From 71f26eab744d1a139c3403eeb0c0b63c3b2307b0 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 11 May 2023 12:19:59 -0700 Subject: [PATCH] add examples to readme of running key functionality from command line --- README.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/README.md b/README.md index 047344b1..dd3bfac6 100644 --- a/README.md +++ b/README.md @@ -32,6 +32,27 @@ The structure of this graph is expected to conform to the Biolink Model standard In addition to the main code-base, KGX also provides a series of [command line operations](https://kgx.readthedocs.io/en/latest/examples.html#using-kgx-cli). +### Example usage +Validate: +```bash +poetry run kgx validate -i tsv tests/resources/merge/test2_nodes.tsv tests/resources/merge/test2_edges.tsv +``` + +Merge: +```bash +poetry run kgx merge —merge-config tests/resources/test-merge.yaml +``` + +Graph Summary: +```bash +poetry run kgx graph-summary -i tests/resources/graph_nodes.tsv -o summary.txt +``` + +Transform: +```bash +poetry run kgx transform —transform-config tests/resources/test-transform-tsv-rdf.yaml +``` + ### Error Detection and Reporting Non-redundant JSON-formatted structured error logging is now provided in KGX Transformer, Validator, GraphSummary and MetaKnowledgeGraph operations. See the various unit tests for the general design pattern (using the Validator as an example here):