From e8de8e7cdbebf4c93ed3dfd347d902a98a3cd127 Mon Sep 17 00:00:00 2001 From: John-Marc Chandonia Date: Tue, 30 Jun 2026 16:15:14 -0700 Subject: [PATCH] add fold02 agent evaluation bundle --- .../fold-02-holdout-15-26/AGENT_ACTION_LOG.md | 63 ++ .../AGENT_INSTRUCTIONS.md | 11 + .../fold-02-holdout-15-26/EVALUATION.md | 45 ++ .../fold-02-holdout-15-26/MANIFEST.json | 36 + .../agent_outputs/curator_bundle.json | 206 +++++ .../agent_outputs/harmonize_heldout.py | 309 ++++++++ .../agent_outputs/heldout_harmonized.csv | 712 ++++++++++++++++++ .../heldout_harmonized_dataset_15.csv | 287 +++++++ .../heldout_harmonized_dataset_26.csv | 426 +++++++++++ .../agent_outputs/mapping.json | 184 +++++ .../agent_outputs/mapping_notes.md | 20 + .../evaluation_metrics.json | 45 ++ 12 files changed, 2344 insertions(+) create mode 100644 evaluations/fold-02-holdout-15-26/AGENT_ACTION_LOG.md create mode 100644 evaluations/fold-02-holdout-15-26/AGENT_INSTRUCTIONS.md create mode 100644 evaluations/fold-02-holdout-15-26/EVALUATION.md create mode 100644 evaluations/fold-02-holdout-15-26/MANIFEST.json create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/curator_bundle.json create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_26.csv create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/mapping.json create mode 100644 evaluations/fold-02-holdout-15-26/agent_outputs/mapping_notes.md create mode 100644 evaluations/fold-02-holdout-15-26/evaluation_metrics.json diff --git a/evaluations/fold-02-holdout-15-26/AGENT_ACTION_LOG.md b/evaluations/fold-02-holdout-15-26/AGENT_ACTION_LOG.md new file mode 100644 index 0000000..c73d5d0 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/AGENT_ACTION_LOG.md @@ -0,0 +1,63 @@ +- 2026-06-30T15:54:23-07:00 | action=command | subject=mkdir -p .runs/fold-02-holdout-15-26/agent_outputs | reason=initialize action log and output directory +- 2026-06-30T15:54:39-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/AGENT_INSTRUCTIONS.md | reason=read mandatory fold-local benchmark instructions +- 2026-06-30T15:54:39-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/MANIFEST.json | reason=read fold manifest for held-out datasets and allowed exemplars +- 2026-06-30T15:54:39-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/skills/essdive_sm_curator/SKILL.md | reason=read fold-local curator skill +- 2026-06-30T15:54:39-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/skills/essdive_sm_harmonizer/SKILL.md | reason=read fold-local harmonizer skill +- 2026-06-30T15:54:50-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/skills/essdive_sm_curator/SKILL.md lines 261-520 | reason=complete fold-local curator skill read +- 2026-06-30T15:54:50-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/skills/essdive_sm_harmonizer/SKILL.md lines 261-620 | reason=complete fold-local harmonizer skill read +- 2026-06-30T15:55:00-07:00 | action=command | subject=wc -l fold-local instruction and skill files | reason=verify complete local skill file lengths before proceeding +- 2026-06-30T15:55:09-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/skills/essdive_sm_curator/SKILL.md lines 521-556 | reason=finish complete fold-local curator skill read +- 2026-06-30T15:55:16-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26 | reason=inventory fold-local sandbox files and allowed exemplars +- 2026-06-30T15:55:23-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/data | reason=locate fold-local exemplar mapping, code, and metadata only +- 2026-06-30T15:55:40-07:00 | action=command | subject=python summarize fold-local sm_data_harmonization_mapping.json | reason=inspect allowed exemplar mapping schema and dataset patterns +- 2026-06-30T15:55:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json | reason=read fold-local exemplar mapping only +- 2026-06-30T15:56:34-07:00 | action=directory_listing | subject=/h/jmc/ess-dive_wfsfa_soil_datasets held-out package directories | reason=locate allowed raw held-out files for package classification +- 2026-06-30T15:56:54-07:00 | action=command | subject=python inspect two held-out raw CSV files | reason=summarize columns, row counts, and sample values for harmonization +- 2026-06-30T15:56:54-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-987726ef1235abc-20230504T210342929747/TDR_survey_ER_20190701.csv | reason=inspect held-out dataset 15 raw payload +- 2026-06-30T15:56:54-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-f782da867133296-20230504T211008637996/ER18_soil_physical.csv | reason=inspect held-out dataset 26 raw payload +- 2026-06-30T15:57:13-07:00 | action=command | subject=sed read fold-local common.py and exemplar dataset scripts | reason=learn allowed code patterns and schema helper behavior +- 2026-06-30T15:57:13-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/data/gold/expert_code/harmonize_sm/common.py | reason=inspect fold-local shared helper functions +- 2026-06-30T15:57:13-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/data/gold/expert_code/harmonize_sm/dataset_09.py | reason=inspect similar discrete TDR/VWC exemplar +- 2026-06-30T15:57:13-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/data/gold/expert_code/harmonize_sm/dataset_18.py | reason=inspect similar discrete lab water-content exemplar +- 2026-06-30T15:57:31-07:00 | action=command | subject=curl ESS-DIVE API metadata for held-out package IDs | reason=retrieve DOI/title metadata for mapping entries without reading forbidden local gold outputs +- 2026-06-30T15:57:42-07:00 | action=command | subject=curl ESS-DIVE API metadata for held-out package IDs with network access | reason=sandbox DNS blocked public metadata lookup needed for DOI/title fields +- 2026-06-30T15:58:04-07:00 | action=command | subject=python parse downloaded ESS-DIVE metadata JSON from /tmp | reason=extract DOI, descriptions, distributions, spatial coverage for held-out curation +- 2026-06-30T15:58:04-07:00 | action=read | subject=/tmp/ess_meta_15.json | reason=read public ESS-DIVE metadata response for held-out dataset 15 +- 2026-06-30T15:58:04-07:00 | action=read | subject=/tmp/ess_meta_26.json | reason=read public ESS-DIVE metadata response for held-out dataset 26 +- 2026-06-30T16:00:46-07:00 | action=command | subject=python generate harmonize_heldout.py | reason=create benchmark harmonization script without apply_patch +- 2026-06-30T16:00:46-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=write final harmonization script under agent_outputs +- 2026-06-30T16:02:54-07:00 | action=command | subject=python regenerate harmonize_heldout.py | reason=fix script generation quoting after failed attempt +- 2026-06-30T16:02:54-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=write final harmonization script under agent_outputs +- 2026-06-30T16:03:02-07:00 | action=command | subject=python agent_outputs/harmonize_heldout.py | reason=run held-out harmonization script to generate final outputs +- 2026-06-30T16:03:02-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=execute generated harmonization script +- 2026-06-30T16:03:34-07:00 | action=command | subject=python edit harmonize_heldout.py remove pyproj dependency | reason=replace unavailable pyproj dependency with local UTM conversion +- 2026-06-30T16:03:34-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=read generated script for dependency fix +- 2026-06-30T16:03:34-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=write generated script with local UTM conversion +- 2026-06-30T16:03:55-07:00 | action=command | subject=python agent_outputs/harmonize_heldout.py | reason=rerun held-out harmonization after dependency fix +- 2026-06-30T16:03:55-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=execute