Merge branch 'main' of github.com:broadinstitute/seqr-loading-pipelines

Author: bpblanken

v03_pipeline/lib/misc/validation.py

@@ -15,7 +15,14 @@
 
 
 class SeqrValidationError(Exception):
-    pass
+    def __init__(
+        self,
+        msg: str,
+        error_body: dict | None = None,
+    ):
+        super().__init__(msg)
+        self.msg = msg
+        self.error_body = error_body if error_body is not None else {}
 
 
 def validate_allele_type(

v03_pipeline/lib/tasks/validate_callset.py

@@ -140,7 +140,10 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable:
         if validation_exceptions:
             write_validation_errors_for_run_task = self.clone(
                 WriteValidationErrorsForRunTask,
-                error_messages=[str(e) for e in validation_exceptions],
+                error_messages=[e.msg for e in validation_exceptions],
+                error_body={
+                    k: v for e in validation_exceptions for k, v in e.error_body.items()
+                },
             )
             write_validation_errors_for_run_task.run()
             raise SeqrValidationError(

v03_pipeline/lib/tasks/write_validation_errors_for_run.py

@@ -50,20 +50,11 @@ def wrapper(self: luigi.Task):
         try:
             return f(self)
         except SeqrValidationError as e:
-            if isinstance(
-                e.args[1],
-                object,
-            ):  # TODO: improve type checking with a pydantic model/typed dict
-                write_validation_errors_for_run_task = self.clone(
-                    WriteValidationErrorsForRunTask,
-                    error_messages=[str(e.args[0])],
-                    error_body=e.args[1],
-                )
-            else:
-                write_validation_errors_for_run_task = self.clone(
-                    WriteValidationErrorsForRunTask,
-                    error_messages=[str(e)],
-                )
+            write_validation_errors_for_run_task = self.clone(
+                WriteValidationErrorsForRunTask,
+                error_messages=[e.msg],
+                error_body=e.error_body,
+            )
             write_validation_errors_for_run_task.run()
             raise SeqrValidationError(
                 write_validation_errors_for_run_task.to_single_error_message(),