src/pybel_tools/definition_utils/summary_independent.py
def merge_namespaces(input_locations, output_path, namespace_name, namespace_keyword, namespace_domain, author_name,
                     citation_name, namespace_description=None, namespace_species=None, namespace_version=None,
                     namespace_query_url=None, namespace_created=None, author_contact=None, author_copyright=None,
                     citation_description=None, citation_url=None, citation_version=None, citation_date=None,
                     case_sensitive=True, delimiter='|', cacheable=True, functions=None, value_prefix='',
                     sort_key=None, check_keywords=True):
    """Merges namespaces from multiple locations to one.

    :param iter input_locations: An iterable of URLs or file paths pointing to BEL namespaces.
    :param str output_path: The path to the file to write the merged namespace
    :param str namespace_name: The namespace name
    :param str namespace_keyword: Preferred BEL Keyword, maximum length of 8
    :param str namespace_domain: One of: :data:`pybel.constants.NAMESPACE_DOMAIN_BIOPROCESS`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_CHEMICAL`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_GENE`, or
                            :data:`pybel.constants.NAMESPACE_DOMAIN_OTHER`
    :param str author_name: The namespace's authors
    :param str citation_name: The name of the citation
    :param str namespace_query_url: HTTP URL to query for details on namespace values (must be valid URL)
    :param str namespace_description: Namespace description
    :param str namespace_species: Comma-separated list of species taxonomy id's
    :param str namespace_version: Namespace version
    :param str namespace_created: Namespace public timestamp, ISO 8601 datetime
    :param str author_contact: Namespace author's contact info/email address
    :param str author_copyright: Namespace's copyright/license information
    :param str citation_description: Citation description
    :param str citation_url: URL to more citation information
    :param str citation_version: Citation version
    :param str citation_date: Citation publish timestamp, ISO 8601 Date
    :param bool case_sensitive: Should this config file be interpreted as case-sensitive?
    :param str delimiter: The delimiter between names and labels in this config file
    :param bool cacheable: Should this config file be cached?
    :param functions: The encoding for the elements in this namespace
    :type functions: iterable of characters
    :param str value_prefix: a prefix for each name
    :param sort_key: A function to sort the values with :func:`sorted`
    :param bool check_keywords: Should all the keywords be the same? Defaults to ``True``
    """
    results = get_merged_namespace_names(input_locations, check_keywords=check_keywords)

    with open(output_path, 'w') as file:
        write_namespace(
            namespace_name=namespace_name,
            namespace_keyword=namespace_keyword,
            namespace_domain=namespace_domain,
            author_name=author_name,
            citation_name=citation_name,
            values=results,
            namespace_species=namespace_species,
            namespace_description=namespace_description,
            namespace_query_url=namespace_query_url,
            namespace_version=namespace_version,
            namespace_created=namespace_created,
            author_contact=author_contact,
            author_copyright=author_copyright,
            citation_description=citation_description,
            citation_url=citation_url,
            citation_version=citation_version,
            citation_date=citation_date,
            case_sensitive=case_sensitive,
            delimiter=delimiter,
            cacheable=cacheable,
            functions=functions,
            value_prefix=value_prefix,
            sort_key=sort_key,
            file=file
        )
def merge_namespaces(input_locations, output_path, namespace_name, namespace_keyword, namespace_domain, author_name,
                     citation_name, namespace_description=None, namespace_species=None, namespace_version=None,
                     namespace_query_url=None, namespace_created=None, author_contact=None, author_copyright=None,
                     citation_description=None, citation_url=None, citation_version=None, citation_date=None,
                     case_sensitive=True, delimiter='|', cacheable=True, functions=None, value_prefix='',
                     sort_key=None, check_keywords=True):
    """Merges namespaces from multiple locations to one.

    :param iter input_locations: An iterable of URLs or file paths pointing to BEL namespaces.
    :param str output_path: The path to the file to write the merged namespace
    :param str namespace_name: The namespace name
    :param str namespace_keyword: Preferred BEL Keyword, maximum length of 8
    :param str namespace_domain: One of: :data:`pybel.constants.NAMESPACE_DOMAIN_BIOPROCESS`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_CHEMICAL`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_GENE`, or
                            :data:`pybel.constants.NAMESPACE_DOMAIN_OTHER`
    :param str author_name: The namespace's authors
    :param str citation_name: The name of the citation
    :param str namespace_query_url: HTTP URL to query for details on namespace values (must be valid URL)
    :param str namespace_description: Namespace description
    :param str namespace_species: Comma-separated list of species taxonomy id's
    :param str namespace_version: Namespace version
    :param str namespace_created: Namespace public timestamp, ISO 8601 datetime
    :param str author_contact: Namespace author's contact info/email address
    :param str author_copyright: Namespace's copyright/license information
    :param str citation_description: Citation description
    :param str citation_url: URL to more citation information
    :param str citation_version: Citation version
    :param str citation_date: Citation publish timestamp, ISO 8601 Date
    :param bool case_sensitive: Should this config file be interpreted as case-sensitive?
    :param str delimiter: The delimiter between names and labels in this config file
    :param bool cacheable: Should this config file be cached?
    :param functions: The encoding for the elements in this namespace
    :type functions: iterable of characters
    :param str value_prefix: a prefix for each name
    :param sort_key: A function to sort the values with :func:`sorted`
    :param bool check_keywords: Should all the keywords be the same? Defaults to ``True``
    """
    results = get_merged_namespace_names(input_locations, check_keywords=check_keywords)