generated harmonization script after dependency fix +- 2026-06-30T16:03:55.620789-07:00 | action=command | subject=harmonize_heldout.py main | reason=generate all held-out benchmark outputs +- 2026-06-30T16:03:55.621017-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-987726ef1235abc-20230504T210342929747/TDR_survey_ER_20190701.csv | reason=read held-out dataset 15 raw CSV for harmonization +- 2026-06-30T16:04:08-07:00 | action=command | subject=python edit harmonize_heldout.py qc_flag dtype | reason=fix NumPy string/NaN dtype promotion issue +- 2026-06-30T16:04:08-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=read generated script for qc_flag fix +- 2026-06-30T16:04:08-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=write generated script with qc_flag dtype fix +- 2026-06-30T16:04:17-07:00 | action=command | subject=python agent_outputs/harmonize_heldout.py | reason=rerun held-out harmonization after qc_flag fix +- 2026-06-30T16:04:17-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py | reason=execute generated harmonization script after qc_flag fix +- 2026-06-30T16:04:17.543179-07:00 | action=command | subject=harmonize_heldout.py main | reason=generate all held-out benchmark outputs +- 2026-06-30T16:04:17.543412-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-987726ef1235abc-20230504T210342929747/TDR_survey_ER_20190701.csv | reason=read held-out dataset 15 raw CSV for harmonization +- 2026-06-30T16:04:17.573359-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-f782da867133296-20230504T211008637996/ER18_soil_physical.csv | reason=read held-out dataset 26 raw CSV for harmonization +- 2026-06-30T16:04:17.592195-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv | reason=write optional per-dataset harmonized rows for held-out index 15 +- 2026-06-30T16:04:17.594437-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_26.csv | reason=write optional per-dataset harmonized rows for held-out index 26 +- 2026-06-30T16:04:17.597450-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv | reason=write concatenated held-out target-schema harmonized rows +- 2026-06-30T16:04:17.601624-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/mapping.json | reason=write held-out mapping entries +- 2026-06-30T16:04:17.603208-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/curator_bundle.json | reason=write curator decisions and structured inputs +- 2026-06-30T16:04:17.603503-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/mapping_notes.md | reason=write harmonization decisions and unresolved assumptions +- 2026-06-30T16:04:40-07:00 | action=directory_listing | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs | reason=verify final output files are present under agent_outputs +- 2026-06-30T16:04:40-07:00 | action=command | subject=python validate held-out output files | reason=check parseability, row counts, and target schema +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv | reason=validate combined held-out harmonized CSV +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv | reason=validate optional dataset 15 CSV +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_26.csv | reason=validate optional dataset 26 CSV +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/mapping.json | reason=validate mapping JSON +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/curator_bundle.json | reason=validate curator bundle JSON +- 2026-06-30T16:04:40-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/agent_outputs/mapping_notes.md | reason=validate mapping notes presence +- 2026-06-30T16:04:56-07:00 | action=command | subject=python scan AGENT_ACTION_LOG.md for forbidden path patterns | reason=perform mandatory anti-leakage log scan +- 2026-06-30T16:04:56-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26/AGENT_ACTION_LOG.md | reason=scan own action log for forbidden path patterns diff --git a/evaluations/fold-02-holdout-15-26/AGENT_INSTRUCTIONS.md b/evaluations/fold-02-holdout-15-26/AGENT_INSTRUCTIONS.md new file mode 100644 index 0000000..1fbb484 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/AGENT_INSTRUCTIONS.md @@ -0,0 +1,11 @@ +# 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-987726ef1235abc-20230504T210342929747` +- `ess-dive-f782da867133296-20230504T211008637996` diff --git a/evaluations/fold-02-holdout-15-26/EVALUATION.md b/evaluations/fold-02-holdout-15-26/EVALUATION.md new file mode 100644 index 0000000..524d1a2 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/EVALUATION.md @@ -0,0 +1,45 @@ +# fold-02-holdout-15-26 Agent Evaluation + +## Scope + +This directory records one sandboxed sub-agent attempt for held-out dataset indices `[15, 26]`. + +- Sandbox: `.runs/fold-02-holdout-15-26` +- Tracked artifact copy: `evaluations/fold-02-holdout-15-26` +- 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 | 711 | 586 | +| Target columns present | 9 / 9 | 9 / 9 | +| Schema exact match | true | n/a | +| Unique keyed rows recovered | 0 | 584 | +| Missing gold keyed rows | 584 | n/a | +| Extra agent keyed rows | 711 | 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: `{"heldout_indices": [15, 26], "note": "cluster mapping literal comparison not computed"}` + + +## 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=True`). diff --git a/evaluations/fold-02-holdout-15-26/MANIFEST.json b/evaluations/fold-02-holdout-15-26/MANIFEST.json new file mode 100644 index 0000000..e51293d --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/MANIFEST.json @@ -0,0 +1,36 @@ +{ + "name": "fold-02-holdout-15-26", + "holdout_indices": [ + 15, + 26 + ], + "holdout_identifiers": [ + "ess-dive-987726ef1235abc-20230504T210342929747", + "ess-dive-f782da867133296-20230504T211008637996" + ], + "exemplar_indices": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 16, + 17, + 18, + 23, + 24, + 25, + 27 + ], + "n_exemplars": 26, + "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-02-holdout-15-26/agent_outputs/curator_bundle.json b/evaluations/fold-02-holdout-15-26/agent_outputs/curator_bundle.json new file mode 100644 index 0000000..ce4a37f --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/agent_outputs/curator_bundle.json @@ -0,0 +1,206 @@ +{ + "datasets": [ + { + "package_id": "ess-dive-987726ef1235abc-20230504T210342929747", + "doi": "doi:10.15485/1648526", + "title": "Time-domain reflectometer survey across the East River Watershed, Colorado", + "curator_decision": "INCLUDE", + "exclusion_reason": null, + "data_payload_files": [ + { + "filename": "TDR_survey_ER_20190701.csv", + "columns": [ + "GPS_id", + "Sample_id", + "id", + "Site", + "Easting_m", + "Northing_m", + "Elevation_m", + "TDR_T(C)_1", + "TDR_T(C)_2", + "TDR_T(C)_3", + "TDR_SM(VWC%)_1", + "TDR_SM(VWC%)_2", + "TDR_SM(VWC%)_3", + "TDR_EC(mS/m)_1", + "TDR_EC(mS/m)_2", + "TDR_EC(mS/m)_3" + ], + "row_count_estimate": 101, + "file_size_bytes": 9944, + "soil_moisture_columns": [ + "TDR_SM(VWC%)_1", + "TDR_SM(VWC%)_2", + "TDR_SM(VWC%)_3" + ] + } + ], + "location_metadata_files": [ + { + "filename": "TDR_survey_ER_20190701.csv", + "columns": [ + "GPS_id", + "Site", + "Easting_m", + "Northing_m", + "Elevation_m" + ] + } + ], + "sensor_metadata_files": null, + "readme_content": null, + "location_resolution": { + "source": "data_payload", + "qc_flag_recommendation": null, + "site_coordinates_preview": [ + { + "site_id": "ss01", + "latitude": 38.919149485550214, + "longitude": -106.94877138958229 + }, + { + "site_id": "ss02", + "latitude": 38.91933691149292, + "longitude": -106.94862400823963 + }, + { + "site_id": "ss03", + "latitude": 38.91978827229731, + "longitude": -106.94838307097369 + }, + { + "site_id": "ss04", + "latitude": 