --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Aug 02 13:52:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Aug 02 14:19:38 2011 -0400 @@ -427,10 +427,12 @@ current_working_dir = os.getcwd() # Update repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) + is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -506,10 +508,12 @@ else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" + is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -550,6 +554,13 @@ metadata = repository_metadata.metadata else: metadata = None + is_malicious = change_set_is_malicious( trans, id, repository.tip ) + if is_malicious: + if trans.app.security_agent.can_push( trans.user, repository ): + message += malicious_error_can_push + else: + message += malicious_error + status = 'error' return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, @@ -558,6 +569,7 @@ display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -669,8 +681,17 @@ repository_metadata = get_repository_metadata( trans, id, repository.tip ) if repository_metadata: metadata = repository_metadata.metadata + is_malicious = repository_metadata.malicious else: metadata = None + is_malicious = False + if is_malicious: + if trans.app.security_agent.can_push( trans.user, repository ): + message += malicious_error_can_push + else: + message += malicious_error + status = 'error' + malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) categories = get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] return trans.fill_template( '/webapps/community/repository/manage_repository.mako', @@ -688,6 +709,8 @@ display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, + malicious_check_box=malicious_check_box, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -713,9 +736,11 @@ 'parent' : ctx.parents()[0] } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) + is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/view_changelog.mako', repository=repository, changesets=changesets, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -740,6 +765,7 @@ diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( self.to_html_escaped( diff ) ) + is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, ctx=ctx, @@ -752,6 +778,7 @@ ignored=ignored, clean=clean, diffs=diffs, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -781,12 +808,14 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) + is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/rate_repository.mako', repository=repository, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, rra=rra, + is_malicious=is_malicious, message=message, status=status ) @web.expose @@ -829,12 +858,27 @@ @web.expose @web.require_login( "set repository metadata" ) def set_metadata( self, trans, id, ctx_str, **kwd ): - message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) - if not message: - message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) + malicious = kwd.get( 'malicious', '' ) + if kwd.get( 'malicious_button', False ): + repository_metadata = get_repository_metadata( trans, id, ctx_str ) + malicious_checked = CheckboxField.is_checked( malicious ) + repository_metadata.malicious = malicious_checked + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + if malicious_checked: + message = "The repository tip has been defined as malicious." + else: + message = "The repository tip has been defined as <b>not</b> malicious." + status = 'done' + else: + # The set_metadata_button was clicked + message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) + if not message: + message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, + malicious=malicious, message=message, status=status ) ) @web.expose @@ -903,12 +947,14 @@ id=repository_id, message=message, status=status ) ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( '/webapps/community/repository/add_tool_data_table_entry.mako', name_attr=name_attr, repository=repository, comment_char=comment_char, loc_filename=loc_filename, column_fields=column_fields, + is_malicious=is_malicious, message=message, status=status ) def __get_column_fields( self, **kwd ): @@ -938,10 +984,12 @@ try: tool = load_tool( trans, os.path.abspath( tool_config ) ) tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, tool=tool, tool_state=tool_state, + is_malicious=is_malicious, message=message, status=status ) except Exception, e: @@ -977,10 +1025,12 @@ metadata = tool_metadata_dict tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) break + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, metadata=metadata, + is_malicious=is_malicious, message=message, status=status ) @web.expose --- a/lib/galaxy/webapps/community/model/__init__.py Tue Aug 02 13:52:02 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue Aug 02 14:19:38 2011 -0400 @@ -153,10 +153,11 @@ fp.close() class RepositoryMetadata( object ): - def __init__( self, repository_id=None, changeset_revision=None, metadata=None ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None, malicious=False ): self.repository_id = repository_id self.changeset_revision = changeset_revision self.metadata = metadata or dict() + self.malicious = malicious class ItemRatingAssociation( object ): def __init__( self, id=None, user=None, item=None, rating=0, comment='' ): --- a/lib/galaxy/webapps/community/model/mapping.py Tue Aug 02 13:52:02 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Tue Aug 02 14:19:38 2011 -0400 @@ -117,7 +117,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), Column( "changeset_revision", TrimmedString( 255 ), index=True ), - Column( "metadata", JSONType, nullable=True ) ) + Column( "metadata", JSONType, nullable=True ), + Column( "malicious", Boolean, default=False ) ) RepositoryRatingAssociation.table = Table( "repository_rating_association", metadata, Column( "id", Integer, primary_key=True ), --- a/lib/galaxy/webapps/community/security/__init__.py Tue Aug 02 13:52:02 2011 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Tue Aug 02 14:19:38 2011 -0400 @@ -6,6 +6,7 @@ from galaxy.util.bunch import Bunch from galaxy.util import listify from galaxy.model.orm import * +from mercurial import hg, ui log = logging.getLogger(__name__) @@ -155,17 +156,8 @@ for group in groups: self.associate_components( user=user, group=group ) def can_push( self, user, repository ): - # TODO: handle this via the mercurial api. - if not user: - return False - # Read the repository's hgrc file - hgrc_file = os.path.abspath( os.path.join( repository.repo_path, ".hg", "hgrc" ) ) - config = ConfigParser.ConfigParser() - config.read( hgrc_file ) - for option in config.options( "web" ): - if option == 'allow_push': - allowed = config.get( "web", option ) - return user.username in allowed + if user: + return user.username in listify( repository.allow_push ) return False def get_permitted_actions( filter=None ): --- a/templates/webapps/community/repository/add_tool_data_table_entry.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/add_tool_data_table_entry.mako Tue Aug 02 14:19:38 2011 -0400 @@ -6,6 +6,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_set_metadata = not is_new can_rate = not is_new and trans.user and repository.user != trans.user @@ -43,6 +44,8 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif + %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> --- a/templates/webapps/community/repository/browse_repository.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Tue Aug 02 14:19:38 2011 -0400 @@ -9,6 +9,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_rate = trans.user and repository.user != trans.user can_manage = is_admin or repository.user == trans.user @@ -80,9 +81,11 @@ %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %endif </div> %endif </ul> @@ -94,6 +97,12 @@ %if can_browse_contents: <div class="toolForm"><div class="toolFormTitle">Browse ${repository.name}</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" > --- a/templates/webapps/community/repository/manage_repository.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Aug 02 14:19:38 2011 -0400 @@ -8,6 +8,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_set_metadata = not is_new can_rate = not is_new and trans.user and repository.user != trans.user @@ -80,6 +81,8 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif + %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> @@ -96,10 +99,12 @@ <div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"><form name="edit_repository" id="edit_repository" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} - </div> + %if can_download: + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div> + %endif <div class="form-row"><label>Name:</label><input name="repo_name" type="textfield" value="${repo_name}" size="40"/> @@ -304,7 +309,7 @@ %endif <p/><div class="toolForm"> - <div class="toolFormTitle">User access</div> + <div class="toolFormTitle">Grant authority to upload or push changes</div><div class="toolFormBody"><table class="grid"><tr> @@ -394,3 +399,24 @@ </div> %endif <p/> +%if not is_new and trans.user_is_admin(): + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Malicious repository tip</div> + <div class="toolFormBody"> + <form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> + <div class="form-row"> + <label>Define repository tip as malicious:</label> + ${malicious_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to define this repository's tip as malicious, restricting it from being download-able. + </div> + </div> + <div class="form-row"> + <input type="submit" name="malicious_button" value="Save"/> + </div> + </form> + </div> + </div> +%endif +<p/> --- a/templates/webapps/community/repository/rate_repository.