1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/6c488ed46f93/ changeset: 6c488ed46f93 user: greg date: 2011-09-26 21:29:19 summary: Fixes for installing tool shed repositories into a local Galaxy instance where the repository includes tools that have parameters that are dynamically generated select lists with various conbinations of tool_data_table entries and index files dependencies. affected #: 6 files (-1 bytes)

--- a/lib/galaxy/tools/__init__.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Sep 26 15:29:19 2011 -0400 @@ -1320,7 +1320,32 @@ errors[ input.name ] = error state[ input.name ] = value return errors - + @property + def params_with_missing_data_table_entry( self ): + """ + Return all parameters that are dynamically generated select lists whose + options require an entry not currently in the tool_data_table_conf.xml file. + """ + params = [] + for input_param in self.input_params: + if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + options = input_param.options + if options and options.missing_tool_data_table_name and input_param not in params: + params.append( input_param ) + return params + @property + def params_with_missing_index_file( self ): + """ + Return all parameters that are dynamically generated + select lists whose options refer to a missing .loc file. + """ + params = [] + for input_param in self.input_params: + if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + options = input_param.options + if options and options.missing_index_file and input_param not in params: + params.append( input_param ) + return params def get_static_param_values( self, trans ): """ Returns a map of parameter names and values if the tool does not

--- a/lib/galaxy/tools/data/__init__.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/data/__init__.py Mon Sep 26 15:29:19 2011 -0400 @@ -106,6 +106,9 @@ self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) self.data = all_rows + def handle_found_index_file( self, filename ): + self.missing_index_file = None + self.data.extend( self.parse_file_fields( open( filename ) ) ) def get_fields( self ): return self.data def parse_column_spec( self, config_element ):

--- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Sep 26 15:29:19 2011 -0400 @@ -399,6 +399,7 @@ self.separator = elem.get( 'separator', '\t' ) self.line_startswith = elem.get( 'startswith', None ) data_file = elem.get( 'from_file', None ) + self.index_file = None self.missing_index_file = None dataset_file = elem.get( 'from_dataset', None ) from_parameter = elem.get( 'from_parameter', None ) @@ -414,15 +415,16 @@ # which the tool_data_table refers does not exist. if self.tool_data_table.missing_index_file: self.missing_index_file = self.tool_data_table.missing_index_file - # Column definitions are optional, but if provided override those from the table - if elem.find( "column" ) is not None: - self.parse_column_definitions( elem ) else: - self.columns = self.tool_data_table.columns + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns else: self.missing_tool_data_table_name = tool_data_table_name log.warn( "Data table named '%s' is required by tool but not configured" % tool_data_table_name ) - # Options are defined by parsing tabular text data from an data file + # Options are defined by parsing tabular text data from a data file # on disk, a dataset, or the value of another parameter elif data_file is not None or dataset_file is not None or from_parameter is not None: self.parse_column_definitions( elem ) @@ -431,6 +433,7 @@ if not os.path.isabs( data_file ): full_path = os.path.join( self.tool_param.tool.app.config.tool_data_path, data_file ) if os.path.exists( full_path ): + self.index_file = data_file self.file_fields = self.parse_file_fields( open( full_path ) ) else: self.missing_index_file = data_file