38.91991967874135, + "longitude": -106.9481283728234 + }, + { + "site_id": "ss05", + "latitude": 38.920330599929436, + "longitude": -106.94777947145542 + }, + { + "site_id": "ss06", + "latitude": 38.92057817593979, + "longitude": -106.9477034701639 + }, + { + "site_id": "ss07", + "latitude": 38.91921055774817, + "longitude": -106.94981682010442 + }, + { + "site_id": "ss08", + "latitude": 38.91935265011536, + "longitude": -106.949706333905 + }, + { + "site_id": "ss09", + "latitude": 38.91951143173095, + "longitude": -106.949515893945 + }, + { + "site_id": "ss10", + "latitude": 38.919869384250404, + "longitude": -106.94931107187196 + } + ], + "site_coordinate_count": 101 + }, + "time_series_inference": { + "is_timeseries": false, + "interval_min": null, + "reasoning": "One spatial survey with repeated TDR readings per point; no row-level time sequence." + }, + "experimental_context": { + "manipulation_detected": false, + "manipulation_type": null, + "has_control_data": null, + "recommendation": "include_all" + }, + "similar_dataset_reference": { + "index": 9, + "reason": "Discrete VWC survey with UTM coordinates and replicate VWC columns." + }, + "open_questions": [ + "Row-level dates are absent; the harmonizer assigns package temporalCoverage startDate 2019-07-02 as the nominal survey date." + ], + "harmonized_rows": 286 + }, + { + "package_id": "ess-dive-f782da867133296-20230504T211008637996", + "doi": "doi:10.15485/1671826", + "title": "Soil bulk density and texture data collected during field survey associated with NEON AOP survey, East River, CO 2018", + "curator_decision": "INCLUDE", + "exclusion_reason": null, + "data_payload_files": [ + { + "filename": "ER18_soil_physical.csv", + "columns": [ + "Unnamed: 0", + "SampleSiteCode", + "SampleID", + "Soil Wet Weight (g)", + "Soil Dry Weight (g)", + "Lab #", + "SiteID", + "Whole sample wt, g", + ">2mm portion wt, g", + "SAND", + "SILT", + "CLAY", + "IGSN", + "Top sample depth_cm", + "Bottom sample depth_cm", + "Collection date", + "BD_tot g/cm3", + "<2mm portion wt, g", + "BD_2mm g/cm3", + "BD_wet g/cm3", + "water content %vol", + "mineral density g/cm3", + "sand density g/cm3", + "silt density g/cm3", + "clay density g/cm3" + ], + "row_count_estimate": 586, + "file_size_bytes": 81011, + "soil_moisture_columns": [ + "water content %vol", + "Soil Wet Weight (g)", + "Soil Dry Weight (g)" + ] + } + ], + "location_metadata_files": null, + "sensor_metadata_files": null, + "readme_content": null, + "location_resolution": { + "source": "package_metadata_bbox_only", + "qc_flag_recommendation": "g2", + "site_coordinates": [], + "site_coordinate_count": 0 + }, + "time_series_inference": { + "is_timeseries": false, + "interval_min": null, + "reasoning": "Discrete soil-core collection dates; no repeated sensor time series per site/depth." + }, + "experimental_context": { + "manipulation_detected": false, + "manipulation_type": null, + "has_control_data": null, + "recommendation": "include_all" + }, + "similar_dataset_reference": { + "index": 18, + "reason": "Discrete lab soil-water-content sampling with dated samples and depth ranges." + }, + "open_questions": [ + "Exact per-site coordinates are not in the payload; package metadata provides only a bounding box.", + "Depth is represented as the midpoint of reported ranges, corresponding to qc_flag d1 in mapping notes." + ], + "harmonized_rows": 425 + } + ] +} diff --git a/evaluations/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py b/evaluations/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py new file mode 100644 index 0000000..2f2524e --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/agent_outputs/harmonize_heldout.py @@ -0,0 +1,309 @@ +from __future__ import annotations + +import json +from datetime import datetime, timezone +from pathlib import Path + +import numpy as np +import pandas as pd +import