biocypher 0.5.19__py3-none-any.whl → 0.5.20__py3-none-any.whl

biocypher/_connect.py

@@ -53,8 +53,6 @@ class _Neo4jDriver:
 
         increment_version (bool): Whether to increment the version number.
 
-        ontology (Ontology): The ontology to use for mapping.
-
         translator (Translator): The translator to use for mapping.
 
     """
@@ -66,14 +64,12 @@ class _Neo4jDriver:
         user: str,
         password: str,
         multi_db: bool,
-        ontology: Ontology,
         translator: Translator,
         wipe: bool = False,
         fetch_size: int = 1000,
         increment_version: bool = True,
     ):
-        self._ontology = ontology
-        self._translator = translator
+        self.translator = translator
 
         self._driver = neo4j_utils.Driver(
             db_name=database_name,
@@ -103,7 +99,7 @@ class _Neo4jDriver:
             "MATCH (v:BioCypher) " "WHERE NOT (v)-[:PRECEDES]->() " "RETURN v",
         )
         # add version node
-        self.add_biocypher_nodes(self._ontology)
+        self.add_biocypher_nodes(self.translator.ontology)
 
         # connect version node to previous
         if db_version[0]:
@@ -111,7 +107,7 @@ class _Neo4jDriver:
             previous_id = previous["v"]["id"]
             e_meta = BioCypherEdge(
                 previous_id,
-                self._ontology.get_dict().get("node_id"),
+                self.translator.ontology.get_dict().get("node_id"),
                 "PRECEDES",
             )
             self.add_biocypher_edges(e_meta)
@@ -142,7 +138,7 @@ class _Neo4jDriver:
         logger.info("Creating constraints for node types in config.")
 
         # get structure
-        for leaf in self._ontology.extended_schema.items():
+        for leaf in self.translator.ontology.mapping.extended_schema.items():
             label = _misc.sentencecase_to_pascalcase(leaf[0])
             if leaf[1]["represented_as"] == "node":
                 s = (
@@ -172,7 +168,7 @@ class _Neo4jDriver:
                 - second entry: Neo4j summary.
         """
 
-        bn = self._translator.translate_nodes(id_type_tuples)
+        bn = self.translator.translate_nodes(id_type_tuples)
         return self.add_biocypher_nodes(bn)
 
     def add_edges(self, id_src_tar_type_tuples: Iterable[tuple]) -> tuple:
@@ -204,7 +200,7 @@ class _Neo4jDriver:
                 - second entry: Neo4j summary.
         """
 
-        bn = self._translator.translate_edges(id_src_tar_type_tuples)
+        bn = self.translator.translate_edges(id_src_tar_type_tuples)
         return self.add_biocypher_edges(bn)
 
     def add_biocypher_nodes(
@@ -375,7 +371,6 @@ class _Neo4jDriver:
 def get_driver(
     dbms: str,
     translator: "Translator",
-    ontology: "Ontology",
 ):
     """
     Function to return the writer class.
@@ -394,7 +389,6 @@ def get_driver(
             user=dbms_config["user"],
             password=dbms_config["password"],
             multi_db=dbms_config["multi_db"],
-            ontology=ontology,
             translator=translator,
         )
 

biocypher/_core.py

@@ -13,8 +13,10 @@ BioCypher core module. Interfaces with the user and distributes tasks to
 submodules.
 """
 from typing import Optional
+import os
 
 from more_itertools import peekable
+import yaml
 
 import pandas as pd
 
@@ -25,7 +27,7 @@ logger.debug(f"Loading module {__name__}.")
 from ._write import get_writer
 from ._config import config as _config
 from ._config import update_from_file as _file_update
-from ._create import BioCypherEdge, BioCypherNode
+from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 from ._pandas import Pandas
 from ._connect import get_driver
 from ._mapping import OntologyMapping
@@ -181,19 +183,6 @@ class BioCypher:
 
         return self._ontology_mapping
 
-    def _get_translator(self) -> Translator:
-        """
-        Create translator if not exists and return.
-        """
-
-        if not self._translator:
-            self._translator = Translator(
-                ontology_mapping=self._get_ontology_mapping(),
-                strict_mode=self._strict_mode,
-            )
-
-        return self._translator
-
     def _get_ontology(self) -> Ontology:
         """
         Create ontology if not exists and return.
@@ -208,17 +197,28 @@ class BioCypher:
 
         return self._ontology
 
+    def _get_translator(self) -> Translator:
+        """
+        Create translator if not exists and return.
+        """
+
+        if not self._translator:
+            self._translator = Translator(
+                ontology=self._get_ontology(),
+                strict_mode=self._strict_mode,
+            )
+
+        return self._translator
+
     def _get_writer(self):
         """
         Create writer if not online. Set as instance variable `self._writer`.
         """
 