--- a/lib/galaxy/web/base/controller.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Mon Sep 26 15:29:19 2011 -0400 @@ -2437,96 +2437,14 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: - # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs - repository_tools_tups = [] - # The sample_files list contains all files whose name ends in .sample - sample_files = [] - for root, dirs, files in os.walk( repo_files_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' ) - # Find all special .sample files first. - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - relative_path = os.path.join( root, name ) - full_path = os.path.abspath( os.path.join( root, name ) ) - try: - repository_tool = trans.app.toolbox.load_tool( full_path ) - if repository_tool: - # Check all of the tool's input parameters, looking for any that are dynamically - # generated using external data files to make sure the files exist. - for input_param in repository_tool.input_params: - if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the - # tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.missing_tool_data_table_name: - # The repository must contain a tool_data_table_conf.xml.sample file. - for sample_file in sample_files: - head, tail = os.path.split( sample_file ) - if tail == 'tool_data_table_conf.xml.sample': - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) - if error: - log.debug( exception_msg ) - break - if options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # The repository must contain the required xxx.loc.sample file. - for sample_file in sample_files: - sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: - copy_sample_loc_file( trans, sample_file ) - break - # At this point, we need to lstrip tool_path from relative_path. - tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) - repository_tools_tups.append( ( tup_path, repository_tool ) ) - except Exception, e: - # We have an inavlid .xml file, so not a tool config. - log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) + sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) if repository_tools_tups: - # Look at each tool to see if it includes a "requirement" that refers to - # a fabric script. For those that do, execute the fabric script to install - # tool dependencies. - for repository_tools_tup in repository_tools_tups: - tup_path, repository_tool = repository_tools_tup - for requirement in repository_tool.requirements: - if requirement.type == 'fabfile': - log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) - fabfile = requirement.fabfile - method = requirement.method - # Find the relative path to the fabfile. - relative_fabfile_path = None - for root, dirs, files in os.walk( repo_files_dir ): - for name in files: - if name == fabfile: - relative_fabfile_path = os.path.join( root, name ) - break - if relative_fabfile_path: - # cmd will look something like: fab -f fabfile.py install_bowtie - cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( repo_files_dir ) - proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode != 0: - # TODO: do something more here than logging the problem. - tmp_stderr = open( tmp_name, 'rb' ) - error = tmp_stderr.read() - tmp_stderr.close() - log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + # Handle missing data table entries for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) + # Handle missing index files for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) + # Handle tools that use fabric scripts to install dependencies. + self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) # Generate an in-memory tool conf section that includes the new tools. new_tool_section = self.__generate_tool_panel_section( repository_name, repository_clone_url, @@ -2585,6 +2503,120 @@ tool_panel_section_select_field=tool_panel_section_select_field, message=message, status=status ) + def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if any have input parameters that are dynamically + # generated select lists that require entries in the tool_data_table_conf.xml file. + missing_data_table_entry = False + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + if repository_tool.params_with_missing_data_table_entry: + missing_data_table_entry = True + break + if missing_data_table_entry: + # The repository must contain a tool_data_table_conf.xml.sample file that includes + # all required entries for all tools in the repository. + for sample_file in sample_files: + head, tail = os.path.split( sample_file ) + if tail == 'tool_data_table_conf.xml.sample': + break + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + if error: + # TODO: Do more here than logging an exception. + log.debug( exception_msg ) + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if it has any input parameters that + # are dynamically generated select lists that depend on a .loc file. + missing_files_handled = [] + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + params_with_missing_index_file = repository_tool.params_with_missing_index_file + for param in params_with_missing_index_file: + options = param.options + missing_head, missing_tail = os.path.split( options.missing_index_file ) + if missing_tail not in missing_files_handled: + # The repository must contain the required xxx.loc.sample file. + for sample_file in sample_files: + sample_head, sample_tail = os.path.split( sample_file ) + if sample_tail == '%s.sample' % missing_tail: + copy_sample_loc_file( trans, sample_file ) + if options.tool_data_table and options.tool_data_table.missing_index_file: + options.tool_data_table.handle_found_index_file( options.missing_index_file ) + missing_files_handled.append( missing_tail ) + break + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ): + # Inspect each tool to see if it includes a "requirement" that refers to a fabric + # script. For those that do, execute the fabric script to install tool dependencies. + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + for requirement in repository_tool.requirements: + if requirement.type == 'fabfile': + log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) + fabfile = requirement.fabfile + method = requirement.method + # Find the relative path to the fabfile. + relative_fabfile_path = None + for root, dirs, files in os.walk( repo_files_dir ): + for name in files: + if name == fabfile: + relative_fabfile_path = os.path.join( root, name ) + break + if relative_fabfile_path: + # cmd will look something like: fab -f fabfile.py install_bowtie + cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode != 0: + # TODO: do something more here than logging the problem. + tmp_stderr = open( tmp_name, 'rb' ) + error = tmp_stderr.read() + tmp_stderr.close() + log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): + # The sample_files list contains all files whose name ends in .sample + sample_files = [] + # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs + repository_tools_tups = [] + for root, dirs, files in os.walk( repo_files_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' ) + # Find all special .sample files first. + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + relative_path = os.path.join( root, name ) + full_path = os.path.abspath( os.path.join( root, name ) ) + try: + repository_tool = trans.app.toolbox.load_tool( full_path ) + if repository_tool: + # At this point, we need to lstrip tool_path from relative_path. + tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) + repository_tools_tups.append( ( tup_path, repository_tool ) ) + except Exception, e: + # We have an invalid .xml file, so not a tool config. + log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) + return sample_files, repository_tools_tups def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): # Add an entry in the shed_tool_conf file. An entry looks something like: # <section name="Filter and Sort" id="filter"> @@ -2704,12 +2736,15 @@ select_field.add_option( option_tup[0], option_tup[1] ) return select_field def copy_sample_loc_file( trans, filename ): - """Copy xxx.loc.sample to ~/tool-data/xxx.loc""" + """Copy xxx.loc.sample to ~/tool-data/xxx.loc.sample and ~/tool-data/xxx.loc""" head, sample_loc_file = os.path.split( filename ) - loc_file = sample_loc_file.rstrip( '.sample' ) + loc_file = sample_loc_file.replace( '.sample', '' ) tool_data_path = os.path.abspath( trans.app.config.tool_data_path ) - if not ( os.path.exists( os.path.join( tool_data_path, loc_file ) ) or os.path.exists( os.path.join( tool_data_path, sample_loc_file ) ) ): - shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) + # It's ok to overwrite the .sample version of the file. + shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) + # Only create the .loc file if it does not yet exist. We don't + # overwrite it in case it contains stuff proprietary to the local instance. + if not os.path.exists( os.path.join( tool_data_path, loc_file ) ): shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) ) def get_user( trans, id ): """Get a User from the database by id.""" @@ -2774,7 +2809,7 @@ if line.find( '</tables>' ) >= 0: for new_table_elem in new_table_elems: new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) - new_tdt_config.write( '</tables>' ) + new_tdt_config.write( '</tables>\n' ) else: new_tdt_config.write( line ) new_tdt_config.close()