math + +FOLD_DIR = Path('/scratch/jmc/data-harmonization-eval/.runs/fold-02-holdout-15-26') +OUT_DIR = FOLD_DIR / 'agent_outputs' +LOG_PATH = FOLD_DIR / 'AGENT_ACTION_LOG.md' +RAW_BASE = Path('/h/jmc/ess-dive_wfsfa_soil_datasets') + +TARGET_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', +] + +DATASETS = { + 15: { + 'package_id': 'ess-dive-987726ef1235abc-20230504T210342929747', + 'doi': 'doi:10.15485/1648526', + 'title': 'Time-domain reflectometer survey across the East River Watershed, Colorado', + 'file': 'TDR_survey_ER_20190701.csv', + 'nominal_date': '2019-07-02', + 'timezone': 'America/Denver', + 'depth_m': 0.25, + 'description': 'Near-surface point measurements of soil temperature, volumetric water content, and electrical conductivity using TDR at 25 cm depth across East River hillslopes in early July 2019.', + 'temporal_coverage': {'startDate': '2019-07-02', 'endDate': '2019-07-07'}, + }, + 26: { + 'package_id': 'ess-dive-f782da867133296-20230504T211008637996', + 'doi': 'doi:10.15485/1671826', + 'title': 'Soil bulk density and texture data collected during field survey associated with NEON AOP survey, East River, CO 2018', + 'file': 'ER18_soil_physical.csv', + 'timezone': 'America/Denver', + 'description': 'Soil cores collected from surface and subsurface depths for bulk density, volumetric water content, and texture across East River and nearby watersheds in summer 2018.', + 'temporal_coverage': {'startDate': '2018-06-12', 'endDate': '2018-10-15'}, + }, +} + + +def log_action(action: str, subject: str, reason: str) -> None: + ts = datetime.now(timezone.utc).astimezone().isoformat() + with LOG_PATH.open('a', encoding='utf-8') as fh: + fh.write(f'- {ts} | action={action} | subject={subject} | reason={reason}\n') + + +def raw_path(idx: int) -> Path: + meta = DATASETS[idx] + return RAW_BASE / meta['package_id'] / meta['file'] + + +def read_raw_csv(idx: int) -> pd.DataFrame: + path = raw_path(idx) + log_action('read', str(path), f'read held-out dataset {idx} raw CSV for harmonization') + return pd.read_csv(path) + + +def parse_local_date_to_utc(series: pd.Series, fmt: str | None = None, tz: str = 'America/Denver') -> pd.Series: + dt = pd.to_datetime(series, format=fmt, errors='coerce') + dt = dt.dt.tz_localize(tz, ambiguous='NaT', nonexistent='shift_forward') + return dt.dt.tz_convert('UTC') + + +def iso_utc(series: pd.Series) -> pd.Series: + return series.dt.strftime('%Y-%m-%dT%H:%M:%SZ') + + + +def utm13n_to_latlon(easting: pd.Series, northing: pd.Series) -> tuple[np.ndarray, np.ndarray]: + # WGS84 inverse Transverse Mercator for UTM zone 13N. + a = 6378137.0 + ecc_sq = 0.0066943799901413165 + k0 = 0.9996 + ecc_prime_sq = ecc_sq / (1.0 - ecc_sq) + e1 = (1.0 - math.sqrt(1.0 - ecc_sq)) / (1.0 + math.sqrt(1.0 - ecc_sq)) + x = pd.to_numeric(easting, errors='coerce').to_numpy(dtype=float) - 500000.0 + y = pd.to_numeric(northing, errors='coerce').to_numpy(dtype=float) + long_origin = -105.0 + m = y / k0 + mu = m / (a * (1.0 - ecc_sq / 4.0 - 3.0 * ecc_sq**2 / 64.0 - 5.0 * ecc_sq**3 / 256.0)) + phi1 = ( + mu + + (3.0 * e1 / 2.0 - 27.0 * e1**3 / 32.0) * np.sin(2.0 * mu) + + (21.0 * e1**2 / 16.0 - 55.0 * e1**4 / 32.0) * np.sin(4.0 * mu) + + (151.0 * e1**3 / 96.0) * np.sin(6.0 * mu) + ) + n1 = a / np.sqrt(1.0 - ecc_sq * np.sin(phi1) ** 2) + t1 = np.tan(phi1) ** 2 + c1 = ecc_prime_sq * np.cos(phi1) ** 2 + r1 = a * (1.0 - ecc_sq) / ((1.0 - ecc_sq * np.sin(phi1) ** 2) ** 1.5) + d = x / (n1 * k0) + lat = phi1 - (n1 * np.tan(phi1) / r1) * ( + d**2 / 2.0 + - (5.0 + 3.0 * t1 + 10.0 * c1 - 4.0 * c1**2 - 9.0 * ecc_prime_sq) * d**4 / 24.0 + + (61.0 + 90.0 * t1 + 298.0 * c1 + 45.0 * t1**2 - 252.0 * ecc_prime_sq - 3.0 * c1**2) * d**6 / 720.0 + ) + lon = np.deg2rad(long_origin) + ( + d + - (1.0 + 2.0 * t1 + c1) * d**3 / 6.0 + + (5.0 - 2.0 * c1 + 28.0 * t1 - 3.0 * c1**2 + 8.0 * ecc_prime_sq + 24.0 * t1**2) * d**5 / 120.0 + ) / np.cos(phi1) + lat = np.rad2deg(lat) + lon = np.rad2deg(lon) + lat[np.isnan(x) | np.isnan(y)] = np.nan + lon[np.isnan(x) | np.isnan(y)] = np.nan + return lon, lat + +def ensure_target_columns(df: pd.DataFrame) -> pd.DataFrame: + for col in TARGET_COLUMNS: + if col not in df.columns: + df[col] = np.nan + return df[TARGET_COLUMNS].copy() + + +def harmonize_dataset_15() -> tuple[pd.DataFrame, pd.DataFrame]: + ddf = read_raw_csv(15) + meta = DATASETS[15] + base = ddf.copy() + base['datetime_UTC'] = iso_utc(parse_local_date_to_utc(pd.Series([meta['nominal_date']] * len(base)), '%Y-%m-%d', meta['timezone'])) + base['site_id'] = base['GPS_id'].astype(str) + base['depth_m'] = float(meta['depth_m']) + base['is_timeseries'] = False + base['interval_min'] = np.nan + base['gravimetric_water_content_gH2O_gs'] = np.nan + base['water_potential_kPa'] = np.nan + + long = base.melt( + id_vars=['datetime_UTC', 'site_id', 'depth_m', 'is_timeseries', 'interval_min', 'gravimetric_water_content_gH2O_gs', 'water_potential_kPa'], + value_vars=['TDR_SM(VWC%)_1', 'TDR_SM(VWC%)_2', 'TDR_SM(VWC%)_3'], + var_name='source_variable', + value_name='volumetric_water_content_m3_m3', + ) + long['replicate'] = pd.to_numeric(long['source_variable'].str.extract(r'_(\d+)$')[0], errors='coerce') + long['volumetric_water_content_m3_m3'] = pd.to_numeric(long['volumetric_water_content_m3_m3'], errors='coerce') / 100.0 + long = long[long['volumetric_water_content_m3_m3'].notna()].copy() + harmonized = ensure_target_columns(long) + + loc_src = ddf[['GPS_id', 'Site', 'Easting_m', 'Northing_m', 'Elevation_m']].copy() + lon, lat = utm13n_to_latlon(loc_src['Easting_m'], loc_src['Northing_m']) + loc_src['site_id'] = loc_src['GPS_id'].astype(str) + loc_src['latitude'] = lat + loc_src['longitude'] = lon + loc_src['source_dataset_id'] = meta['package_id'] + loc_src['qc_flag'] = pd.Series(np.nan, index=loc_src.index, dtype=object) + loc_src.loc[loc_src['latitude'].isna() | loc_src['longitude'].isna(), 'qc_flag'] = 'g2' + loc = loc_src[['site_id', 'Site', 'Easting_m', 'Northing_m', 'Elevation_m', 'latitude', 'longitude', 'source_dataset_id', 'qc_flag']].drop_duplicates() + return harmonized, loc + + +def harmonize_dataset_26() -> tuple[pd.DataFrame, pd.DataFrame]: + ddf = read_raw_csv(26) + meta = DATASETS[26] + x = ddf.copy() + x['datetime_UTC'] = iso_utc(parse_local_date_to_utc(x['Collection date'], '%m/%d/%y', meta['timezone'])) + x['site_id'] = x['SampleSiteCode'].astype(str) + top = pd.to_numeric(x['Top sample depth_cm'], errors='coerce') + bottom = pd.to_numeric(x['Bottom sample depth_cm'], errors='coerce') + x['depth_m'] = ((top + bottom) / 2.0) / 100.0 + x['replicate'] = np.nan + x['is_timeseries'] = False + x['interval_min'] = np.nan + x['volumetric_water_content_m3_m3'] = pd.to_numeric(x['water content %vol'], errors='coerce') / 100.0 + wet = pd.to_numeric(x['Soil Wet Weight (g)'], errors='coerce') + dry = pd.to_numeric(x['Soil Dry Weight (g)'], errors='coerce') + x['gravimetric_water_content_gH2O_gs'] = (wet - dry) / dry + x.loc[(dry <= 0) | wet.isna() | dry.isna(), 'gravimetric_water_content_gH2O_gs'] = np.nan + x['water_potential_kPa'] = np.nan + x = x[x['volumetric_water_content_m3_m3'].notna() | x['gravimetric_water_content_gH2O_gs'].notna()].copy() + harmonized = ensure_target_columns(x) + loc = pd.DataFrame({ + 'site_id': sorted(ddf['SampleSiteCode'].dropna().astype(str).unique()), + 'latitude': np.nan, + 'longitude': np.nan, + 'source_dataset_id': meta['package_id'], + 'qc_flag': 'g2', + }) + return harmonized, loc + + +def build_mapping() -> list[dict]: + return [ + { + 'index': 15, + 'dataset_identifier': DATASETS[15]['package_id'], + 'doi': DATASETS[15]['doi'], + 'archive_repository': 'ESS-DIVE', + 'data_payload_files': [DATASETS[15]['file']], + 'location_metadata_files': [DATASETS[15]['file']], + 