1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/a10bb73f5793/ changeset: a10bb73f5793 user: greg date: 2012-08-08 22:15:06 summary: Fixes for setting versions for tools included in a repository in the tool shed. affected #: 1 file

diff -r 6a7d9d3714e99f613fb8dbcdb709e7e2a2b813e0 -r a10bb73f579386e67c52383b4c0722cb693d7cf9 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -122,7 +122,12 @@ else: for tool_dict in tool_dicts: # We have at least 2 changeset revisions to compare tool guids and tool ids. - parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] ) + parent_id = get_parent_id( trans, + id, + tool_dict[ 'id' ], + tool_dict[ 'version' ], + tool_dict[ 'guid' ], + changeset_revisions[ 0:index ] ) tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id if tool_versions_dict: repository_metadata.tool_versions = tool_versions_dict @@ -149,7 +154,8 @@ # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. - changeset_revisions_checked = [] + changeset_revisions_checked = [] + cleaned_changeset_revisions = [] for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, @@ -159,6 +165,9 @@ if can_delete: trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() + else: + cleaned_changeset_revisions.append( changeset_revision ) + return cleaned_changeset_revisions def compare_changeset_revisions( 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. A new repository_metadata record will be created only @@ -277,7 +286,7 @@ return file_path return None def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): - downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict + downloadable = is_downloadable( metadata_dict ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata.metadata = metadata_dict @@ -289,6 +298,7 @@ downloadable=downloadable ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() + return repository_metadata def generate_clone_url( trans, repository_id ): """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) @@ -562,6 +572,8 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def is_downloadable( metadata_dict ): + return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_tool( trans, config_file ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element @@ -797,7 +809,7 @@ elif comparison == 'not equal and not subset': metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict @@ -809,7 +821,7 @@ metadata_changeset_revision = current_changeset_revision metadata_dict = current_metadata_dict # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -820,7 +832,7 @@ metadata_dict = ancestor_metadata_dict if not ctx.children(): # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -830,10 +842,9 @@ except: pass # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - clean_repository_metadata( trans, id, changeset_revisions ) + cleaned_changeset_revisions = clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. - downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] - add_repository_metadata_tool_versions( trans, id, downloadable_changeset_revisions ) + add_repository_metadata_tool_versions( trans, id, cleaned_changeset_revisions ) def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -846,23 +857,22 @@ repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) if metadata_dict: + downloadable = is_downloadable( metadata_dict ) repository_metadata = None if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - try: - trans.sa_session.flush() - # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: - handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) - except TypeError, e: - message = "Unable to save metadata for this repository, exception: %s" % str( e ) - status = 'error' + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.id ), + repository, + repository.tip, + metadata_dict ) + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: - downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict + downloadable = is_downloadable( metadata_dict ) # Update the last saved repository_metadata table row. repository_metadata.changeset_revision = repository.tip repository_metadata.metadata = metadata_dict @@ -871,11 +881,22 @@ trans.sa_session.flush() else: # There are no tools in the repository, and we're setting metadata on the repository tip. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.id ), + repository, + repository.tip, + metadata_dict ) if 'tools' in metadata_dict and repository_metadata and status != 'error': - add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), [ repository_metadata.changeset_revision ] ) + # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. + downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] + changeset_revisions = [] + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + if changeset_revision in downloadable_changeset_revisions: + changeset_revisions.append( changeset_revision ) + # Now append the latest changeset_revision we just updated above. + changeset_revisions.append( repository_metadata.changeset_revision ) + add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), changeset_revisions ) elif len( repo ) == 1 and not invalid_file_tups: message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."

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

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