biocypher 0.6.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

biocypher/_core.py

@@ -1,43 +1,32 @@
-#!/usr/bin/env python
-
-#
-# Copyright 2021, Heidelberg University Clinic
-#
-# File author(s): Sebastian Lobentanzer
-#                 ...
-#
-# Distributed under MIT licence, see the file `LICENSE`.
-#
-"""
-BioCypher core module. Interfaces with the user and distributes tasks to
-submodules.
-"""
-from typing import Optional
-from datetime import datetime
-import os
-import json
+"""BioCypher core module.
 
-from more_itertools import peekable
-import yaml
+Interfaces with the user and distributes tasks to submodules.
+"""
 
-import pandas as pd
+import itertools
+import json
+import os
 
-from ._logger import logger
+from datetime import datetime
 
-logger.debug(f"Loading module {__name__}.")
+import yaml
 
+from ._config import (
+    config as _config,
+    update_from_file as _file_update,
+)
+from ._create import BioCypherNode
+from ._deduplicate import Deduplicator
 from ._get import Downloader
-from ._config import config as _config
-from ._config import update_from_file as _file_update
-from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
+from ._logger import logger
 from ._mapping import OntologyMapping
 from ._ontology import Ontology
 from ._translate import Translator
-from ._deduplicate import Deduplicator
-from .output.in_memory._pandas import Pandas
+from .output.connect._get_connector import get_connector
+from .output.in_memory._get_in_memory_kg import IN_MEMORY_DBMS, get_in_memory_kg
 from .output.write._get_writer import DBMS_TO_CLASS, get_writer
-from .output.connect._neo4j_driver import get_driver
 
+logger.debug(f"Loading module {__name__}.")
 __all__ = ["BioCypher"]
 
 SUPPORTED_DBMS = DBMS_TO_CLASS.keys()
@@ -51,17 +40,18 @@ REQUIRED_CONFIG = [
 
 
 class BioCypher:
-    """
-    Orchestration of BioCypher operations. Instantiate this class to interact
-    with BioCypher.
+    """Orchestration of BioCypher operations.
 
-    Args:
+    Instantiate this class to interact with BioCypher.
 
+    Args:
+    ----
         dbms (str): The database management system to use. For supported
             systems see SUPPORTED_DBMS.
 
-        offline (bool): Whether to run in offline mode. If True, no
-            connection to the database will be made.
+        offline (bool): Whether to run in offline mode. In offline mode
+            the Knowledge Graph is written to files. In online mode, it
+            is written to a database or hold in memory.
 
         strict_mode (bool): Whether to run in strict mode. If True, the
             translator will raise an error if a node or edge does not
@@ -81,6 +71,8 @@ class BioCypher:
         output_directory (str): Path to the output directory. If not
             provided, the default value 'biocypher-out' will be used.
 
+        cache_directory (str): Path to the cache directory.
+
     """
 
     def __init__(
@@ -105,7 +97,7 @@ class BioCypher:
             logger.warning(
                 "The parameter `db_name` is deprecated. Please set the "
                 "`database_name` setting in the `biocypher_config.yaml` file "
-                "instead."
+                "instead.",
             )
             _config(**{db_name: {"database_name": db_name}})
 
@@ -115,7 +107,8 @@ class BioCypher:
         # Check for required configuration
         for key in REQUIRED_CONFIG:
             if key not in self.base_config:
-                raise ValueError(f"Configuration key {key} is required.")
+                msg = f"Configuration key {key} is required."
+                raise ValueError(msg)
 
         # Set configuration - mandatory
         self._dbms = dbms or self.base_config["dbms"]
@@ -131,34 +124,32 @@ class BioCypher:
             self._strict_mode = strict_mode
 
         self._schema_config_path = schema_config_path or self.base_config.get(
-            "schema_config_path"
+            "schema_config_path",
         )
 
         if not self._schema_config_path:
             logger.warning("Running BioCypher without schema configuration.")
         else:
             logger.info(
-                f"Running BioCypher with schema configuration from {self._schema_config_path}."
+                f"Running BioCypher with schema configuration from {self._schema_config_path}.",
             )
 
         self._head_ontology = head_ontology or self.base_config["head_ontology"]
 
