Add functional tests for augur export v2

This sets up a template for testing `augur export v2` which is rather complex in the different ways it can be called. The tests here are only intended to cover features introduced by this PR.
nextstrain · Jun 8, 2021 · 73649be · 73649be
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diff --git a/tests/functional/export_v2.t b/tests/functional/export_v2.t
@@ -0,0 +1,33 @@
+Integration tests for augur export v2.
+
+  $ pushd "$TESTDIR" > /dev/null
+  $ export AUGUR="../../bin/augur"
+
+Minimal export
+
+  $ ${AUGUR} export v2 \
+  >   --tree export_v2/tree.nwk \
+  >   --node-data export_v2/div_node-data.json \
+  >   --output "$TMP/minimal.json" &>/dev/null
+  [2]
+
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  export_v2/minimal.json "$TMP/minimal.json" \
+  >   --exclude-paths "root['meta']['updated']"
+  {}
+
+Future test:
+Run augur export _without_ any node-data JSONs when this can read divergence values from the newick file
+and compare this to the tree using `div_node-data.json` - they should be identical.
+See https://github.com/nextstrain/augur/issues/273 for more
+
+
+Export with auspice config JSON which defines scale & legend settings
+  $ ${AUGUR} export v2 \
+  >   --tree export_v2/tree.nwk \
+  >   --node-data export_v2/div_node-data.json export_v2/location_node-data.json \
+  >   --auspice-config export_v2/auspice_config1.json \
+  >   --output "$TMP/dataset1.json" &>/dev/null
+
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  export_v2/dataset1.json "$TMP/dataset1.json" \
+  >   --exclude-paths "root['meta']['updated']"
+  {}
diff --git a/tests/functional/export_v2/auspice_config1.json b/tests/functional/export_v2/auspice_config1.json
@@ -0,0 +1,32 @@
+{
+  "colorings": [
+    {
+      "key": "location",
+      "title": "Location",
+      "type": "categorical",
+      "legend": [
+        {"value": "alpha", "display": "α"},
+        {"value": "beta"}
+      ],
+      "scale": [
+        ["beta", "#bd0026"],
+        ["gamma", "#6a51a3"]
+      ]
+    },
+    {
+      "key": "mutation_length",
+      "title": "Mutations per branch",
+      "type": "continuous",
+      "legend": [
+        {"value": 1, "display": "0-2", "bounds": [-1,2]},
+        {"value": 3, "display": "3-5", "bounds": [2,5]},
+        {"value": 5, "display": ">5", "bounds": [5, 10]}
+      ],
+      "scale": [
+        [1, "#081d58"],
+        [3, "#1d91c0"],
+        [5, "#c7e9b4"]
+      ]
+    }
+  ]
+}
diff --git a/tests/functional/export_v2/dataset1.json b/tests/functional/export_v2/dataset1.json
@@ -0,0 +1,224 @@
+{
+  "meta": {
+    "colorings": [
+      {
+        "key": "location",
+        "legend": [
+          {
+            "display": "\u03b1",
+            "value": "alpha"
+          },
+          {
+            "value": "beta"
+          }
+        ],
+        "scale": [
+          [
+            "beta",
+            "#bd0026"
+          ],
+          [
+            "gamma",
+            "#6a51a3"
+          ]
+        ],
+        "title": "Location",
+        "type": "categorical"
+      },
+      {
+        "key": "mutation_length",
+        "legend": [
+          {
+            "bounds": [
+              -1,
+              2
+            ],
+            "display": "0-2",
+            "value": 1
+          },
+          {
+            "bounds": [
+              2,
+              5
+            ],
+            "display": "3-5",
+            "value": 3
+          },
+          {
+            "bounds": [
+              5,
+              10
+            ],
+            "display": ">5",
+            "value": 5
+          }
+        ],
+        "scale": [
+          [
+            1,
+            "#081d58"
+          ],
+          [
+            3,
+            "#1d91c0"
+          ],
+          [
+            5,
+            "#c7e9b4"
+          ]
+        ],
+        "title": "Mutations per branch",
+        "type": "continuous"
+      },
+      {
+        "key": "location",
+        "legend": [
+          {
+            "display": "\u03b1",
+            "value": "alpha"
+          },
+          {
+            "value": "beta"
