"""SSSOM parsers."""
import io
import itertools as itt
import json
import logging as _logging
import re
import typing
from collections import ChainMap, Counter
from pathlib import Path
from typing import Any, Callable, Dict, Iterable, List, Optional, TextIO, Tuple, Union, cast
from xml.dom import Node, minidom
from xml.dom.minidom import Document
import curies
import numpy as np
import pandas as pd
import requests
import yaml
from curies import Converter
from linkml_runtime.loaders.json_loader import JSONLoader
from linkml_runtime.loaders.rdflib_loader import RDFLibLoader
from pandas.errors import EmptyDataError
from rdflib import Graph
from sssom_schema import Mapping, MappingSet
from sssom.constants import (
CONFIDENCE,
CURIE_MAP,
DEFAULT_MAPPING_PROPERTIES,
LICENSE,
MAPPING_JUSTIFICATION,
MAPPING_JUSTIFICATION_UNSPECIFIED,
MAPPING_SET_ID,
OBJECT_ID,
OBJECT_LABEL,
OBJECT_SOURCE,
OBJECT_SOURCE_ID,
OBO_HAS_DB_XREF_URI,
OWL_EQUIV_CLASS_URI,
PREDICATE_ID,
RDF_TYPE,
RDF_TYPE_URI,
RDFS_SUBCLASS_OF,
SKOS_BROAD_MATCH,
SKOS_BROAD_MATCH_URI,
SKOS_EXACT_MATCH,
SKOS_EXACT_MATCH_URI,
SKOS_NARROW_MATCH,
SKOS_NARROW_MATCH_URI,
SUBJECT_ID,
SUBJECT_LABEL,
SUBJECT_SOURCE,
SUBJECT_SOURCE_ID,
MetadataType,
_get_sssom_schema_object,
get_default_metadata,
)
from .context import ConverterHint, _get_built_in_prefix_map, ensure_converter
from .sssom_document import MappingSetDocument
from .util import (
SSSOM_DEFAULT_RDF_SERIALISATION,
MappingSetDataFrame,
get_file_extension,
is_multivalued_slot,
raise_for_bad_path,
safe_compress,
to_mapping_set_dataframe,
)
logging = _logging.getLogger(__name__)
# * *******************************************************
# Parsers (from file)
def _open_input(input: Union[str, Path, TextIO]) -> io.StringIO:
"""Transform a URL, a filepath (from pathlib), or a string (with file contents) to a StringIO object.
:param input: A string representing a URL, a filepath, or file contents,
or a Path object representing a filepath.
:return: A StringIO object containing the input data.
"""
# If the import already is a StrinIO, return it
if isinstance(input, io.StringIO):
return input
elif isinstance(input, Path):
input = str(input)
if isinstance(input, str):
if input.startswith("http://") or input.startswith("https://"):
# It's a URL
data = requests.get(input, timeout=30).content
return io.StringIO(data.decode("utf-8"))
elif "\n" in input or "\r" in input:
# It's string data
return io.StringIO(input)
else:
# It's a local file path
with open(input, "r") as file:
file_content = file.read()
return io.StringIO(file_content)
raise IOError(f"Could not determine the type of input {input}")
def _separate_metadata_and_table_from_stream(s: io.StringIO):
s.seek(0)
# Create a new StringIO object for filtered data
table_component = io.StringIO()
metadata_component = io.StringIO()
header_section = True
# Filter out lines starting with '#'
for line in s:
if not line.startswith("#"):
table_component.write(line)
if header_section:
header_section = False
elif header_section:
metadata_component.write(line)
else:
logging.info(
f"Line {line} is starting with hash symbol, but header section is already passed. "
f"This line is skipped"
)
# Reset the cursor to the start of the new StringIO object
table_component.seek(0)
metadata_component.seek(0)
return table_component, metadata_component
def _read_pandas_and_metadata(input: io.StringIO, sep: str = None):
"""Read a tabular data file by wrapping func:`pd.read_csv` to handles comment lines correctly.
:param input: The file to read. If no separator is given, this file should be named.
