Provide expanded vrs 2 output

sallybg · sallybg · commit 9635256c3ea1 · 2024-08-01T09:15:22.000-07:00
Workaround for issue where model_dump_json picks an IRI rather
than a SequenceLocation to represent an Allele or Haplotype's
location.
diff --git a/src/dcd_mapping/annotate.py b/src/dcd_mapping/annotate.py
@@ -535,7 +535,7 @@ def save_mapped_output_json(
     _logger.info("Saving mapping output to %s", output_path)
     with output_path.open("w") as file:
         json.dump(
-            json.loads(output.model_dump_json(exclude_unset=True, exclude_none=True)),
+            output.model_dump(exclude_unset=True, exclude_none=True),
             file,
             indent=4,
         )

Original file line number	Diff line number	Diff line change
`@@ -535,7 +535,7 @@ def save_mapped_output_json(`
`535`	`535`	`_logger.info("Saving mapping output to %s", output_path)`
`536`	`536`	`with output_path.open("w") as file:`
`537`	`537`	`json.dump(`
`538`		`- json.loads(output.model_dump_json(exclude_unset=True, exclude_none=True)),`
	`538`	`+ output.model_dump(exclude_unset=True, exclude_none=True),`
`539`	`539`	`file,`
`540`	`540`	`indent=4,`
`541`	`541`	`)`