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clades: Add test for --skip-validation
Note: I didn't actually use a command to generate `aa_muts_generated_by.json`. I just copied the "generated_by" entry from another JSON file.
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Integration tests for augur clades. | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Node-data JSONs produced from a different major version of augur | ||
are not allowed. | ||
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$ ${AUGUR} clades \ | ||
> --tree "$TESTDIR/../data/tree.nwk" \ | ||
> --mutations "$TESTDIR/../data/aa_muts_generated_by.json" \ | ||
> --clades "$TESTDIR/../data/clades.tsv" \ | ||
> --output-node-data clades.json | ||
ERROR: Augur version incompatibility detected: the JSON .*aa_muts_generated_by\.json.* was generated by \{'program': 'augur', 'version': '21.1.0'\}, which is incompatible with the current augur version \([.0-9]+\). We suggest you rerun the pipeline using the current version of augur. (re) | ||
[2] | ||
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Skipping validation allows mismatched augur versions to be used without error. | ||
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$ ${AUGUR} clades \ | ||
> --tree "$TESTDIR/../data/tree.nwk" \ | ||
> --mutations "$TESTDIR/../data/aa_muts_generated_by.json" \ | ||
> --clades "$TESTDIR/../data/clades.tsv" \ | ||
> --output-node-data clades.json \ | ||
> --skip-validation &>/dev/null |
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{ | ||
"generated_by": { | ||
"program": "augur", | ||
"version": "21.1.0" | ||
}, | ||
"nodes": { | ||
"BRA/2016/FC_6706": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"COL/FLR_00008/2015": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"L169I", | ||
"G292E" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"Colombia/2016/ZC204Se": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [ | ||
"N17K" | ||
] | ||
} | ||
}, | ||
"DOM/2016/BB_0183": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"D208G" | ||
], | ||
"NS2A": [ | ||
"L152M" | ||
], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"I322V", | ||
"Q650R", | ||
"D878E" | ||
], | ||
"PRO": [] | ||
} | ||
}, | ||
"EcEs062_16": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"HND/2016/HU_ME59": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"G100A" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [ | ||
"M572L" | ||
], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"R525C" | ||
], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000001": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [ | ||
"D107E" | ||
], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"R324W" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"T833A" | ||
], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000002": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"M349V" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000003": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000004": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000005": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000006": { | ||
"aa_muts": {} | ||
}, | ||
"NODE_0000007": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"NODE_0000008": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"PAN/CDC_259359_V1_V3/2015": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [ | ||
"M32I" | ||
], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [], | ||
"PRO": [] | ||
} | ||
}, | ||
"PRVABC59": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [ | ||
"I80T" | ||
], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"A91V" | ||
], | ||
"PRO": [] | ||
} | ||
}, | ||
"VEN/UF_1/2016": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [ | ||
"E76D" | ||
], | ||
"ENV": [], | ||
"MP": [], | ||
"NS1": [ | ||
"T301P" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"A833T" | ||
], | ||
"PRO": [] | ||
} | ||
}, | ||
"ZKC2/2016": { | ||
"aa_muts": { | ||
"2K": [], | ||
"CA": [ | ||
"S109N" | ||
], | ||
"ENV": [ | ||
"K419R" | ||
], | ||
"MP": [], | ||
"NS1": [ | ||
"R324Q" | ||
], | ||
"NS2A": [], | ||
"NS2B": [], | ||
"NS3": [], | ||
"NS4A": [], | ||
"NS4B": [], | ||
"NS5": [ | ||
"V114M", | ||
"N624S", | ||
"K670R" | ||
], | ||
"PRO": [] | ||
} | ||
} | ||
} | ||
} |