:param sep: File separator for pandas
:return: A pandas dataframe
"""
table_stream, metadata_stream = _separate_metadata_and_table_from_stream(input)
try:
df = pd.read_csv(table_stream, sep=sep, dtype=str, engine="python")
df.fillna("", inplace=True)
except EmptyDataError as e:
logging.warning(f"Seems like the dataframe is empty: {e}")
df = pd.DataFrame(
columns=[
SUBJECT_ID,
SUBJECT_LABEL,
PREDICATE_ID,
OBJECT_ID,
MAPPING_JUSTIFICATION,
]
)
if isinstance(df, pd.DataFrame):
sssom_metadata = _read_metadata_from_table(metadata_stream)
return df, sssom_metadata
return None, None
def _get_seperator_symbol_from_file_path(file):
r"""
Take as an input a filepath and return the seperate symbol used, for example, by pandas.
:param file: the file path
:return: the seperator symbols as a string, e.g. '\t'
"""
if isinstance(file, Path) or isinstance(file, str):
extension = get_file_extension(file)
if extension == "tsv":
return "\t"
elif extension == "csv":
return ","
logging.warning(f"Could not guess file extension for {file}")
return None
[docs]def parse_sssom_table(
file_path: Union[str, Path, TextIO],
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
**kwargs,
) -> MappingSetDataFrame:
"""Parse a TSV to a :class:`MappingSetDocument` to a :class:`MappingSetDataFrame`."""
if isinstance(file_path, Path) or isinstance(file_path, str):
raise_for_bad_path(file_path)
stream: io.StringIO = _open_input(file_path)
sep_new = _get_seperator_symbol_from_file_path(file_path)
df, sssom_metadata = _read_pandas_and_metadata(stream, sep_new)
if meta is None:
meta = {}
# The priority order for combining prefix maps are:
# 1. Built-in prefix map
# 2. Internal prefix map inside the document
# 3. Prefix map passed through this function inside the ``meta``
# 4. Prefix map passed through this function to ``prefix_map`` (handled with ensure_converter)
converter = curies.chain(
[
_get_built_in_prefix_map(),
Converter.from_prefix_map(sssom_metadata.pop(CURIE_MAP, {})),
Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
ensure_converter(prefix_map, use_defaults=False),
]
)
# The priority order for combining metadata is:
# 1. Metadata appearing in the SSSOM document
# 2. Metadata passed through ``meta`` to this function
# 3. Default metadata
combine_meta = dict(
ChainMap(
sssom_metadata,
meta,
get_default_metadata(),
)
)
msdf = from_sssom_dataframe(df, prefix_map=converter, meta=combine_meta)
return msdf
[docs]def parse_sssom_rdf(
file_path: str,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
serialisation=SSSOM_DEFAULT_RDF_SERIALISATION,
**kwargs,
# mapping_predicates: Optional[List[str]] = None,
) -> MappingSetDataFrame:
"""Parse a TSV to a :class:`MappingSetDocument` to a :class:`MappingSetDataFrame`."""
raise_for_bad_path(file_path)
g = Graph()
g.parse(file_path, format=serialisation)
# Initialize meta if it's None
if meta is None:
meta = {}
# The priority order for combining prefix maps are:
# 1. Built-in prefix map
# 2. Internal prefix map inside the document
# 3. Prefix map passed through this function inside the ``meta``
# 4. Prefix map passed through this function to ``prefix_map`` (handled with ensure_converter)
converter = curies.chain(
[
_get_built_in_prefix_map(),
Converter.from_rdflib(g),
Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
ensure_converter(prefix_map, use_defaults=False),
]
)
msdf = from_sssom_rdf(g, prefix_map=converter, meta=meta)
# df: pd.DataFrame = msdf.df
# if mapping_predicates and not df.empty():
# msdf.df = df[df["predicate_id"].isin(mapping_predicates)]
return msdf
[docs]def parse_sssom_json(
file_path: str, prefix_map: ConverterHint = None, meta: Optional[MetadataType] = None, **kwargs
) -> MappingSetDataFrame:
"""Parse a TSV to a :class:`MappingSetDocument` to a :class:`MappingSetDataFrame`."""
raise_for_bad_path(file_path)
with open(file_path) as json_file:
jsondoc = json.load(json_file)
# Initialize meta if it's None
if meta is None:
meta = {}
# The priority order for combining prefix maps are:
# 1. Built-in prefix map
# 2. Internal prefix map inside the document
# 3. Prefix map passed through this function inside the ``meta``
# 4. Prefix map passed through this function to ``prefix_map`` (handled with ensure_converter)
converter = curies.chain(
[
_get_built_in_prefix_map(),
Converter.from_jsonld(file_path),
Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
ensure_converter(prefix_map, use_defaults=False),
]
)
msdf = from_sssom_json(jsondoc=jsondoc, prefix_map=converter, meta=meta)
return msdf
# Import methods from external file formats
[docs]def parse_obographs_json(
file_path: str,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
mapping_predicates: Optional[List[str]] = None,
) -> MappingSetDataFrame:
"""Parse an obographs file as a JSON object and translates it into a MappingSetDataFrame.
