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biocypher/_create.py
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356
biocypher/_create.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 'create' module. Handles the creation of BioCypher node and edge
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dataclasses.
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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 Union
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from dataclasses import field, dataclass
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import os
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__all__ = [
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"BioCypherEdge",
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"BioCypherNode",
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"BioCypherRelAsNode",
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]
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@dataclass(frozen=True)
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class BioCypherNode:
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"""
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Handoff class to represent biomedical entities as Neo4j nodes.
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Has id, label, property dict; id and label (in the Neo4j sense of a
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label, ie, the entity descriptor after the colon, such as
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":Protein") are non-optional and called node_id and node_label to
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avoid confusion with "label" properties. Node labels are written in
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PascalCase and as nouns, as per Neo4j consensus.
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Args:
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node_id (string): consensus "best" id for biological entity
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node_label (string): primary type of entity, capitalised
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**properties (kwargs): collection of all other properties to be
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passed to neo4j for the respective node (dict)
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Todo:
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- check and correct small inconsistencies such as capitalisation
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of ID names ("uniprot" vs "UniProt")
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- check for correct ID patterns (eg "ENSG" + string of numbers,
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uniprot length)
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- ID conversion using pypath translation facilities for now
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"""
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node_id: str
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node_label: str
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preferred_id: str = "id"
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properties: dict = field(default_factory=dict)
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def __post_init__(self):
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"""
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Add id field to properties.
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Check for reserved keywords.
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Replace unwanted characters in properties.
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"""
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self.properties["id"] = self.node_id
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self.properties["preferred_id"] = self.preferred_id or None
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# TODO actually make None possible here; as is, "id" is the default in
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# the dataclass as well as in the configuration file
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if ":TYPE" in self.properties.keys():
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logger.warning(
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"Keyword ':TYPE' is reserved for Neo4j. "
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"Removing from properties.",
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# "Renaming to 'type'."
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)
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# self.properties["type"] = self.properties[":TYPE"]
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del self.properties[":TYPE"]
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for k, v in self.properties.items():
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if isinstance(v, str):
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self.properties[k] = (
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v.replace(
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os.linesep,
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" ",
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)
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.replace(
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"\n",
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" ",
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)
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.replace(
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"\r",
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" ",
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)
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)
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elif isinstance(v, list):
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#modified biocypher, because the data contained intgers in lists
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self.properties[k] = [
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(str(val) if isinstance(val, (int, float)) else val)
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.replace(os.linesep, " ")
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.replace("\n", " ")
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.replace("\r", " ")
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for val in v
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]
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def get_id(self) -> str:
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"""
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Returns primary node identifier.
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Returns:
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str: node_id
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"""
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return self.node_id
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def get_label(self) -> str:
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"""
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Returns primary node label.
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Returns:
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str: node_label
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"""
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return self.node_label
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def get_type(self) -> str:
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"""
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Returns primary node label.
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Returns:
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str: node_label
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"""
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return self.node_label
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def get_preferred_id(self) -> str:
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"""
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Returns preferred id.
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Returns:
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str: preferred_id
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"""
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return self.preferred_id
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def get_properties(self) -> dict:
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"""
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Returns all other node properties apart from primary id and
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label as key-value pairs.
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Returns:
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dict: properties
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"""
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return self.properties
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def get_dict(self) -> dict:
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"""
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Return dict of id, labels, and properties.
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Returns:
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dict: node_id and node_label as top-level key-value pairs,
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properties as second-level dict.
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"""
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return {
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"node_id": self.node_id,
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"node_label": self.node_label,
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"properties": self.properties,
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}
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@dataclass(frozen=True)
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class BioCypherEdge:
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"""
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Handoff class to represent biomedical relationships in Neo4j.
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Has source and target ids, label, property dict; ids and label (in
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the Neo4j sense of a label, ie, the entity descriptor after the
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colon, such as ":TARGETS") are non-optional and called source_id,
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target_id, and relationship_label to avoid confusion with properties
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called "label", which usually denotes the human-readable form.
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Relationship labels are written in UPPERCASE and as verbs, as per
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Neo4j consensus.
