make sure loculus is not called in unit tests

loculus-project · Sep 23, 2024 · cd19482 · cd19482
1 parent ca0d0d9
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diff --git a/ingest/README.md b/ingest/README.md
@@ -138,7 +138,14 @@ The ingest pipeline requires config files, found in the directory `config`. The
 
 ## Testing
 
-Currently, there is not automated testing other than running the pipeline manually and in preview deployments.
+Tests can be found in the `tests` folder, they can be run using
+
+```sh
+micromamba activate loculus-ingest
+pytest tests/
+```
+
+`.github/workflows/ingest-tests.yaml` runs these tests,
 
 ## Roadmap
 

diff --git a/ingest/tests/test_ingest.py b/ingest/tests/test_ingest.py
@@ -62,6 +62,7 @@ def test_snakemake():
     destination_directory = CONFIG_DIR
     source_directory = TEST_DATA_DIR / "config_cchf"
     copy_files(source_directory, destination_directory)
+    run_snakemake("get_loculus_submissions", touch=True)  # Do not call_loculus
     run_snakemake("group_segments")
     run_snakemake("get_previous_submissions", touch=True)  # Do not call_loculus
     run_snakemake("compare_hashes")