1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/82b5aef7a1da/ Changeset: 82b5aef7a1da User: greg Date: 2014-01-17 19:49:10 Summary: Enhance setting tool shed repository metadata to support tool dependency recipes that define installation of a binary but do not also include a recipe for installing and compiling from source. Affected #: 3 files

diff -r 79c1a31e269d4668d125c1a277549617d34dae13 -r 82b5aef7a1da9e4129ba2a3920a54048642cc991 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -303,7 +303,8 @@ with make_tmp_dir() as work_dir: with lcd( work_dir ): # The first action in the list of actions will be the one that defines the installation process. There - # are currently only two supported processes; download_by_url and clone via a "shell_command" action type. + # are currently three supported processes; download_binary, download_by_url and clone via a "shell_command" + # action type. action_type, action_dict = actions[ 0 ] if action_type == 'download_binary': url = action_dict[ 'url' ] @@ -316,11 +317,13 @@ downloaded_filename = td_common_util.download_binary( url, work_dir ) # Filter out any actions that are not download_binary, chmod, or set_environment. filtered_actions = filter_actions_after_binary_installation( actions[ 1: ] ) - # Set actions to the same, so that the current download_binary doesn't get re-run in the filtered actions below. + # Set actions to the same, so that the current download_binary doesn't get re-run in the + # filtered actions below. actions = filtered_actions except Exception, e: log.exception( str( e ) ) - # No binary exists, or there was an error downloading the binary from the generated URL. Proceed with the remaining actions. + # No binary exists, or there was an error downloading the binary from the generated URL. + # Proceed with the remaining actions. filtered_actions = actions[ 1: ] action_type, action_dict = filtered_actions[ 0 ] # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that @@ -345,8 +348,9 @@ is_binary = action_dict.get( 'is_binary', False ) log.debug( 'Attempting to download via url: %s', url ) if 'target_filename' in action_dict: - # Sometimes compressed archives extract their content to a folder other than the default defined file name. Using this - # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. + # Sometimes compressed archives extract their content to a folder other than the default + # defined file name. Using this attribute will ensure that the file name is set appropriately + # and can be located after download, decompression and extraction. downloaded_filename = action_dict[ 'target_filename' ] else: downloaded_filename = os.path.split( url )[ -1 ] @@ -374,8 +378,9 @@ filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] if 'target_filename' in action_dict: - # Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this - # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. + # Sometimes compressed archives extracts their content to a folder other than the default + # defined file name. Using this attribute will ensure that the file name is set appropriately + # and can be located after download, decompression and extraction. filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ]

diff -r 79c1a31e269d4668d125c1a277549617d34dae13 -r 82b5aef7a1da9e4129ba2a3920a54048642cc991 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -324,31 +324,37 @@