         # Set configuration - optional
         self._output_directory = output_directory or self.base_config.get(
-            "output_directory"
+            "output_directory",
         )
         self._cache_directory = cache_directory or self.base_config.get(
-            "cache_directory"
+            "cache_directory",
         )
         self._tail_ontologies = tail_ontologies or self.base_config.get(
-            "tail_ontologies"
+            "tail_ontologies",
         )
 
         if self._dbms not in SUPPORTED_DBMS:
-            raise ValueError(
-                f"DBMS {self._dbms} not supported. "
-                f"Please select from {SUPPORTED_DBMS}."
-            )
+            msg = f"DBMS {self._dbms} not supported. Please select from {SUPPORTED_DBMS}."
+            raise ValueError(msg)
 
         # Initialize
         self._ontology_mapping = None
@@ -167,23 +158,97 @@ class BioCypher:
         self._downloader = None
         self._ontology = None
         self._writer = None
-        self._pd = None
+        self._driver = None
+        self._in_memory_kg = None
 
-    def _get_deduplicator(self) -> Deduplicator:
+        self._in_memory_kg = None
+        self._nodes = None
+        self._edges = None
+
+    def _initialize_in_memory_kg(self) -> None:
+        """Create in-memory KG instance.
+
+        Set as instance variable `self._in_memory_kg`.
         """
-        Create deduplicator if not exists and return.
+        if not self._in_memory_kg:
+            self._in_memory_kg = get_in_memory_kg(
+                dbms=self._dbms,
+                deduplicator=self._get_deduplicator(),
+            )
+
+    def add_nodes(self, nodes) -> None:
+        """Add new nodes to the internal representation.
+
+        Initially, receive nodes data from adaptor and create internal
+        representation for nodes.
+
+        Args:
+        ----
+            nodes(iterable): An iterable of nodes
+
+        """
+        if isinstance(nodes, list):
+            self._nodes = list(itertools.chain(self._nodes, nodes))
+        else:
+            self._nodes = itertools.chain(self._nodes, nodes)
+
+    def add_edges(self, edges) -> None:
+        """Add new edges to the internal representation.
+
+        Initially, receive edges data from adaptor and create internal
+        representation for edges.
+
+        Args:
+        ----
+             edges(iterable): An iterable of edges.
+
         """
+        if isinstance(edges, list):
+            self._edges = list(itertools.chain(self._edges, edges))
+        else:
+            self._edges = itertools.chain(self._edges, edges)
+
+    def to_df(self):
+        """Create DataFrame using internal representation.
+
+        TODO: to_df implies data frame, should be specifically that use case
+        """
+        return self._to_KG()
+
+    def to_networkx(self):
+        """Create networkx using internal representation."""
+        return self._to_KG()
+
+    def _to_KG(self):
+        """Convert the internal representation to knowledge graph.
+
+        The knowledge graph is returned based on the `dbms` parameter in
+        the biocypher configuration file.
+
+        Returns
+        -------
+             Any: knowledge graph.
+
+        """
+        if not self._in_memory_kg:
+            self._initialize_in_memory_kg()
+        if not self._translator:
+            self._get_translator()
+        tnodes = self._translator.translate_entities(self._nodes)
+        tedges = self._translator.translate_entities(self._edges)
+        self._in_memory_kg.add_nodes(tnodes)
+        self._in_memory_kg.add_edges(tedges)
+        return self._in_memory_kg.get_kg()
 
+    def _get_deduplicator(self) -> Deduplicator:
+        """Create deduplicator if not exists and return."""
         if not self._deduplicator:
             self._deduplicator = Deduplicator()
 
         return self._deduplicator
 
     def _get_ontology_mapping(self) -> OntologyMapping:
-        """
-        Create ontology mapping if not exists and return.
-        """
-
+        """Create ontology mapping if not exists and return."""
         if not self._schema_config_path:
             self._ontology_mapping = OntologyMapping()
 
@@ -195,10 +260,7 @@ class BioCypher:
         return self._ontology_mapping
 
     def _get_ontology(self) -> Ontology:
-        """
-        Create ontology if not exists and return.
-        """
-
+        """Create ontology if not exists and return."""
         if not self._ontology:
             self._ontology = Ontology(
                 ontology_mapping=self._get_ontology_mapping(),
@@ -209,10 +271,7 @@ class BioCypher:
         return self._ontology
 
     def _get_translator(self) -> Translator:
-        """
-        Create translator if not exists and return.
-        """
-
+        """Create translator if not exists and return."""
         if not self._translator:
             self._translator = Translator(
                 ontology=self._get_ontology(),
@@ -222,14 +281,18 @@ class BioCypher:
         return self._translator
 
     def _get_writer(self):
-        """
-        Create writer if not online. Set as instance variable `self._writer`.
-        """
+        """Create writer if not online.
 