-        # Get worker
         if self._offline:
             self._writer = get_writer(
                 dbms=self._dbms,
                 translator=self._get_translator(),
-                ontology=self._get_ontology(),
                 deduplicator=self._get_deduplicator(),
                 output_directory=self._output_directory,
                 strict_mode=self._strict_mode,
@@ -235,7 +235,6 @@ class BioCypher:
             self._driver = get_driver(
                 dbms=self._dbms,
                 translator=self._get_translator(),
-                ontology=self._get_ontology(),
                 deduplicator=self._get_deduplicator(),
             )
         else:
@@ -318,14 +317,15 @@ class BioCypher:
         if not self._pd:
             self._pd = Pandas(
                 translator=self._get_translator(),
-                ontology=self._get_ontology(),
                 deduplicator=self._get_deduplicator(),
             )
 
         entities = peekable(entities)
 
-        if isinstance(entities.peek(), BioCypherNode) or isinstance(
-            entities.peek(), BioCypherEdge
+        if (
+            isinstance(entities.peek(), BioCypherNode)
+            or isinstance(entities.peek(), BioCypherEdge)
+            or isinstance(entities.peek(), BioCypherRelAsNode)
         ):
             tentities = entities
         elif len(entities.peek()) < 4:
@@ -504,6 +504,73 @@ class BioCypher:
 
         self._writer.write_import_call()
 
+    def write_schema_info(self) -> 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
+        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`.
+
+        We start by using the `extended_schema` dictionary from the ontology
+        class instance, which contains all expanded entities and relationships.
+        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."
+            )
+
+        ontology = self._get_ontology()
+        schema = ontology.mapping.extended_schema
+        schema["is_schema_info"] = True
+
+        deduplicator = self._get_deduplicator()
+        for node in deduplicator.entity_types:
+            if node in schema.keys():
+                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."
+                )
+
+        # find 'label_as_edge' cases in schema entries
+        changed_labels = {}
+        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():
+                    changed_labels[v["label_as_edge"]] = k
+
+        for edge in deduplicator.seen_relationships.keys():
+            if edge in changed_labels.keys():
+                edge = changed_labels[edge]
+            if edge in schema.keys():
+                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."
+                )
+
+        # write to output directory as YAML file
+        path = os.path.join(self._output_directory, "schema_info.yaml")
+        with open(path, "w") as f:
+            f.write(yaml.dump(schema))
+
+        return schema
+
     # TRANSLATION METHODS ###
 
     def translate_term(self, term: str) -> str:

biocypher/_deduplicate.py

@@ -2,7 +2,7 @@ from ._logger import logger
 
 logger.debug(f"Loading module {__name__}.")
 
-from ._create import BioCypherEdge, BioCypherNode
+from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 
 
 class Deduplicator:
@@ -19,15 +19,17 @@ class Deduplicator:
     """
 
     def __init__(self):
-        self.seen_node_ids = set()
-        self.duplicate_node_ids = set()
-        self.duplicate_node_types = set()
+        self.seen_entity_ids = set()
+        self.duplicate_entity_ids = set()
 
-        self.seen_edges = {}
-        self.duplicate_edge_ids = set()
-        self.duplicate_edge_types = set()
+        self.entity_types = set()
+        self.duplicate_entity_types = set()
 
-    def node_seen(self, node: BioCypherNode) -> bool:
+        self.seen_relationships = {}
+        self.duplicate_relationship_ids = set()
+        self.duplicate_relationship_types = set()
+
+    def node_seen(self, entity: BioCypherNode) -> bool:
         """
         Adds a node to the instance and checks if it has been seen before.
 
@@ -37,19 +39,22 @@ class Deduplicator:
         Returns:
             True if the node has been seen before, False otherwise.
         """
-        if node.get_id() in self.seen_node_ids:
-            self.duplicate_node_ids.add(node.get_id())
-            if node.get_label() not in self.duplicate_node_types:
+        if entity.get_label() not in self.entity_types:
+            self.entity_types.add(entity.get_label())
+
+        if entity.get_id() in self.seen_entity_ids:
+            self.duplicate_entity_ids.add(entity.get_id())
+            if entity.get_label() not in self.duplicate_entity_types:
                 logger.warning(
-                    f"Duplicate node type {node.get_label()} found. "
+                    f"Duplicate node type {entity.get_label()} found. "
                 )
-                self.duplicate_node_types.add(node.get_label())
+                self.duplicate_entity_types.add(entity.get_label())
             return True
 
-        self.seen_node_ids.add(node.get_id())
+        self.seen_entity_ids.add(entity.get_id())
         return False
 
-    def edge_seen(self, edge: BioCypherEdge) -> bool:
+    def edge_seen(self, relationship: BioCypherEdge) -> bool:
         """
         Adds an edge to the instance and checks if it has been seen before.
 