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Tue Aug 02 14:19:38 2011 -0400 @@ -1,5 +1,6 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/webapps/community/common/common.mako" import="*" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /><% from galaxy.web.framework.helpers import time_ago @@ -8,6 +9,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user @@ -86,9 +88,11 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %endif </div> %endif </ul> @@ -96,6 +100,12 @@ %if repository.user != trans.user: <div class="toolForm"><div class="toolFormTitle">${repository.name}</div> + %if can_download: + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div> + %endif <div class="toolFormBody"><div class="form-row"><label>Description:</label> --- a/templates/webapps/community/repository/tool_form.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Aug 02 14:19:38 2011 -0400 @@ -11,6 +11,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_rate = trans.user and repository.user != trans.user can_manage = is_admin or repository.user == trans.user @@ -130,9 +131,11 @@ %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %endif </div> %endif </ul> --- a/templates/webapps/community/repository/view_changelog.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Tue Aug 02 14:19:38 2011 -0400 @@ -12,6 +12,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_rate = trans.user and repository.user != trans.user can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) if can_push: browse_label = 'Browse or delete repository files' else: @@ -55,9 +56,11 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %endif </div></ul> @@ -65,18 +68,26 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} +%if can_download: + <div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div></div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"> - <div class="toolFormTitle">Changesets</div> + <% + if can_download: + title_str = 'Changesets' + else: + title_str = '%s changesets' % repository.name + %> + <div class="toolFormTitle">${title_str}</div><% test_date = None %><div class="toolFormBody"><table class="grid"> --- a/templates/webapps/community/repository/view_changeset.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Tue Aug 02 14:19:38 2011 -0400 @@ -13,6 +13,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_view_change_log = not is_new can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) if can_push: browse_label = 'Browse or delete repository files' else: @@ -59,9 +60,11 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %endif </div></ul> @@ -69,18 +72,26 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} +%if can_download: + <div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div></div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"> - <div class="toolFormTitle">Changeset ${ctx}</div> + <% + if can_download: + title_str = 'Changeset %s' % ctx + else: + title_str = '%s changeset %s' % ( repository.name, ctx ) + %> + <div class="toolFormTitle">${title_str}</div><div class="toolFormBody"><table class="grid"> %if modified: @@ -155,14 +166,19 @@ %endif %for diff in diffs: <% - # Read the first line of diff - line = diff.split( '\n' )[0] + # Read at most the first 10 lines of diff to determine the anchor + ctr = 0 + lines = diff.split( '\n' ) diff = diff.replace( '\n', '<br/>' ) anchor_str = '' - for anchor in anchors: - if line.find( anchor ) >= 0: - anchor_str = '<a name="%s">%s</a>' % ( anchor, anchor ) + for line in lines: + if ctr > 9: break + for anchor in anchors: + if line.find( anchor ) >= 0: + anchor_str = '<a name="%s">%s</a>' % ( anchor, anchor ) + break + ctr += 1 %><tr><td bgcolor="#E0E0E0">${anchor_str}</td></tr><tr><td>${diff}</td></tr> --- a/templates/webapps/community/repository/view_repository.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Aug 02 14:19:38 2011 -0400 @@ -9,6 +9,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_view_change_log = not is_new if can_push: @@ -79,6 +80,8 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif + %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> @@ -94,10 +97,12 @@ <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} - </div> + %if can_download: + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div> + %endif <div class="form-row"><label>Name:</label> %if can_browse_contents: --- a/templates/webapps/community/repository/view_tool_metadata.mako Tue Aug 02 13:52:02 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Tue Aug 02 14:19:38 2011 -0400 @@ -10,6 +10,7 @@ is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push + can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user @@ -50,9 +51,11 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), 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 ), file_type='zip' )}">Download as a zip file</a> + %endif </div> %endif </ul> @@ -61,25 +64,21 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} +%if can_download: + <div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div></div></div> -</div> +%else: + <b>Repository name:</b><br/> + ${repository.name} +%endif %if metadata: -## "{"tools": -## [{"description": "data on any column using simple expressions", -## "id": "Filter1", -## "name": "Filter", -## "requirements": [], -## "tests": [{ -## "inputs": [["input", "1.bed", {"children": [], "value": "1.bed"}], ["cond", "c1=='chr22'", {"children": [], "value": "c1=='chr22'"}]], "name": "Test-1", -## "outputs": [["out_file1", "filter1_test1.bed", {"compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], -## "required_files": [["1.bed", {"children": [], "value": "1.bed"}]]}, {"inputs": [["input", "7.bed", {"children": [], "value": "7.bed"}], ["cond", "c1=='chr1' and c3-c2>=2000 and c6=='+'", {"children": [], "value": "c1=='chr1' and c3-c2>=2000 and c6=='+'"}]], "name": "Test-2", "outputs": [["out_file1", "filter1_test2.bed", {"compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["7.bed", {"children": [], "value": "7.bed"}]]}], "tool_config": "database/community_files/000/repo_1/filtering.xml", "version": "1.0.1", "version_string_cmd": null}], "workflows": [{"a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Workflow constructed from history 'Unnamed history'", "steps": {"0": {"annotation": "", "id": 0, "input_connections": {}, "inputs": [{"description": "", "name": "Input Dataset"}], "name": "Input dataset", "outputs": [], "position": {"left": 10, "top": 10}, "tool_errors": null, "tool_id": null, "tool_state": "{\\"name\\": \\"Input Dataset\\"}", "tool_version": null, "type": "data_input", "user_outputs": []}, "1": {"annotation": "", "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "name": "Filter", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 230, "top": 10}, "post_job_actions": {}, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\\"__page__\\": 0, \\"cond\\": \\"\\\\\\"c1=='chr1'\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/Users/gvk/workspaces_2008/central_051111/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"input\\": \\"null\\"}", "tool_version": null, "type": "tool", "user_outputs": []}, "2": {"annotation": "", "id": 2, "input_connections": {"input1": {"id": 0, "output_name": "output"}, "input2": {"id": 1, "output_name": "out_file1"}}, "inputs": [], "name": "Subtract Whole Dataset", "outputs": [{"name": "output", "type": "input"}], "position": {"left": 450, "top": 10}, "post_job_actions": {}, "tool_errors": null, "tool_id": "subtract_query1", "tool_state": "{\\"input2\\": \\"null\\", \\"__page__\\": 0, \\"end_col\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"None\\\\\\"}\\", \\"begin_col\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"None\\\\\\"}\\", \\"input1\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/Users/gvk/workspaces_2008/central_051111/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", "tool_version": null, "type": "tool", "user_outputs": []}}}]}" <p/><div class="toolForm"><div class="toolFormTitle">${metadata[ 'name' ]} tool metadata</div> @@ -89,26 +88,34 @@ <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ] )}">${metadata[ 'name' ]}</a><div style="clear: both"></div></div> - <div class="form-row"> - <label>Description:</label> - ${metadata[ 'description' ]} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Id:</label> - ${metadata[ 'id' ]} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Version:</label> - ${metadata[ 'version' ]} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Version command string:</label> - ${metadata[ 'version_string_cmd' ]} - <div style="clear: both"></div> - </div> + %if 'description' in metadata: + <div class="form-row"> + <label>Description:</label> + ${metadata[ 'description' ]} + <div style="clear: both"></div> + </div> + %endif + %if 'id' in metadata: + <div class="form-row"> + <label>Id:</label> + ${metadata[ 'id' ]} + <div style="clear: both"></div> + </div> + %endif + %if 'version' in metadata: + <div class="form-row"> + <label>Version:</label> + ${metadata[ 'version' ]} + <div style="clear: both"></div> + </div> + %endif + %if 'version_string_cmd' in metadata: + <div class="form-row"> + <label>Version command string:</label> + ${metadata[ 'version_string_cmd' ]} + <div style="clear: both"></div> + </div> + %endif <div class="form-row"><label>Command:</label><pre>${tool.command}</pre> 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: Trackster: refactor post-draw actions into their own methods.