+          }
+        ],
+        "scale": [
+          [
+            "beta",
+            "#bd0026"
+          ],
+          [
+            "gamma",
+            "#6a51a3"
+          ]
+        ],
+        "title": "Location",
+        "type": "categorical"
+      }
+    ],
+    "filters": [
+      "location"
+    ],
+    "panels": [
+      "tree"
+    ],
+    "updated": "2021-06-09"
+  },
+  "tree": {
+    "branch_attrs": {},
+    "children": [
+      {
+        "branch_attrs": {},
+        "name": "tipA",
+        "node_attrs": {
+          "div": 1,
+          "location": {
+            "value": "delta"
+          },
+          "mutation_length": {
+            "value": 1
+          }
+        }
+      },
+      {
+        "branch_attrs": {},
+        "children": [
+          {
+            "branch_attrs": {},
+            "name": "tipB",
+            "node_attrs": {
+              "div": 3,
+              "location": {
+                "value": "gamma"
+              },
+              "mutation_length": {
+                "value": 1
+              }
+            }
+          },
+          {
+            "branch_attrs": {},
+            "name": "tipC",
+            "node_attrs": {
+              "div": 3,
+              "location": {
+                "value": "gamma"
+              },
+              "mutation_length": {
+                "value": 1
+              }
+            }
+          }
+        ],
+        "name": "internalBC",
+        "node_attrs": {
+          "div": 2,
+          "mutation_length": {
+            "value": 2
+          }
+        }
+      },
+      {
+        "branch_attrs": {},
+        "children": [
+          {
+            "branch_attrs": {},
+            "name": "tipD",
+            "node_attrs": {
+              "div": 8,
+              "location": {
+                "value": "alpha"
+              },
+              "mutation_length": {
+                "value": 3
+              }
+            }
+          },
+          {
+            "branch_attrs": {},
+            "name": "tipE",
+            "node_attrs": {
+              "div": 9,
+              "location": {
+                "value": "alpha"
+              },
+              "mutation_length": {
+                "value": 4
+              }
+            }
+          },
+          {
+            "branch_attrs": {},
+            "name": "tipF",
+            "node_attrs": {
+              "div": 6,
+              "location": {
+                "value": "beta"
+              },
+              "mutation_length": {
+                "value": 1
+              }
+            }
+          }
+        ],
+        "name": "internalDEF",
+        "node_attrs": {
+          "div": 5,
+          "location": {
+            "value": "alpha"
+          },
+          "mutation_length": {
+            "value": 5
+          }
+        }
+      }
+    ],
+    "name": "ROOT",
+    "node_attrs": {
+      "div": 0,
+      "mutation_length": {
+        "value": 0
+      }
+    }
+  },
+  "version": "v2"
+}
diff --git a/tests/functional/export_v2/div_node-data.json b/tests/functional/export_v2/div_node-data.json
@@ -0,0 +1,31 @@
+{
+  "nodes": {
+    "ROOT": {
+      "mutation_length": 0
+    },
+    "tipA": {
+      "mutation_length": 1
+    },
+    "internalBC": {
+      "mutation_length": 2
+    },
+    "tipB": {
+      "mutation_length": 1
+    },
+    "tipC": {
+      "mutation_length": 1
+    },
+    "internalDEF": {
+      "mutation_length": 5
+    },
+    "tipD": {
+      "mutation_length": 3
+    },
+    "tipE": {
+      "mutation_length": 4
+    },
+    "tipF": {
+      "mutation_length": 1
+    }
+  }
+} 
diff --git a/tests/functional/export_v2/location_node-data.json b/tests/functional/export_v2/location_node-data.json
@@ -0,0 +1,25 @@
+{
+  "nodes": {
+    "tipA": {
+      "location": "delta"
+    },
+    "tipB": {
+      "location": "gamma"
+    },
+    "tipC": {
+      "location": "gamma"
+    },
+    "internalDEF": {
+      "location": "alpha"
+    },
+    "tipD": {
+      "location": "alpha"
+    },
+    "tipE": {
+      "location": "alpha"
+    },
+    "tipF": {
+      "location": "beta"
+    }
+  }
+}