:param file_path: The path to the obographs file
:param prefix_map: an optional prefix map
:param meta: an optional dictionary of metadata elements
:param mapping_predicates: an optional list of mapping predicates that should be extracted
:return: A SSSOM MappingSetDataFrame
"""
raise_for_bad_path(file_path)
converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
with open(file_path) as json_file:
jsondoc = json.load(json_file)
return from_obographs(
jsondoc,
prefix_map=converter,
meta=meta,
mapping_predicates=mapping_predicates,
)
def _get_prefix_map_and_metadata(
prefix_map: ConverterHint = None, meta: Optional[MetadataType] = None
) -> Tuple[Converter, MetadataType]:
if meta is None:
meta = get_default_metadata()
converter = curies.chain(
[
_get_built_in_prefix_map(),
Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
ensure_converter(prefix_map, use_defaults=False),
]
)
return converter, meta
def _address_multivalued_slot(k: str, v: Any) -> Union[str, List[str]]:
if isinstance(v, str) and is_multivalued_slot(k):
# IF k is multivalued, then v = List[values]
return [s.strip() for s in v.split("|")]
else:
return v
def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet:
_metadata = dict(ChainMap(meta or {}, get_default_metadata()))
mapping_set = MappingSet(mapping_set_id=_metadata[MAPPING_SET_ID], license=_metadata[LICENSE])
_set_metadata_in_mapping_set(mapping_set=mapping_set, metadata=meta)
return mapping_set
def _get_mapping_dict(
row: pd.Series, bad_attrs: Counter, mapping_slots: typing.Set[str]
) -> Dict[str, Any]:
"""Generate a mapping dictionary from a given row of data.
It also updates the 'bad_attrs' counter for keys that are not present
in the sssom_schema_object's mapping_slots.
"""
# Populate the mapping dictionary with key-value pairs from the row,
# only if the value exists, is not NaN, and the key is in the schema's mapping slots.
# The value could be a string or a list and is handled accordingly via _address_multivalued_slot().
mdict = {
k: _address_multivalued_slot(k, v)
for k, v in row.items()
if v and pd.notna(v) and k in mapping_slots
}
# Update bad_attrs for keys not in mapping_slots
bad_keys = set(row.keys()) - mapping_slots
for bad_key in bad_keys:
bad_attrs[bad_key] += 1
return mdict
[docs]def parse_alignment_xml(
file_path: str,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
mapping_predicates: Optional[List[str]] = None,
) -> MappingSetDataFrame:
"""Parse a TSV -> MappingSetDocument -> MappingSetDataFrame."""
raise_for_bad_path(file_path)
converter, meta = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
logging.info("Loading from alignment API")
xmldoc = minidom.parse(file_path)
msdf = from_alignment_minidom(
xmldoc,
prefix_map=converter,
meta=meta,
mapping_predicates=mapping_predicates,
)
return msdf
# Readers (from object)
[docs]def from_sssom_dataframe(
df: pd.DataFrame,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
) -> MappingSetDataFrame:
"""Convert a dataframe to a MappingSetDataFrame.
:param df: A mappings dataframe
:param prefix_map: A prefix map
:param meta: A metadata dictionary
:return: MappingSetDataFrame
"""
converter = ensure_converter(prefix_map)
# Need to revisit this solution.
# This is to address: A value is trying to be set on a copy of a slice from a DataFrame
if CONFIDENCE in df.columns:
df2 = df.copy()
df2[CONFIDENCE].replace(r"^\s*$", np.NaN, regex=True, inplace=True)
df = df2
mapping_set = _get_mapping_set_from_df(df=df, meta=meta)
doc = MappingSetDocument(mapping_set=mapping_set, converter=converter)
return to_mapping_set_dataframe(doc)
[docs]def from_sssom_rdf(
g: Graph,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
) -> MappingSetDataFrame:
"""Convert an SSSOM RDF graph into a SSSOM data table.
