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:
closuredownload: Downloads data defined in download.yamlexportjsonlmerge: Merge nodes and edges into kgrelease: Copy data to Monarch GCP data bucketssolrsqlitetransform: Run Koza transformation on specified...
ingest closure
Usage:
$ ingest closure [OPTIONS]
Options:
--help: Show this message and exit.
ingest download
Downloads data defined in download.yaml
Usage:
$ ingest download [OPTIONS]
Options:
--ingests TEXT: Which ingests to download data for--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 export
Usage:
$ ingest export [OPTIONS]
Options:
--help: Show this message and exit.
ingest jsonl
Usage:
$ ingest jsonl [OPTIONS]
Options:
--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--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.
ingest solr
Usage:
$ ingest solr [OPTIONS]
Options:
--help: Show this message and exit.
ingest sqlite
Usage:
$ ingest sqlite [OPTIONS]
Options:
--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)--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.