nextstrain · joverlee521 · Jan 23, 2025 · Jan 13, 2025 · Jan 13, 2025 · Jan 13, 2025
diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,12 @@
 
 ## __NEXT__
 
+### Major Changes
+
+* export v2: The string "none" is now an invalid value for `--color-by-metadata` and `--metadata-columns` options and will be ignored to prevent clashes with Auspice's internal use of "none". [#1113][] (@joverlee521)
+* schema: The string "none" is now an invalid branch label, node_attr key, and coloring key. [#1113][] (@joverlee521)
+
+[#1113]: https://github.com/nextstrain/augur/pull/1113
 
 ## 27.2.0 (22 January 2025)
 

diff --git a/augur/data/schema-auspice-config-v2.json b/augur/data/schema-auspice-config-v2.json
@@ -22,7 +22,8 @@
                 "properties": {
                     "key": {
                         "description": "They key used to access the value of this coloring on each node",
-                        "type": "string"
+                        "type": "string",
+                        "not": {"const": "none"}
                     },
                     "title": {
                         "description": "Text to be displayed in the \"color by\" dropdown and legends",
@@ -265,7 +266,7 @@
             "$comment": "These columns will not be used as coloring options in Auspice but will be visible in the tree.",
             "type": "array",
             "uniqueItems": true,
-            "items": {"type": "string"}
+            "items": {"type": "string", "not": {"const": "none"}}
         },
         "extensions": {
             "description": "Data to be passed through to the the resulting dataset JSON",

diff --git a/augur/data/schema-export-v2.json b/augur/data/schema-export-v2.json
@@ -281,7 +281,8 @@
                                     "type": "number"
                                 }
                             }
-                        }
+                        },
+                        "^none$": false
                     }
                 },
                 "branch_attrs": {
@@ -296,7 +297,8 @@
                                     "$comment": "e.g. clade->3c3a",
                                     "$comment": "string is parsed unchanged by Auspice",
                                     "type": "string"
-                                }
+                                },
+                                "^none$": false
                             }
                         },
                         "mutations": {

diff --git a/augur/export_v2.py b/augur/export_v2.py
@@ -25,6 +25,9 @@
 
 MINIFY_THRESHOLD_MB = 5
 
+# Invalid metadata columns because they are used internally by Auspice
+INVALID_METADATA_COLUMNS = ("none")
+
 
 # Set up warnings & exceptions
 warn = warnings.warn
@@ -401,6 +404,10 @@ def _is_valid(coloring):
         if key != "gt" and not trait_values:
             warn(f"Requested color-by field {key!r} does not exist and will not be used as a coloring or exported.")
             return False
+        if key in INVALID_METADATA_COLUMNS:
+            warn(f"You asked for a color-by for trait {key!r}, but this is an invalid coloring key.\n"
+                  "It will be ignored during export, please rename field if you would like to use it as a coloring.")
+            return False
         return True
 
     def _get_colorings():
@@ -950,10 +957,13 @@ def register_parser(parent_subparsers):
     config.add_argument('--description', metavar="description.md", help="Markdown file with description of build and/or acknowledgements to be displayed by Auspice")
     config.add_argument('--warning', metavar="text or file", help="Text or file in Markdown format to be displayed as a warning banner by Auspice")
     config.add_argument('--geo-resolutions', metavar="trait", nargs='+', action=ExtendOverwriteDefault, help="Geographic traits to be displayed on map")
-    config.add_argument('--color-by-metadata', metavar="trait", nargs='+', action=ExtendOverwriteDefault, help="Metadata columns to include as coloring options")
+    config.add_argument('--color-by-metadata', metavar="trait", nargs='+', action=ExtendOverwriteDefault,
+        help="Metadata columns to include as coloring options. " +
+             f"Ignores columns named {INVALID_METADATA_COLUMNS!r}, so please rename them if you would like to include them as colorings.")
     config.add_argument('--metadata-columns', nargs="+", action=ExtendOverwriteDefault,
-                                 help="Metadata columns to export in addition to columns provided by --color-by-metadata or colorings in the Auspice configuration file. " +
-                                      "These columns will not be used as coloring options in Auspice but will be visible in the tree.")
+        help="Metadata columns to export in addition to columns provided by --color-by-metadata or colorings in the Auspice configuration file. " +
+             "These columns will not be used as coloring options in Auspice but will be visible in the tree. " +
+             f"Ignores columns named {INVALID_METADATA_COLUMNS!r}, so please rename them if you would like to include them as metadata fields.")
     config.add_argument('--panels', metavar="panels", nargs='+', action=ExtendOverwriteDefault, choices=['tree', 'map', 'entropy', 'frequencies', 'measurements'], help="Restrict panel display in auspice. Options are %(choices)s. Ignore this option to display all available panels.")
 