@@ -59,23 +64,57 @@ class Deduplicator:
         Returns:
             True if the edge has been seen before, False otherwise.
         """
-        if edge.get_type() not in self.seen_edges:
-            self.seen_edges[edge.get_type()] = set()
+        if relationship.get_type() not in self.seen_relationships:
+            self.seen_relationships[relationship.get_type()] = set()
 
         # concatenate source and target if no id is present
-        if not edge.get_id():
-            _id = f"{edge.get_source_id()}_{edge.get_target_id()}"
+        if not relationship.get_id():
+            _id = (
+                f"{relationship.get_source_id()}_{relationship.get_target_id()}"
+            )
         else:
-            _id = edge.get_id()
+            _id = relationship.get_id()
+
+        if _id in self.seen_relationships[relationship.get_type()]:
+            self.duplicate_relationship_ids.add(_id)
+            if relationship.get_type() not in self.duplicate_relationship_types:
+                logger.warning(
+                    f"Duplicate edge type {relationship.get_type()} found. "
+                )
+                self.duplicate_relationship_types.add(relationship.get_type())
+            return True
+
+        self.seen_relationships[relationship.get_type()].add(_id)
+        return False
+
+    def rel_as_node_seen(self, rel_as_node: BioCypherRelAsNode) -> bool:
+        """
+        Adds a rel_as_node to the instance (one entity and two relationships)
+        and checks if it has been seen before. Only the node is relevant for
+        identifying the rel_as_node as a duplicate.
+
+        Args:
+            rel_as_node: BioCypherRelAsNode to be added.
+
+        Returns:
+            True if the rel_as_node has been seen before, False otherwise.
+        """
+        node = rel_as_node.get_node()
+
+        if node.get_label() not in self.seen_relationships:
+            self.seen_relationships[node.get_label()] = set()
+
+        # rel as node always has an id
+        _id = node.get_id()
 
-        if _id in self.seen_edges[edge.get_type()]:
-            self.duplicate_edge_ids.add(_id)
-            if edge.get_type() not in self.duplicate_edge_types:
-                logger.warning(f"Duplicate edge type {edge.get_type()} found. ")
-                self.duplicate_edge_types.add(edge.get_type())
+        if _id in self.seen_relationships[node.get_type()]:
+            self.duplicate_relationship_ids.add(_id)
+            if node.get_type() not in self.duplicate_relationship_types:
+                logger.warning(f"Duplicate edge type {node.get_type()} found. ")
+                self.duplicate_relationship_types.add(node.get_type())
             return True
 
-        self.seen_edges[edge.get_type()].add(_id)
+        self.seen_relationships[node.get_type()].add(_id)
         return False
 
     def get_duplicate_nodes(self):
@@ -86,8 +125,8 @@ class Deduplicator:
             list: list of duplicate nodes
         """
 
-        if self.duplicate_node_types:
-            return (self.duplicate_node_types, self.duplicate_node_ids)
+        if self.duplicate_entity_types:
+            return (self.duplicate_entity_types, self.duplicate_entity_ids)
         else:
             return None
 
@@ -99,7 +138,10 @@ class Deduplicator:
             list: list of duplicate edges
         """
 
-        if self.duplicate_edge_types:
-            return (self.duplicate_edge_types, self.duplicate_edge_ids)
+        if self.duplicate_relationship_types:
+            return (
+                self.duplicate_relationship_types,
+                self.duplicate_relationship_ids,
+            )
         else:
             return None

biocypher/_metadata.py

@@ -19,7 +19,7 @@ import importlib.metadata
 
 import toml
 
-_VERSION = "0.5.19"
+_VERSION = "0.5.20"
 
 
 def get_metadata():

biocypher/_ontology.py

@@ -269,7 +269,7 @@ class Ontology:
         """
 
         self._head_ontology_meta = head_ontology
-        self.extended_schema = ontology_mapping.extended_schema
+        self.mapping = ontology_mapping
         self._tail_ontology_meta = tail_ontologies
 
         self._tail_ontologies = None
@@ -403,7 +403,7 @@ class Ontology:
         if not self._nx_graph:
             self._nx_graph = self._head_ontology.get_nx_graph().copy()
 
-        for key, value in self.extended_schema.items():
+        for key, value in self.mapping.extended_schema.items():
             if not value.get("is_a"):
                 if self._nx_graph.has_node(value.get("synonym_for")):
                     continue
@@ -485,7 +485,7 @@ class Ontology:
         setting the synonym as the primary node label.
         """
 
-        for key, value in self.extended_schema.items():
+        for key, value in self.mapping.extended_schema.items():
             if key in self._nx_graph.nodes:
                 self._nx_graph.nodes[key].update(value)
 
