Output Writing
Writer Retrieval
Return the writer class based on the selection in the config file.
dbms: the database management system; for options, see DBMS_TO_CLASS.
translator: the Translator object.
deduplicator: the Deduplicator object.
output_directory: the directory to output.write the output files to.
strict_mode: whether to use strict mode.
instance: an instance of the selected writer class.
Source code in biocypher/output/write/_get_writer.py
Writer Base Class
Bases: 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
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.
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'
Source code in biocypher/output/write/_writer.py
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__init__(translator, deduplicator, output_directory=None, strict_mode=False, *args, **kwargs)
Abstract class for writing node and edge representations to disk.
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.
Source code in biocypher/output/write/_writer.py
write_edges(edges, batch_size=int(1000000.0), force=False)
Wrapper for writing edges.
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.
bool: The return value. True for success, False otherwise.
Source code in biocypher/output/write/_writer.py
write_import_call()
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.
Source code in biocypher/output/write/_writer.py
write_nodes(nodes, batch_size=int(1000000.0), force=False)
Wrapper for writing nodes.
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.
bool: The return value. True for success, False otherwise.
Source code in biocypher/output/write/_writer.py
Batch Writer Base Class
Bases: _Writer
, ABC
Abstract batch writer class.
Source code in biocypher/output/write/_batch_writer.py
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import_call_file_prefix
property
Property for output directory path.
__init__(translator, deduplicator, delimiter, array_delimiter=',', quote='"', output_directory=None, db_name='neo4j', import_call_bin_prefix=None, import_call_file_prefix=None, wipe=True, strict_mode=False, skip_bad_relationships=False, skip_duplicate_nodes=False, db_user=None, db_password=None, db_host=None, db_port=None, file_format=None, rdf_namespaces={}, labels_order='Ascending', **kwargs)
Write node and edge representations to disk.
Abstract parent class for writing node and edge representations to disk using the format specified by each database type. The database-specific functions are implemented by the respective child-classes. This abstract class contains all methods expected by a bach writer instance, some of which need to be overwritten by the child classes.
Each batch writer instance has a fixed representation that needs to be
passed at instantiation via the attr:
schema
argument. The instance
also expects an ontology adapter via attr:
ontology_adapter
to be
able to convert and extend the hierarchy.
Requires the following methods to be overwritten by database-specific writer classes:
- _write_node_headers
- _write_edge_headers
- _construct_import_call
- _write_array_string
- _get_import_script_name
translator:
Instance of :py:class:`Translator` to enable translation of
nodes and manipulation of properties.
deduplicator:
Instance of :py:class:`Deduplicator` to enable deduplication
of nodes and edges.
delimiter:
The delimiter to use for the CSV files.
array_delimiter:
The delimiter to use for array properties.
quote:
The quote character to use for the CSV files.
output_directory:
Path for exporting CSV files.
db_name:
Name of the database that will be used in the generated
commands.
import_call_bin_prefix:
Path prefix for the admin import call binary.
import_call_file_prefix:
Path prefix for the data files (headers and parts) in the import
call.
wipe:
Whether to force import (removing existing DB content).
(Specific to Neo4j.)
strict_mode:
Whether to enforce source, version, and license properties.
skip_bad_relationships:
Whether to skip relationships that do not have a valid
start and end node. (Specific to Neo4j.)
skip_duplicate_nodes:
Whether to skip duplicate nodes. (Specific to Neo4j.)
db_user:
The database user.
db_password:
The database password.
db_host:
The database host. Defaults to localhost.
db_port:
The database port.
file_format:
The format of RDF.
rdf_namespaces:
The namespaces for RDF.
labels_order:
The order of labels, to reflect the hierarchy (or not).
Default: "Ascending" (from more specific to more generic).
Source code in biocypher/output/write/_batch_writer.py
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get_import_call()
Eeturn the import call.
Return the import call detailing folder and individual node and edge headers and data files, as well as delimiters and database name.
Returns
str: a bash command for the database import
Source code in biocypher/output/write/_batch_writer.py
write_edges(edges, batch_size=int(1000000.0))
Write edges and their headers.
edges (BioCypherEdge): a list or generator of edges in
:py:class:`BioCypherEdge` or :py:class:`BioCypherRelAsNode`
format
bool: The return value. True for success, False otherwise.
Source code in biocypher/output/write/_batch_writer.py
write_import_call()
Write the import call.
Function to 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.
Source code in biocypher/output/write/_batch_writer.py
write_nodes(nodes, batch_size=int(1000000.0), force=False)
Write nodes and their headers.
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.
bool: The return value. True for success, False otherwise.
Source code in biocypher/output/write/_batch_writer.py
Neo4j Batch Writer
Bases: _BatchWriter
Class for writing node and edge representations to disk using the
format specified by Neo4j for the use of admin import. Each batch
writer instance has a fixed representation that needs to be passed
at instantiation via the attr:
schema
argument. The instance
also expects an ontology adapter via attr:
ontology_adapter
to be able
to convert and extend the hierarchy.
This class inherits from the abstract class "_BatchWriter" and implements the Neo4j-specific methods:
- _write_node_headers
- _write_edge_headers
- _construct_import_call
- _write_array_string
Source code in biocypher/output/write/graph/_neo4j.py
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__init__(*args, **kwargs)
Constructor.
