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.
nextstrain · Oct 23, 2024 · c0b6dac · c0b6dac
1 parent feef8d5
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diff --git a/tests/functional/clades/cram/augur-version-mismatch.t b/tests/functional/clades/cram/augur-version-mismatch.t
@@ -0,0 +1,23 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+Node-data JSONs produced from a different major version of augur
+are not allowed.
+
+  $ ${AUGUR} clades \
+  >   --tree "$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]
+
+Skipping validation allows mismatched augur versions to be used without error.
+
+  $ ${AUGUR} clades \
+  >   --tree "$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
diff --git a/tests/functional/clades/data/aa_muts_generated_by.json b/tests/functional/clades/data/aa_muts_generated_by.json
@@ -0,0 +1,332 @@
+{
+  "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": []
+      }
+    }
+  }
+}