1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/4c6f1004071d/ changeset: 4c6f1004071d user: greg date: 2011-11-18 22:44:10 summary: Add the ability to reset all metadata (for every change set) in a tool shed repository (currently restricted to an admin), and add a fix for checking security when making changes to tool shed repository information on the Manage repsoitory page. affected #: 4 files

diff -r 07df6866125adb6f3723aec8303e9300338e4cdc -r 4c6f1004071d5055c9bf2d0b35f5bfe077b79e1e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -343,6 +343,127 @@ mimetype=mimetype ) ) metadata_dict[ 'datatypes' ] = datatypes return metadata_dict +def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ): + # Browse the repository tip files on disk to generate metadata. This is faster than + # the generate_metadata_for_changeset_revision() method below because fctx.data() does + # not have to be written to disk to load tools. also, since changeset_revision is the + # repository tip, we handle things like .loc.sample files here. + metadata_dict = {} + invalid_files = [] + sample_files = [] + datatypes_config = None + # Find datatypes_conf.xml if it exists. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + # Find all special .sample files. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + # Find all tool configs and exported workflows. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # Find all tool configs. + if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) + try: + tool = load_tool( trans, full_path ) + valid = True + except Exception, e: + valid = False + invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of 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 ) + # 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 ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + # 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 ) ) ) + return metadata_dict, invalid_files +def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ): + # Browse repository files within a change set to generate metadata. + metadata_dict = {} + invalid_files = [] + sample_files = [] + datatypes_config = None + # Find datatypes_conf.xml if it exists. + for filename in ctx: + if filename == 'datatypes_conf.xml': + fctx = ctx[ filename ] + datatypes_config = fctx.data() + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + # 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. + if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ): + fctx = ctx[ filename ] + # Write the contents of the old tool config to a temporary file. + # TODO: figure out how to enhance the load_tool method so that a + # temporary disk file is not necessary in order to pass the tool + # config. + 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 ) + valid = True + except Exception, e: + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + # Update the list of 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. + # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository + # tip, we do not have to handle any .loc.sample files since they would have been handled previously. + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + try: + os.unlink( tmp_filename ) + except: + pass + # Find all exported workflows. + elif filename.endswith( '.ga' ): + try: + fctx = ctx[ filename ] + workflow_text = fctx.data() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + # 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 ) ) ) + return metadata_dict, invalid_files def set_repository_metadata( trans, id, changeset_revision, **kwd ): """Set repository metadata""" message = '' @@ -350,102 +471,12 @@ repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - invalid_files = [] - sample_files = [] - datatypes_config = None ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: - metadata_dict = {} if changeset_revision == repository.tip: - # Find datatypes_conf.xml if it exists. - for root, dirs, files in os.walk( repo_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == 'datatypes_conf.xml': - datatypes_config = os.path.abspath( os.path.join( root, name ) ) - break - if datatypes_config: - metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) - # Find all special .sample files. - for root, dirs, files in os.walk( repo_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) - # Find all tool configs and exported workflows. - for root, dirs, files in os.walk( repo_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - # Find all tool configs. - if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) - try: - tool = load_tool( trans, full_path ) - valid = True - except Exception, e: - valid = False - invalid_files.append( ( name, str( e ) ) ) - if valid and tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of 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 ) - # 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 ) - if exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - # 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 ) ) ) + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ) else: - # Find all special .sample files first. - for filename in ctx: - if filename.endswith( '.sample' ): - sample_files.append( os.path.abspath( filename ) ) - # 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 - we do not have to update metadata for workflows or datatypes in anything - # but repository tips (handled above) since at the time this code was written, no workflows or - # dataytpes_conf.xml files exist in tool shed repositories, so they can only be added in future tips. - 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 ) - valid = True - except Exception, e: - invalid_files.append( ( filename, str( e ) ) ) - valid = False - if valid and tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of 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 ) - try: - os.unlink( tmp_filename ) - except: - pass + metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ) if metadata_dict: if changeset_revision == repository.tip: if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): @@ -467,8 +498,8 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - message = "Revision '%s' includes no tools or exported workflows for which metadata can be defined " % str( changeset_revision ) - message += "so this revision cannot be automatically installed into a local Galaxy instance." + message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( changeset_revision ) + message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" else: # change_set is None