+        Set as instance variable `self._writer`.
+        """
         if self._offline:
-            timestamp = lambda: datetime.now().strftime("%Y%m%d%H%M%S")
+
+            def timestamp() -> str:
+                return datetime.now().strftime("%Y%m%d%H%M%S")
+
             outdir = self._output_directory or os.path.join(
-                "biocypher-out", timestamp()
+                "biocypher-out",
+                timestamp(),
             )
             self._output_directory = os.path.abspath(outdir)
 
@@ -241,240 +304,270 @@ class BioCypher:
                 strict_mode=self._strict_mode,
             )
         else:
-            raise NotImplementedError("Cannot get writer in online mode.")
+            msg = "Cannot get writer in online mode."
+            raise NotImplementedError(msg)
+
+        return self._writer
 
     def _get_driver(self):
-        """
-        Create driver if not exists. Set as instance variable `self._driver`.
-        """
+        """Create driver if not exists.
 
+        Set as instance variable `self._driver`.
+        """
         if not self._offline:
-            self._driver = get_driver(
+            self._driver = get_connector(
                 dbms=self._dbms,
                 translator=self._get_translator(),
-                deduplicator=self._get_deduplicator(),
             )
         else:
-            raise NotImplementedError("Cannot get driver in offline mode.")
+            msg = "Cannot get driver in offline mode."
+            raise NotImplementedError(msg)
 
-    def write_nodes(
-        self, nodes, batch_size: int = int(1e6), force: bool = False
-    ) -> bool:
+        return self._driver
+
+    def _get_in_memory_kg(self):
+        """Create in-memory KG instance.
+
+        Set as instance variable `self._in_memory_kg`.
         """
-        Write nodes to database. Either takes an iterable of tuples (if given,
-        translates to ``BioCypherNode`` objects) or an iterable of
-        ``BioCypherNode`` objects.
+        if not self._in_memory_kg:
+            self._in_memory_kg = get_in_memory_kg(
+                dbms=self._dbms,
+                deduplicator=self._get_deduplicator(),
+            )
 
-        Args:
-            nodes (iterable): An iterable of nodes to write to the database.
+        return self._in_memory_kg
 
-            batch_size (int): The batch size to use when writing to disk.
+    def _add_nodes(
+        self,
+        nodes,
+        batch_size: int = int(1e6),
+        force: bool = False,
+    ):
+        """Add nodes to the BioCypher KG.
 
-            force (bool): Whether to force writing to the output directory even
-                if the node type is not present in the schema config file.
+        First uses the `_translator` to translate the nodes to `BioCypherNode`
+        objects. Depending on the configuration the translated nodes are then
+        passed to the
 
-        Returns:
-            bool: True if successful.
-        """
+        - `_writer`: if `_offline` is set to `False`
 
-        if not self._writer:
-            self._get_writer()
+        - `_in_memory_kg`: if `_offline` is set to `False` and the `_dbms` is an
+            `IN_MEMORY_DBMS`
 
-        nodes = peekable(nodes)
-        if not isinstance(nodes.peek(), BioCypherNode):
-            tnodes = self._translator.translate_nodes(nodes)
-        else:
-            tnodes = nodes
-        # write node files
-        return self._writer.write_nodes(
-            tnodes, batch_size=batch_size, force=force
-        )
+        - `_driver`: if `_offline` is set to `True` and the `_dbms` is not an
+            `IN_MEMORY_DBMS`
 
-    def write_edges(self, edges, batch_size: int = int(1e6)) -> bool:
         """
-        Write edges to database. Either takes an iterable of tuples (if given,
-        translates to ``BioCypherEdge`` objects) or an iterable of
-        ``BioCypherEdge`` objects.
+        if not self._translator:
+            self._get_translator()
+        translated_nodes = self._translator.translate_entities(nodes)
 
-        Args:
-            edges (iterable): An iterable of edges to write to the database.
+        if self._offline:
+            passed = self._get_writer().write_nodes(
+                translated_nodes,
+                batch_size=batch_size,
+                force=force,
+            )
+        elif self._is_online_and_in_memory():
+            passed = self._get_in_memory_kg().add_nodes(translated_nodes)
+        else:
+            passed = self._get_driver().add_biocypher_nodes(translated_nodes)
 
-        Returns:
-            bool: True if successful.
-        """
+        return passed
 
-        if not self._writer:
-            self._get_writer()
+    def _add_edges(self, edges, batch_size: int = int(1e6)):
+        """Add edges to the BioCypher KG.
 