by Bitbucket 02 Aug '11

02 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5feafa125856/ changeset: 5feafa125856 user: jgoecks date: 2011-08-02 19:52:02 summary: Trackster: refactor post-draw actions into their own methods. affected #: 1 file (396 bytes) --- a/static/scripts/trackster.js Tue Aug 02 12:16:22 2011 -0400 +++ b/static/scripts/trackster.js Tue Aug 02 13:52:02 2011 -0400 @@ -2021,7 +2021,8 @@ var tile_index = Math.floor( low / resolution / DENSITY ); // A list of tiles drawn/retrieved. var drawn_tiles = []; - var tile_count = 0 + var tile_count = 0; + // Draw or fetch and show tiles. while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = gen_key(width, w_scale, tile_index); @@ -2029,7 +2030,7 @@ var tile_low = tile_index * DENSITY * this.view.resolution; var tile_high = tile_low + DENSITY * this.view.resolution; if (!force && cached) { - drawn_tiles[drawn_tiles.length] = cached; + drawn_tiles.push(cached); this.show_tile(cached, parent_element, w_scale); } else { this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); @@ -2039,128 +2040,14 @@ } // - // Post-draw actions: + // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. // var track = this; var intervalId = setInterval(function() { if (drawn_tiles.length === tile_count) { // All tiles have been drawn. clearInterval(intervalId); - - // Clear tiles? - if (clear_after) { - // Clear out track content in order to show the most recent content. - // Most recent content is the div with children (tiles) most recently appended to track. - // However, do not delete recently-appended empty content as calls to draw() may still be active - // and using these divs. - var track_content = track.content_div.children(); - var remove = false; - for (var i = track_content.length-1, len = 0; i >= len; i--) { - var child = $(track_content[i]); - if (remove) { - child.remove(); - } - else if (child.children().length !== 0) { - // Found most recent content with tiles: set remove to start removing old elements. - remove = true; - } - } - } - - // - // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. - // - // HACK: use track type b/c LineTrack histograms are different; what's needed is different - // post-draw actions for different line tracks. - if (track instanceof FeatureTrack && track.mode == "Histogram") { - // Get global max. - var global_max = -1; - for (var i = 0; i < drawn_tiles.length; i++) { - var cur_max = drawn_tiles[i].max_val; - if (cur_max > global_max) { - global_max = cur_max; - } - } - - for (var i = 0; i < drawn_tiles.length; i++) { - if (drawn_tiles[i].max_val !== global_max) { - var tile = drawn_tiles[i]; - tile.canvas.remove(); - track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index, - tile.resolution, parent_element, w_scale, [], { max: global_max }); - } - } - } - - // - // Update filter attributes, UI. - // - - // Update filtering UI. - if (track.filters_manager) { - var filters = track.filters_manager.filters; - for (var f = 0; f < filters.length; f++) { - filters[f].update_ui_elt(); - } - - // Determine if filters are available; this is based on the tiles' data. - var filters_available = false, - example_feature; - for (var i = 0; i < drawn_tiles.length; i++) { - if (drawn_tiles[i].data.length) { - example_feature = drawn_tiles[i].data[0]; - for (var f = 0; f < filters.length; f++) { - if (filters[f].applies_to(example_feature)) { - filters_available = true; - break; - } - } - } - } - - // If filter availability changed, hide filter div if necessary and update menu. - if (track.filters_available !== filters_available) { - track.filters_available = filters_available; - if (!track.filters_available) { - track.filters_div.hide(); - } - track.make_name_popup_menu(); - } - } - - // - // If some tiles have messages, set padding of tiles without messages - // so features and rows align. - // - var messages_to_show = false; - for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { - if (drawn_tiles[tile_index].message) { - messages_to_show = true; - break; - } - } - if (messages_to_show) { - for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { - tile = drawn_tiles[tile_index]; - if (!tile.message) { - // Need to align with other tile(s) that have message(s). - tile.canvas.css("padding-top", ERROR_PADDING); - } - } - } - - // Store initial canvas in case we need to use it for overview - /* This is completely broken, just saves the first tile it sees - regardless of if it should be the overview - if (!track.initial_canvas && !window.G_vmlCanvasManager) { - track.initial_canvas = $(tile_element).clone(); - var src_ctx = tile_element.get(0).getContext("2d"); - var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); - var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - tgt_ctx.putImageData(data, 0, 0); - track.set_overview(); - } - */ + track.postdraw_actions(drawn_tiles, clear_after); } }, 50); @@ -2170,7 +2057,51 @@ for (var i = 0; i < this.child_tracks.length; i++) { this.child_tracks[i].draw(force, clear_after); } - }, + }, + /** + * Actions to be taken after draw has been completed. Draw is completed when all tiles have been + * drawn/fetched and shown. + */ + postdraw_actions: function(tiles, clear_after) { + var track = this; + + // + // If some tiles have messages, set padding of tiles without messages + // so features and rows align. + // + var messages_to_show = false; + for (var tile_index = 0; tile_index < tiles.length; tile_index++) { + if (tiles[tile_index].message) { + messages_to_show = true; + break; + } + } + if (messages_to_show) { + for (var tile_index = 0; tile_index < tiles.length; tile_index++) { + tile = tiles[tile_index]; + if (!tile.message) { + // Need to align with other tile(s) that have message(s). + tile.canvas.css("padding-top", ERROR_PADDING); + } + } + } + + // Store initial canvas in case we need to use it for overview + /* This is completely broken, just saves the first tile it sees + regardless of if it should be the overview + if (!track.initial_canvas && !window.G_vmlCanvasManager) { + track.initial_canvas = $(tile_element).clone(); + var src_ctx = tile_element.get(0).getContext("2d"); + var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); + var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); + tgt_ctx.putImageData(data, 0, 0); + track.set_overview(); + } + */ + }, + /** + * Do actual tile drawing. + */ delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { var track = this, tile_low = tile_index * DENSITY * resolution, @@ -2187,7 +2118,7 @@ return; } track.show_tile(tile, parent_element, w_scale); - drawn_tiles[drawn_tiles.length] = tile; + drawn_tiles.push(tile); }; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data var id = setTimeout(function() { @@ -2196,7 +2127,7 @@ var tile = (force ? undefined : track.tile_cache.get(key)); if (tile) { track.show_tile(tile, parent_element, w_scale); - drawn_tiles[drawn_tiles.length] = tile; + drawn_tiles.push(tile); } else { // @@ -2585,6 +2516,94 @@ this.painter = painters.LinkedFeaturePainter; }; extend(FeatureTrack.prototype, TiledTrack.prototype, { + /** + * Actions to be taken after draw has been completed. Draw is completed when all tiles have been + * drawn/fetched and shown. + */ + postdraw_actions: function(tiles, clear_after) { + TiledTrack.prototype.postdraw_actions.call(this, tiles, clear_after); + + var track = this; + + // Clear tiles? + if (clear_after) { + // Clear out track content in order to show the most recent content. + // Most recent content is the div with children (tiles) most recently appended to track. + // However, do not delete recently-appended empty content as calls to draw() may still be active + // and using these divs. + var track_content = track.content_div.children(); + var remove = false; + for (var i = track_content.length-1, len = 0; i >= len; i--) { + var child = $(track_content[i]); + if (remove) { + child.remove(); + } + else if (child.children().length !== 0) { + // Found most recent content with tiles: set remove to start removing old elements. + remove = true; + } + } + } + + // + // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. + // + if (track.mode == "Histogram") { + // Get global max. + var global_max = -1; + for (var i = 0; i < tiles.length; i++) { + var cur_max = tiles[i].max_val; + if (cur_max > global_max) { + global_max = cur_max; + } + } + + for (var i = 0; i < tiles.length; i++) { + if (tiles[i].max_val !== global_max) { + var tile = tiles[i]; + tile.canvas.remove(); + track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index, + tile.resolution, parent_element, w_scale, [], { max: global_max }); + } + } + } + + // + // Update filter attributes, UI. + // + + // Update filtering UI. + if (track.filters_manager) { + var filters = track.filters_manager.filters; + for (var f = 0; f < filters.length; f++) { + filters[f].update_ui_elt(); + } + + // Determine if filters are available; this is based on the tiles' data. + var filters_available = false, + example_feature; + for (var i = 0; i < tiles.length; i++) { + if (tiles[i].data.length) { + example_feature = tiles[i].data[0]; + for (var f = 0; f < filters.length; f++) { + if (filters[f].applies_to(example_feature)) { + filters_available = true; + break; + } + } + } + } + + // If filter availability changed, hide filter div if necessary and update menu. + if (track.filters_available !== filters_available) { + track.filters_available = filters_available; + if (!track.filters_available) { + track.filters_div.hide(); + } + track.make_name_popup_menu(); + } + } + }, update_auto_mode: function( mode ) { if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for 2 comments in templates/dataset/security_common.mako.
