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biocypher/_mapping.py
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307
biocypher/_mapping.py
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#!/usr/bin/env python
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#
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# Copyright 2021, Heidelberg University Clinic
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#
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# File author(s): Sebastian Lobentanzer
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# ...
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#
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# Distributed under MIT licence, see the file `LICENSE`.
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#
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"""
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BioCypher 'mapping' module. Handles the mapping of user-defined schema to the
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underlying ontology.
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"""
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from ._logger import logger
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logger.debug(f"Loading module {__name__}.")
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from typing import Optional
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from urllib.request import urlopen
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import yaml
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from . import _misc
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from ._config import config as _config
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class OntologyMapping:
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"""
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Class to store the ontology mapping and extensions.
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"""
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def __init__(self, config_file: str = None):
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self.schema = self._read_config(config_file)
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self.extended_schema = self._extend_schema()
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def _read_config(self, config_file: str = None):
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"""
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Read the configuration file and store the ontology mapping and extensions.
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"""
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if config_file is None:
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schema_config = {}
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# load yaml file from web
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elif config_file.startswith("http"):
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with urlopen(config_file) as f:
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schema_config = yaml.safe_load(f)
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# get graph state from config (assume file is local)
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else:
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with open(config_file, "r") as f:
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schema_config = yaml.safe_load(f)
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return schema_config
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def _extend_schema(self, d: Optional[dict] = None) -> dict:
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"""
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Get leaves of the tree hierarchy from the data structure dict
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contained in the `schema_config.yaml`. Creates virtual leaves
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(as children) from entries that provide more than one preferred
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id type (and corresponding inputs).
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Args:
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d:
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Data structure dict from yaml file.
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"""
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d = d or self.schema
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extended_schema = dict()
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# first pass: get parent leaves with direct representation in ontology
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for k, v in d.items():
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# k is not an entity
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if "represented_as" not in v:
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continue
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# preferred_id optional: if not provided, use `id`
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if not v.get("preferred_id"):
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v["preferred_id"] = "id"
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# k is an entity that is present in the ontology
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if "is_a" not in v:
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extended_schema[k] = v
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# second pass: "vertical" inheritance
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d = self._vertical_property_inheritance(d)
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for k, v in d.items():
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if "is_a" in v:
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# prevent loops
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if k == v["is_a"]:
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logger.warning(
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f"Loop detected in ontology mapping: {k} -> {v}. "
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"Removing item. Please fix the inheritance if you want "
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"to use this item."
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)
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continue
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extended_schema[k] = v
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# "horizontal" inheritance: create siblings for multiple identifiers or
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# sources -> virtual leaves or implicit children
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mi_leaves = {}
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ms_leaves = {}
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for k, v in d.items():
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# k is not an entity
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if "represented_as" not in v:
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continue
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if isinstance(v.get("preferred_id"), list):
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mi_leaves = self._horizontal_inheritance_pid(k, v)
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extended_schema.update(mi_leaves)
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elif isinstance(v.get("source"), list):
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ms_leaves = self._horizontal_inheritance_source(k, v)
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extended_schema.update(ms_leaves)
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return extended_schema
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def _vertical_property_inheritance(self, d):
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"""
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Inherit properties from parents to children and update `d` accordingly.
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"""
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for k, v in d.items():
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# k is not an entity
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if "represented_as" not in v:
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continue
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# k is an entity that is present in the ontology
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if "is_a" not in v:
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continue
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# "vertical" inheritance: inherit properties from parent
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if v.get("inherit_properties", False):
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# get direct ancestor
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if isinstance(v["is_a"], list):
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parent = v["is_a"][0]
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else:
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parent = v["is_a"]
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# ensure child has properties and exclude_properties
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if "properties" not in v:
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v["properties"] = {}
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if "exclude_properties" not in v:
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v["exclude_properties"] = {}
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# update properties of child
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parent_props = self.schema[parent].get("properties", {})
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if parent_props:
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v["properties"].update(parent_props)
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parent_excl_props = self.schema[parent].get(
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"exclude_properties", {}
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)
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if parent_excl_props:
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v["exclude_properties"].update(parent_excl_props)
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# update schema (d)
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d[k] = v
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return d
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def _horizontal_inheritance_pid(self, key, value):
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"""
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Create virtual leaves for multiple preferred id types or sources.
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If we create virtual leaves, input_label/label_in_input always has to be
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a list.
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"""
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leaves = {}
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preferred_id = value["preferred_id"]
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input_label = value.get("input_label") or value["label_in_input"]
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represented_as = value["represented_as"]
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# adjust lengths
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max_l = max(
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[
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len(_misc.to_list(preferred_id)),
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len(_misc.to_list(input_label)),
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len(_misc.to_list(represented_as)),
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],
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)
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# adjust pid length if necessary
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if isinstance(preferred_id, str):
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pids = [preferred_id] * max_l
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else:
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pids = preferred_id
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# adjust rep length if necessary
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if isinstance(represented_as, str):
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reps = [represented_as] * max_l
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else:
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reps = represented_as
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for pid, lab, rep in zip(pids, input_label, reps):
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skey = pid + "." + key
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svalue = {
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"preferred_id": pid,
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"input_label": lab,
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"represented_as": rep,
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# mark as virtual
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"virtual": True,
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}
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# inherit is_a if exists
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if "is_a" in value.keys():
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# treat as multiple inheritance
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if isinstance(value["is_a"], list):
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v = list(value["is_a"])
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v.insert(0, key)
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svalue["is_a"] = v
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else:
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svalue["is_a"] = [key, value["is_a"]]
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else:
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# set parent as is_a
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svalue["is_a"] = key
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# inherit everything except core attributes
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for k, v in value.items():
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if k not in [
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"is_a",
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"preferred_id",
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"input_label",
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"label_in_input",
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"represented_as",
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]:
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svalue[k] = v
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leaves[skey] = svalue
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return leaves
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def _horizontal_inheritance_source(self, key, value):
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"""
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Create virtual leaves for multiple sources.
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If we create virtual leaves, input_label/label_in_input always has to be
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a list.
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"""
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leaves = {}
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source = value["source"]
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input_label = value.get("input_label") or value["label_in_input"]
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represented_as = value["represented_as"]
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# adjust lengths
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src_l = len(source)
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# adjust label length if necessary
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if isinstance(input_label, str):
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labels = [input_label] * src_l
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else:
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labels = input_label
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# adjust rep length if necessary
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if isinstance(represented_as, str):
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reps = [represented_as] * src_l
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else:
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reps = represented_as
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for src, lab, rep in zip(source, labels, reps):
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skey = src + "." + key
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svalue = {
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"source": src,
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"input_label": lab,
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"represented_as": rep,
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# mark as virtual
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"virtual": True,
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}
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# inherit is_a if exists
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if "is_a" in value.keys():
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# treat as multiple inheritance
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if isinstance(value["is_a"], list):
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v = list(value["is_a"])
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v.insert(0, key)
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svalue["is_a"] = v
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else:
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svalue["is_a"] = [key, value["is_a"]]
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else:
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# set parent as is_a
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svalue["is_a"] = key
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# inherit everything except core attributes
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for k, v in value.items():
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if k not in [
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"is_a",
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"source",
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"input_label",
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"label_in_input",
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"represented_as",
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]:
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svalue[k] = v
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leaves[skey] = svalue
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return leaves
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