-        edges = peekable(edges)
-        if not isinstance(edges.peek(), BioCypherEdge):
-            tedges = self._translator.translate_edges(edges)
-        else:
-            tedges = edges
-        # write edge files
-        return self._writer.write_edges(tedges, batch_size=batch_size)
+        First uses the `_translator` to translate the edges to `BioCypherEdge`
+        objects. Depending on the configuration the translated edges are then
+        passed to the
 
-    def to_df(self) -> list[pd.DataFrame]:
-        """
-        Convert entities to a pandas DataFrame for each entity type and return
-        a list.
+        - `_writer`: if `_offline` is set to `False`
 
-        Args:
-            entities (iterable): An iterable of entities to convert to a
-                DataFrame.
+        - `_in_memory_kg`: if `_offline` is set to `False` and the `_dbms` is an
+            `IN_MEMORY_DBMS`
+
+        - `_driver`: if `_offline` is set to `True` and the `_dbms` is not an
+            `IN_MEMORY_DBMS`
 
-        Returns:
-            pd.DataFrame: A pandas DataFrame.
         """
-        if not self._pd:
-            raise ValueError(
-                "No pandas instance found. Please call `add()` first."
+        if not self._translator:
+            self._get_translator()
+        translated_edges = self._translator.translate_entities(edges)
+
+        if self._offline:
+            if not self._writer:
+                self._initialize_writer()
+            passed = self._writer.write_edges(
+                translated_edges,
+                batch_size=batch_size,
             )
+        elif self._is_online_and_in_memory():
+            if not self._in_memory_kg:
+                self._initialize_in_memory_kg()
+            passed = self._in_memory_kg.add_edges(translated_edges)
+        else:
+            if not self._driver:
+                self._initialize_driver()
+            passed = self._driver.add_biocypher_nodes(translated_edges)
 
-        return self._pd.dfs
+        return passed
 
-    def add(self, entities) -> None:
-        """
-        Function to add entities to the in-memory database. Accepts an iterable
-        of tuples (if given, translates to ``BioCypherNode`` or
-        ``BioCypherEdge`` objects) or an iterable of ``BioCypherNode`` or
-        ``BioCypherEdge`` objects.
+    def _is_online_and_in_memory(self) -> bool:
+        """Return True if in online mode and in-memory dbms is used."""
+        return (not self._offline) & (self._dbms in IN_MEMORY_DBMS)
+
+    def write_nodes(
+        self,
+        nodes,
+        batch_size: int = int(1e6),
+        force: bool = False,
+    ) -> bool:
+        """Write nodes to database.
+
+        Either takes an iterable of tuples (if given, translates to
+        ``BioCypherNode`` objects) or an iterable of ``BioCypherNode`` objects.
 
         Args:
-            entities (iterable): An iterable of entities to add to the database.
-                Can be 3-tuples (nodes) or 5-tuples (edges); also accepts
-                4-tuples for edges (deprecated).
+        ----
+            nodes (iterable): An iterable of nodes to write to the database.
+            batch_size (int): The batch size to use when writing to disk.
+            force (bool): Whether to force writing to the output directory even
+                if the node type is not present in the schema config file.
 
         Returns:
-            None
-        """
-        if not self._pd:
-            self._pd = Pandas(
-                translator=self._get_translator(),
-                deduplicator=self._get_deduplicator(),
-            )
-
-        entities = peekable(entities)
+        -------
+            bool: True if successful.
 
-        if (
-            isinstance(entities.peek(), BioCypherNode)
-            or isinstance(entities.peek(), BioCypherEdge)
-            or isinstance(entities.peek(), BioCypherRelAsNode)
-        ):
-            tentities = entities
-        elif len(entities.peek()) < 4:
-            tentities = self._translator.translate_nodes(entities)
-        else:
-            tentities = self._translator.translate_edges(entities)
+        """
+        return self._add_nodes(nodes, batch_size=batch_size, force=force)
 
-        self._pd.add_tables(tentities)
+    def write_edges(self, edges, batch_size: int = int(1e6)) -> bool:
+        """Write edges to database.
 