@@ -541,9 +541,9 @@ class Ontology:
 
         if not full:
             # set of leaves and their intermediate parents up to the root
-            filter_nodes = set(self.extended_schema.keys())
+            filter_nodes = set(self.mapping.extended_schema.keys())
 
-            for node in self.extended_schema.keys():
+            for node in self.mapping.extended_schema.keys():
                 filter_nodes.update(self.get_ancestors(node).nodes)
 
             # filter graph
@@ -557,11 +557,13 @@ class Ontology:
             tree = _misc.create_tree_visualisation(G)
 
             # add synonym information
-            for node in self.extended_schema:
-                if self.extended_schema[node].get("synonym_for"):
+            for node in self.mapping.extended_schema:
+                if not isinstance(self.mapping.extended_schema[node], dict):
+                    continue
+                if self.mapping.extended_schema[node].get("synonym_for"):
                     tree.nodes[node].tag = (
                         f"{node} = "
-                        f"{self.extended_schema[node].get('synonym_for')}"
+                        f"{self.mapping.extended_schema[node].get('synonym_for')}"
                     )
 
             tree.show()
@@ -602,7 +604,7 @@ class Ontology:
             "node_id": self._get_current_id(),
             "node_label": "BioCypher",
             "properties": {
-                "schema": "self.extended_schema",
+                "schema": "self.ontology_mapping.extended_schema",
             },
         }
 

biocypher/_pandas.py

@@ -1,11 +1,10 @@
 import pandas as pd
 
-from ._create import BioCypherEdge, BioCypherNode
+from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 
 
 class Pandas:
-    def __init__(self, ontology, translator, deduplicator):
-        self.ontology = ontology
+    def __init__(self, translator, deduplicator):
         self.translator = translator
         self.deduplicator = deduplicator
 
@@ -18,22 +17,48 @@ class Pandas:
         """
         lists = {}
         for entity in entities:
-            if not isinstance(entity, BioCypherNode) and not isinstance(
-                entity, BioCypherEdge
+            if (
+                not isinstance(entity, BioCypherNode)
+                and not isinstance(entity, BioCypherEdge)
+                and not isinstance(entity, BioCypherRelAsNode)
             ):
                 raise TypeError(
-                    f"Expected a BioCypherNode or BioCypherEdge, got {type(entity)}."
+                    "Expected a BioCypherNode / BioCypherEdge / "
+                    f"BioCypherRelAsNode, got {type(entity)}."
                 )
 
             if isinstance(entity, BioCypherNode):
                 seen = self.deduplicator.node_seen(entity)
             elif isinstance(entity, BioCypherEdge):
                 seen = self.deduplicator.edge_seen(entity)
+            elif isinstance(entity, BioCypherRelAsNode):
+                seen = self.deduplicator.rel_as_node_seen(entity)
 
             if seen:
                 continue
 
-            _type = entity.get_label()
+            if isinstance(entity, BioCypherRelAsNode):
+                node = entity.get_node()
+                source_edge = entity.get_source_edge()
+                target_edge = entity.get_target_edge()
+
+                _type = node.get_type()
+                if not _type in lists:
+                    lists[_type] = []
+                lists[_type].append(node)
+
+                _source_type = source_edge.get_type()
+                if not _source_type in lists:
+                    lists[_source_type] = []
+                lists[_source_type].append(source_edge)
+
+                _target_type = target_edge.get_type()
+                if not _target_type in lists:
+                    lists[_target_type] = []
+                lists[_target_type].append(target_edge)
+                continue
+
+            _type = entity.get_type()
             if not _type in lists:
                 lists[_type] = []
             lists[_type].append(entity)

biocypher/_translate.py

@@ -23,7 +23,7 @@ from more_itertools import peekable
 
 from . import _misc
 from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
-from ._mapping import OntologyMapping
+from ._ontology import Ontology
 
 __all__ = ["BiolinkAdapter", "Translator"]
 
@@ -41,9 +41,7 @@ class Translator:
     and cypher queries.
     """
 
-    def __init__(
-        self, ontology_mapping: "OntologyMapping", strict_mode: bool = False
-    ):
+    def __init__(self, ontology: "Ontology", strict_mode: bool = False):
         """
         Args:
             leaves:
@@ -57,7 +55,7 @@ class Translator:
                 carry source, licence, and version information.
         """
 
-        self.extended_schema = ontology_mapping.extended_schema
+        self.ontology = ontology
         self.strict_mode = strict_mode
 
         # record nodes without biolink type configured in schema_config.yaml
@@ -71,7 +69,7 @@ class Translator:
 
     def translate_nodes(
         self,
-        id_type_prop_tuples: Iterable,
+        node_tuples: Iterable,
     ) -> Generator[BioCypherNode, None, None]:
         """
         Translates input node representation to a representation that
@@ -79,16 +77,16 @@ class Translator:
         requires explicit statement of node type on pass.
 
