1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/058c507d05fd/ changeset: 058c507d05fd user: greg date: 2011-11-21 17:21:23 summary: Subtle but critical fixes in resetting all metadata for tool shed repositories ( and some code clean up ). affected #: 4 files

diff -r 66038323cb438066cb76e255fd436fc245056bfd -r 058c507d05fd41694261f9f679b7cccafe295faf lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1622,51 +1622,56 @@ if len( repo ) == 1: message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) else: - # The following will be a list of changeset_revisions that have been created or updated. - # When the following loop completes, we'll delete all repository_metadata records for - # this repository that do not have a changeset_revision value in this list. + # The list of changeset_revisions refers to repository_metadata records that have been + # created or updated. When the following loop completes, we'll delete all repository_metadata + # records for this repository that do not have a changeset_revision value in this list. changeset_revisions = [] - repository_metadata_tup_for_comparison = () + ancestor_changeset_revision = None + ancestor_metadata_dict = None for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - current_changeset_revision = str( ctx ) + current_changeset_revision = str( repo.changectx( changeset ) ) ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir ) if current_metadata_dict: - if repository_metadata_tup_for_comparison: - ancestor_changeset_revision, ancestor_metadata_dict = repository_metadata_tup_for_comparison - comparison = self.__compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) - # The value of comparsion will be one of: + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparsion will be one of: # 'no metadata' - no metadata for either ancestor or current, so continue from current # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current # 'subset' - ancestor metadata is a subset of current metadata, so continue from current # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. + comparison = self.__compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) if comparison in [ 'no metadata', 'equal', 'subset' ]: - repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict ) + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict elif comparison == 'not equal and not subset': self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) - # keep track of the changeset_revisions that we've persisted. + # Keep track of the changeset_revisions that we've persisted. changeset_revisions.append( ancestor_changeset_revision ) - repository_metadata_tup_for_comparison = () + ancestor_changeset_revision = None + ancestor_metadata_dict = None else: - # We're at the first change set in the change log. - repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict ) + # We're either at the first change set in the change log or we have just created or updated + # a repository_metadata record. At this point we set the ancestor changeset to the current + # changeset for comparison in the next iteration. + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict if not ctx.children(): # We're at the end of the change log. self.__create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict ) changeset_revisions.append( current_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None elif ancestor_metadata_dict: # Our current change set has no metadata, but our ancestor change set has metadata, so save it. self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) - # keep track of the changeset_revisions that we've persisted. + # Keep track of the changeset_revisions that we've persisted. changeset_revisions.append( ancestor_changeset_revision ) - repository_metadata_tup_for_comparison = () - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = None + ancestor_metadata_dict = None self.__clean_repository_metadata( trans, id, changeset_revisions ) if not message: message = "Repository metadata has been reset." @@ -1699,6 +1704,12 @@ def __compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision # is an ancestor of current_changeset_revision which is associated with current_metadata_dict. + # + # TODO: a new repository_metadata record will be created only when this method returns the string + # 'not equal and not subset'. However, we're currently also returning the strings 'no metadata', + # 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave things this way + # for the current time in case we discover a use for these additional result strings. + # # Get information about tools. if 'tools' in ancestor_metadata_dict: ancestor_tools = ancestor_metadata_dict[ 'tools' ] @@ -1735,7 +1746,7 @@ else: current_datatypes = [] # Handle case where no metadata exists for either changeset. - if not ( ancestor_guids or current_guids or ancestor_workflows or current_workflows or ancestor_datatypes or current_datatypes ): + if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: return 'no metadata' workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows ) datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes ) @@ -1758,9 +1769,13 @@ for ancestor_workflow in ancestor_workflows: # Currently the only way to differentiate workflows is by name. ancestor_workflow_name = ancestor_workflow[ 'name' ] + num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] ) found_in_current = False for current_workflow in current_workflows: - if current_workflow[ 'name' ] == ancestor_workflow_name: + # Assume that if the name and number of steps are euqal, + # then the workflows are the same. Of course, this may + # not be true... + if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps: found_in_current = True break if not found_in_current:

diff -r 66038323cb438066cb76e255fd436fc245056bfd -r 058c507d05fd41694261f9f679b7cccafe295faf lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -194,7 +194,7 @@ categories=relation( RepositoryCategoryAssociation ), ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ), user=relation( User.mapper ), - downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.id ) ) ) ) + downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) )

assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ) ) )

diff -r 66038323cb438066cb76e255fd436fc245056bfd -r 058c507d05fd41694261f9f679b7cccafe295faf templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -181,7 +181,7 @@ <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a></td><td> - %if 'steps' in workflow_dict: + %if steps: ${len( steps )} %else: unknown

diff -r 66038323cb438066cb76e255fd436fc245056bfd -r 058c507d05fd41694261f9f679b7cccafe295faf templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -107,7 +107,7 @@ else: ctx_parent_str = "%s:%s" % ( ctx_parent_rev, ctx_parent ) if changeset[ 'has_metadata' ]: - has_metadata_str = 'Repository metadata is associated with this change set.' + has_metadata_str = '<table border="0" bgcolor="#D8D8D8"><tr><td>Repository metadata is associated with this change set.</td></tr></table>' else: has_metadata_str = '' %>

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

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