-    def add_nodes(self, nodes) -> None:
-        """
-        Wrapper for ``add()`` to add nodes to the in-memory database.
+        Either takes an iterable of tuples (if given, translates to
+        ``BioCypherEdge`` objects) or an iterable of ``BioCypherEdge`` objects.
 
         Args:
-            nodes (iterable): An iterable of node tuples to add to the database.
+        ----
+            edges (iterable): An iterable of edges to write to the database.
 
         Returns:
-            None
-        """
-        self.add(nodes)
+        -------
+            bool: True if successful.
 
-    def add_edges(self, edges) -> None:
         """
-        Wrapper for ``add()`` to add edges to the in-memory database.
+        return self._add_edges(edges, batch_size=batch_size)
+
+    def add(self, entities) -> None:
+        """Add entities to the in-memory database.
+
+        Accepts an iterable of tuples (if given, translates to
+        ``BioCypherNode`` or ``BioCypherEdge`` objects) or an iterable of
+        ``BioCypherNode`` or ``BioCypherEdge`` objects.
 
         Args:
-            edges (iterable): An iterable of edge tuples to add to the database.
+        ----
+            entities (iterable): An iterable of entities to add to the database.
+                Can be 3-tuples (nodes) or 5-tuples (edges); also accepts
+                4-tuples for edges (deprecated).
 
         Returns:
+        -------
             None
+
         """
-        self.add(edges)
+        return self._add_nodes(entities)
 
     def merge_nodes(self, nodes) -> bool:
-        """
-        Merge nodes into database. Either takes an iterable of tuples (if given,
-        translates to ``BioCypherNode`` objects) or an iterable of
-        ``BioCypherNode`` objects.
+        """Merge nodes into database.
+
+        Either takes an iterable of tuples (if given, translates to
+        ``BioCypherNode`` objects) or an iterable of ``BioCypherNode`` objects.
 
         Args:
+        ----
             nodes (iterable): An iterable of nodes to merge into the database.
 
         Returns:
+        -------
             bool: True if successful.
-        """
-
-        if not self._driver:
-            self._get_driver()
 
-        nodes = peekable(nodes)
-        if not isinstance(nodes.peek(), BioCypherNode):
-            tnodes = self._translator.translate_nodes(nodes)
-        else:
-            tnodes = nodes
-        # write node files
-        return self._driver.add_biocypher_nodes(tnodes)
+        """
+        return self._add_nodes(nodes)
 
     def merge_edges(self, edges) -> bool:
-        """
-        Merge edges into database. Either takes an iterable of tuples (if given,
-        translates to ``BioCypherEdge`` objects) or an iterable of
-        ``BioCypherEdge`` objects.
+        """Merge edges into database.
+
+        Either takes an iterable of tuples (if given, translates to
+        ``BioCypherEdge`` objects) or an iterable of ``BioCypherEdge`` objects.
 
         Args:
+        ----
             edges (iterable): An iterable of edges to merge into the database.
 
         Returns:
+        -------
             bool: True if successful.
+
         """
+        return self._add_edges(edges)
 
-        if not self._driver:
-            self._get_driver()
+    def get_kg(self):
+        """Get the in-memory KG instance.
 
-        edges = peekable(edges)
-        if not isinstance(edges.peek(), BioCypherEdge):
-            tedges = self._translator.translate_edges(edges)
-        else:
-            tedges = edges
-        # write edge files
-        return self._driver.add_biocypher_edges(tedges)
+        Depending on the specified `dbms` this could either be a list of Pandas
+        dataframes or a NetworkX DiGraph.
+        """
+        if not self._is_online_and_in_memory():
+            msg = (f"Getting the in-memory KG is only available in online mode for {IN_MEMORY_DBMS}.",)
+            raise ValueError(msg)
+        if not self._in_memory_kg:
+            msg = "No in-memory KG instance found. Please call `add()` first."
+            raise ValueError(msg)
 
-    # DOWNLOAD AND CACHE MANAGEMENT METHODS ###
+        if not self._in_memory_kg:
+            self._initialize_in_memory_kg()
+        return self._in_memory_kg.get_kg()
 
-    def _get_downloader(self, cache_dir: Optional[str] = None):
-        """
-        Create downloader if not exists.
-        """
+    # DOWNLOAD AND CACHE MANAGEMENT METHODS ###
 
+    def _get_downloader(self, cache_dir: str | None = None):
+        """Create downloader if not exists."""
         if not self._downloader:
             self._downloader = Downloader(self._cache_directory)
 
     def download(self, *resources) -> None:
-        """
-        Use the :class:`Downloader` class to download or load from cache the
-        resources given by the adapter.
-        """
+        """Download or load from cache the resources given by the adapter.
 