         Args:
-            id_type_tuples (list of tuples): collection of tuples
+            node_tuples (list of tuples): collection of tuples
                 representing individual nodes by their unique id and a type
                 that is translated from the original database notation to
                 the corresponding BioCypher notation.
 
         """
 
-        self._log_begin_translate(id_type_prop_tuples, "nodes")
+        self._log_begin_translate(node_tuples, "nodes")
 
-        for _id, _type, _props in id_type_prop_tuples:
+        for _id, _type, _props in node_tuples:
             # check for strict mode requirements
             required_props = ["source", "licence", "version"]
 
@@ -132,8 +130,9 @@ class Translator:
         """
 
         return (
-            self.extended_schema[_bl_type]["preferred_id"]
-            if "preferred_id" in self.extended_schema.get(_bl_type, {})
+            self.ontology.mapping.extended_schema[_bl_type]["preferred_id"]
+            if "preferred_id"
+            in self.ontology.mapping.extended_schema.get(_bl_type, {})
             else "id"
         )
 
@@ -142,7 +141,9 @@ class Translator:
         Filters properties for those specified in schema_config if any.
         """
 
-        filter_props = self.extended_schema[bl_type].get("properties", {})
+        filter_props = self.ontology.mapping.extended_schema[bl_type].get(
+            "properties", {}
+        )
 
         # strict mode: add required properties (only if there is a whitelist)
         if self.strict_mode and filter_props:
@@ -150,7 +151,7 @@ class Translator:
                 {"source": "str", "licence": "str", "version": "str"},
             )
 
-        exclude_props = self.extended_schema[bl_type].get(
+        exclude_props = self.ontology.mapping.extended_schema[bl_type].get(
             "exclude_properties", []
         )
 
@@ -188,7 +189,7 @@ class Translator:
 
     def translate_edges(
         self,
-        id_src_tar_type_prop_tuples: Iterable,
+        edge_tuples: Iterable,
     ) -> Generator[Union[BioCypherEdge, BioCypherRelAsNode], None, None]:
         """
         Translates input edge representation to a representation that
@@ -197,7 +198,7 @@ class Translator:
 
         Args:
 
-            id_src_tar_type_prop_tuples (list of tuples):
+            edge_tuples (list of tuples):
 
                 collection of tuples representing source and target of
                 an interaction via their unique ids as well as the type
@@ -206,18 +207,18 @@ class Translator:
                 Can optionally possess its own ID.
         """
 
-        self._log_begin_translate(id_src_tar_type_prop_tuples, "edges")
+        self._log_begin_translate(edge_tuples, "edges")
 
         # legacy: deal with 4-tuples (no edge id)
         # TODO remove for performance reasons once safe
-        id_src_tar_type_prop_tuples = peekable(id_src_tar_type_prop_tuples)
-        if len(id_src_tar_type_prop_tuples.peek()) == 4:
-            id_src_tar_type_prop_tuples = [
+        edge_tuples = peekable(edge_tuples)
+        if len(edge_tuples.peek()) == 4:
+            edge_tuples = [
                 (None, src, tar, typ, props)
-                for src, tar, typ, props in id_src_tar_type_prop_tuples
+                for src, tar, typ, props in edge_tuples
             ]
 
-        for _id, _src, _tar, _type, _props in id_src_tar_type_prop_tuples:
+        for _id, _src, _tar, _type, _props in edge_tuples:
             # check for strict mode requirements
             if self.strict_mode:
                 if not "source" in _props:
@@ -239,7 +240,9 @@ class Translator:
                 # filter properties for those specified in schema_config if any
                 _filtered_props = self._filter_props(bl_type, _props)
 
-                rep = self.extended_schema[bl_type]["represented_as"]
+                rep = self.ontology.mapping.extended_schema[bl_type][
+                    "represented_as"
+                ]
 
                 if rep == "node":
                     if _id:
@@ -295,9 +298,9 @@ class Translator:
                     yield BioCypherRelAsNode(n, e_s, e_t)
 
                 else:
-                    edge_label = self.extended_schema[bl_type].get(
-                        "label_as_edge"
-                    )
+                    edge_label = self.ontology.mapping.extended_schema[
+                        bl_type
+                    ].get("label_as_edge")
 
                     if edge_label is None:
                         edge_label = bl_type
@@ -356,7 +359,7 @@ class Translator:
 
         self._ontology_mapping = {}
 
-        for key, value in self.extended_schema.items():
+        for key, value in self.ontology.mapping.extended_schema.items():
             labels = value.get("input_label") or value.get("label_in_input")
 
             if isinstance(labels, str):

biocypher/_write.py

@@ -125,7 +125,6 @@ class _BatchWriter(ABC):
 
     def __init__(
         self,
-        ontology: "Ontology",
         translator: "Translator",
         deduplicator: "Deduplicator",
         delimiter: str,
@@ -167,10 +166,6 @@ class _BatchWriter(ABC):
             - _get_import_script_name
 
