ingest
Usage:
$ ingest [OPTIONS] COMMAND [ARGS]...
Options:
--version--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.
Commands:
download: Downloads data defined in download.yamltransform: Run Koza transformation on specified...merge: Merge nodes and edges into kgclosurejsonlneo4j-csvsqlitesolrexportreport: Run Koza QC on specified Monarch ingestsgraph-stats: Generate graph statistics from merged KG...release: Copy data to Monarch GCP data buckets
ingest download
Downloads data defined in download.yaml
Usage:
$ ingest download [OPTIONS]
Options:
-i, --ingest TEXT: Run a single ingest (see download.yaml for a list)--ingests TEXT: Which ingests to download data for--ingest_file PATH: A yaml file which has a newline seperated list of ingests to perform.--all / --no-all: Download all ingest datasets [default: no-all]--write-metadata / --no-write-metadata: Write versions of ingests to metadata.yaml [default: no-write-metadata]--help: Show this message and exit.
ingest transform
Run Koza transformation on specified Monarch ingests
Usage:
$ ingest transform [OPTIONS]
Options:
-o, --output-dir TEXT: Directory to output data [default: output]-i, --ingest TEXT: Run a single ingest (see ingests.yaml for a list)--ingests TEXT: Which ingests to download data for--ingest_file PATH: A yaml file which has a newline seperated list of ingests to perform.--phenio / --no-phenio: Run the phenio transform [default: no-phenio]-a, --all: Ingest all sources-f, --force: Force ingest, even if output exists (on by default for single ingests)--rdf / --no-rdf: Output rdf files along with tsv [default: no-rdf]-d, --debug / -q, --quiet: Use --quiet to suppress log output, --debug for verbose, including Koza logs-l, --log: Write DEBUG level logs to ./logs/ for each ingest-n, --row-limit INTEGER: Number of rows to process--write-metadata / --no-write-metadata: Write data/package versions to output_dir/metadata.yaml [default: no-write-metadata]--help: Show this message and exit.
ingest merge
Merge nodes and edges into kg
Usage:
$ ingest merge [OPTIONS]
Options:
--input-dir TEXT: Directory with nodes and edges to be merged [default: output/transform_output]--output-dir TEXT: Directory to output data [default: output]-d, --debug / -q, --quiet: Use --quiet to suppress log output, --debug for verbose--closure / --no-closure: Apply closure to merged graph [default: no-closure]--kg-name, --kg_name TEXT: The name of the kg being produced. Merge artificat will be ultimately be stored in output/$KG_NAME.tar.gz [default: monarch-kg]--help: Show this message and exit.
ingest closure
Usage:
$ ingest closure [OPTIONS]
Options:
--help: Show this message and exit.
ingest jsonl
Usage:
$ ingest jsonl [OPTIONS]
Options:
--help: Show this message and exit.
ingest neo4j-csv
Usage:
$ ingest neo4j-csv [OPTIONS]
Options:
--help: Show this message and exit.
ingest sqlite
Usage:
$ ingest sqlite [OPTIONS]
Options:
--help: Show this message and exit.
ingest solr
Usage:
$ ingest solr [OPTIONS]
Options:
--help: Show this message and exit.
ingest export
Usage:
$ ingest export [OPTIONS]
Options:
--help: Show this message and exit.
ingest report
Run Koza QC on specified Monarch ingests
Usage:
$ ingest report [OPTIONS]
Options:
--help: Show this message and exit.
ingest graph-stats
Generate graph statistics from merged KG database
Usage:
$ ingest graph-stats [OPTIONS]
Options:
-i, --input-db TEXT: Path to input DuckDB database [default: output/monarch-kg.duckdb]-o, --output TEXT: Output YAML file path [default: output/merged_graph_stats.yaml]-b, --backend TEXT: Backend to use: 'koza' (new) or 'kgx' (legacy) [default: koza]--help: Show this message and exit.
ingest release
Copy data to Monarch GCP data buckets
Usage:
$ ingest release [OPTIONS]
Options:
--dir TEXT: Directory with kg to be released [default: output]--kghub / --no-kghub: Also release to kghub S3 bucket [default: no-kghub]--help: Show this message and exit.