Check the version of Neo4j and adds a command scope if version >= 5.
Returns
_Neo4jBatchWriter: An instance of the writer.
Source code in biocypher/output/write/graph/_neo4j.py
ArangoDB Batch Writer
Bases: _Neo4jBatchWriter
Class for writing node and edge representations to disk.
Uses the format specified by ArangoDB for the use of "arangoimport". Output files are similar to Neo4j, but with a different header format.
Source code in biocypher/output/write/graph/_arangodb.py
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RDF Writer
Bases: _BatchWriter
Write BioCypher's property graph into an RDF format.
Uses rdflib
and all the extensions it supports (RDF/XML, N3, NTriples,
N-Quads, Turtle, TriX, Trig and JSON-LD). By default, the conversion
is done keeping only the minimum information about node and edges,
skipping all properties.
Source code in biocypher/output/write/graph/_rdf.py
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add_property_to_graph(graph, rdf_subject, rdf_object, rdf_predicate)
Add the properties to an RDF node.
It takes the graph, the subject, object, and predicate of the RDF triple. It checks if the property is a list and adds it to the graph accordingly. Otherwise it checks if the string represents a list. If it does, it transforms it to a list and adds it to the graph. If not, it adds the property to the graph as a literal. If the property is neither a list or string, it will also be added as a literal.
graph (RDFLib.Graph): The RDF graph to add the nodes to.
rdf_subject (str): The subject of the RDF triple.
rdf_object (str): The object of the RDF triple.
rdf_predicate (str): The predicate of the RDF triple.
None
Source code in biocypher/output/write/graph/_rdf.py
as_uri(name, namespace='')
Return an RDFlib object with the given namespace as a URI.
There is often a default for empty namespaces, which would have been
loaded with the ontology, and put in self.namespace
by
self._init_namespaces
.
name (str): The name to be transformed.
namespace (str): The namespace to be used.
str: The URI for the given name and namespace.
Source code in biocypher/output/write/graph/_rdf.py
property_to_uri(property_name)
Convert a property name to its corresponding URI.
This function takes a property name and searches for its corresponding URI in various namespaces. It first checks the core namespaces for rdflib, including owl, rdf, rdfs, xsd, and xml.
property_name (str): The property name to be converted to a URI.
str: The corresponding URI for the input property name.
Source code in biocypher/output/write/graph/_rdf.py
to_uri(subject)
Extract the namespace from the given subject.
Split the subject's string on ":". Then convert the subject to a proper URI, if the namespace is known. If namespace is unknown, defaults to the default prefix of the ontology.
subject (str): The subject to be converted to a URI.
str: The corresponding URI for the subject.
Source code in biocypher/output/write/graph/_rdf.py
transform_string_to_list(string_list)
Transform a string representation of a list into a list.
string_list (str): The string representation of the list.
list: The list representation of the input string.
Source code in biocypher/output/write/graph/_rdf.py
write_edges(edges, batch_size=int(1000000.0))
Write edges in RDF format.
edges (BioCypherEdge): a list or generator of edges in
:py:class:`BioCypherEdge` format
batch_size (int): The number of edges to write in each batch.
bool: The return value. True for success, False otherwise.
Source code in biocypher/output/write/graph/_rdf.py
write_nodes(nodes, batch_size=int(1000000.0), force=False)
Write nodes in RDF format.
nodes (list or generator): A list or generator of nodes in
BioCypherNode format.
batch_size (int): The number of nodes to write in each batch.
force (bool): Flag to force the writing even if the output file
already exists.
bool: True if the writing is successful, False otherwise.
Source code in biocypher/output/write/graph/_rdf.py
NetworkX Writer
Bases: _Writer
Class for writing the in-memory networkx DiGraph to file.
Call _construct_import_call
to write the networkx DiGraph to a pickle
file and return the Python call to load it.
TODO: this is a non-intuitive name, should be adjusted.
Source code in biocypher/output/write/graph/_networkx.py
PostgreSQL Batch Writer
Bases: _BatchWriter
Write node and edge representations for PostgreSQL.
Class for writing node and edge representations to disk using the
format specified by PostgreSQL for the use of "COPY FROM...". Each batch
writer instance has a fixed representation that needs to be passed
at instantiation via the attr:
schema
argument. The instance
also expects an ontology adapter via attr:
ontology_adapter
to be able
to convert and extend the hierarchy.
This class inherits from the abstract class "_BatchWriter" and implements the PostgreSQL-specific methods:
- _write_node_headers
- _write_edge_headers
- _construct_import_call
- _write_array_string
Source code in biocypher/output/write/relational/_postgresql.py
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SQLite Batch Writer
Bases: _PostgreSQLBatchWriter
Class for writing node and edge representations to a SQLite database. It uses the _PostgreSQLBatchWriter class under the hood, which already implements the logic to write the nodes/edges to a relational DBMS. Only the import bash script differs between PostgreSQL and SQLite and is therefore implemented in this class.
- _construct_import_call
Source code in biocypher/output/write/relational/_sqlite.py
Pandas CSV Writer
Bases: _Writer
Class for writing node and edge representations to CSV files.