:param g: the Graph (rdflib)
:param prefix_map: A dictionary containing the prefix map, defaults to None
:param meta: Potentially additional metadata, defaults to None
:return: MappingSetDataFrame object
"""
converter = ensure_converter(prefix_map)
mapping_set = cast(
MappingSet,
RDFLibLoader().load(
source=g,
target_class=MappingSet,
schemaview=_get_sssom_schema_object().view,
prefix_map=converter.bimap,
ignore_unmapped_predicates=True,
),
)
# The priority order for combining metadata is:
# 1. Metadata appearing in the SSSOM document
# 2. Metadata passed through ``meta`` to this function
# 3. Default metadata
# As the Metadata appearing in the SSSOM document is already parsed by LinkML
# we only need to overwrite the metadata from 2 and 3 if it is not present
combine_meta = dict(
ChainMap(
meta or {},
get_default_metadata(),
)
)
_set_metadata_in_mapping_set(mapping_set, metadata=combine_meta, overwrite=False)
mdoc = MappingSetDocument(mapping_set=mapping_set, converter=converter)
return to_mapping_set_dataframe(mdoc)
[docs]def from_sssom_json(
jsondoc: Union[str, dict, TextIO],
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
) -> MappingSetDataFrame:
"""Load a mapping set dataframe from a JSON object.
:param jsondoc: JSON document
:param prefix_map: Prefix map
:param meta: metadata used to augment the metadata existing in the mapping set
:return: MappingSetDataFrame object
"""
converter = ensure_converter(prefix_map)
mapping_set = cast(MappingSet, JSONLoader().load(source=jsondoc, target_class=MappingSet))
# The priority order for combining metadata is:
# 1. Metadata appearing in the SSSOM document
# 2. Metadata passed through ``meta`` to this function
# 3. Default metadata
# As the Metadata appearing in the SSSOM document is already parsed by LinkML
# we only need to overwrite the metadata from 2 and 3 if it is not present
combine_meta = dict(
ChainMap(
meta or {},
get_default_metadata(),
)
)
_set_metadata_in_mapping_set(mapping_set, metadata=combine_meta, overwrite=False)
mapping_set_document = MappingSetDocument(mapping_set=mapping_set, converter=converter)
return to_mapping_set_dataframe(mapping_set_document)
[docs]def from_alignment_minidom(
dom: Document,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
mapping_predicates: Optional[List[str]] = None,
) -> MappingSetDataFrame:
"""Read a minidom Document object.
:param dom: XML (minidom) object
:param prefix_map: A prefix map
:param meta: Optional meta data
:param mapping_predicates: Optional list of mapping predicates to extract
:return: MappingSetDocument
:raises ValueError: for alignment format: xml element said, but not set to yes. Only XML is supported!
"""
converter = ensure_converter(prefix_map)
ms = _init_mapping_set(meta)
mlist: List[Mapping] = []
# bad_attrs = {}
if not mapping_predicates:
mapping_predicates = DEFAULT_MAPPING_PROPERTIES
alignments = dom.getElementsByTagName("Alignment")
for n in alignments:
for e in n.childNodes:
if e.nodeType == Node.ELEMENT_NODE:
node_name = e.nodeName
if node_name == "map":
cell = e.getElementsByTagName("Cell")
for c_node in cell:
mdict: Dict[str, Any] = _cell_element_values(
c_node, converter, mapping_predicates=mapping_predicates
)
_add_valid_mapping_to_list(mdict, mlist, flip_superclass_assertions=True)
elif node_name == "xml":
if e.firstChild.nodeValue != "yes":
raise ValueError(
"Alignment format: xml element said, but not set to yes. Only XML is supported!"
)
elif node_name == "onto1":
ms[SUBJECT_SOURCE_ID] = e.firstChild.nodeValue
elif node_name == "onto2":
ms[OBJECT_SOURCE_ID] = e.firstChild.nodeValue
elif node_name == "uri1":
ms[SUBJECT_SOURCE] = e.firstChild.nodeValue
elif node_name == "uri2":
ms[OBJECT_SOURCE] = e.firstChild.nodeValue
ms.mappings = mlist # type: ignore
mapping_set_document = MappingSetDocument(mapping_set=ms, converter=converter)
return to_mapping_set_dataframe(mapping_set_document)
def _get_obographs_predicate_id(obographs_predicate: str):
if obographs_predicate == "is_a":
return RDFS_SUBCLASS_OF
return obographs_predicate
[docs]def from_obographs(
jsondoc: Dict,
prefix_map: ConverterHint = None,
meta: Optional[MetadataType] = None,
mapping_predicates: Optional[List[str]] = None,
) -> MappingSetDataFrame:
"""Convert a obographs json object to an SSSOM data frame.
