biocypher 0.5.42__py3-none-any.whl → 0.5.44__py3-none-any.whl

biocypher/_config/biocypher_config.yaml

@@ -131,3 +131,11 @@ sqlite:
   delimiter: '\t'
   # import_call_bin_prefix: '' # path to "sqlite3"
   # import_call_file_prefix: '/path/to/files'
+
+csv:
+  ### CSV/Pandas configuration ###
+  delimiter: ","
+
+networkx:
+  ### NetworkX configuration ###
+  some_config: some_value # placeholder for technical reasons TODO

biocypher/_core.py

@@ -26,17 +26,17 @@ from ._logger import logger
 
 logger.debug(f"Loading module {__name__}.")
 
-from biocypher.write._write import DBMS_TO_CLASS, get_writer
 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 ._pandas import Pandas
-from ._connect import get_driver
 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.write._get_writer import DBMS_TO_CLASS, get_writer
+from .output.connect._neo4j_driver import get_driver
 
 __all__ = ["BioCypher"]
 

biocypher/_metadata.py

@@ -19,7 +19,7 @@ import importlib.metadata
 
 import toml
 
-_VERSION = "0.5.42"
+_VERSION = "0.5.44"
 
 
 def get_metadata():

biocypher/{_connect.py → output/connect/_neo4j_driver.py}

@@ -13,7 +13,7 @@ BioCypher 'online' mode. Handles connection and manipulation of a running DBMS.
 """
 import subprocess
 
-from ._logger import logger
+from biocypher._logger import logger
 
 logger.debug(f"Loading module {__name__}.")
 
@@ -22,10 +22,10 @@ import itertools
 
 import neo4j_utils
 
-from . import _misc
-from ._config import config as _config
-from ._create import BioCypherEdge, BioCypherNode
-from ._translate import Translator
+from biocypher import _misc
+from biocypher._config import config as _config
+from biocypher._create import BioCypherEdge, BioCypherNode
+from biocypher._translate import Translator
 
 __all__ = ["_Neo4jDriver"]
 

biocypher/{_pandas.py → output/in_memory/_pandas.py}

@@ -1,6 +1,6 @@
 import pandas as pd
 
-from ._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
+from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 
 
 class Pandas:
@@ -87,3 +87,4 @@ class Pandas:
             self.dfs[_type] = pd.concat(
                 [self.dfs[_type], df], ignore_index=True
             )
+        return self.dfs[_type]

biocypher/{write → output/write}/_batch_writer.py

@@ -6,16 +6,18 @@ import os
 import re
 import glob
 
-from rdflib import Graph
 from more_itertools import peekable
 
 from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 from biocypher._logger import logger
 from biocypher._translate import Translator
 from biocypher._deduplicate import Deduplicator
+from biocypher.output.write._writer import _Writer
 
 
-class _BatchWriter(ABC):
+class _BatchWriter(_Writer, ABC):
+    """Abstract batch writer class"""
+
     @abstractmethod
     def _get_default_import_call_bin_prefix(self):
         """
@@ -41,7 +43,7 @@ class _BatchWriter(ABC):
             str: The database-specific string representation of an array
         """
         raise NotImplementedError(
-            "Database writer must override '_write_node_headers'"
+            "Database writer must override '_write_array_string'"
         )
 
     @abstractmethod
@@ -206,6 +208,12 @@ class _BatchWriter(ABC):
             rdf_namespaces:
                 The namespaces for RDF.
         """
+        super().__init__(
+            translator=translator,
+            deduplicator=deduplicator,
+            output_directory=output_directory,
+            strict_mode=strict_mode,
+        )
         self.db_name = db_name
         self.db_user = db_user
         self.db_password = db_password
@@ -239,32 +247,15 @@ class _BatchWriter(ABC):
         self.import_call_nodes = set()
         self.import_call_edges = set()
 