--- a/lib/galaxy/webapps/community/controllers/common.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Sep 26 15:29:19 2011 -0400 @@ -176,8 +176,8 @@ # tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options: - if options.missing_tool_data_table_name: - # See if the repository contains a tool_data_table_conf.xml.sample file. + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. sample_found = False for sample_file in sample_files: head, tail = os.path.split( sample_file ) @@ -187,6 +187,8 @@ if error: can_set_metadata = False invalid_files.append( ( tail, correction_msg ) ) + else: + options.missing_tool_data_table_name = None break if not sample_found: can_set_metadata = False @@ -194,20 +196,24 @@ correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " correction_msg += "that includes the required entry to resolve this issue.<br/>" invalid_files.append( ( name, correction_msg ) ) - elif options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # See if the repository contains the required xxx.loc.sample file. + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_head, index_tail = os.path.split( index_file ) sample_found = False for sample_file in sample_files: sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: + if sample_tail == '%s.sample' % index_tail: copy_sample_loc_file( trans, sample_file ) + options.index_file = index_tail + options.missing_index_file = None + options.tool_data_table.missing_index_file = None sample_found = True break if not sample_found: can_set_metadata = False - correction_msg = "This file refers to a missing file <b>%s</b>. " % str( options.missing_index_file ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( missing_tail ) + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_tail ) invalid_files.append( ( name, correction_msg ) ) return can_set_metadata, invalid_files def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ):

--- a/templates/tool_form.mako Mon Sep 26 10:23:15 2011 -0400 +++ b/templates/tool_form.mako Mon Sep 26 15:29:19 2011 -0400 @@ -250,20 +250,15 @@ <% # Render an error message if a dynamically generated select list is missing a required # index file or entry in the tool_data_table_conf.xml file. - from galaxy.tools.parameters.basic import SelectToolParameter message = "" - for input_param in tool.input_params: - if isinstance( input_param, SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the - # tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.missing_tool_data_table_name: - message = "Data table named '%s' is required by tool but not configured" % options.missing_tool_data_table_name - break - if options.missing_index_file: - message = "Index file named '%s' is required by tool but not availble" % options.missing_index_file - break + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file

# Handle calculating the redirect url for the special case where we have nginx proxy # upload and need to do url_for on the redirect portion of the tool action.

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