KGX CLI¶

Knowledge Graph Exchange CLI entrypoint.

KGX CLI [OPTIONS] COMMAND [ARGS]...

Options

--debug¶: Prints the stack trace if error occurs

--version¶: Show the version and exit.

edge-summary¶

Loads and summarizes a knowledge graph edge set, where the input is a file.

KGX CLI edge-summary [OPTIONS] FILEPATH

Options

--input-type <input_type>¶

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

-m, --max_rows <max_rows>¶: The maximum number of rows to return

-o, --output <output>¶

Arguments

FILEPATH¶: Required argument

load-and-merge¶

Load nodes and edges from files and KGs, as defined in a config YAML, and merge them into a single graph. The merge happens in-memory. This merged graph can then be written to a local/remote Neo4j instance OR be serialized into a file.

KGX CLI load-and-merge [OPTIONS] LOAD_CONFIG

Arguments

LOAD_CONFIG¶: Required argument

neo4j-download¶

Download nodes and edges from Neo4j database.

KGX CLI neo4j-download [OPTIONS]

Options

-a, --address <address>¶: [required]

-u, --username <username>¶: [required]

-p, --password <password>¶: [required]

-o, --output <output>¶: [required]

--output-type <output_type>¶

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

--subject-label <subject_label>¶

--object-label <object_label>¶

--edge-label <edge_label>¶

--directed <directed>¶: Whether the edges are directed

--stop-after <stop_after>¶: Once this many edges are downloaded the application will finish

--page-size <page_size>¶: The size of pages to download for each batch

neo4j-edge-summary¶

Get a summary of all the edges in a Neo4j database.

KGX CLI neo4j-edge-summary [OPTIONS]

Options

-a, --address <address>¶: [required]

-u, --username <username>¶: [required]

-p, --password <password>¶: [required]

-o, --output <output>¶

neo4j-node-summary¶

Get a summary of all the nodes in a Neo4j database.

KGX CLI neo4j-node-summary [OPTIONS]

Options

-a, --address <address>¶: [required]

-u, --username <username>¶: [required]

-p, --password <password>¶: [required]

-o, --output <output>¶

neo4j-upload¶

Upload a set of nodes/edges to a Neo4j database.

KGX CLI neo4j-upload [OPTIONS] INPUTS...

Options

--input-type <input_type>¶

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

--use-unwind¶: Loads using UNWIND cypher clause, which is quicker

-a, --address <address>¶: [required]

-u, --username <username>¶

-p, --password <password>¶

Arguments

INPUTS¶: Required argument(s)

node-summary¶

Loads and summarizes a knowledge graph node set, where the input is a file.

KGX CLI node-summary [OPTIONS] FILEPATH

Options

--input-type <input_type>¶

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

-m, --max-rows <max_rows>¶: The maximum number of rows to return

-o, --output <output>¶

Arguments

FILEPATH¶: Required argument

transform¶

Transform a Knowledge Graph from one serialization form to another.

KGX CLI transform [OPTIONS] INPUTS...

Options

--input-type <input_type>¶

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

-o, --output <output>¶: [required]

--output-type <output_type>¶

[required]

Options: tar|txt|csv|tsv|graphml|ttl|json|rq|owl

--mapping <mapping>¶

--preserve¶

Arguments

INPUTS¶: Required argument(s)

validate¶

Run KGX validation on an input file to check for BioLink Model compliance.

KGX CLI validate [OPTIONS] PATH

Options

-o, --output <output>¶: The path to a text file to append the output to. [required]

-d, --output-dir <output_dir>¶: The path to a directory to save a series of text files to.

Arguments

PATH¶: Required argument