def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ - Parse a <package> element within a tool dependency definition and return a list of action tuples. This method is called when setting - metadata on a repository that includes a tool_dependencies.xml file or when installing a repository that includes a tool_dependencies.xml - file. If installing, platform_info_dict must be a valid dictionary and include_after_install_actions must be True. + Parse a <package> element within a tool dependency definition and return a list of action tuples. + This method is called when setting metadata on a repository that includes a tool_dependencies.xml + file or when installing a repository that includes a tool_dependencies.xml file. If installing, + platform_info_dict must be a valid dictionary and include_after_install_actions must be True. """ - # The actions_elem_tuples list contains <actions> tag sets (possibly inside of an <actions_group> tag set) to be processed in the order - # they are defined in the tool_dependencies.xml file. + # The actions_elem_tuples list contains <actions> tag sets (possibly inside of an <actions_group> + # tag set) to be processed in the order they are defined in the tool_dependencies.xml file. actions_elem_tuples = [] - # The tag sets that will go into the actions_elem_list are those that install a compiled binary if the architecture and operating system - # match it's defined attributes. If compiled binary is not installed, the first <actions> tag set [following those that have the os and - # architecture attributes] that does not have os or architecture attributes will be processed. This tag set must contain the recipe for - # downloading and compiling source. + # The tag sets that will go into the actions_elem_list are those that install a compiled binary if + # the architecture and operating system match it's defined attributes. If compiled binary is not + # installed, the first <actions> tag set [following those that have the os and architecture attributes] + # that does not have os or architecture attributes will be processed. This tag set must contain the + # recipe for downloading and compiling source. actions_elem_list = [] for elem in package_elem: if elem.tag == 'actions': - # We have an <actions> tag that should not be matched against a specific combination of architecture and operating system. + # We have an <actions> tag that should not be matched against a specific combination of + # architecture and operating system. in_actions_group = False actions_elem_tuples.append( ( in_actions_group, elem ) ) elif elem.tag == 'actions_group': - # We have an actions_group element, and its child <actions> elements should therefore be compared with the current operating system + # We have an actions_group element, and its child <actions> elements should therefore be compared + # with the current operating system # and processor architecture. in_actions_group = True - # Record the number of <actions> elements so we can filter out any <action> elements that precede <actions> elements. + # Record the number of <actions> elements so we can filter out any <action> elements that precede + # <actions> elements. actions_elem_count = len( elem.findall( 'actions' ) ) - # Record the number of <actions> elements that have both architecture and os specified, in order to filter out any - # platform-independent <actions> elements that come before platform-specific <actions> elements. + # Record the number of <actions> elements that have both architecture and os specified, in order + # to filter out any platform-independent <actions> elements that come before platform-specific + # <actions> elements. platform_actions_elements = [] for actions_elem in elem.findall( 'actions' ): if actions_elem.get( 'architecture' ) is not None and actions_elem.get( 'os' ) is not None: @@ -356,8 +362,9 @@ platform_actions_element_count = len( platform_actions_elements ) platform_actions_elements_processed = 0 actions_elems_processed = 0 - # The tag sets that will go into the after_install_actions list are <action> tags instead of <actions> tags. These will be processed - # only if they are at the very end of the <actions_group> tag set (after all <actions> tag sets). See below for details. + # The tag sets that will go into the after_install_actions list are <action> tags instead of <actions> + # tags. These will be processed only if they are at the very end of the <actions_group> tag set (after + # all <actions> tag sets). See below for details. after_install_actions = [] # Inspect the <actions_group> element and build the actions_elem_list and the after_install_actions list. for child_element in elem: @@ -365,60 +372,71 @@ actions_elems_processed += 1 system = child_element.get( 'os' ) architecture = child_element.get( 'architecture' ) - # Skip <actions> tags that have only one of architecture or os specified, in order for the count in - # platform_actions_elements_processed to remain accurate. + # Skip <actions> tags that have only one of architecture or os specified, in order for the + # count in platform_actions_elements_processed to remain accurate. if ( system and not architecture ) or ( architecture and not system ): log.debug( 'Error: Both architecture and os attributes must be specified in an <actions> tag.' ) continue - # Since we are inside an <actions_group> tag set, compare it with our current platform information and filter the <actions> - # tag sets that don't match. Require both the os and architecture attributes to be defined in order to find a match. + # Since we are inside an <actions_group> tag set, compare it with our current platform information + # and filter the <actions> tag sets that don't match. Require both the os and architecture attributes + # to be defined in order to find a match. if system and architecture: platform_actions_elements_processed += 1 - # If either the os or architecture do not match the platform, this <actions> tag will not be considered a match. Skip - # it and proceed with checking the next one. + # If either the os or architecture do not match the platform, this <actions> tag will not be + # considered a match. Skip it and proceed with checking the next one. if platform_info_dict: if platform_info_dict[ 'os' ] != system or platform_info_dict[ 'architecture' ] != architecture: continue else: - # We must not be installing a repository into Galaxy, so determining if we can install a binary is not necessary. + # We must not be installing a repository into Galaxy, so determining if we can install a + # binary is not necessary. continue else: - # <actions> tags without both os and architecture attributes are only allowed to be specified after platform-specific - # <actions> tags. If we find a platform-independent <actions> tag before all platform-specific <actions> tags have been - # processed. + # <actions> tags without both os and architecture attributes are only allowed to be specified + # after platform-specific <actions> tags. If we find a platform-independent <actions> tag before + # all platform-specific <actions> tags have been processed. if platform_actions_elements_processed < platform_actions_element_count: - message = 'Error: <actions> tags without os and architecture attributes are only allowed after all <actions> tags with ' - message += 'os and architecture attributes have been defined. Skipping the <actions> tag set with no os or architecture ' - message += 'attributes that has been defined between two <actions> tag sets that have these attributes defined. ' - log.debug( message ) + debug_msg = 'Error: <actions> tags without os and architecture attributes are only allowed ' + debug_msg += 'after all <actions> tags with os and architecture attributes have been defined. ' + debug_msg += 'Skipping the <actions> tag set with no os or architecture attributes that has ' + debug_msg += 'been defined between two <actions> tag sets that have these attributes defined. ' + log.debug( debug_msg ) continue - # If we reach this point, it means one of two things: 1) The system and architecture attributes are not defined in this - # <actions> tag, or 2) The system and architecture attributes are defined, and they are an exact match for the current - # platform. Append the child element to the list of elements to process. + # If we reach this point, it means one of two things: 1) The system and architecture attributes are + # not defined in this <actions> tag, or 2) The system and architecture attributes are defined, and + # they are an exact match for the current platform. Append the child element to the list of elements + # to process. actions_elem_list.append( child_element ) elif child_element.tag == 'action': # Any <action> tags within an <actions_group> tag set must come after all <actions> tags. if actions_elems_processed == actions_elem_count: - # If all <actions> elements have been processed, then this <action> element can be appended to the list of actions to - # execute within this group. + # If all <actions> elements have been processed, then this <action> element can be appended to the + # list of actions to execute within this group. after_install_actions.append( child_element ) else: - # If any <actions> elements remain to be processed, then log a message stating that <action> elements are not allowed - # to precede any <actions> elements within an <actions_group> tag set. - message = 'Error: <action> tags are only allowed at the end of an <actions_group> tag set after all <actions> tags. ' - message += 'Skipping <%s> element with type %s.' % ( child_element.tag, child_element.get( 'type' ) ) - log.debug( message ) + # If any <actions> elements remain to be processed, then log a message stating that <action> + # elements are not allowed to precede any <actions> elements within an <actions_group> tag set. + debug_msg = 'Error: <action> tags are only allowed at the end of an <actions_group> tag set after ' + debug_msg += 'all <actions> tags. Skipping <%s> element with type %s.' % \ + ( child_element.tag, child_element.get( 'type', 'unknown' ) ) + log.debug( debug_msg ) continue if platform_info_dict is None and not include_after_install_actions: # We must be setting metadata on a repository. - actions_elem_tuples.append( ( in_actions_group, actions_elem_list[ 0 ] ) ) + if len( actions_elem_list ) >= 1: + actions_elem_tuples.append( ( in_actions_group, actions_elem_list[ 0 ] ) ) + else: + # We are processing a recipe that contains only an <actions_group> tag set for installing a binary, + # but does not include an additional recipe for installing and compiling from source. + actions_elem_tuples.append( ( in_actions_group, [] ) ) elif platform_info_dict is not None and include_after_install_actions: # We must be installing a repository. if after_install_actions: actions_elem_list.extend( after_install_actions ) actions_elem_tuples.append( ( in_actions_group, actions_elem_list ) ) else: - # Skip any element that is not <actions> or <actions_group> - this will skip comments, <repository> tags and <readme> tags. + # Skip any element that is not <actions> or <actions_group> - this will skip comments, <repository> tags + # and <readme> tags. in_actions_group = False continue return actions_elem_tuples