         Args:
-            ontology:
-                Instance of :py:class:`Ontology` to enable translation and
-                ontology queries
-
             translator:
                 Instance of :py:class:`Translator` to enable translation of
                 nodes and manipulation of properties.
@@ -251,8 +246,6 @@ class _BatchWriter(ABC):
         self.wipe = wipe
         self.strict_mode = strict_mode
 
-        self.extended_schema = ontology.extended_schema
-        self.ontology = ontology
         self.translator = translator
         self.deduplicator = deduplicator
         self.node_property_dict = {}
@@ -352,34 +345,34 @@ class _BatchWriter(ABC):
             bool: The return value. True for success, False otherwise.
         """
         passed = False
-        # unwrap generator in one step
         edges = list(edges)  # force evaluation to handle empty generator
         if edges:
-            z = zip(
-                *(
-                    (
-                        e.get_node(),
-                        [
-                            e.get_source_edge(),
-                            e.get_target_edge(),
-                        ],
-                    )
-                    if isinstance(e, BioCypherRelAsNode)
-                    else (None, [e])
-                    for e in edges
-                )
-            )
-            nod, edg = (list(a) for a in z)
-            nod = [n for n in nod if n]
-            edg = [val for sublist in edg for val in sublist]  # flatten
+            nodes_flat = []
+            edges_flat = []
+            for edge in edges:
+                if isinstance(edge, BioCypherRelAsNode):
+                    # check if relationship has already been written, if so skip
+                    if self.deduplicator.rel_as_node_seen(edge):
+                        continue
 
-            if nod and edg:
-                passed = self.write_nodes(nod) and self._write_edge_data(
-                    edg,
+                    nodes_flat.append(edge.get_node())
+                    edges_flat.append(edge.get_source_edge())
+                    edges_flat.append(edge.get_target_edge())
+
+                else:
+                    # check if relationship has already been written, if so skip
+                    if self.deduplicator.edge_seen(edge):
+                        continue
+
+                    edges_flat.append(edge)
+
+            if nodes_flat and edges_flat:
+                passed = self.write_nodes(nodes_flat) and self._write_edge_data(
+                    edges_flat,
                     batch_size,
                 )
             else:
-                passed = self._write_edge_data(edg, batch_size)
+                passed = self._write_edge_data(edges_flat, batch_size)
 
         else:
             # is this a problem? if the generator or list is empty, we
@@ -451,8 +444,12 @@ class _BatchWriter(ABC):
                     bin_l[label] = 1
 
                     # get properties from config if present
-                    cprops = self.extended_schema.get(label).get(
-                        "properties",
+                    cprops = (
+                        self.translator.ontology.mapping.extended_schema.get(
+                            label
+                        ).get(
+                            "properties",
+                        )
                     )
                     if cprops:
                         d = dict(cprops)
@@ -486,7 +483,7 @@ class _BatchWriter(ABC):
 
                     # get label hierarchy
                     # multiple labels:
-                    all_labels = self.ontology.get_ancestors(label)
+                    all_labels = self.translator.ontology.get_ancestors(label)
 
                     if all_labels:
                         # convert to pascal case
@@ -682,10 +679,6 @@ class _BatchWriter(ABC):
             # for each label to check for consistency and their type
             # for now, relevant for `int`
             for edge in edges:
-                # check for duplicates
-                if self.deduplicator.edge_seen(edge):
-                    continue
-
                 if not (edge.get_source_id() and edge.get_target_id()):
                     logger.error(
                         "Edge must have source and target node. "
@@ -706,13 +699,23 @@ class _BatchWriter(ABC):
                     # (may not be if it is an edge that carries the
                     # "label_as_edge" property)
                     cprops = None
-                    if label in self.extended_schema:
-                        cprops = self.extended_schema.get(label).get(
+                    if (
+                        label
+                        in self.translator.ontology.mapping.extended_schema
+                    ):
+                        cprops = self.translator.ontology.mapping.extended_schema.get(
+                            label
+                        ).get(
                             "properties",
                         )
                     else:
                         # try via "label_as_edge"
-                        for k, v in self.extended_schema.items():
+                        for (
+                            k,
+                            v,
+                        ) in (
+                            self.translator.ontology.mapping.extended_schema.items()
+                        ):
                             if isinstance(v, dict):
                                 if v.get("label_as_edge") == label:
                                     cprops = v.get("properties")
@@ -873,9 +876,14 @@ class _BatchWriter(ABC):
 