-        self._outdir = output_directory
+        self.outdir = output_directory
 
         self._import_call_file_prefix = import_call_file_prefix
 
-        if os.path.exists(self.outdir):
-            logger.warning(
-                f"Output directory `{self.outdir}` already exists. "
-                "If this is not planned, file consistency may be compromised."
-            )
-        else:
-            logger.info(f"Creating output directory `{self.outdir}`.")
-            os.makedirs(self.outdir)
-
         self.parts = {}  # dict to store the paths of part files for each label
 
         # TODO not memory efficient, but should be fine for most cases; is
         # there a more elegant solution?
 
-    @property
-    def outdir(self):
-        """
-        Property for output directory path.
-        """
-
-        return self._outdir
-
     @property
     def import_call_file_prefix(self):
         """
@@ -272,7 +263,7 @@ class _BatchWriter(ABC):
         """
 
         if self._import_call_file_prefix is None:
-            return self._outdir
+            return self.outdir
         else:
             return self._import_call_file_prefix
 
@@ -1005,7 +996,9 @@ class _BatchWriter(ABC):
         """
 
         file_path = os.path.join(self.outdir, self._get_import_script_name())
-        logger.info(f"Writing {self.db_name} import call to `{file_path}`.")
+        logger.info(
+            f"Writing {self.db_name + ' ' if self.db_name else ''}import call to `{file_path}`."
+        )
 
         with open(file_path, "w", encoding="utf-8") as f:
             f.write(self._construct_import_call())

biocypher/{write/_write.py → output/write/_get_writer.py}

@@ -14,11 +14,13 @@ suitable for import into a DBMS.
 """
 
 from biocypher._logger import logger
-from biocypher.write.graph._rdf import _RDFWriter
-from biocypher.write.graph._neo4j import _Neo4jBatchWriter
-from biocypher.write.graph._arangodb import _ArangoDBBatchWriter
-from biocypher.write.relational._sqlite import _SQLiteBatchWriter
-from biocypher.write.relational._postgresql import _PostgreSQLBatchWriter
+from biocypher.output.write.graph._rdf import _RDFWriter
+from biocypher.output.write.graph._neo4j import _Neo4jBatchWriter
+from biocypher.output.write.graph._arangodb import _ArangoDBBatchWriter
+from biocypher.output.write.graph._networkx import _NetworkXWriter
+from biocypher.output.write.relational._csv import _PandasCSVWriter
+from biocypher.output.write.relational._sqlite import _SQLiteBatchWriter
+from biocypher.output.write.relational._postgresql import _PostgreSQLBatchWriter
 
 logger.debug(f"Loading module {__name__}.")
 
@@ -46,6 +48,12 @@ DBMS_TO_CLASS = {
     "sqlite3": _SQLiteBatchWriter,
     "rdf": _RDFWriter,
     "RDF": _RDFWriter,
+    "csv": _PandasCSVWriter,
+    "CSV": _PandasCSVWriter,
+    "pandas": _PandasCSVWriter,
+    "Pandas": _PandasCSVWriter,
+    "networkx": _NetworkXWriter,
+    "NetworkX": _NetworkXWriter,
 }
 
 
@@ -61,19 +69,14 @@ def get_writer(
     file.
 
     Args:
-
         dbms: the database management system; for options, see DBMS_TO_CLASS.
-
         translator: the Translator object.
-
-        output_directory: the directory to write the output files to.
-
+        deduplicator: the Deduplicator object.
+        output_directory: the directory to output.write the output files to.
         strict_mode: whether to use strict mode.
 
     Returns:
-
         instance: an instance of the selected writer class.
-
     """
 
     dbms_config = _config(dbms)

