diff --git a/evaluations/fold-07-holdout-9/AGENT_ACTION_LOG.md b/evaluations/fold-07-holdout-9/AGENT_ACTION_LOG.md new file mode 100644 index 0000000..4cc1937 --- /dev/null +++ b/evaluations/fold-07-holdout-9/AGENT_ACTION_LOG.md @@ -0,0 +1,38 @@ +- 2026-06-30T16:01:04-07:00 | action=command | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9 initialize output directory | reason=start benchmark run with required outputs directory +- 2026-06-30T16:01:04-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/AGENT_INSTRUCTIONS.md | reason=read fold-local task instructions +- 2026-06-30T16:01:04-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/MANIFEST.json | reason=read fold manifest for allowed inputs +- 2026-06-30T16:01:04-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/skills/essdive_sm_curator/SKILL.md | reason=read required fold-local curator skill +- 2026-06-30T16:01:04-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/skills/essdive_sm_harmonizer/SKILL.md | reason=read required fold-local harmonizer skill +- 2026-06-30T16:01:04-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9 | reason=inspect fold-local sandbox structure only +- 2026-06-30T16:01:26-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/skills/essdive_sm_harmonizer/SKILL.md lines 321-700 | reason=complete required fold-local harmonizer skill read +- 2026-06-30T16:01:26-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data | reason=inspect allowed fold-local exemplar data files +- 2026-06-30T16:01:26-07:00 | action=directory_listing | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802 | reason=inspect allowed raw held-out package files +- 2026-06-30T16:01:38-07:00 | action=directory_listing | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802 recursive | reason=inspect all allowed raw held-out files +- 2026-06-30T16:01:38-07:00 | action=command | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802 file type summary | reason=identify parseable raw held-out file types +- 2026-06-30T16:01:38-07:00 | action=file_read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802/NEON_plot_TDR.csv header | reason=inspect held-out candidate soil moisture payload columns and sample rows +- 2026-06-30T16:02:00-07:00 | action=directory_listing | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802/ess-dive-64109adb5fba6b5-20260114T183043578 | reason=inspect nested raw held-out folder listed in package +- 2026-06-30T16:02:00-07:00 | action=search | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9 package identifier | reason=look for fold-local metadata or notes for held-out identifier without leaving sandbox +- 2026-06-30T16:02:00-07:00 | action=search | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/gold/expert_code/harmonize_sm | reason=find fold-local exemplar code using Easting Northing UTM or VWC patterns +- 2026-06-30T16:02:00-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json header | reason=inspect fold-local mapping schema and entries +- 2026-06-30T16:02:53-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/gold/expert_code/harmonize_sm/common.py | reason=inspect fold-local helper schema and UTM conversion conventions +- 2026-06-30T16:02:53-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/gold/expert_code/harmonize_sm/dataset_15.py | reason=inspect fold-local TDR/VWC percent and UTM exemplar +- 2026-06-30T16:02:53-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/gold/expert_code/harmonize_sm/dataset_17.py | reason=inspect fold-local embedded location metadata exemplar +- 2026-06-30T16:02:53-07:00 | action=command | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json selected entries | reason=inspect relevant fold-local mapping examples only +- 2026-06-30T16:03:24-07:00 | action=search | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802 | reason=search allowed raw held-out package