:param jsondoc: The JSON object representing the ontology in obographs format
:param prefix_map: The prefix map to be used
:param meta: Any additional metadata that needs to be added to the resulting SSSOM data frame, defaults to None
:param mapping_predicates: Optional list of mapping predicates to extract
:raises Exception: When there is no CURIE
:return: An SSSOM data frame (MappingSetDataFrame)
"""
converter = ensure_converter(prefix_map)
ms = _init_mapping_set(meta)
mlist: List[Mapping] = []
if not mapping_predicates:
mapping_predicates = DEFAULT_MAPPING_PROPERTIES
graphs = jsondoc.get("graphs")
if not graphs:
raise Exception("No graphs element in obographs file, wrong format?")
#: A dictionary of node URIs to node labels
labels: Mapping[str, str] = {
node["id"]: node.get("lbl")
for graph in graphs
for node in graph.get("nodes", [])
if node.get("lbl")
}
for graph in graphs:
for node in graph.get("nodes", []):
meta = node.get("meta")
if not meta:
continue
node_uri = node["id"]
if OBO_HAS_DB_XREF_URI in mapping_predicates:
for xref in meta.get("xrefs", []):
mdict = _make_mdict(
node_uri, OBO_HAS_DB_XREF_URI, xref["val"], converter, labels
)
_add_valid_mapping_to_list(mdict, mlist)
for value in meta.get("basicPropertyValues", []):
predicate_uri = value["pred"]
if predicate_uri not in mapping_predicates:
continue
mdict = _make_mdict(node_uri, predicate_uri, value["val"], converter, labels)
_add_valid_mapping_to_list(mdict, mlist)
for edge in graph.get("edges", []):
predicate_uri = _get_obographs_predicate_id(edge["pred"])
if predicate_uri not in mapping_predicates:
continue
mdict = _make_mdict(edge["sub"], predicate_uri, edge["obj"], converter, labels)
_add_valid_mapping_to_list(mdict, mlist)
if OWL_EQUIV_CLASS_URI in mapping_predicates:
for equivalents in graph.get("equivalentNodesSets", []):
node_uris = equivalents.get("nodeIds")
if not node_uris:
continue
for subject_uri, object_uri in itt.product(node_uris, repeat=2):
if subject_uri == object_uri:
continue
mdict = _make_mdict(
subject_uri, OWL_EQUIV_CLASS_URI, object_uri, converter, labels
)
_add_valid_mapping_to_list(mdict, mlist)
ms.mappings = mlist # type: ignore
mdoc = MappingSetDocument(mapping_set=ms, converter=converter)
return to_mapping_set_dataframe(mdoc)
def _make_mdict(
subject_id: str,
predicate_id: str,
object_id: str,
converter: Converter,
labels: typing.Mapping[str, str],
):
mdict = {
MAPPING_JUSTIFICATION: MAPPING_JUSTIFICATION_UNSPECIFIED,
}
try:
subject_curie = safe_compress(subject_id, converter)
except ValueError as e:
logging.debug("could not parse subject %s - %s", subject_id, e)
else:
mdict[SUBJECT_ID] = subject_curie
try:
predicate_curie = safe_compress(predicate_id, converter)
except ValueError as e:
logging.debug("could not parse predicate %s - %s", predicate_id, e)
else:
mdict[PREDICATE_ID] = predicate_curie
try:
object_curie = safe_compress(object_id, converter)
except ValueError as e:
logging.debug("could not parse object %s - %s", object_id, e)
else:
mdict[OBJECT_ID] = object_curie
if subject_id in labels:
mdict[SUBJECT_LABEL] = labels[subject_id]
if object_id in labels:
mdict[OBJECT_LABEL] = labels[object_id]
return mdict
# All from_* take as an input a python object (data frame, json, etc.) and return a MappingSetDataFrame
# All read_* take as an input a file handle and return a MappingSetDataFrame (usually wrapping a from_* method)
PARSING_FUNCTIONS: typing.Mapping[str, Callable] = {
"tsv": parse_sssom_table,
"obographs-json": parse_obographs_json,
"alignment-api-xml": parse_alignment_xml,
"json": parse_sssom_json,
"rdf": parse_sssom_rdf,
}
[docs]def get_parsing_function(input_format: Optional[str], filename: str) -> Callable:
"""Return appropriate parser function based on input format of file.