biocypher/output/write/_writer.py

@@ -0,0 +1,200 @@
+from abc import ABC, abstractmethod
+from typing import Union, Optional
+from collections.abc import Iterable
+import os
+
+from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
+from biocypher._logger import logger
+from biocypher._translate import Translator
+from biocypher._deduplicate import Deduplicator
+
+__all__ = ["_Writer"]
+
+
+class _Writer(ABC):
+    """Abstract class for writing node and edge representations to disk.
+    Specifics of the different writers (e.g. neo4j, postgresql, csv, etc.)
+    are implemented in the child classes. Any concrete writer needs to
+    implement at least:
+    - _write_node_data
+    - _write_edge_data
+    - _construct_import_call
+    - _get_import_script_name
+
+    Args:
+        translator (Translator): Instance of :py:class:`Translator` to enable translation of
+            nodes and manipulation of properties.
+        deduplicator (Deduplicator): Instance of :py:class:`Deduplicator` to enable deduplication
+            of nodes and edges.
+        output_directory (str, optional): Path for exporting CSV files. Defaults to None.
+        strict_mode (bool, optional): Whether to enforce source, version, and license properties. Defaults to False.
+    strict_mode (bool, optional): Whether to enforce source, version, and license properties. Defaults to False.
+
+    Raises:
+        NotImplementedError: Writer implementation must override '_write_node_data'
+        NotImplementedError: Writer implementation must override '_write_edge_data'
+        NotImplementedError: Writer implementation must override '_construct_import_call'
+        NotImplementedError: Writer implementation must override '_get_import_script_name'
+    """
+
+    def __init__(
+        self,
+        translator: Translator,
+        deduplicator: Deduplicator,
+        output_directory: Optional[str] = None,
+        strict_mode: bool = False,
+        *args,
+        **kwargs,
+    ):
+        """Abstract class for writing node and edge representations to disk.
+
+        Args:
+            translator (Translator): Instance of :py:class:`Translator` to enable translation of
+                nodes and manipulation of properties.
+            deduplicator (Deduplicator): Instance of :py:class:`Deduplicator` to enable deduplication
+                of nodes and edges.
+            output_directory (str, optional): Path for exporting CSV files. Defaults to None.
+            strict_mode (bool, optional): Whether to enforce source, version, and license properties. Defaults to False.
+        strict_mode (bool, optional): Whether to enforce source, version, and license properties. Defaults to False.
+        """
+        self.translator = translator
+        self.deduplicator = deduplicator
+        self.strict_mode = strict_mode
+        self.output_directory = output_directory
+
+        if os.path.exists(self.output_directory):
+            if kwargs.get("write_to_file", True):
+                logger.warning(
+                    f"Output directory `{self.output_directory}` already exists. "
+                    "If this is not planned, file consistency may be compromised."
+                )
+        else:
+            logger.info(f"Creating output directory `{self.output_directory}`.")
+            os.makedirs(self.output_directory)
+
+    @abstractmethod
+    def _write_node_data(
+        self,
+        nodes: Iterable[
+            Union[BioCypherNode, BioCypherEdge, BioCypherRelAsNode]
+        ],
+    ) -> bool:
+        """Implement how to output.write nodes to disk.
+
+        Args:
+            nodes (Iterable): An iterable of BioCypherNode / BioCypherEdge / BioCypherRelAsNode objects.
+
+        Returns:
+            bool: The return value. True for success, False otherwise.
+        """
+        raise NotImplementedError(
+            "Writer implementation must override 'write_nodes'"
+        )
+
+    @abstractmethod
+    def _write_edge_data(
+        self,
+        edges: Iterable[
+            Union[BioCypherNode, BioCypherEdge, BioCypherRelAsNode]
+        ],
+    ) -> bool:
+        """Implement how to output.write edges to disk.
+
+        Args:
+            edges (Iterable): An iterable of BioCypherNode / BioCypherEdge / BioCypherRelAsNode objects.
+
+        Returns:
+            bool: The return value. True for success, False otherwise.
+        """
+        raise NotImplementedError(
+            "Writer implementation must override 'write_edges'"
+        )
+
+    @abstractmethod
+    def _construct_import_call(self) -> str:
+        """
+        Function to construct the import call detailing folder and
+        individual node and edge headers and data files, as well as
+        delimiters and database name. Built after all data has been
+        processed to ensure that nodes are called before any edges.
+
+        Returns:
+            str: command for importing the output files into a DBMS.
+        """
+        raise NotImplementedError(
+            "Writer implementation must override '_construct_import_call'"
+        )
+
+    @abstractmethod
+    def _get_import_script_name(self) -> str:
+        """Returns the name of the import script.
+
+        Returns:
+            str: The name of the import script (ending in .sh)
+        """
+        raise NotImplementedError(
+            "Writer implementation must override '_get_import_script_name'"
+        )
+
+    def write_nodes(
+        self, nodes, batch_size: int = int(1e6), force: bool = False
+    ):
+        """Wrapper for writing nodes.
+
+        Args:
+            nodes (BioCypherNode): a list or generator of nodes in
+                :py:class:`BioCypherNode` format
+            batch_size (int): The batch size for writing nodes.
+            force (bool): Whether to force writing nodes even if their type is
+                not present in the schema.
+
+        Returns:
+            bool: The return value. True for success, False otherwise.
+        """
+        passed = self._write_node_data(nodes)
+        if not passed:
+            logger.error("Error while writing node data.")
+            return False
+        return True
+
+    def write_edges(
+        self, edges, batch_size: int = int(1e6), force: bool = False
+    ):
+        """Wrapper for writing edges.
+
+        Args:
+            nodes (BioCypherNode): a list or generator of nodes in
+                :py:class:`BioCypherNode` format
+            batch_size (int): The batch size for writing nodes.
+            force (bool): Whether to force writing nodes even if their type is
+                not present in the schema.
+
+        Returns:
+            bool: The return value. True for success, False otherwise.
+        """
+        passed = self._write_edge_data(edges)
+        if not passed:
+            logger.error("Error while writing edge data.")
+            return False
+        return True
+
+    def write_import_call(self):
+        """
+        Function to output.write the import call detailing folder and
+        individual node and edge headers and data files, as well as
+        delimiters and database name, to the export folder as txt.
+
+        Returns:
+            str: The path of the file holding the import call.
+        """
+        file_path = os.path.join(
+            self.output_directory, self._get_import_script_name()
+        )
+        logger.info(
+            f"Writing {self.__class__.__name__} import call to `{file_path}`."
+        )
+
+        with open(file_path, "w", encoding="utf-8") as f:
+            f.write(self._construct_import_call())
+
+        return file_path