diff -r 79c1a31e269d4668d125c1a277549617d34dae13 -r 82b5aef7a1da9e4129ba2a3920a54048642cc991 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -791,26 +791,30 @@ if sub_elem.tag == 'readme': requirements_dict[ 'readme' ] = sub_elem.text elif sub_elem.tag == 'repository': - # We have a complex repository dependency. If the returned value of repository_dependency_is_valid is True, the tool - # dependency definition will be set as invalid. This is currently the only case where a tool dependency definition is - # considered invalid. - repository_dependency_tup, repository_dependency_is_valid, error_message = handle_repository_elem( app=app, - repository_elem=sub_elem, - only_if_compiling_contained_td=False ) + # We have a complex repository dependency. If the returned value of repository_dependency_is_valid + # is True, the tool dependency definition will be set as invalid. This is currently the only case + # where a tool dependency definition is considered invalid. + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + handle_repository_elem( app=app, repository_elem=sub_elem, only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': - # Complex repository dependencies can be defined within the last <actions> tag set contained in an <actions_group> tag set. - # Comments, <repository> tag sets and <readme> tag sets will be skipped in td_common_util.parse_package_elem(). - actions_elem_tuples = td_common_util.parse_package_elem( sub_elem, platform_info_dict=None, include_after_install_actions=False ) + # Complex repository dependencies can be defined within the last <actions> tag set contained in an + # <actions_group> tag set. Comments, <repository> tag sets and <readme> tag sets will be skipped + # in td_common_util.parse_package_elem(). + actions_elem_tuples = td_common_util.parse_package_elem( sub_elem, + platform_info_dict=None, + include_after_install_actions=False ) if actions_elem_tuples: - # We now have a list of a single tuple that looks something like: [(True, <Element 'actions' at 0x104017850>)] + # We now have a list of a single tuple that looks something like: + # [(True, <Element 'actions' at 0x104017850>)] actions_elem_tuple = actions_elem_tuples[ 0 ] in_actions_group, actions_elem = actions_elem_tuple if in_actions_group: - # Since we're inside an <actions_group> tag set, inspect the actions_elem to see if a complex repository dependency - # is defined. By definition, complex repository dependency definitions contained within the last <actions> tag set - # within an <actions_group> tag set will have the value of "only_if_compiling_contained_td" set to True in + # Since we're inside an <actions_group> tag set, inspect the actions_elem to see if a complex + # repository dependency is defined. By definition, complex repository dependency definitions + # contained within the last <actions> tag set within an <actions_group> tag set will have the + # value of "only_if_compiling_contained_td" set to True in for action_elem in actions_elem: if action_elem.tag == 'package': # <package name="libgtextutils" version="0.6"> @@ -834,7 +838,8 @@ # Append the error message to the requirements_dict. requirements_dict[ 'error' ] = error_message invalid_tool_dependencies_dict[ dependency_key ] = requirements_dict - return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, repository_dependency_is_valid, error_message + return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, \ + repository_dependency_is_valid, error_message

def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): """ @@ -1986,7 +1991,8 @@ content_alert_str=content_alert_str, **kwd ) if error_message: - # FIXME: This probably should not redirect since this method is called from the upload controller as well as the repository controller. + # FIXME: This probably should not redirect since this method is called from the upload controller as well + # as the repository controller. # If there is an error, display it. return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository',

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