Title: Interface for the 'Neo4j Bolt' Protocol
Version: 1.4.0
Description: Querying, extracting, and processing large-scale network data from Neo4j databases using the 'Neo4j Bolt' https://neo4j.com/docs/bolt/current/bolt/ protocol. This interface supports efficient data retrieval, batch processing for large datasets, and seamless conversion of query results into R data frames, making it ideal for bioinformatics, computational biology, and other graph-based applications.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (≥ 4.1.0)
Imports: data.table, glue, purrr, reticulate
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-22 23:55:09 UTC; wanjun
Author: Wanjun Gu ORCID iD [aut, cre]
Maintainer: Wanjun Gu <wanjun.gu@ucsf.edu>
Repository: CRAN
Date/Publication: 2025-02-25 11:50:02 UTC

Convert a Query Result into a Data Frame

Description

This function takes a query result object and transforms it into a data frame with specified field names. For each entry in the query result, it attempts to extract values corresponding to the given field names. If a particular field does not exist in the entry, it is replaced with NA.

Usage

convert_df(
  query_result,
  field_names = c("node_id", "n.identifier", "n.name", "n.source")
)

Arguments

query_result

A list (or similar structure) representing the query result, typically containing entries from which fields can be extracted.

field_names

A character vector of field names to be extracted from each entry in query_result. Defaults to c("node_id", "n_identifier", "n.name", "n.source").

Value

A data frame with one row per entry in query_result, and columns corresponding to the specified field_names. Missing fields are filled with NA.

Examples


# Suppose query_result is a list of named lists:
query_result = list(
  list(node_id = 1, n = list(identifier = 1, name = "some node", source = "internet")),
  list(node_id = 2, n = list(identifier = 2, name = "some other node", source = "library"))
)

query_result_df = convert_df(
  query_result,
  field_names = c("node_id", "n.identifier", "n.name", "n.source")
)

Batch Query and Save Data from Neo4j

Description

This function performs batch queries to a Neo4j database and appends the results to a TSV file.

Usage

run_batch_query(
  uri,
  user,
  password,
  query,
  field_names,
  filename = NULL,
  batch_size = 1000
)

Arguments

uri

A string specifying the URI for the Neo4j database connection.

user

A string specifying the username for the Neo4j database.

password

A string specifying the password for the Neo4j database.

query

A string containing the Cypher query to execute. The query should not include SKIP or LIMIT, as these are appended for batching.

field_names

A character vector specifying the column names to use for the resulting data.

filename

A string specifying the name of the TSV file to save the results. If NULL, a temporary file will be used.

batch_size

An integer specifying the number of records to fetch per batch. Default is 1000.

Value

No return value, called for side effects.

Examples

## Not run: 
run_batch_query(
  uri = "bolt://localhost:7687",
  user = "<Username for Neo4j>",
  password = "<Password for Neo4j>",
  query = "MATCH (n) RETURN n LIMIT 10",
  field_names = c("id", "name"),
  filename = NULL,  # Writes to a temp file by default
  batch_size = 1000
)

## End(Not run)

Connect to Neo4j and Run a Simple Query

Description

This function demonstrates connecting to a Neo4j database via the Python neo4j driver and using pandas to manipulate the returned data.

Usage

run_query(uri, user, password, query)

Arguments

uri

Neo4j URI, e.g., "bolt://localhost:7687"

user

Username for Neo4j

password

Password for Neo4j

query

A Cypher query to execute, e.g. "MATCH (n) RETURN n LIMIT 5"

Value

A data.frame containing the query results.

Set up the Conda environment for bolt4jr

Description

This function initializes the Conda environment required for the bolt4jr package. If no Conda binary is found, it installs Miniconda. If the required Conda environment (bolt4jr) is not found, it creates the environment and installs the necessary dependencies.

Usage

setup_bolt4jr()

Details

The function ensures that:

Call this function manually before using any functionality that relies on Python.

Value

No return value, called for side effects.