biocypher/{write → output/write}/graph/_arangodb.py

@@ -1,7 +1,7 @@
 import os
 
 from biocypher._logger import logger
-from biocypher.write.graph._neo4j import _Neo4jBatchWriter
+from biocypher.output.write.graph._neo4j import _Neo4jBatchWriter
 
 
 class _ArangoDBBatchWriter(_Neo4jBatchWriter):

biocypher/{write → output/write}/graph/_neo4j.py

@@ -1,9 +1,7 @@
 import os
-import re
-import subprocess
 
 from biocypher._logger import logger
-from biocypher.write._batch_writer import parse_label, _BatchWriter
+from biocypher.output.write._batch_writer import parse_label, _BatchWriter
 
 
 class _Neo4jBatchWriter(_BatchWriter):
@@ -49,7 +47,7 @@ class _Neo4jBatchWriter(_BatchWriter):
 
     def _write_array_string(self, string_list):
         """
-        Abstract method to write the string representation of an array into a .csv file
+        Abstract method to output.write the string representation of an array into a .csv file
         as required by the neo4j admin-import.
 
         Args:
@@ -303,11 +301,13 @@ class _Neo4jBatchWriter(_BatchWriter):
         Returns:
             str: The import call.
         """
-        import_call = (
-            f"{self.import_call_bin_prefix}neo4j-admin {import_cmd} "
-            f'--delimiter="{self.escaped_delim}" '
-            f'--array-delimiter="{self.escaped_adelim}" '
-        )
+        import_call = f"{self.import_call_bin_prefix}neo4j-admin {import_cmd} "
+
+        import_call += f"{database_cmd}{self.db_name} "
+
+        import_call += f'--delimiter="{self.escaped_delim}" '
+
+        import_call += f'--array-delimiter="{self.escaped_adelim}" '
 
         if self.quote == "'":
             import_call += f'--quote="{self.quote}" '
@@ -329,6 +329,4 @@ class _Neo4jBatchWriter(_BatchWriter):
         for header_path, parts_path in self.import_call_edges:
             import_call += f'--relationships="{header_path},{parts_path}" '
 