:param input_format: File format
:param filename: Filename
:raises Exception: Unknown file format
:return: Appropriate 'read' function
"""
if input_format is None:
input_format = get_file_extension(filename)
func = PARSING_FUNCTIONS.get(input_format)
if func is None:
raise Exception(f"Unknown input format: {input_format}")
return func
def _flip_superclass_assertion(mapping: Mapping) -> Mapping:
if mapping.predicate_id != "sssom:superClassOf":
return mapping
mapping.predicate_id = "rdfs:subClassOf"
return _swap_object_subject(mapping)
def _swap_object_subject(mapping: Mapping) -> Mapping:
members = [
attr.replace("subject_", "")
for attr in dir(mapping)
if not callable(getattr(mapping, attr))
and not attr.startswith("__")
and attr.startswith("subject_")
]
for var in members:
subject_val = getattr(mapping, "subject_" + var)
object_val = getattr(mapping, "object_" + var)
setattr(mapping, "subject_" + var, object_val)
setattr(mapping, "object_" + var, subject_val)
return mapping
def _read_metadata_from_table(stream: io.StringIO) -> Dict[str, Any]:
yamlstr = ""
for line in stream:
if line.startswith("#"):
yamlstr += re.sub("^#", "", line)
else:
break
if yamlstr:
meta = yaml.safe_load(yamlstr)
logging.info(f"Meta={meta}")
return meta
return {}
def _set_metadata_in_mapping_set(
mapping_set: MappingSet, metadata: Optional[MetadataType] = None, overwrite: bool = True
) -> None:
if metadata is None:
logging.info("Tried setting metadata but none provided.")
else:
for k, v in metadata.items():
if k != CURIE_MAP:
if (
hasattr(mapping_set, k)
and getattr(mapping_set, k) is not None
and not overwrite
):
continue
mapping_set[k] = _address_multivalued_slot(k, v)
def _cell_element_values(cell_node, converter: Converter, mapping_predicates) -> Dict[str, Any]:
mdict: Dict[str, Any] = {}
for child in cell_node.childNodes:
if child.nodeType == Node.ELEMENT_NODE:
try:
if child.nodeName == "entity1":
mdict[SUBJECT_ID] = safe_compress(child.getAttribute("rdf:resource"), converter)
elif child.nodeName == "entity2":
mdict[OBJECT_ID] = safe_compress(child.getAttribute("rdf:resource"), converter)
elif child.nodeName == "measure":
mdict[CONFIDENCE] = child.firstChild.nodeValue
elif child.nodeName == "relation":
relation = child.firstChild.nodeValue
if (relation == "=") and (SKOS_EXACT_MATCH_URI in mapping_predicates):
mdict[PREDICATE_ID] = SKOS_EXACT_MATCH
elif (relation == "<") and (SKOS_BROAD_MATCH_URI in mapping_predicates):
mdict[PREDICATE_ID] = SKOS_BROAD_MATCH
elif (relation == ">") and (SKOS_NARROW_MATCH_URI in mapping_predicates):
mdict[PREDICATE_ID] = SKOS_NARROW_MATCH
# elif (relation == "%") and (SOMETHING in mapping_predicates)
# # Incompatible.
# pass
# elif (relation == "HasInstance") and (SOMETHING in mapping_predicates):
# pass
elif (relation == "InstanceOf") and (RDF_TYPE_URI in mapping_predicates):
mdict[PREDICATE_ID] = RDF_TYPE
else:
logging.warning(f"{relation} not a recognised relation type.")
else:
logging.warning(f"Unsupported alignment api element: {child.nodeName}")
except ValueError as e:
logging.warning(e)
mdict[MAPPING_JUSTIFICATION] = MAPPING_JUSTIFICATION_UNSPECIFIED
return mdict
# The following methods dont really belong in the parser package..
[docs]def to_mapping_set_document(msdf: MappingSetDataFrame) -> MappingSetDocument:
"""Convert a MappingSetDataFrame to a MappingSetDocument."""