by Bitbucket 02 Aug '11

02 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f60dfcc77165/ changeset: f60dfcc77165 user: dan date: 2011-08-02 18:16:22 summary: Fix for 2 comments in templates/dataset/security_common.mako. affected #: 1 file (2 bytes) --- a/templates/dataset/security_common.mako Tue Aug 02 08:55:57 2011 -0400 +++ b/templates/dataset/security_common.mako Tue Aug 02 12:16:22 2011 -0400 @@ -109,8 +109,8 @@ %for k, v in permitted_actions: %if k not in do_not_render: <div class="form-row"> - # LIBRARY_ACCESS is a special case because we need to render all roles instead of - # roles derived from the roles associated with LIBRARY_ACCESS. + ## LIBRARY_ACCESS is a special case because we need to render all roles instead of + ## roles derived from the roles associated with LIBRARY_ACCESS. <% render_all_roles = k == 'LIBRARY_ACCESS' %> %if render_all_roles: ${render_select( current_actions, k, v, all_roles )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update EuPathDB datasource configuration file. Contributed by Mark Heiges.
by Bitbucket 02 Aug '11

02 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9cae773f70ed/ changeset: 9cae773f70ed user: dan date: 2011-08-02 14:55:57 summary: Update EuPathDB datasource configuration file. Contributed by Mark Heiges. affected #: 1 file (1.2 KB) --- a/tools/data_source/eupathdb.xml Mon Aug 01 17:35:18 2011 -0400 +++ b/tools/data_source/eupathdb.xml Tue Aug 02 08:55:57 2011 -0400 @@ -1,30 +1,10 @@ - -<tool name="EuPathDB" id="eupathdb" tool_type="data_source"> +<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="post"> + <inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="get"><display>go to EuPathDB server $GALAXY_URL</display><param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /></inputs> - <request_param_translation> - <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> - <request_param galaxy_name="URL" remote_name="URL" missing=""> - <append_param separator="&" first_separator="?" join="="> - <value name="dbkey" missing="?" /> - <value name="wdk_history_id" missing="" /> - <value name="wdkReportFormat" missing="tabular" /> - <value name="selectedFields" missing="" /> - <value name="includeHeader" missing="yes" /> - <value name="downloadType" missing="plain" /> - </append_param> - </request_param> - <request_param galaxy_name="format" remote_name="wdkReportFormat" missing="tabular" /> - <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> - </request_param_translation><uihints minwidth="800"/><outputs><data name="output" format="txt" /> 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: kanwei: LibraryDataset Parameter:
by Bitbucket 01 Aug '11

01 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2573ac2b9c58/ changeset: 2573ac2b9c58 user: kanwei date: 2011-08-01 23:35:18 summary: LibraryDataset Parameter: - Now allows multiple dataset selection instead of just one. As a result, the ValueWrapper is now an iterator that iterates over each selected library dataset. - Move #templates method to become an attribute of LDDAs instead of a helper method in ValueWrapper. affected #: 5 files (1.6 KB) --- a/lib/galaxy/model/__init__.py Fri Jul 29 14:33:34 2011 -0400 +++ b/lib/galaxy/model/__init__.py Mon Aug 01 17:35:18 2011 -0400 @@ -4,7 +4,9 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ - +import pkg_resources +pkg_resources.require( "simplejson" ) +import simplejson import galaxy.datatypes from galaxy.util.bunch import Bunch from galaxy import util @@ -1415,6 +1417,22 @@ else: return template.get_widgets( trans.user ) return [] + def templates_dict( self ): + """ + Returns a dict of template info + """ + template_data = {} + for temp_info in self.info_association: + template = temp_info.template + content = temp_info.info.content + tmp_dict = {} + for field in template.fields: + tmp_dict[field['label']] = content[field['name']] + template_data[template.name] = tmp_dict + return template_data + def templates_json( self ): + return simplejson.dumps( self.templates_dict() ) + def get_display_name( self ): """ LibraryDatasetDatasetAssociation name can be either a string or a unicode object. --- a/lib/galaxy/tools/__init__.py Fri Jul 29 14:33:34 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Aug 01 17:35:18 2011 -0400 @@ -1,7 +1,7 @@ """ Classes encapsulating galaxy tools and tool configuration. """ -import pkg_resources; +import pkg_resources pkg_resources.require( "simplejson" ) @@ -2026,21 +2026,16 @@ self.input = input self.value = value self._other_values = other_values + self.counter = 0 def __str__( self ): - return self.value.name - def templates( self ): - """ Returns JSON dict of templates => data """ - if not self.value: - return None - template_data = {} - for temp_info in self.value.info_association: - template = temp_info.template - content = temp_info.info.content - tmp_dict = {} - for field in template.fields: - tmp_dict[field['label']] = content[field['name']] - template_data[template.name] = tmp_dict - return simplejson.dumps( template_data ) + return self.value + def __iter__( self ): + return self + def next( self ): + if self.counter >= len(self.value): + raise StopIteration + self.counter += 1 + return self.value[self.counter-1] def __getattr__( self, key ): return getattr( self.value, key ) --- a/lib/galaxy/tools/parameters/basic.py Fri Jul 29 14:33:34 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Aug 01 17:35:18 2011 -0400 @@ -725,7 +725,7 @@ dynamic options, we need to check whether the other parameters which determine what options are valid have been set. For the old style dynamic options which do not specify dependencies, this is always true - (must valiate at runtime). + (must validate at runtime). """ # Option list is statically defined, never need late validation if not self.is_dynamic: @@ -804,7 +804,7 @@ Select list that sets the last used genome build for the current history as "selected". - >>> # Create a mock transcation with 'hg17' as the current build + >>> # Create a mock transaction with 'hg17' as the current build >>> from galaxy.util.bunch import Bunch >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames ) @@ -1539,20 +1539,26 @@ def from_html( self, value, trans, other_values={} ): if not value: return None - elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ): + elif isinstance( value, list ): return value else: - return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( value ) ) + decoded_lst = [] + for encoded_id in value.split("||"): + decoded_lst.append( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( encoded_id ) ) ) + return decoded_lst def to_string( self, value, app ): if not value: - return None - return value.id + return value + return [ldda.id for ldda in value] def to_python( self, value, app ): if not value: return value - return app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( value ) + lddas = [] + for ldda_id in value: + lddas.append( app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) ) + return lddas # class RawToolParameter( ToolParameter ): # """ --- a/lib/galaxy/web/form_builder.py Fri Jul 29 14:33:34 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Mon Aug 01 17:35:18 2011 -0400 @@ -656,17 +656,17 @@ class LibraryField( BaseField ): def __init__( self, name, value=None, trans=None ): self.name = name - self.ldda = value + self.lddas = value self.trans = trans def get_html( self, prefix="", disabled=False ): - if not self.ldda: - ldda = "" - text = "Choose a library dataset" + if not self.lddas: + ldda_ids = "" + text = "Select library dataset(s)" else: - ldda = self.trans.security.encode_id(self.ldda.id) - text = self.ldda.name + ldda_ids = "||".join( [ self.trans.security.encode_id( ldda.id ) for ldda in self.lddas ] ) + text = "<br />".join( [ "%s. %s" % (i+1, ldda.name) for i, ldda in enumerate(self.lddas)] ) return '<a href="javascript:void(0);" class="add-librarydataset">%s</a> \ - <input type="hidden" name="%s%s" value="%s">' % ( text, prefix, self.name, escape( str(ldda), quote=True ) ) + <input type="hidden" name="%s%s" value="%s">' % ( text, prefix, self.name, escape( str(ldda_ids), quote=True ) ) def get_display_text(self): if self.ldda: --- a/templates/tool_form.mako Fri Jul 29 14:33:34 2011 -0400 +++ b/templates/tool_form.mako Mon Aug 01 17:35:18 2011 -0400 @@ -79,12 +79,18 @@ hide_modal(); }, "Select": function() { + var names = []; + var ids = []; + counter = 1; $('input[name=ldda_ids]:checked').each(function() { var name = $.trim( $(this).siblings("div").find("a").text() ); var id = $(this).val(); - link.text(name); - link.siblings("input[type=hidden]").val(id); + names.push( counter + ". " + name ); + counter += 1; + ids.push(id); }); + link.html( names.join("<br/>") ); + link.siblings("input[type=hidden]").val( ids.join("||") ); hide_modal(); } } 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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