for DOI or metadata strings +- 2026-06-30T16:03:24-07:00 | action=command | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802/NEON_plot_TDR.csv dataframe profile | reason=inspect held-out payload dimensions, nulls, unique values, and VWC ranges +- 2026-06-30T16:03:55-07:00 | action=command | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802/NEON_plot_TDR.csv invalid row inspection | reason=inspect sentinel rows before filtering +- 2026-06-30T16:03:55-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json lines 980-1060 | reason=inspect fold-local excluded/prior-version mapping context mentioning held-out package +- 2026-06-30T16:03:55-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/data/gold/expert_code/harmonize_sm/dataset_26.py | reason=inspect fold-local discrete sampling date/depth pattern exemplar +- 2026-06-30T16:05:31-07:00 | action=command | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs generate benchmark outputs | reason=write required held-out curation, mapping, notes, and script files +- 2026-06-30T16:05:31-07:00 | action=file_write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/curator_bundle.json | reason=record curation decision and raw file interpretation +- 2026-06-30T16:05:31-07:00 | action=file_write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/mapping.json | reason=write harmonization mapping entry for held-out dataset +- 2026-06-30T16:05:31-07:00 | action=file_write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/mapping_notes.md | reason=document inclusion, filtering, and unresolved assumptions +- 2026-06-30T16:05:31-07:00 | action=file_write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/harmonize_heldout.py | reason=create standalone script to generate heldout_harmonized.csv +- 2026-06-30T16:05:47-07:00 | action=command | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/harmonize_heldout.py | reason=run harmonization script to create heldout_harmonized.csv +- 2026-06-30T16:05:47-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/heldout_harmonized.csv summary | reason=validate generated harmonized output schema and values +- 2026-06-30T16:05:48-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/mapping.json | reason=validate mapping JSON parses +- 2026-06-30T16:05:48-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs/curator_bundle.json | reason=validate curator bundle JSON parses +- 2026-06-30T16:05:48-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/agent_outputs | reason=confirm required output files exist +- 2026-06-30T16:06:15-07:00 | action=command | subject=/tmp/fold07_mapping_check.json /tmp/fold07_bundle_check.json cleanup | reason=remove transient JSON validation files so retained outputs stay under agent_outputs +- 2026-06-30T16:06:15-07:00 | action=file_write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/AGENT_ACTION_LOG.md correction note for transient validation files | reason=record that prior JSON validation command wrote temporary files under /tmp and they were removed +- 2026-06-30T16:06:15-07:00 | action=file_read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-07-holdout-9/AGENT_ACTION_LOG.md forbidden path pattern scan | reason=scan action log for leakage-forbidden path patterns diff --git a/evaluations/fold-07-holdout-9/AGENT_INSTRUCTIONS.md b/evaluations/fold-07-holdout-9/AGENT_INSTRUCTIONS.md new file mode 100644 index 0000000..d6f8b6b --- /dev/null +++ b/evaluations/fold-07-holdout-9/AGENT_INSTRUCTIONS.md @@ -0,0 +1,10 @@ +# Run environment — leave-one-cluster-out + +Harmonize the held-out dataset(s) below using ONLY: +- the skills in `skills/`, +- the exemplars in `data/processed/.../sm_data_harmonization_mapping.json` and the code patterns in `data/gold/expert_code/harmonize_sm/` (both have the held-out cluster removed), +- the shared raw inputs under `~/ess-dive_wfsfa_soil_datasets/` and the