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Args:
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source_id (string): consensus "best" id for biological entity
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target_id (string): consensus "best" id for biological entity
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relationship_label (string): type of interaction, UPPERCASE
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properties (dict): collection of all other properties of the
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respective edge
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"""
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source_id: str
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target_id: str
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relationship_label: str
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relationship_id: str = None
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properties: dict = field(default_factory=dict)
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def __post_init__(self):
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"""
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Check for reserved keywords.
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"""
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if ":TYPE" in self.properties.keys():
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logger.debug(
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"Keyword ':TYPE' is reserved for Neo4j. "
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"Removing from properties.",
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# "Renaming to 'type'."
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)
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# self.properties["type"] = self.properties[":TYPE"]
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del self.properties[":TYPE"]
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elif "id" in self.properties.keys():
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logger.debug(
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"Keyword 'id' is reserved for Neo4j. "
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"Removing from properties.",
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# "Renaming to 'type'."
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)
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# self.properties["type"] = self.properties[":TYPE"]
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del self.properties["id"]
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elif "_ID" in self.properties.keys():
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logger.debug(
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"Keyword '_ID' is reserved for Postgres. "
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"Removing from properties.",
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# "Renaming to 'type'."
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)
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# self.properties["type"] = self.properties[":TYPE"]
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del self.properties["_ID"]
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def get_id(self) -> Union[str, None]:
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"""
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Returns primary node identifier or None.
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Returns:
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str: node_id
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"""
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return self.relationship_id
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def get_source_id(self) -> str:
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"""
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Returns primary node identifier of relationship source.
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Returns:
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str: source_id
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"""
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return self.source_id
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def get_target_id(self) -> str:
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"""
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Returns primary node identifier of relationship target.
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Returns:
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str: target_id
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"""
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return self.target_id
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def get_label(self) -> str:
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"""
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Returns relationship label.
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Returns:
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str: relationship_label
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"""
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return self.relationship_label
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def get_type(self) -> str:
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"""
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Returns relationship label.
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Returns:
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str: relationship_label
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"""
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return self.relationship_label
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def get_properties(self) -> dict:
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"""
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Returns all other relationship properties apart from primary ids
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and label as key-value pairs.
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Returns:
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dict: properties
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"""
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return self.properties
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def get_dict(self) -> dict:
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"""
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Return dict of ids, label, and properties.
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Returns:
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dict: source_id, target_id and relationship_label as
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top-level key-value pairs, properties as second-level
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dict.
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"""
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return {
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"relationship_id": self.relationship_id or None,
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"source_id": self.source_id,
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"target_id": self.target_id,
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"relationship_label": self.relationship_label,
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"properties": self.properties,
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}
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@dataclass(frozen=True)
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class BioCypherRelAsNode:
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"""
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Class to represent relationships as nodes (with in- and outgoing
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edges) as a triplet of a BioCypherNode and two BioCypherEdges. Main
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usage in type checking (instances where the receiving function needs
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to check whether it receives a relationship as a single edge or as
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a triplet).
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Args:
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node (BioCypherNode): node representing the relationship
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source_edge (BioCypherEdge): edge representing the source of the
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relationship
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target_edge (BioCypherEdge): edge representing the target of the
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relationship
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"""
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node: BioCypherNode
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source_edge: BioCypherEdge
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target_edge: BioCypherEdge
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def __post_init__(self):
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if not isinstance(self.node, BioCypherNode):
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raise TypeError(
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f"BioCypherRelAsNode.node must be a BioCypherNode, "
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f"not {type(self.node)}.",
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)
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if not isinstance(self.source_edge, BioCypherEdge):
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raise TypeError(
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f"BioCypherRelAsNode.source_edge must be a BioCypherEdge, "
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f"not {type(self.source_edge)}.",
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)
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if not isinstance(self.target_edge, BioCypherEdge):
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raise TypeError(
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f"BioCypherRelAsNode.target_edge must be a BioCypherEdge, "
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f"not {type(self.target_edge)}.",
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)
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def get_node(self) -> BioCypherNode:
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return self.node
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def get_source_edge(self) -> BioCypherEdge:
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return self.source_edge
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def get_target_edge(self) -> BioCypherEdge:
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return self.target_edge
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