             if label in ["IS_SOURCE_OF", "IS_TARGET_OF", "IS_PART_OF"]:
                 skip_id = True
-            elif not self.extended_schema.get(label):
+            elif not self.translator.ontology.mapping.extended_schema.get(
+                label
+            ):
                 # find label in schema by label_as_edge
-                for k, v in self.extended_schema.items():
+                for (
+                    k,
+                    v,
+                ) in self.translator.ontology.mapping.extended_schema.items():
                     if v.get("label_as_edge") == label:
                         schema_label = k
                         break
@@ -884,7 +892,9 @@ class _BatchWriter(ABC):
 
             if schema_label:
                 if (
-                    self.extended_schema.get(schema_label).get("use_id")
+                    self.translator.ontology.mapping.extended_schema.get(
+                        schema_label
+                    ).get("use_id")
                     == False
                 ):
                     skip_id = True
@@ -1009,6 +1019,7 @@ class _Neo4jBatchWriter(_BatchWriter):
 
     This class inherits from the abstract class "_BatchWriter" and implements the
     Neo4j-specific methods:
+
         - _write_node_headers
         - _write_edge_headers
         - _construct_import_call
@@ -1181,9 +1192,14 @@ class _Neo4jBatchWriter(_BatchWriter):
 
             if label in ["IS_SOURCE_OF", "IS_TARGET_OF", "IS_PART_OF"]:
                 skip_id = True
-            elif not self.extended_schema.get(label):
+            elif not self.translator.ontology.mapping.extended_schema.get(
+                label
+            ):
                 # find label in schema by label_as_edge
-                for k, v in self.extended_schema.items():
+                for (
+                    k,
+                    v,
+                ) in self.translator.ontology.mapping.extended_schema.items():
                     if v.get("label_as_edge") == label:
                         schema_label = k
                         break
@@ -1194,7 +1210,9 @@ class _Neo4jBatchWriter(_BatchWriter):
 
             if schema_label:
                 if (
-                    self.extended_schema.get(schema_label).get("use_id")
+                    self.translator.ontology.mapping.extended_schema.get(
+                        schema_label
+                    ).get("use_id")
                     == False
                 ):
                     skip_id = True
@@ -1352,9 +1370,9 @@ class _ArangoDBBatchWriter(_Neo4jBatchWriter):
                 f.write(row)
 
             # add collection from schema config
-            collection = self.extended_schema[label].get(
-                "db_collection_name", None
-            )
+            collection = self.translator.ontology.mapping.extended_schema[
+                label
+            ].get("db_collection_name", None)
 
             # add file path to neo4 admin import statement
             # do once for each part file
@@ -1433,16 +1451,19 @@ class _ArangoDBBatchWriter(_Neo4jBatchWriter):
                 f.write(row)
 
             # add collection from schema config
-            if not self.extended_schema.get(label):
-                for _, v in self.extended_schema.items():
+            if not self.translator.ontology.mapping.extended_schema.get(label):
+                for (
+                    _,
+                    v,
+                ) in self.translator.ontology.mapping.extended_schema.items():
                     if v.get("label_as_edge") == label:
                         collection = v.get("db_collection_name", None)
                         break
 
             else:
-                collection = self.extended_schema[label].get(
-                    "db_collection_name", None
-                )
+                collection = self.translator.ontology.mapping.extended_schema[
+                    label
+                ].get("db_collection_name", None)
 
             # add file path to neo4 admin import statement (import call path
             # may be different from actual output path)
@@ -1520,6 +1541,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
 
     This class inherits from the abstract class "_BatchWriter" and implements the
     PostgreSQL-specific methods:
+
         - _write_node_headers
         - _write_edge_headers
         - _construct_import_call
@@ -1839,7 +1861,6 @@ DBMS_TO_CLASS = {
 def get_writer(
     dbms: str,
     translator: "Translator",
-    ontology: "Ontology",
     deduplicator: "Deduplicator",
     output_directory: str,
     strict_mode: bool,
@@ -1854,8 +1875,6 @@ def get_writer(
 
         translator: the Translator object.
 
-        ontology: the Ontology object.
-
         output_directory: the directory to write the output files to.
 
         strict_mode: whether to use strict mode.
@@ -1879,7 +1898,6 @@ def get_writer(
 
     if writer is not None:
         return writer(
-            ontology=ontology,
             translator=translator,
             deduplicator=deduplicator,
             delimiter=dbms_config.get("delimiter"),

