add Payu JSON profiling parser

Author: edoyango

src/access/parsers/payujson_profiling.py

@@ -0,0 +1,63 @@
+# Copyright 2025 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0
+
+"""Parser for payu JSON walltime data generated by payu.
+The data to be parsed is written in the following form:
+
+{
+    "scheduler_job_id": "149764665.gadi-pbs",
+    "scheduler_type": "pbs",
+    # ... many more fields ...
+    "timings": {
+        "payu_start_time": "2025-09-16T08:52:50.748807",
+        "payu_setup_duration_seconds": 47.73822930175811,
+        "payu_model_run_duration_seconds": 6776.044810215011,
+        "payu_run_duration_seconds": 6779.385873348918,
+        "payu_archive_duration_seconds": 8.063649574294686,
+        "payu_finish_time": "2025-09-16T10:46:48.974451",
+        "payu_total_duration_seconds": 6838.225644
+    },
+    # ... more fields
+}
+"""
+
+from access.parsers.profiling import ProfilingParser
+import json
+
+
+class PayuJSONProfilingParser(ProfilingParser):
+    """Payu JSON job output profiling parser."""
+
+    def __init__(self):
+        """Instantiate Payu JSON profiling parser."""
+        super().__init__()
+        self._metrics = ["walltime"]
+
+    @property
+    def metrics(self) -> list:
+        return self._metrics
+
+    def read(self, stream: str) -> dict:
+
+        try:
+            timings = json.loads(stream)["timings"]
+        except KeyError:
+            raise KeyError('"timings" key missing in stream.')
+        except json.JSONDecodeError:
+            raise ValueError("Invalid JSON supplied.")
+
+        # remove known keys not relevant to profiling
+        for unwanted_key in ("payu_start_time", "payu_finish_time"):
+            try:
+                del timings[unwanted_key]
+            except KeyError:
+                continue
+
+        result = {"regions": [], "walltime": []}
+
+        # transpose dict to be consistent with other profiling parsers.
+        for k, v in timings.items():
+            result["regions"].append(k)
+            result["walltime"].append(v)
+
+        return result

tests/test_payujson_profiling.py

@@ -0,0 +1,62 @@
+# Copyright 2025 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0
+
+import pytest
+import datetime
+
+from access.parsers.payujson_profiling import PayuJSONProfilingParser
+
+
+@pytest.fixture(scope="module")
+def payujson_parser():
+    """Fixture instantiating the Payu JSON parser."""
+    return PayuJSONProfilingParser()
+
+
+@pytest.fixture(scope="module")
+def payujson_profiling():
+    """Fixture returning a dict holding the parsed FMS timing content without hits."""
+    return {
+        "regions": [
+            "payu_setup_duration_seconds",
+            "payu_model_run_duration_seconds",
+            "payu_run_duration_seconds",
+            "payu_archive_duration_seconds",
+            "payu_total_duration_seconds",
+        ],
+        "walltime": [47.73822930175811, 6776.044810215011, 6779.385873348918, 8.063649574294686, 6838.225644],
+    }
+
+
+@pytest.fixture(scope="module")
+def payujson_log_file():
+    """Fixture returning the FMS timing content without hits column."""
+    return """{
+    "scheduler_job_id": "149764665.gadi-pbs",
+    "timings": {
+        "payu_start_time": "2025-09-16T08:52:50.748807",
+        "payu_setup_duration_seconds": 47.73822930175811,
+        "payu_model_run_duration_seconds": 6776.044810215011,
+        "payu_run_duration_seconds": 6779.385873348918,
+        "payu_archive_duration_seconds": 8.063649574294686,
+        "payu_finish_time": "2025-09-16T10:46:48.974451",
+        "payu_total_duration_seconds": 6838.225644
+    },
+    "payu_run_id": "5c9027104cc39a5d39814624537c21440b68beb7",
+    "payu_model_run_status": 0,
+    "model_finish_time": "1844-01-01T00:00:00",
+    "model_start_time": "1843-01-01T00:00:00",
+    "model_calendar": "proleptic_gregorian",
+    "payu_run_status": 0
+}
+"""
+
+
+def test_payujson_profiling(payujson_parser, payujson_log_file, payujson_profiling):
+    """Test the correct parsing of Payu JSON timing information."""
+    parsed_log = payujson_parser.read(payujson_log_file)
+    for idx, region in enumerate(payujson_profiling.keys()):
+        assert region in parsed_log, f"{region} not found in Payu JSON parsed log"
+        assert (
+            payujson_profiling["walltime"][idx] == parsed_log["walltime"][idx]
+        ), f"Incorrect walltime for region {region} (idx: {idx})."