-        # Database needs to be at the end starting with Neo4j 5.0+.
-        import_call += f"{database_cmd}{self.db_name} "
         return import_call

biocypher/output/write/graph/_networkx.py

@@ -0,0 +1,76 @@
+import pickle
+
+import networkx as nx
+
+from biocypher._logger import logger
+from biocypher.output.write._writer import _Writer
+from biocypher.output.write.relational._csv import _PandasCSVWriter
+
+
+class _NetworkXWriter(_Writer):
+    """
+    Class for writing node and edges to a networkx DiGraph.
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.csv_writer = _PandasCSVWriter(*args, write_to_file=False, **kwargs)
+        self.G = nx.DiGraph()
+
+    def _construct_import_call(self) -> str:
+        """Function to construct the Python code to load all node and edge csv files again into Pandas dfs.
+
+        Returns:
+            str: Python code to load the csv files into Pandas dfs.
+        """
+        logger.info(
+            f"Writing networkx {self.G} to pickle file networkx_graph.pkl."
+        )
+        with open(f"{self.output_directory}/networkx_graph.pkl", "wb") as f:
+            pickle.dump(self.G, f)
+
+        import_call = "import pickle\n"
+        import_call += "with open('./networkx_graph.pkl', 'rb') as f:\n\tG_loaded = pickle.load(f)"
+        return import_call
+
+    def _get_import_script_name(self) -> str:
+        """Function to return the name of the import script."""
+        return "import_networkx.py"
+
+    def _write_node_data(self, nodes) -> bool:
+        passed = self.csv_writer._write_entities_to_file(nodes)
+        self.add_to_networkx()
+        return passed
+
+    def _write_edge_data(self, edges) -> bool:
+        passed = self.csv_writer._write_entities_to_file(edges)
+        self.add_to_networkx()
+        return passed
+
+    def add_to_networkx(self) -> bool:
+        all_dfs = self.csv_writer.stored_dfs
+        node_dfs = [
+            df
+            for df in all_dfs.values()
+            if df.columns.str.contains("node_id").any()
+        ]
+        edge_dfs = [
+            df
+            for df in all_dfs.values()
+            if df.columns.str.contains("source_id").any()
+            and df.columns.str.contains("target_id").any()
+        ]
+        for df in node_dfs:
+            nodes = df.set_index("node_id").to_dict(orient="index")
+            self.G.add_nodes_from(nodes.items())
+        for df in edge_dfs:
+            edges = df.set_index(["source_id", "target_id"]).to_dict(
+                orient="index"
+            )
+            self.G.add_edges_from(
+                (
+                    (source, target, attrs)
+                    for (source, target), attrs in edges.items()
+                )
+            )
+        return True

biocypher/{write → output/write}/graph/_rdf.py

@@ -24,11 +24,10 @@ from rdflib.namespace import (
 
 from biocypher._create import BioCypherEdge, BioCypherNode
 from biocypher._logger import logger
-from biocypher.write._batch_writer import _BatchWriter
+from biocypher.output.write._batch_writer import _BatchWriter
 
 
 class _RDFWriter(_BatchWriter):
-
     """
     Class to write BioCypher's property graph into an RDF format using
     rdflib and all the extensions it supports (RDF/XML, N3, NTriples,
@@ -125,7 +124,7 @@ class _RDFWriter(_BatchWriter):
 
         # create file name
         file_name = os.path.join(
-            self._outdir, f"{label_pascal}.{self.extension}"
+            self.outdir, f"{label_pascal}.{self.extension}"
         )
 
         # write data in graph
@@ -287,7 +286,7 @@ class _RDFWriter(_BatchWriter):
 
         # create file name
         file_name = os.path.join(
-            self._outdir, f"{label_pascal}.{self.extension}"
+            self.outdir, f"{label_pascal}.{self.extension}"
         )
 