{biocypher-0.5.19.dist-info → biocypher-0.5.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.5.19
+Version: 0.5.20
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT
@@ -38,7 +38,9 @@ Description-Content-Type: text/markdown
 ![Python](https://img.shields.io/badge/python-3.10-blue.svg)
 [![PyPI version](https://badge.fury.io/py/biocypher.svg)](https://badge.fury.io/py/biocypher)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-![Docs build](https://github.com/biocypher/biocypher/actions/workflows/sphinx_autodoc.yml/badge.svg)
+[![CI](https://github.com/biocypher/biocypher/actions/workflows/ci_cd.yaml/badge.svg)](https://github.com/biocypher/biocypher/actions/workflows/ci_cd.yaml)
+![Coverage](https://raw.githubusercontent.com/biocypher/biocypher/coverage/coverage.svg)
+[![Docs build](https://github.com/biocypher/biocypher/actions/workflows/sphinx_autodoc.yaml/badge.svg)](https://github.com/biocypher/biocypher/actions/workflows/sphinx_autodoc.yaml)
 [![Downloads](https://static.pepy.tech/badge/biocypher)](https://pepy.tech/project/biocypher)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com)

{biocypher-0.5.19.dist-info → biocypher-0.5.20.dist-info}/RECORD

@@ -5,19 +5,19 @@ biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsX
 biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
 biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
 biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
-biocypher/_connect.py,sha256=i62424Cbdnm2oI4ECLkcMF2V2A6aShCK2eSSwaGLbVE,12603
-biocypher/_core.py,sha256=Sg7ESentsTsqp9KbzPC_jh1fRAqOGzyy98Xzma7BBkw,17100
+biocypher/_connect.py,sha256=0oSyO6CEIlKL8rHo-HHE7y0FzGfSi4vnEXSDy1TnIUE,12456
+biocypher/_core.py,sha256=fA0tRorzy3R1mgzzT77mFk-l6oQ01ZAfjg8l6KbPQYM,19882
 biocypher/_create.py,sha256=vpUchUdEpWupZi1LgFLxAWMtqoBwnWbP7PwEDUCBS4A,10202
-biocypher/_deduplicate.py,sha256=ah2i6ONx6ml4MbQMXIe6NfbVzf1bjav0l3gLj1xGDE0,3288
+biocypher/_deduplicate.py,sha256=BBvfpXzu6L5YDY5FdtXxnf8YlsbJpbCE8RdUoKsm0n0,4949
 biocypher/_logger.py,sha256=soYtz1DiduLFw3XrMnphWWUxeuJqvSof4AYhlafxl08,2933
 biocypher/_mapping.py,sha256=XJZjmXTPnXVkyub1ZU0h3EKXQ2YROaGaJOaGyPMqgy4,9338
-biocypher/_metadata.py,sha256=24UdhQ8vslHBfHf0S6oF9A5asyiM9SVOjfVqvRPnFvY,1658
+biocypher/_metadata.py,sha256=Hmz4g_CSuqikUJ6EtLEq2GS7Z0BawtAsL0Wk-7AiE8c,1658
 biocypher/_misc.py,sha256=wsjGVOqBDVM5hxbE_TEaZ69u1kJc8HXwRAtQHUgE8XQ,4545
-biocypher/_ontology.py,sha256=vCGIHJn_IH5bmOMTA6GJQZB-eNVOlyjYnMzwmwfni0Q,21375
-biocypher/_pandas.py,sha256=2qaCtUCk_nhr8dCqXqUr8zgMhCetPh9EDq-3z-8Qxi0,2021
-biocypher/_translate.py,sha256=e5XhPxbPArd0aK-Zk7F533ECV12jMR_ZzoAlGD3TAzc,16540
-biocypher/_write.py,sha256=kOb_l1LMu_weu5RLxEDLvSrpgdU1PZZe7ObaNhJRkdU,66943
-biocypher-0.5.19.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
-biocypher-0.5.19.dist-info/WHEEL,sha256=vxFmldFsRN_Hx10GDvsdv1wroKq8r5Lzvjp6GZ4OO8c,88
-biocypher-0.5.19.dist-info/METADATA,sha256=_7DNxOzmag2EO1vxTpjE7dcsX7YclymnoIVEkoMXlJ4,9103
-biocypher-0.5.19.dist-info/RECORD,,
+biocypher/_ontology.py,sha256=pHc4hO8iZx-yg9gzqfBR9khoIni-lKAxWgnRFyNP91E,21530
+biocypher/_pandas.py,sha256=GVCFM68J7yBjh40MpkNVgD8qT1RFMrrIjMOtD3iKsf4,3040
+biocypher/_translate.py,sha256=nj4Y60F0U3JBH36N2dh5pFcC8Ot86rskJ2ChJwje9dI,16494
+biocypher/_write.py,sha256=2ynF-VkvTr8WT2qPt2wji3iupP3WON94TlT6NpfDvCs,67738
+biocypher-0.5.20.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
+biocypher-0.5.20.dist-info/WHEEL,sha256=vxFmldFsRN_Hx10GDvsdv1wroKq8r5Lzvjp6GZ4OO8c,88
+biocypher-0.5.20.dist-info/METADATA,sha256=B3VOakjkLgCjusCElMML-neoPoc869g4jNI45Bchibo,9429
+biocypher-0.5.20.dist-info/RECORD,,