1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/34c190323b36/ changeset: 34c190323b36 user: greg date: 2011-07-11 19:34:23 summary: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata. affected #: 5 files (4.3 KB)

--- a/lib/galaxy/webapps/community/controllers/common.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 13:34:23 2011 -0400 @@ -75,9 +75,100 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def set_repository_metadata( trans, id, ctx_str, **kwd ): + """Set repository metadata""" + message = '' + status = 'done' + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) + change_set = get_change_set( trans, repo, ctx_str ) + invalid_tool_configs = [] + flush_needed = False + if change_set is not None: + for root, dirs, files in os.walk( repo_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = load_tool( trans, full_path ) + if tool is not None: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + tool_requirements = [] + for tr in tool.requirements: + requirement_dict = dict( name=tr.name, + type=tr.type, + version=tr.version ) + tool_requirements.append( requirement_dict ) + tool_dict = dict( id = tool.id, + name = tool.name, + version = tool.version, + description = tool.description, + tool_config = os.path.join( root, name ), + requirements = tool_requirements ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + metadata_tools = metadata[ 'tools' ] + found = False + for tool_metadata_dict in metadata_tools: + if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ + 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: + found = True + tool_metadata_dict[ 'name' ] = tool.name + tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) + tool_metadata_dict[ 'requirements' ] = tool_requirements + flush_needed = True + if not found: + metadata_tools.append( tool_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'tools' ] = [ tool_dict ] + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + metadata_dict = dict( tools = [ tool_dict ] ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + except Exception, e: + invalid_tool_configs.append( ( name, str( e ) ) ) + else: + message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + status = 'error' + if invalid_tool_configs: + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) + for itc_tup in invalid_tool_configs: + message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) + status = 'error' + elif flush_needed: + # We only flush if there are no tool config errors, so change sets will only have metadata + # if everything in them is valid. + trans.sa_session.flush() + return message, status def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() +def get_change_set( trans, repo, ctx_str, **kwd ): + """Retrieve a specified change set from a repository""" + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + if str( ctx ) == ctx_str: + return ctx + return None def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) @@ -184,77 +275,3 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def set_repository_metadata( trans, id, ctx_str, **kwd ): - """Set repository metadata""" - message = '' - status = 'done' - repository = get_repository( trans, id ) - repo_dir = repository.repo_path - repo = hg.repository( ui.ui(), repo_dir ) - found = False - invalid_tool_configs = [] - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if found: - for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - tool = load_tool( trans, full_path ) - if tool is not None: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) - # TODO: add more stuff, like requirements - tool_dict = dict( id = tool.id, - name = tool.name, - version = tool.version, - description = tool.description, - tool_config = full_path ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'tools' in metadata: - metadata_tools = metadata[ 'tools' ] - found = False - for tool_metadata_dict in metadata_tools: - if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ - 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: - found = True - tool_metadata_dict[ 'name' ] = tool.name - tool_metadata_dict[ 'description' ] = tool.description - tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) - # TODO: add more stuff, like tool requirements, code files, etc - if not found: - metadata_tools.append( tool_dict ) - else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'tools' ] = [ tool_dict ] - trans.sa_session.add( repository_metadata ) - else: - metadata_dict = dict( tools = [ tool_dict ] ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - except Exception, e: - invalid_tool_configs.append( ( name, str( e ) ) ) - else: - message = "Repository does not include changeset revision '%s'." % str( ctx_str ) - status = 'error' - if invalid_tool_configs: - message = "The following tool configs are invalid and were not added to the repository metadata:<br/>" - for itc_tup in invalid_tool_configs: - message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) - status = 'error' - return message, status

--- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:34:23 2011 -0400 @@ -643,13 +643,8 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - found = False - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if not found: + ctx = get_change_set( trans, repo, ctx_str ) + if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', @@ -753,6 +748,8 @@ @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 ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id,

--- a/templates/webapps/community/repository/manage_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -160,11 +160,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td> - <td>version: ${tool_dict[ 'version' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table>

--- a/templates/webapps/community/repository/tool_form.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Mon Jul 11 13:34:23 2011 -0400 @@ -15,6 +15,10 @@ 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 + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><html> @@ -116,6 +120,9 @@ %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif

--- a/templates/webapps/community/repository/view_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -155,11 +155,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td><td>version: ${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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