+        Args:
+        ----
+            resources (iterable): An iterable of resources to download or load
+                from cache.
+
+        Returns:
+        -------
+            None
+
+        """
         self._get_downloader()
         return self._downloader.download(*resources)
 
     # OVERVIEW AND CONVENIENCE METHODS ###
 
-    def log_missing_input_labels(self) -> Optional[dict[str, list[str]]]:
-        """
+    def log_missing_input_labels(self) -> dict[str, list[str]] | None:
+        """Log missing input labels.
 
         Get the set of input labels encountered without an entry in the
         `schema_config.yaml` and print them to the logger.
 
-        Returns:
-
+        Returns
+        -------
             Optional[Dict[str, List[str]]]: A dictionary of Biolink types
             encountered without an entry in the `schema_config.yaml` file.
 
         """
-
         mt = self._translator.get_missing_biolink_types()
 
         if mt:
@@ -495,11 +588,11 @@ class BioCypher:
             return None
 
     def log_duplicates(self) -> None:
-        """
+        """Log duplicate nodes and edges.
+
         Get the set of duplicate nodes and edges encountered and print them to
         the logger.
         """
-
         dn = self._deduplicator.get_duplicate_nodes()
 
         if dn:
@@ -543,11 +636,10 @@ class BioCypher:
             logger.info("No duplicate edges in input.")
 
     def show_ontology_structure(self, **kwargs) -> None:
-        """
-        Show the ontology structure using treelib or write to GRAPHML file.
+        """Show the ontology structure using treelib or write to GRAPHML file.
 
         Args:
-
+        ----
             to_disk (str): If specified, the ontology structure will be saved
                 to disk as a GRAPHML file, to be opened in your favourite
                 graph visualisation tool.
@@ -555,36 +647,37 @@ class BioCypher:
             full (bool): If True, the full ontology structure will be shown,
                 including all nodes and edges. If False, only the nodes and
                 edges that are relevant to the extended schema will be shown.
-        """
 
+        """
         if not self._ontology:
             self._get_ontology()
 
         return self._ontology.show_ontology_structure(**kwargs)
 
     def write_import_call(self) -> str:
-        """
-        Write a shell script to import the database depending on the chosen
-        DBMS.
+        """Write a shell script to import the database.
 
-        Returns:
+        Shell script is written depending on the chosen DBMS.
+
+        Returns
+        -------
             str: path toward the file holding the import call.
-        """
 
+        """
         if not self._offline:
-            raise NotImplementedError(
-                "Cannot write import call in online mode."
-            )
+            msg = "Cannot write import call in online mode."
+            raise NotImplementedError(msg)
 
         return self._writer.write_import_call()
 
     def write_schema_info(self, as_node: bool = False) -> None:
-        """
-        Write an extended schema info YAML file that extends the
-        `schema_config.yaml` with run-time information of the built KG. For
-        instance, include information on whether something present in the actual
-        knowledge graph, whether it is a relationship (which is important in the
-        case of representing relationships as nodes) and the actual sources and
+        """Write an extended schema info to file or node.
+
+        Creates a YAML file or KG node that extends the `schema_config.yaml`
+        with run-time information of the built KG. For instance, include
+        information on whether something present in the actual knowledge graph,
+        whether it is a relationship (which is important in the case of
+        representing relationships as nodes) and the actual sources and
         targets of edges. Since this file can be used in place of the original
         `schema_config.yaml` file, it indicates that it is the extended schema
         by setting `is_schema_info` to `true`.
@@ -594,12 +687,16 @@ class BioCypher:
         The information of whether something is a relationship can be gathered
         from the deduplicator instance, which keeps track of all entities that
         have been seen.
-        """
 