         # write data in graph

biocypher/output/write/relational/_csv.py

@@ -0,0 +1,76 @@
+from more_itertools import peekable
+
+from biocypher._logger import logger
+from biocypher.output.write._writer import _Writer
+from biocypher.output.in_memory._pandas import Pandas
+
+
+class _PandasCSVWriter(_Writer):
+    """
+    Class for writing node and edge representations to a CSV file.
+    """
+
+    def __init__(self, *args, write_to_file: bool = True, **kwargs):
+        kwargs["write_to_file"] = write_to_file
+        super().__init__(*args, **kwargs)
+        self.in_memory_dfs = {}
+        self.stored_dfs = {}
+        self.pandas_in_memory = Pandas(
+            translator=self.translator,
+            deduplicator=self.deduplicator,
+        )
+        self.delimiter = kwargs.get("delimiter")
+        if not self.delimiter:
+            self.delimiter = ","
+        self.write_to_file = write_to_file
+
+    def _construct_import_call(self) -> str:
+        """Function to construct the Python code to load all node and edge csv files again into Pandas dfs.
+
+        Returns:
+            str: Python code to load the csv files into Pandas dfs.
+        """
+        import_call = "import pandas as pd\n\n"
+        for df_name in self.stored_dfs.keys():
+            import_call += f"{df_name} = pd.read_csv('./{df_name}.csv', header=0, index_col=0)\n"
+        return import_call
+
+    def _get_import_script_name(self) -> str:
+        """Function to return the name of the import script."""
+        return "import_pandas_csv.py"
+
+    def _write_node_data(self, nodes) -> bool:
+        passed = self._write_entities_to_file(nodes)
+        return passed
+
+    def _write_edge_data(self, edges) -> bool:
+        passed = self._write_entities_to_file(edges)
+        return passed
+
+    def _write_entities_to_file(self, entities: iter) -> bool:
+        """Function to output.write the entities to a CSV file.
+
+        Args:
+            entities (iterable): An iterable of BioCypherNode / BioCypherEdge / BioCypherRelAsNode objects.
+        """
+        entities = peekable(entities)
+        entity_list = self.pandas_in_memory._separate_entity_types(entities)
+        for entity_type, entities in entity_list.items():
+            self.in_memory_dfs[
+                entity_type
+            ] = self.pandas_in_memory._add_entity_df(entity_type, entities)
+        for entity_type in self.in_memory_dfs.keys():
+            entity_df = self.in_memory_dfs[entity_type]
+            if " " in entity_type or "." in entity_type:
+                entity_type = entity_type.replace(" ", "_").replace(".", "_")
+            if self.write_to_file:
+                logger.info(
+                    f"Writing {entity_df.shape[0]} entries to {entity_type}.csv."
+                )
+                entity_df.to_csv(
+                    f"{self.output_directory}/{entity_type}.csv",
+                    sep=self.delimiter,
+                )
+            self.stored_dfs[entity_type] = entity_df
+        self.in_memory_dfs = {}
+        return True

biocypher/{write → output/write}/relational/_postgresql.py

@@ -2,7 +2,7 @@ import os
 import glob
 
 from biocypher._logger import logger
-from biocypher.write._batch_writer import _BatchWriter
+from biocypher.output.write._batch_writer import _BatchWriter
 
 
 class _PostgreSQLBatchWriter(_BatchWriter):
@@ -59,7 +59,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
 
     def _write_array_string(self, string_list) -> str:
         """
-        Abstract method to write the string representation of an array into a .csv file
+        Abstract method to output.write the string representation of an array into a .csv file
         as required by the postgresql COPY command, with '{','}' brackets and ',' separation.
 
         Args:

biocypher/{write → output/write}/relational/_sqlite.py

@@ -1,4 +1,4 @@
-from biocypher.write.relational._postgresql import _PostgreSQLBatchWriter
+from biocypher.output.write.relational._postgresql import _PostgreSQLBatchWriter
 
 
 class _SQLiteBatchWriter(_PostgreSQLBatchWriter):

{biocypher-0.5.42.dist-info → biocypher-0.5.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.5.42
+Version: 0.5.44
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT

biocypher-0.5.44.dist-info/RECORD

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biocypher-0.5.42.dist-info/RECORD

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