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Update top/traj metadata to append rather than replace logfile extrac… #51

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Merged
jkalayan merged 2 commits into from
Sep 25, 2026
Merged

Update top/traj metadata to append rather than replace logfile extrac… #51

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8102d52
Update top/traj metadata to append rather than replace logfile extrac…
jkalayan Sep 25, 2026
ec04f1f
Merge top/traj metadata into existing extracted data
jkalayan Sep 25, 2026
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19 changes: 19 additions & 0 deletions biosim_extractor/helpers/metadata_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,3 +31,22 @@ def round_floats(obj, decimals=3, preserve_below=1e-3):
return {k: round_floats(v, decimals, preserve_below) for k, v in obj.items()}

return obj


def merge_metadata(existing, incoming):
if not existing:
return incoming
if not incoming:
return existing

for key, value in incoming.items():
if (
key in existing
and isinstance(existing[key], dict)
and isinstance(value, dict)
):
merge_metadata(existing[key], value)
else:
existing[key] = value

return existing
8 changes: 5 additions & 3 deletions biosim_extractor/metadata/populatemetadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@

from biosim_extractor.amber.amberlog import AmberLogParser
from biosim_extractor.gromacs.gromacslog import GromacsLogParser
from biosim_extractor.helpers.metadata_utils import round_floats
from biosim_extractor.helpers.metadata_utils import merge_metadata, round_floats
from biosim_extractor.mdanalysis.toptraj import TopTrajParser
from biosim_extractor.metadata.fetchschema import get_schema, update_schema
from biosim_extractor.metadata.filemetadata import files_metadata, group_files
Expand Down Expand Up @@ -257,7 +257,9 @@ def populate(self):
self.data = self.apply_mapping()

if self.top_file and self.traj_file:
self.data = self.populate_toptraj()
toptraj_data = self.populate_toptraj()
if toptraj_data is not None:
self.data = merge_metadata(self.data, toptraj_data)

# self.data["SimulationMetadata"]["@type"] = "SimulationMetadata"
result = self.data["SimulationMetadata"]
Expand Down Expand Up @@ -526,7 +528,6 @@ def resolve_schema_inputs(args):
mapping_path = args.mappingschema
biosim_path = args.biosimschema

# If either path is missing, fetch a schema bundle and fill defaults.
if not mapping_path or not biosim_path:
bundle = (
update_schema(
Expand All @@ -539,6 +540,7 @@ def resolve_schema_inputs(args):
cache_dir=args.schema_cache_dir,
)
)

mapping_path = mapping_path or str(bundle.mapping_json)
biosim_path = biosim_path or str(bundle.schema_yaml)

Expand Down
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