ms = _get_mapping_set_from_df(df=msdf.df, meta=msdf.metadata)
return MappingSetDocument(mapping_set=ms, converter=msdf.converter)
def _get_mapping_set_from_df(df: pd.DataFrame, meta: Optional[MetadataType] = None) -> MappingSet:
mapping_set = _init_mapping_set(meta)
bad_attrs: Counter = Counter()
mapping_slots = set(_get_sssom_schema_object().mapping_slots)
df.apply(
lambda row: _add_valid_mapping_to_list(
_get_mapping_dict(row, bad_attrs, mapping_slots), mapping_set.mappings
),
axis=1,
)
for k, v in bad_attrs.items():
logging.warning(f"No attr for {k} [{v} instances]")
return mapping_set
[docs]def split_dataframe(
msdf: MappingSetDataFrame,
) -> Dict[str, MappingSetDataFrame]:
"""Group the mapping set dataframe into several subdataframes by prefix.
:param msdf: MappingSetDataFrame object
:raises RuntimeError: DataFrame object within MappingSetDataFrame is None
:return: Mapping object
"""
subject_prefixes = set(msdf.df[SUBJECT_ID].str.split(":", n=1, expand=True)[0])
object_prefixes = set(msdf.df[OBJECT_ID].str.split(":", n=1, expand=True)[0])
relations = set(msdf.df[PREDICATE_ID])
return split_dataframe_by_prefix(
msdf=msdf,
subject_prefixes=subject_prefixes,
object_prefixes=object_prefixes,
relations=relations,
)
[docs]def split_dataframe_by_prefix(
msdf: MappingSetDataFrame,
subject_prefixes: Iterable[str],
object_prefixes: Iterable[str],
relations: Iterable[str],
) -> Dict[str, MappingSetDataFrame]:
"""Split a mapping set dataframe by prefix.
:param msdf: An SSSOM MappingSetDataFrame
:param subject_prefixes: a list of prefixes pertaining to the subject
:param object_prefixes: a list of prefixes pertaining to the object
:param relations: a list of relations of interest
:return: a dict of SSSOM data frame names to MappingSetDataFrame
"""
df = msdf.df
meta = msdf.metadata
split_to_msdf: Dict[str, MappingSetDataFrame] = {}
for subject_prefix, object_prefix, relation in itt.product(
subject_prefixes, object_prefixes, relations
):
relation_prefix, relation_id = relation.split(":")
split = f"{subject_prefix.lower()}_{relation_id.lower()}_{object_prefix.lower()}"
if subject_prefix not in msdf.converter.bimap:
logging.warning(f"{split} - missing subject prefix - {subject_prefix}")
continue
if object_prefix not in msdf.converter.bimap:
logging.warning(f"{split} - missing object prefix - {object_prefix}")
continue
df_subset = df[
(df[SUBJECT_ID].str.startswith(subject_prefix + ":"))
& (df[PREDICATE_ID] == relation)
& (df[OBJECT_ID].str.startswith(object_prefix + ":"))
]
if 0 == len(df_subset):
logging.debug(f"No matches ({len(df_subset)} matches found)")
continue
subconverter = msdf.converter.get_subconverter(
[subject_prefix, object_prefix, relation_prefix]
)
split_to_msdf[split] = from_sssom_dataframe(
df_subset, prefix_map=dict(subconverter.bimap), meta=meta
)
return split_to_msdf
def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):
"""
Return a valid mapping object if it can be constructed, else None.
:param mdict: A dictionary containing the mapping metadata.
:return: A valid Mapping object, or None.
"""
mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED)
try:
m = Mapping(**mdict)
except ValueError as e:
logging.warning(
f"One mapping in the mapping set is not well-formed, "
f"and therfore not included in the mapping set ({mdict}). Error: {e}"
)
return None
else:
return m
def _add_valid_mapping_to_list(
mdict: Dict[str, Any], mlist: List[Mapping], *, flip_superclass_assertions=False
):
"""
Validate the mapping and append to the list if valid.
Parameters:
- mdict (dict): A dictionary containing the mapping metadata.
- mlist (list): The list to which the valid mapping should be appended.
- flip_superclass_assertions (bool): an optional paramter that flips sssom:superClassOf to rdfs:subClassOf
"""
mapping = _ensure_valid_mapping_from_dict(mdict)
if not mapping:
return None
if flip_superclass_assertions:
mapping = _flip_superclass_assertion(mapping)
mlist.append(mapping)