-        if not self._offline:
-            raise NotImplementedError(
-                "Cannot write schema info in online mode."
-            )
+        Args:
+        ----
+            as_node (bool): If True, the schema info is written as a KG node.
+                If False, the schema info is written to a YAML file.
+
+        """
+        if (not self._offline) and self._dbms not in IN_MEMORY_DBMS:
+            msg = "Cannot write schema info in online mode."
+            raise NotImplementedError(msg)
 
         ontology = self._get_ontology()
         schema = ontology.mapping.extended_schema.copy()
@@ -607,13 +704,12 @@ class BioCypher:
 
         deduplicator = self._get_deduplicator()
         for node in deduplicator.entity_types:
-            if node in schema.keys():
+            if node in schema:
                 schema[node]["present_in_knowledge_graph"] = True
                 schema[node]["is_relationship"] = False
             else:
                 logger.info(
-                    f"Node {node} not present in extended schema. "
-                    "Skipping schema info."
+                    f"Node {node} not present in extended schema. Skipping schema info.",
                 )
 
         # find 'label_as_edge' cases in schema entries
@@ -621,21 +717,20 @@ class BioCypher:
         for k, v in schema.items():
             if not isinstance(v, dict):
                 continue
-            if "label_as_edge" in v.keys():
-                if v["label_as_edge"] in deduplicator.seen_relationships.keys():
+            if "label_as_edge" in v:
+                if v["label_as_edge"] in deduplicator.seen_relationships:
                     changed_labels[v["label_as_edge"]] = k
 
-        for edge in deduplicator.seen_relationships.keys():
-            if edge in changed_labels.keys():
+        for edge in deduplicator.seen_relationships:
+            if edge in changed_labels:
                 edge = changed_labels[edge]
-            if edge in schema.keys():
+            if edge in schema:
                 schema[edge]["present_in_knowledge_graph"] = True
                 schema[edge]["is_relationship"] = True
                 # TODO information about source and target nodes
             else:
                 logger.info(
-                    f"Edge {edge} not present in extended schema. "
-                    "Skipping schema info."
+                    f"Edge {edge} not present in extended schema. Skipping schema info.",
                 )
 
         # write to output directory as YAML file
@@ -660,74 +755,77 @@ class BioCypher:
     # TRANSLATION METHODS ###
 
     def translate_term(self, term: str) -> str:
-        """
-        Translate a term to its BioCypher equivalent.
+        """Translate a term to its BioCypher equivalent.
 
         Args:
+        ----
             term (str): The term to translate.
 
         Returns:
+        -------
             str: The BioCypher equivalent of the term.
-        """
 
+        """
         # instantiate adapter if not exists
         self.start_ontology()
 
         return self._translator.translate_term(term)
 
     def summary(self) -> None:
-        """
-        Wrapper for showing ontology structure and logging duplicates and
-        missing input types.
-        """
+        """Call convenience and reporting methods.
 
+        Shows ontology structure and logs duplicates and missing input types.
+        """
         self.show_ontology_structure()
         self.log_duplicates()
         self.log_missing_input_labels()
 
     def reverse_translate_term(self, term: str) -> str:
-        """
-        Reverse translate a term from its BioCypher equivalent.
+        """Reverse translate a term from its BioCypher equivalent.
 
         Args:
+        ----
             term (str): The BioCypher term to reverse translate.
 
         Returns:
+        -------
             str: The original term.
-        """
 
+        """
         # instantiate adapter if not exists
         self.start_ontology()
 
         return self._translator.reverse_translate_term(term)
 
     def translate_query(self, query: str) -> str:
-        """
-        Translate a query to its BioCypher equivalent.
+        """Translate a query to its BioCypher equivalent.
 
         Args:
+        ----
             query (str): The query to translate.
 
         Returns:
+        -------
             str: The BioCypher equivalent of the query.
-        """
 
+        """
         # instantiate adapter if not exists
         self.start_ontology()
 
         return self._translator.translate(query)
 
     def reverse_translate_query(self, query: str) -> str:
-        """
-        Reverse translate a query from its BioCypher equivalent.
+        """Reverse translate a query from its BioCypher equivalent.
 
         Args:
+        ----
             query (str): The BioCypher query to reverse translate.
 
         Returns:
+        -------
             str: The original query.
-        """
 
+        """
         # instantiate adapter if not exists
         self.start_ontology()