cached metadata under `data/external/ess-dive_meta/`. + +Do NOT look up the held-out dataset's existing harmonized output, expert code, or mapping entry from any other location. The held-out datasets are: + +- `ess-dive-460e696d8210ed3-20260309T155937802` diff --git a/evaluations/fold-07-holdout-9/EVALUATION.md b/evaluations/fold-07-holdout-9/EVALUATION.md new file mode 100644 index 0000000..1be212d --- /dev/null +++ b/evaluations/fold-07-holdout-9/EVALUATION.md @@ -0,0 +1,52 @@ +# fold-07-holdout-9 Agent Evaluation + +## Scope + +This directory records one sandboxed sub-agent attempt for held-out dataset indices `[9]`. + +- Sandbox: `.runs/fold-07-holdout-9` +- Tracked artifact copy: `evaluations/fold-07-holdout-9` +- Successful agent trace: `AGENT_ACTION_LOG.md` + +## Anti-Leakage Audit + +The successful trace was scanned for root gold data, root processed data, other fold sandboxes, held-out expert module names, and explicit `violation` markers. Result: `0` matches. + +## Output Equivalence Against Gold + +| Metric | Agent | Gold | +| --- | ---: | ---: | +| Rows | 664 | 672 | +| Target columns present | 9 / 9 | 9 / 9 | +| Schema exact match | true | n/a | +| Unique keyed rows recovered | 0 | 672 | +| Missing gold keyed rows | 672 | n/a | +| Extra agent keyed rows | 664 | n/a | +| Row precision | 0.000 | n/a | +| Gold recall | 0.000 | n/a | + +Shared-row value matches after key merge: + +| Column | Matched rows | +| --- | ---: | +| `interval_min` | 0/0 | +| `volumetric_water_content_m3_m3` | 0/0 | +| `gravimetric_water_content_gH2O_gs` | 0/0 | +| `water_potential_kPa` | 0/0 | +| `is_timeseries` | 0/0 | + +## JSON Mapping Match + +- Summary: `{"extra_agent_categories": ["gravimetric_water_content"], "field_exact_matches_by_name": {"destination_variable": "8/8", "source_files": "8/8", "source_pattern": "5/8", "transformation": "0/8", "unit_conversion": "6/8"}, "field_level_exact_matches": "27/40", "gold_mapping_categories_present": "8/8", "missing_gold_categories": [], "top_level_exact_matches": "7/7", "top_level_matches": {"archive_repository": true, "data_payload_files": true, "dataset_identifier": true, "doi": true, "index": true, "location_metadata_files": true, "sensor_metadata_files": true}}` + +| Field | Exact matches | +| --- | ---: | +| `destination_variable` | 8/8 | +| `source_pattern` | 5/8 | +| `source_files` | 8/8 | +| `transformation` | 0/8 | +| `unit_conversion` | 6/8 | + +## Overall Assessment + +See `evaluation_metrics.json` for machine-readable details. The run passed the targeted local no-gold path audit. Output equivalence should be interpreted with the key policy recorded in the metrics (`key_includes_dataset_index=False`). diff --git a/evaluations/fold-07-holdout-9/MANIFEST.json b/evaluations/fold-07-holdout-9/MANIFEST.json new file mode 100644 index 0000000..4d36488 --- /dev/null +++ b/evaluations/fold-07-holdout-9/MANIFEST.json @@ -0,0 +1,35 @@ +{ + "name": "fold-07-holdout-9", + "holdout_indices": [ + 9 + ], + "holdout_identifiers": [ + "ess-dive-460e696d8210ed3-20260309T155937802" + ], + "exemplar_indices": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 10, + 15, + 16, + 17, + 18, + 23, + 24, + 25, + 26, + 27 + ], + "n_exemplars": 27, + "sources": { + "package": "data/gold/expert_code/harmonize_sm", + "mapping": "data/gold/sm_data_harmonization_mapping.json", + "skills": "skills" + } +} \ No newline at end of file diff --git a/evaluations/fold-07-holdout-9/agent_outputs/curator_bundle.json b/evaluations/fold-07-holdout-9/agent_outputs/curator_bundle.json new file mode 100644 index 0000000..f44473c --- /dev/null +++ b/evaluations/fold-07-holdout-9/agent_outputs/curator_bundle.json @@ -0,0 +1,68 @@ +{ + "dataset_identifier": "ess-dive-460e696d8210ed3-20260309T155937802", + "doi": "doi:10.15485/3013006", + "doi_source": "Fold-local mapping entry for prior package version ess-dive-64109adb5fba6b5-20260114T183043578 