Validation mode warn no longer exits code 2

The help message for `--validation-mode` is very specific:

> 'error' mode causes a non-zero exit status if any validation checks
> failed, while 'warn' does not.

In the actual implementation however we would print an error and exit
with code 2 for any validation check _except_ the augur version check.
Now, for `ValidationMode.WARN` we catch these errors and turn them into
warnings such that augur can exit code 0 as specified.

Author: jameshadfield

augur/util_support/node_data_file.py

@@ -63,49 +63,49 @@ def validate(self):
         if self.validation_mode is ValidationMode.SKIP:
             return # don't perform validation (i.e. skip it)
 
-        if self.annotations:
-            try:
-                validate_json(
-                    self.annotations,
-                    load_json_schema("schema-annotations.json"),
-                    self.fname,
+        try:
+            if self.annotations:
+                try:
+                    validate_json(
+                        self.annotations,
+                        load_json_schema("schema-annotations.json"),
+                        self.fname,
+                    )
+                except ValidateError as err:
+                    raise AugurError(
+                        f"{self.fname} contains an `annotations` attribute of an invalid JSON format. Was it "
+                        "produced by different version of augur the one you are currently using "
+                        f" ({__version__})? Please check the program that produced that JSON file."
+                    ) from err
+
+            if not isinstance(self.nodes, dict):
+                raise AugurError(
+                    f"`nodes` value in {self.fname} is not a dictionary. Please check the formatting of this JSON!"
                 )
-            except ValidateError as err:
+
+            if not isinstance(self.branches, dict):
                 raise AugurError(
-                    f"{self.fname} contains an `annotations` attribute of an invalid JSON format. Was it "
-                    "produced by different version of augur the one you are currently using "
-                    f" ({__version__})? Please check the program that produced that JSON file."
-                ) from err
-
-        if not isinstance(self.nodes, dict):
-            raise AugurError(
-                f"`nodes` value in {self.fname} is not a dictionary. Please check the formatting of this JSON!"
-            )
-
-        if not isinstance(self.branches, dict):
-            raise AugurError(
-                f"`branches` value in {self.fname} is not a dictionary. Please check the formatting of this JSON!"
-            )
-
-        if not self.nodes and not self.branches:
-            print_err(
-                f"WARNING: {self.fname} has empty or nonexistent `nodes` and `branches`. Please check the formatting of this JSON!"
-            )
-
-        if self.is_generated_by_incompatible_augur:
-            msg = (
-                f"Augur version incompatibility detected: the JSON {self.fname} was generated by "
-                f"{self.generated_by}, which is incompatible with the current augur version "
-                f"({__version__}). We suggest you rerun the pipeline using the current version of "
-                "augur."
-            )
-            if self.validation_mode is ValidationMode.ERROR:
+                    f"`branches` value in {self.fname} is not a dictionary. Please check the formatting of this JSON!"
+                )
+
+            if not self.nodes and not self.branches:
+                print_err(
+                    f"WARNING: {self.fname} has empty or nonexistent `nodes` and `branches`. Please check the formatting of this JSON!"
+                )
+
+            if self.is_generated_by_incompatible_augur:
+                msg = (
+                    f"Augur version incompatibility detected: the JSON {self.fname} was generated by "
+                    f"{self.generated_by}, which is incompatible with the current augur version "
+                    f"({__version__}). We suggest you rerun the pipeline using the current version of "
+                    "augur."
+                )
                 raise AugurError(msg)
-            elif self.validation_mode is ValidationMode.WARN:
-                print_err(f"WARNING: {msg}")
+        except AugurError as e:
+            if self.validation_mode is ValidationMode.WARN:
+                print_err(f"WARNING: {e.args[0]}")
             else:
-                raise ValueError(f"unknown validation mode: {self.validation_mode!r}")
-
+                raise e
 
 
 class NodeDataObject(NodeDataFile):