1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/8607202c00cc/ changeset: 8607202c00cc branch: next-stable user: inithello date: 2013-03-20 14:33:34 summary: Display an error message when cookies are blocked between the tool shed and galaxy. affected #: 2 files

diff -r c92d41cb71440de8564112e6e89a75598388268c -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -317,9 +317,9 @@ @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + kwd[ 'galaxy_url' ] = galaxy_url if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. @@ -346,11 +346,14 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_repositories', **kwd ) ) + log.debug("CCC In browse_valid_categories, just before returning valid_category_grid, kwd: %s" % str( kwd )) return self.valid_category_grid( trans, **kwd )

@web.expose def browse_valid_repositories( self, trans, **kwd ): - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + kwd[ 'galaxy_url' ] = galaxy_url repository_id = kwd.get( 'id', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -359,8 +362,6 @@ category = suc.get_category_by_name( trans, category_name ) # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method. kwd[ 'id' ] = trans.security.encode_id( category.id ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": @@ -423,7 +424,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -437,11 +438,14 @@ if from_update_manager: update = 'true' no_update = 'false' - else: + elif galaxy_url: # Start building up the url to redirect back to the calling Galaxy instance. url = suc.url_join( galaxy_url, 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + else: + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: @@ -746,9 +750,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -833,9 +835,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -952,7 +952,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -1443,18 +1442,23 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) - galaxy_url = kwd.get( 'galaxy_url', None ) if not repository_ids: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_ids = trans.security.encode_id( repository.id ) - if not galaxy_url: - # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed. - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # Redirect back to local Galaxy to perform install. - url = suc.url_join( galaxy_url, - 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) - return trans.response.send_redirect( url ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + # Redirect back to local Galaxy to perform install. + url = suc.url_join( galaxy_url, + 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) + return trans.response.send_redirect( url ) + else: + message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + status = 'error' + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_valid_categories', + message=message, + status=status ) )

@web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): @@ -1854,8 +1858,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None )

diff -r c92d41cb71440de8564112e6e89a75598388268c -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -116,6 +116,7 @@ return False

def changeset_is_valid( app, repository, changeset_revision ): + """Make sure a changeset hash is valid for a specified repository.""" repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) @@ -124,6 +125,7 @@ return False

def clean_repository_clone_url( repository_clone_url ): + """Return a URL that can be used to clone a tool shed repository, eliminating the protocol and user if either exists.""" if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: # http://test@bx.psu.edu:9009/repos/some_username/column @@ -139,6 +141,7 @@ return tmp_url

def clean_tool_shed_url( tool_shed_url ): + """Return a tool shed URL, eliminating the port if it exists.""" if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. return tool_shed_url.split( ':' )[ 0 ] @@ -186,6 +189,10 @@

def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): + """ + Update a tool shed repository record i the Galaxy database with the new information received. If a record defined by the received tool shed, repository name + and owner does not exists, create a new record with the received information. + """ # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed. log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) @@ -272,6 +279,7 @@ return sharable_url

def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): + """Create and return an ElementTree tool Element.""" if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) else: @@ -429,6 +437,7 @@ return _ui

def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): + """Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the combination of a name, owner and changeset revision.""" url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() @@ -448,6 +457,7 @@ return None, None

def get_file_context_from_ctx( ctx, filename ): + """Return the mercurial file context for a specified file.""" # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario @@ -473,6 +483,7 @@ return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )

def get_named_tmpfile_from_ctx( ctx, filename, dir ): + """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" filename = strip_path( filename ) for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -958,6 +969,14 @@ except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." )

+def handle_galaxy_url( trans, **kwd ): + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + else: + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + return galaxy_url + def open_repository_files_folder( trans, folder_path ): """Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy.""" try:

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

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