uses this DOI and is marked as a prior version of the held-out package.", + "raw_package_dir": "/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-460e696d8210ed3-20260309T155937802", + "files": [ + { + "name": "NEON_plot_TDR.csv", + "category": "data_payload_and_location_metadata", + "columns": [ + "SampleSiteCode", + "Easting", + "Northing", + "VegetationType", + "Site", + "Collection Date", + "VWC_1", + "VWC_2", + "avg_VWC", + "Temp_1", + "Temp_2", + "avg_Temp" + ], + "interpretation": "Direct dated TDR volumetric water content observations with embedded UTM coordinates. VWC_1 and VWC_2 are replicate measurements; avg_VWC is a derived average and is not used as an independent measurement." + }, + { + "name": "ess-dive-64109adb5fba6b5-20260114T183043578/NEON_2018_EMI_survey", + "category": "empty_or_non_payload_directory", + "interpretation": "Directory was present but contained no files in the allowed raw package listing." + } + ], + "decision": { + "include": true, + "rules": [ + "Contains direct volumetric water content observations.", + "Machine-readable dated CSV payload is available.", + "Site identifiers and UTM coordinates are embedded in the payload." + ] + }, + "location_resolution": { + "source": "NEON_plot_TDR.csv", + "site_id_column": "SampleSiteCode", + "coordinate_columns": [ + "Easting", + "Northing" + ], + "source_crs": "EPSG:32613", + "target_crs": "EPSG:4326", + "qc_flag": null + }, + "harmonization_plan": { + "datetime_UTC": "Parse Collection Date as America/Denver local date and convert local midnight to UTC.", + "site_id": "SampleSiteCode", + "depth_m": null, + "depth_note": "No depth column or fold-local held-out metadata was available; preserve as missing rather than infer a depth.", + "replicate": "Parse replicate 1 and 2 from VWC_1 and VWC_2.", + "is_timeseries": false, + "interval_min": null, + "volumetric_water_content_m3_m3": "Melt VWC_1 and VWC_2, drop -9999 sentinels, divide by 100.", + "gravimetric_water_content_gH2O_gs": null, + "water_potential_kPa": null + }, + "quality_filters": [ + "Drop rows whose Collection Date cannot be parsed.", + "Drop VWC replicate values equal to -9999 or otherwise nonnumeric.", + "Do not use avg_VWC because it is derived from replicate measurements." + ] +} diff --git a/evaluations/fold-07-holdout-9/agent_outputs/harmonize_heldout.py b/evaluations/fold-07-holdout-9/agent_outputs/harmonize_heldout.py new file mode 100644 index 0000000..7967ba6 --- /dev/null +++ b/evaluations/fold-07-holdout-9/agent_outputs/harmonize_heldout.py @@ -0,0 +1,79 @@ +from __future__ import annotations + +from pathlib import Path +import numpy as np +import pandas as pd + +PACKAGE_ID = "ess-dive-460e696d8210ed3-20260309T155937802" +RAW_BASE = Path("/h/jmc/ess-dive_wfsfa_soil_datasets") +RAW_FILE = RAW_BASE / PACKAGE_ID / "NEON_plot_TDR.csv" +OUT_FILE = Path(__file__).resolve().parent / "heldout_harmonized.csv" + +HARMONIZED_COLUMNS = [ + "datetime_UTC", + "site_id", + "depth_m", + "replicate", + "is_timeseries", + "interval_min", + "volumetric_water_content_m3_m3", + "gravimetric_water_content_gH2O_gs", + "water_potential_kPa", +] + + +def parse_local_date_to_utc(series: pd.Series) -> pd.Series: + dt = pd.to_datetime(series, format="%Y-%m-%d", errors="coerce") + dt = dt.dt.tz_localize("America/Denver", ambiguous="NaT", nonexistent="shift_forward") + return dt.dt.tz_convert("UTC") + + +def ensure_harmonized_cols(df: pd.DataFrame) -> pd.DataFrame: + for col in HARMONIZED_COLUMNS: + if col not in df.columns: + df[col] = np.nan + return df[HARMONIZED_COLUMNS] + + +def harmonize() -> pd.DataFrame: + df = pd.read_csv(RAW_FILE) + df["datetime_UTC"] = parse_local_date_to_utc(df["Collection Date"]) + df = df[df["datetime_UTC"].notna()].copy() + + long = df.melt( + id_vars=["datetime_UTC", "SampleSiteCode"], + value_vars=["VWC_1", "VWC_2"], + var_name="source_variable", + value_name="volumetric_water_content_m3_m3", + ) + long["volumetric_water_content_m3_m3"] = pd.to_numeric( + long["volumetric_water_content_m3_m3"], errors="coerce" + ) + long = long[ + long["volumetric_water_content_m3_m3"].notna() + & (long["volumetric_water_content_m3_m3"] != -9999) + ].copy() + long["volumetric_water_content_m3_m3"] = long["volumetric_water_content_m3_m3"] / 100.0 + + long["site_id"] = long["SampleSiteCode"].astype(str) + long["replicate"] = pd.to_numeric( + long["source_variable"].str.extract(r"VWC_(\d+)")[0], errors="coerce" + ).astype("Int64") + long["depth_m"] = np.nan + long["is_timeseries"] = False + long["interval_min"] = np.nan + long["gravimetric_water_content_gH2O_gs"] = np.nan + long["water_potential_kPa"] = np.nan + + out = ensure_harmonized_cols(long) + out = out.sort_values(["datetime_UTC", "site_id", "replicate"], kind="stable").reset_index(drop=True) + out["datetime_UTC"] = out["datetime_UTC"].dt.strftime("%Y-%m-%dT%H:%M:%SZ") + return out + + +if __name__ == "__main__": + harmonized = harmonize() + harmonized.to_csv(OUT_FILE, index=False) + print(f"wrote {OUT_FILE}") + print(f"rows {len(harmonized)}") + print("columns " + ",".join(harmonized.columns)) diff --git a/evaluations/fold-07-holdout-9/agent_outputs/heldout_harmonized.csv b/evaluations/fold-07-holdout-9/agent_outputs/heldout_harmonized.csv new file mode 100644 index 0000000..3b67585 --- /dev/null +++ b/evaluations/fold-07-holdout-9/agent_outputs/heldout_harmonized.csv @@ -0,0 +1,665 @@ +datetime_UTC,site_id,depth_m,replicate,is_timeseries,interval_min,volumetric_water_content_m3_m3,gravimetric_water_content_gH2O_gs,water_potential_kPa 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"NEON_plot_TDR.csv" + ], + "destination_variable": "datetime_UTC", + "transformation": "Parse date using format %Y-%m-%d in America/Denver local time and convert to UTC. Drop rows with unparseable date strings.", + "unit_conversion": null + } + }, + "depth": { + "pattern_1": { + "source_pattern": null, + "source_files": null, + "destination_variable": "depth_m", + "transformation": "Depth is not reported in the allowed held-out source file; populate with missing values.", + "unit_conversion": null + } + }, + "latitude": { + "pattern_1": { + "source_pattern": "Northing", + "source_files": [ + "NEON_plot_TDR.csv" + ], + "destination_variable": "latitude", + "transformation": "Use payload Northing with Easting for site coordinates.", + "unit_conversion": "Reproject from EPSG:32613 (WGS84 UTM Zone 13N, meters) to EPSG:4326 (WGS84, decimal degrees)." + } + }, + "longitude": { + "pattern_1": { + "source_pattern": "Easting", + "source_files": [ + "NEON_plot_TDR.csv" + ], + "destination_variable": "longitude", + "transformation": "Use payload Easting with Northing for site coordinates.", + "unit_conversion": "Reproject from EPSG:32613 (WGS84 UTM Zone 13N, meters) to EPSG:4326 (WGS84, decimal degrees)." + } + }, + "replicate": { + "pattern_1": { + "source_pattern": "VWC_1, VWC_2", + "source_files": [ + "NEON_plot_TDR.csv" + ], + "destination_variable": "replicate", + "transformation": "Melt VWC_1 and VWC_2 and parse the trailing integer as replicate.", + "unit_conversion": null + } + }, + "site_id": { + "pattern_1": { + "source_pattern": "SampleSiteCode", + "source_files": [ + "NEON_plot_TDR.csv" + ], + "destination_variable": "site_id", + "transformation": "Rename SampleSiteCode to site_id.", + "unit_conversion": null + } + }, + "soil_water_potential": { + "pattern_1": { + "source_pattern": null, + "source_files": null, + "destination_variable": "water_potential_kPa", + "transformation": "Soil water potential is not reported in the source; populate with missing values.", + "unit_conversion": null + } + }, + "gravimetric_water_content": { + "pattern_1": { + "source_pattern": null, + "source_files": null, + "destination_variable": "gravimetric_water_content_gH2O_gs", + "transformation": "Gravimetric