diff -r 07df6866125adb6f3723aec8303e9300338e4cdc -r 4c6f1004071d5055c9bf2d0b35f5bfe077b79e1e lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1311,15 +1311,14 @@ if params.get( 'edit_repository_button', False ): flush_needed = False # TODO: add a can_manage in the security agent. - if user != repository.user or not trans.user_is_admin(): + if not ( user.email == repository.user.email or trans.user_is_admin() ): message = "You are not the owner of this repository, so you cannot manage it." - status = error return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, webapp='community', message=message, - status=status ) ) + status='error' ) ) if description != repository.description: repository.description = description flush_needed = True @@ -1447,6 +1446,10 @@ changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) + if get_repository_metadata_by_changeset_revision( trans, id, str( ctx ) ): + has_metadata = True + else: + has_metadata = False t, tz = ctx.date() date = datetime( *time.gmtime( float( t ) - tz )[:6] ) display_date = date.strftime( "%Y-%m-%d" ) @@ -1457,7 +1460,8 @@ 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), - 'parent' : ctx.parents()[0] } + 'parent' : ctx.parents()[0], + 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) is_malicious = change_set_is_malicious( trans, id, repository.tip ) @@ -1608,6 +1612,190 @@ message=message, status=status ) ) @web.expose + def reset_all_metadata( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + 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. + changeset_revisions = [] + repository_metadata_tup_for_comparison = () + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + current_changeset_revision = str( ctx ) + 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: + # '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. + if comparison in [ 'no metadata', 'equal', 'subset' ]: + repository_metadata_tup_for_comparison = ( current_changeset_revision, 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. + changeset_revisions.append( ancestor_changeset_revision ) + repository_metadata_tup_for_comparison = () + else: + # We're at the first change set in the change log. + repository_metadata_tup_for_comparison = ( current_changeset_revision, 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 ) + 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. + changeset_revisions.append( ancestor_changeset_revision ) + repository_metadata_tup_for_comparison = () + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + self.__clean_repository_metadata( trans, id, changeset_revisions ) + if not message: + message = "Repository metadata has been reset." + status = 'done' + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + message=message, + status=status ) ) + def __clean_repository_metadata( self, trans, id, changeset_revisions ): + # Delete all repository_metadata reecords associated with the repository + # that have a changeset_revision that is not in 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 ) ): + if repository_metadata.changeset_revision not in changeset_revisions: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + def __create_or_update_repository_metadata( self, trans, id, repository, changeset_revision, metadata_dict ): + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + # Update RepositoryMetadata.metadata. + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # 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() + 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. + # Get information about tools. + if 'tools' in ancestor_metadata_dict: + ancestor_tools = ancestor_metadata_dict[ 'tools' ] + else: + ancestor_tools = [] + if 'tools' in current_metadata_dict: + current_tools = current_metadata_dict[ 'tools' ] + else: + current_tools = [] + ancestor_guids = [] + for tool_dict in ancestor_tools: + ancestor_guids.append( tool_dict[ 'guid' ] ) + ancestor_guids.sort() + current_guids = [] + for tool_dict in current_tools: + current_guids.append( tool_dict[ 'guid' ] ) + current_guids.sort() + # Get information about workflows. + if 'workflows' in ancestor_metadata_dict: + ancestor_workflows = ancestor_metadata_dict[ 'workflows' ] + else: + ancestor_workflows = [] + if 'workflows' in current_metadata_dict: + current_workflows = current_metadata_dict[ 'workflows' ] + else: + current_workflows = [] + # Get information about datatypes. + if 'datatypes' in ancestor_metadata_dict: + ancestor_datatypes = ancestor_metadata_dict[ 'datatypes' ] + else: + ancestor_datatypes = [] + if 'datatypes' in current_metadata_dict: + current_datatypes = current_metadata_dict[ 'datatypes' ] + 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 ): + return 'no metadata' + workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows ) + datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes ) + # Handle case where all metadata is the same. + if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': + return 'equal' + if workflow_comparison == 'subset' and datatype_comparison == 'subset': + is_subset = True + for guid in ancestor_guids: + if guid not in current_guids: + is_subset = False + break + if is_subset: + return 'subset' + return 'not equal and not subset' + def __compare_workflows( self, ancestor_workflows, current_workflows ): + # Determine if ancestor_workflows is the same as current_workflows + # or if ancestor_workflows is a subset of current_workflows. + if len( ancestor_workflows ) <= len( current_workflows ): + for ancestor_workflow in ancestor_workflows: + # Currently the only way to differentiate workflows is by name. + ancestor_workflow_name = ancestor_workflow[ 'name' ] + found_in_current = False + for current_workflow in current_workflows: + if current_workflow[ 'name' ] == ancestor_workflow_name: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_workflows ) == len( current_workflows ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' + def __compare_datatypes( self, ancestor_datatypes, current_datatypes ): + # Determine if ancestor_datatypes is the same as current_datatypes + # or if ancestor_datatypes is a subset of current_datatypes. Each + # datatype dict looks something like: + # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} + if len( ancestor_datatypes ) <= len( current_datatypes ): + for ancestor_datatype in ancestor_datatypes: + # Currently the only way to differentiate datatypes is by name. + ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] + ancestor_datatype_extension = ancestor_datatype[ 'extension' ] + ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ] + found_in_current = False + for current_datatype in current_datatypes: + if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ + current_datatype[ 'extension' ] == ancestor_datatype_extension and \ + current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_datatypes ) == len( current_datatypes ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' + @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) )

diff -r 07df6866125adb6f3723aec8303e9300338e4cdc -r 4c6f1004071d5055c9bf2d0b35f5bfe077b79e1e templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -20,6 +20,7 @@ else: browse_label = 'Browse repository tip files' can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip + can_reset_all_metadata = is_admin and len( repo ) > 0 %><%! @@ -88,6 +89,9 @@ %if can_contact_owner: <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> %endif + %if can_reset_all_metadata: + <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ), webapp='community' )}">Reset all repository metadata</a> + %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>

diff -r 07df6866125adb6f3723aec8303e9300338e4cdc -r 4c6f1004071d5055c9bf2d0b35f5bfe077b79e1e templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -106,6 +106,10 @@ ctx_parent_str = 'None' 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.' + else: + has_metadata_str = '' %><% display_date = changeset[ 'display_date' ] %> %if test_date != display_date: @@ -113,6 +117,11 @@ %endif <tr><td> + %if is_admin and has_metadata_str: + <div class="form-row"> + ${has_metadata_str} + </div> + %endif <div class="form-row"><label>Description:</label><a href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_str )}">${changeset[ 'description' ]}</a>

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

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