def expand(curie: str, prefix_maps: Optional[List[dict]] = None, fallback: bool = True) -> str:
"""
Expand a given CURIE to an URI, based on mappings from `prefix_map`.
This method will return the CURIE as the IRI if there is no mapping found.
Parameters
----------
curie: str
A CURIE
prefix_maps: Optional[List[dict]]
A list of prefix maps to use for mapping
fallback: bool
Determines whether to fallback to default prefix mappings, as determined
by `prefixcommons.curie_util`, when CURIE prefix is not found in `prefix_maps`.
Returns
-------
str
A URI corresponding to the CURIE
"""
default_curie_maps = [get_jsonld_context('monarch_context'), get_jsonld_context('obo_context')]
if prefix_maps:
uri = expand_uri(curie, prefix_maps)
if uri == curie and fallback:
uri = expand_uri(curie, default_curie_maps)
else:
uri = expand_uri(curie, default_curie_maps)
return uri
def __init__(
self,
verbose: bool = False,
progress_monitor: Optional[Callable[[GraphEntityType, List], None]] = None,
schema: Optional[str] = None,
error_log: str = None
):
ErrorDetecting.__init__(self, error_log)
# formal arguments
self.verbose: bool = verbose
self.progress_monitor: Optional[
Callable[[GraphEntityType, List], None]
] = progress_monitor
# TODO: fix... this attribute is not used anywhere at the moment?
self.schema: Optional[str] = schema
# internal attributes
# associated currently active _currently_active_toolkit with this Validator instance
self.validating_toolkit = self.get_toolkit()
self.prefix_manager = PrefixManager()
self.jsonld = get_jsonld_context()
self.prefixes = self.get_all_prefixes(self.jsonld)
self.required_node_properties = self.get_required_node_properties()
self.required_edge_properties = self.get_required_edge_properties()
def get_all_prefixes(jsonld: Optional[Dict] = None) -> set:
"""
Get all prefixes from Biolink Model JSON-LD context.
It also sets ``self.prefixes`` for subsequent access.
Parameters
---------
jsonld: Optional[Dict]
The JSON-LD context
Returns
-------
Optional[Dict]
A set of prefixes
"""
if not jsonld:
jsonld = get_jsonld_context()
prefixes: Set = set(
k
for k, v in jsonld.items()
if isinstance(v, str)
or (isinstance(v, dict) and v.setdefault("@prefix", False))
) # @type: ignored
if "biolink" not in prefixes:
prefixes.add("biolink")
return prefixes
def contract(uri: str,
prefix_maps: Optional[List[Dict]] = None,
fallback: bool = True) -> str:
"""
Contract a given URI to a CURIE, based on mappings from `prefix_maps`.
If no prefix map is provided then will use defaults from prefixcommons-py.
This method will return the URI as the CURIE if there is no mapping found.
Parameters
----------
uri: str
A URI
prefix_maps: Optional[List[Dict]]
A list of prefix maps to use for mapping
fallback: bool
Determines whether to fallback to default prefix mappings, as determined
by `prefixcommons.curie_util`, when URI prefix is not found in `prefix_maps`.
Returns
-------
str
A CURIE corresponding to the URI
"""
curie = uri
default_curie_maps = [
get_jsonld_context("monarch_context"),
get_jsonld_context("obo_context"),
]
if prefix_maps:
curie_list = contract_uri(uri, prefix_maps)
if len(curie_list) == 0:
if fallback:
curie_list = contract_uri(uri, default_curie_maps)
if curie_list:
curie = curie_list[0]
else:
curie = curie_list[0]
else:
curie_list = contract_uri(uri, default_curie_maps)
if len(curie_list) > 0:
curie = curie_list[0]
return curie
def __init__(self, verbose: bool = False):
self.toolkit = get_toolkit()
self.prefix_manager = PrefixManager()
self.jsonld = get_jsonld_context()
self.prefixes = Validator.get_all_prefixes(self.jsonld)
self.required_node_properties = Validator.get_required_node_properties(
)
self.required_edge_properties = Validator.get_required_edge_properties(
)
self.verbose = verbose
def __init__(self, url: str = None):
"""
Initialize an instance of PrefixManager.
Parameters
----------
url: str
The URL from which to read a JSON-LD context for prefix mappings
"""
if url:
context = cu.read_remote_jsonld_context(url)
else:
context = get_jsonld_context()
self.set_prefix_map(context)
def get_all_prefixes(jsonld: dict = None) -> set:
"""
Get all prefixes from Biolink Model JSON-LD context.
It also sets ``self.prefixes`` for subsequent access.
Returns
-------
set
A set of prefixes
"""
if not jsonld:
jsonld = get_jsonld_context()
prefixes = set(k for k, v in jsonld.items() if isinstance(v, str))
if 'biolink' not in prefixes:
prefixes.add('biolink')
return prefixes
def __init__(self,
verbose: bool = False,
progress_monitor: Optional[Callable[[GraphEntityType, List],
None]] = None):
# formal arguments
self.verbose: bool = verbose
self.progress_monitor: Optional[Callable[[GraphEntityType, List],
None]] = progress_monitor
# internal attributes
self.toolkit = get_toolkit()
self.prefix_manager = PrefixManager()
self.jsonld = get_jsonld_context()
self.prefixes = Validator.get_all_prefixes(self.jsonld)
self.required_node_properties = Validator.get_required_node_properties(
)
self.required_edge_properties = Validator.get_required_edge_properties(
)
self.errors: List[ValidationError] = list()
def get_all_prefixes(jsonld: Optional[Dict] = None) -> set:
"""
Get all prefixes from Biolink Model JSON-LD context.
It also sets ``self.prefixes`` for subsequent access.
Parameters
---------
jsonld: Optional[Dict]
The JSON-LD context
Returns
-------
Optional[Dict]
A set of prefixes
"""
if not jsonld:
jsonld = get_jsonld_context()
prefixes = set(jsonld.keys())
if 'biolink' not in prefixes:
prefixes.add('biolink')
return prefixes