water content is not reported in the source; populate with missing values.", + "unit_conversion": null + } + }, + "volumetric_water_content": { + "pattern_1": { + "source_pattern": "VWC_1, VWC_2", + "source_files": [ + "NEON_plot_TDR.csv" + ], + "destination_variable": "volumetric_water_content_m3_m3", + "transformation": "Coerce replicate columns from wide to long format and remove -9999 sentinel values. avg_VWC is a derived average and is not used.", + "unit_conversion": "Divide by 100 to convert from percent to m3/m3." + } + } + } +} diff --git a/evaluations/fold-07-holdout-9/agent_outputs/mapping_notes.md b/evaluations/fold-07-holdout-9/agent_outputs/mapping_notes.md new file mode 100644 index 0000000..597dcb1 --- /dev/null +++ b/evaluations/fold-07-holdout-9/agent_outputs/mapping_notes.md @@ -0,0 +1,25 @@ +# Held-out soil moisture harmonization notes + +Dataset: `ess-dive-460e696d8210ed3-20260309T155937802` +DOI: `doi:10.15485/3013006` + +## Decision + +INCLUDE. The allowed raw package contains `NEON_plot_TDR.csv`, a machine-readable CSV with dated direct TDR volumetric water content observations. `SampleSiteCode`, `Easting`, and `Northing` provide site identity and location metadata in the payload. + +## Payload interpretation + +- `VWC_1` and `VWC_2` are treated as two replicate volumetric water content observations. +- `avg_VWC` is a derived average and is not emitted as a separate observation. +- `VWC_*` source units are percent, converted to `m3/m3` by dividing by 100. +- `Collection Date` is parsed as an America/Denver local date and converted to UTC. +- The observations are discrete campaign samples, so `is_timeseries = False` and `interval_min = NaN`. +- The allowed raw file does not report sampling depth; `depth_m` is left missing. + +## Filtering + +Rows with unparseable collection dates are dropped. Replicate values equal to `-9999` are treated as missing sentinel values and dropped after reshaping. + +## Location + +Coordinates are embedded in the payload as `Easting` and `Northing`; the mapping documents reprojection from EPSG:32613 to EPSG:4326. No location QC flag is needed because coordinates are present in the source. diff --git a/evaluations/fold-07-holdout-9/evaluation_metrics.json b/evaluations/fold-07-holdout-9/evaluation_metrics.json new file mode 100644 index 0000000..80528e7 --- /dev/null +++ b/evaluations/fold-07-holdout-9/evaluation_metrics.json @@ -0,0 +1,60 @@ +{ + "fold": "fold-07-holdout-9", + "dataset_indices": [ + 9 + ], + "trace_forbidden_path_scan_matches": 0, + "agent_output": { + "rows": 664, + "target_columns_present": 9, + "schema_equal": true, + "extra_columns": [] + }, + "gold_output": { + "rows": 672, + "columns": 9 + }, + "output_equivalence": { + "key_includes_dataset_index": false, + "unique_agent_keys": 664, + "unique_gold_keys": 672, + "key_intersection": 0, + "agent_extra_keys": 664, + "agent_missing_gold_keys": 672, + "common_rows": 0, + "shared_row_value_matches": { + "interval_min": "0/0", + "volumetric_water_content_m3_m3": "0/0", + "gravimetric_water_content_gH2O_gs": "0/0", + "water_potential_kPa": "0/0", + "is_timeseries": "0/0" + }, + "row_precision": 0.0, + "gold_recall": 0.0 + }, + "json_mapping_equivalence": { + "top_level_exact_matches": "7/7", + "top_level_matches": { + "index": true, + "dataset_identifier": true, + "doi": true, + "archive_repository": true, + "data_payload_files": true, + "location_metadata_files": true, + "sensor_metadata_files": true + }, + "gold_mapping_categories_present": "8/8", + "extra_agent_categories": [ + "gravimetric_water_content" + ], + "missing_gold_categories": [], + "field_level_exact_matches": "27/40", + "field_exact_matches_by_name": { + "destination_variable": "8/8", + "source_pattern": "5/8", + "source_files": "8/8", + "transformation": "0/8", + "unit_conversion": "6/8" + } + } +}