     optional_inputs = parser.add_argument_group(
@@ -1195,6 +1205,10 @@ def get_additional_metadata_columns(config, command_line_metadata_columns, metad
 
     additional_metadata_columns = []
     for col in potential_metadata_columns:
+        if col in INVALID_METADATA_COLUMNS:
+            warn(f"You asked for a metadata field {col!r}, but this is an invalid field.\n"
+                  "It will be ignored during export, please rename field if you would like to include as a metadata field.")
+            continue
         # Match the column names corrected within parse_node_data_and_metadata
         corrected_col = update_deprecated_names(col)
         if corrected_col not in metadata_names:

diff --git a/tests/functional/export_v2/cram/metadata-with-none-column.t b/tests/functional/export_v2/cram/metadata-with-none-column.t
@@ -0,0 +1,39 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Run export with metadata that contains "none" column and asked to use as coloring.
+This is expected to output a warning that "none" is an invalid coloring column and skip it in colorings.
+
+  $ ${AUGUR} export v2 \
+  >   --tree "$TESTDIR/../data/tree.nwk" \
+  >   --node-data "$TESTDIR/../data/div_node-data.json" "$TESTDIR/../data/location_node-data.json" \
+  >   --metadata "$TESTDIR/../data/none_column_metadata.tsv" \
+  >   --color-by-metadata "none" \
+  >   --maintainers "Nextstrain Team" \
+  >   --output dataset1.json >/dev/null
+  WARNING: You asked for a color-by for trait 'none', but this is an invalid coloring key.
+  It will be ignored during export, please rename field if you would like to use it as a coloring.
+  \s{0} (re)
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/dataset-without-none-column.json" dataset1.json \
+  >   --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']"
+  {}
+
+Run export with metadata that contains "none" column and asked to use as metadata.
+This is expected to output a warning that "none" is an invalid node_attr and skip it in metadata.
+
+  $ ${AUGUR} export v2 \
+  >   --tree "$TESTDIR/../data/tree.nwk" \
+  >   --node-data "$TESTDIR/../data/div_node-data.json" "$TESTDIR/../data/location_node-data.json" \
+  >   --metadata "$TESTDIR/../data/none_column_metadata.tsv" \
+  >   --metadata-column "none" \
+  >   --maintainers "Nextstrain Team" \
+  >   --output dataset2.json >/dev/null
+  WARNING: You asked for a metadata field 'none', but this is an invalid field.
+  It will be ignored during export, please rename field if you would like to include as a metadata field.
+  \s{0} (re)
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/dataset-without-none-column.json" dataset2.json \
+  >   --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']"
+  {}
diff --git a/tests/functional/export_v2/data/dataset-without-none-column.json b/tests/functional/export_v2/data/dataset-without-none-column.json
@@ -0,0 +1,114 @@
+{
+  "version": "v2",
+  "meta": {
+    "updated": "2025-01-13",
+    "maintainers": [
+      {
+        "name": "Nextstrain Team"
+      }
+    ],
+    "colorings": [
+      {
+        "key": "location",
+        "title": "location",
+        "type": "categorical"
+      }
+    ],
+    "filters": [
+      "location"
+    ],
+    "panels": [
+      "tree"
+    ]
+  },
+  "tree": {
+    "name": "ROOT",
+    "node_attrs": {
+      "div": 0
+    },
+    "branch_attrs": {},
+    "children": [
+      {
+        "name": "tipA",
+        "node_attrs": {
+          "div": 1,
+          "location": {
+            "value": "delta"
+          }
+        },
+        "branch_attrs": {}
+      },
+      {
+        "name": "internalBC",
+        "node_attrs": {
+          "div": 2
+        },
+        "branch_attrs": {},
+        "children": [
+          {
+            "name": "tipB",
+            "node_attrs": {
+              "div": 3,
+              "location": {
+                "value": "gamma"
+              }
+            },
+            "branch_attrs": {}
+          },
+          {
+            "name": "tipC",
+            "node_attrs": {
+              "div": 3,
+              "location": {
+                "value": "gamma"
+              }
+            },
+            "branch_attrs": {}
+          }
+        ]
+      },
+      {
+        "name": "internalDEF",
+        "node_attrs": {
+          "div": 5,
+          "location": {
+            "value": "alpha"
+          }
+        },
+        "branch_attrs": {},
+        "children": [
+          {
+            "name": "tipD",
+            "node_attrs": {
+              "div": 8,
+              "location": {
+                "value": "alpha"
+              }
+            },
+            "branch_attrs": {}
+          },
+          {
+            "name": "tipE",
+            "node_attrs": {
+              "div": 9,
+              "location": {
+                "value": "alpha"
+              }
+            },
+            "branch_attrs": {}
+          },
+          {
+            "name": "tipF",
+            "node_attrs": {
+              "div": 6,
+              "location": {
+                "value": "beta"
+              }
+            },
+            "branch_attrs": {}
+          }
+        ]
+      }
+    ]
+  }
+}
diff --git a/tests/functional/export_v2/data/none_column_metadata.tsv b/tests/functional/export_v2/data/none_column_metadata.tsv
@@ -0,0 +1,4 @@
+name	none
+tipA	true
+tipB	true
+tipC	true