    with open(output_path, 'w') as file:
        write_namespace(
            namespace_name=namespace_name,
            namespace_keyword=namespace_keyword,
            namespace_domain=namespace_domain,
            author_name=author_name,
            citation_name=citation_name,
            values=results,
            namespace_species=namespace_species,
            namespace_description=namespace_description,
            namespace_query_url=namespace_query_url,
            namespace_version=namespace_version,
            namespace_created=namespace_created,
            author_contact=author_contact,
            author_copyright=author_copyright,
            citation_description=citation_description,
            citation_url=citation_url,
            citation_version=citation_version,
            citation_date=citation_date,
            case_sensitive=case_sensitive,
            delimiter=delimiter,
            cacheable=cacheable,
            functions=functions,
            value_prefix=value_prefix,
            sort_key=sort_key,
            file=file
        )
def merge_namespaces ( input_locations , output_path , namespace_name , namespace_keyword , namespace_domain , author_name , citation_name , namespace_description = None , namespace_species = None , namespace_version = None , namespace_query_url = None , namespace_created = None , author_contact = None , author_copyright = None , citation_description = None , citation_url = None , citation_version = None , citation_date = None , case_sensitive = True , delimiter = '|' , cacheable = True , functions = None , value_prefix = '' , sort_key = None , check_keywords = True ) : results = get_merged_namespace_names ( input_locations , check_keywords = check_keywords ) with open ( output_path , 'w' ) as file : write_namespace ( namespace_name = namespace_name , namespace_keyword = namespace_keyword , namespace_domain = namespace_domain , author_name = author_name , citation_name = citation_name , values = results , namespace_species = namespace_species , namespace_description = namespace_description , namespace_query_url = namespace_query_url , namespace_version = namespace_version , namespace_created = namespace_created , author_contact = author_contact , author_copyright = author_copyright , citation_description = citation_description , citation_url = citation_url , citation_version = citation_version , citation_date = citation_date , case_sensitive = case_sensitive , delimiter = delimiter , cacheable = cacheable , functions = functions , value_prefix = value_prefix , sort_key = sort_key , file = file )
Merges namespaces from multiple locations to one.

    :param iter input_locations: An iterable of URLs or file paths pointing to BEL namespaces.
    :param str output_path: The path to the file to write the merged namespace
    :param str namespace_name: The namespace name
    :param str namespace_keyword: Preferred BEL Keyword, maximum length of 8
    :param str namespace_domain: One of: :data:`pybel.constants.NAMESPACE_DOMAIN_BIOPROCESS`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_CHEMICAL`,
                            :data:`pybel.constants.NAMESPACE_DOMAIN_GENE`, or
                            :data:`pybel.constants.NAMESPACE_DOMAIN_OTHER`
    :param str author_name: The namespace's authors
    :param str citation_name: The name of the citation
    :param str namespace_query_url: HTTP URL to query for details on namespace values (must be valid URL)
    :param str namespace_description: Namespace description
    :param str namespace_species: Comma-separated list of species taxonomy id's
    :param str namespace_version: Namespace version
    :param str namespace_created: Namespace public timestamp, ISO 8601 datetime
    :param str author_contact: Namespace author's contact info/email address
    :param str author_copyright: Namespace's copyright/license information
    :param str citation_description: Citation description
    :param str citation_url: URL to more citation information
    :param str citation_version: Citation version
    :param str citation_date: Citation publish timestamp, ISO 8601 Date
    :param bool case_sensitive: Should this config file be interpreted as case-sensitive?
    :param str delimiter: The delimiter between names and labels in this config file
    :param bool cacheable: Should this config file be cached?
    :param functions: The encoding for the elements in this namespace
    :type functions: iterable of characters
    :param str value_prefix: a prefix for each name
    :param sort_key: A function to sort the values with :func:`sorted`
    :param bool check_keywords: Should all the keywords be the same? Defaults to ``True``
Merges namespaces from multiple locations to one .