1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/7547a3131862/ changeset: 7547a3131862 user: greg date: 2011-09-09 17:18:05 summary: Add the ability for a tool shed repository owner to reset the repository metadata for any change set revision that has associated repository metadata (previously could only be reset for repository tip) affected #: 5 files (3.1 KB)

--- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 09 11:18:05 2011 -0400 @@ -110,7 +110,7 @@ """Get last metadata defined for a specified repository from the database""" return 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.update_time.desc() ) \ + .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ @@ -163,7 +163,7 @@ repository.name, tool.id, tool.version ) -def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ): +def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received tool. @@ -189,7 +189,7 @@ version=tool.version, description=tool.description, version_string_cmd = tool.version_string_cmd, - tool_config=os.path.join( root, name ), + tool_config=tool_config, requirements=tool_requirements, tests=tool_tests ) if 'tools' in metadata_dict: @@ -249,49 +249,87 @@ ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} - 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: - # Update the list metadata dictionaries for tools in metadata_dict. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) - # Find all exported workflows - elif name.endswith( '.ga' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - # Convert workflow data from json - fp = open( full_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) + if changeset_revision == repository.tip: + 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: + # Update the list metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + # Update the list of metadata dictionaries for workflows in metadata_dict. + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + else: + # Get all tool config file names from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + for filename in ctx: + # Find all tool configs - should not have to update metadata for workflows. + if filename.endswith( '.xml' ): + fctx = ctx[ filename ] + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + if tool is not None: + # Update the list metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + try: + os.unlink( tmp_filename ) + except: + pass if metadata_dict: - if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): - # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + if changeset_revision == repository.tip: + if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): + # Create a new repository_metadata table row. + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # Update the last saved repository_metadata table row. + repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: - # Update the last saved repository_metadata table row. - repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.changeset_revision = changeset_revision + # We're re-generating metadata for an old repository revision. + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) repository_metadata.metadata = metadata_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush()

--- a/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 09 11:18:05 2011 -0400 @@ -1237,22 +1237,26 @@ # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None for filename in ctx: if filename == old_tool_config_file_name: fctx = ctx[ filename ] break - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - tool = load_tool( trans, tmp_filename ) - try: - os.unlink( tmp_filename ) - except: - pass + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + tool = load_tool( trans, tmp_filename ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None 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",

--- a/lib/galaxy/webapps/community/model/mapping.py Fri Sep 09 10:16:48 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Sep 09 11:18:05 2011 -0400 @@ -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.update_time ) ) ) ) + downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.id ) ) ) )

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

--- a/templates/webapps/community/repository/common.mako Fri Sep 09 10:16:48 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Fri Sep 09 11:18:05 2011 -0400 @@ -176,20 +176,16 @@ %endif %endif %if can_set_metadata: - %if repository.tip == changeset_revision: - ## TODO: when we support previewing older versions of tools, we - ## should allow resetting metadata on the older versions as well. - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/></div> - </form> - %endif + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div> + </div> + </form> %endif </div></div>

--- a/templates/webapps/community/repository/tool_form.mako Fri Sep 09 10:16:48 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Fri Sep 09 11:18:05 2011 -0400 @@ -152,26 +152,30 @@ ${render_msg( message, status )} %endif

- <div class="toolForm" id="${tool.id}"> - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> - <div class="toolFormBody"> - <form id="tool_form" name="tool_form" action="" method="get"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} - </form> + %if tool: + <div class="toolForm" id="${tool.id}"> + <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> + <div class="toolFormBody"> + <form id="tool_form" name="tool_form" action="" method="get"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} + </form> + </div></div> - </div> - %if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - # Convert to unicode to display non-ascii characters. - if type( tool.help ) is not unicode: - tool.help = unicode( tool.help, 'utf-8') - %> - ${tool.help} - </div> - </div> + %if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + # Convert to unicode to display non-ascii characters. + if type( tool.help ) is not unicode: + tool.help = unicode( tool.help, 'utf-8') + %> + ${tool.help} + </div> + </div> + %endif + %else: + Tool not properly loaded. %endif </body></html>

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

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