'sensor_metadata_files': None, + 'harmonization_mappings': { + 'datetime': {'pattern_1': {'source_pattern': 'package temporalCoverage startDate; filename date TDR_survey_ER_20190701.csv', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'datetime_UTC', 'transformation': 'Assign nominal survey date from package temporal coverage start (2019-07-02) and convert local America/Denver date to UTC.', 'unit_conversion': None}}, + 'site_id': {'pattern_1': {'source_pattern': 'GPS_id', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'site_id', 'transformation': 'Use GPS_id as the point-level site identifier because each row has separate coordinates.', 'unit_conversion': None}}, + 'depth': {'pattern_1': {'source_pattern': 'package description reports TDR at 25 cm', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'depth_m', 'transformation': 'Assign constant sampling depth 0.25 m.', 'unit_conversion': 'Divide reported 25 cm depth by 100 to convert to m.'}}, + 'replicate': {'pattern_1': {'source_pattern': 'TDR_SM(VWC%)_1, TDR_SM(VWC%)_2, TDR_SM(VWC%)_3', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'replicate', 'transformation': 'Parse trailing integer from repeated TDR VWC columns after wide-to-long reshape.', 'unit_conversion': None}}, + 'volumetric_water_content': {'pattern_1': {'source_pattern': 'TDR_SM(VWC%)_i', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'volumetric_water_content_m3_m3', 'transformation': 'Reshape replicate VWC percent columns to long rows and drop missing readings.', 'unit_conversion': 'Divide by 100 to convert percent VWC to m3/m3.'}}, + 'latitude': {'pattern_1': {'source_pattern': 'Northing_m', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'latitude', 'transformation': 'Reproject EPSG:32613 northing/easting to WGS84 latitude for location metadata.', 'unit_conversion': 'EPSG:32613 to EPSG:4326.'}}, + 'longitude': {'pattern_1': {'source_pattern': 'Easting_m', 'source_files': [DATASETS[15]['file']], 'destination_variable': 'longitude', 'transformation': 'Reproject EPSG:32613 easting/northing to WGS84 longitude for location metadata.', 'unit_conversion': 'EPSG:32613 to EPSG:4326.'}}, + }, + }, + { + 'index': 26, + 'dataset_identifier': DATASETS[26]['package_id'], + 'doi': DATASETS[26]['doi'], + 'archive_repository': 'ESS-DIVE', + 'data_payload_files': [DATASETS[26]['file']], + 'location_metadata_files': None, + 'sensor_metadata_files': None, + 'harmonization_mappings': { + 'datetime': {'pattern_1': {'source_pattern': 'Collection date', 'source_files': [DATASETS[26]['file']], 'destination_variable': 'datetime_UTC', 'transformation': 'Parse collection date as local America/Denver date and convert to UTC.', 'unit_conversion': None}}, + 'site_id': {'pattern_1': {'source_pattern': 'SampleSiteCode', 'source_files': [DATASETS[26]['file']], 'destination_variable': 'site_id', 'transformation': 'Direct column mapping.', 'unit_conversion': None}}, + 'depth': {'pattern_1': {'source_pattern': 'Top sample depth_cm, Bottom sample depth_cm', 'source_files': [DATASETS[26]['file']], 'destination_variable': 'depth_m', 'transformation': 'Use midpoint of reported depth range.', 'unit_conversion': 'Average top and bottom depths in cm, then divide by 100 to convert to m.'}}, + 'volumetric_water_content': {'pattern_1': {'source_pattern': 'water content %vol', 'source_files': [DATASETS[26]['file']], 'destination_variable': 'volumetric_water_content_m3_m3', 'transformation': 'Direct calculated volumetric water-content column from source data; rows without any moisture measure are excluded.', 'unit_conversion': 'Divide by 100 to convert percent volumetric water content to m3/m3.'}}, + 'gravimetric_water_content': {'pattern_1': {'source_pattern': 'Soil Wet Weight (g), Soil Dry Weight (g)', 'source_files': [DATASETS[26]['file']], 'destination_variable': 'gravimetric_water_content_gH2O_gs', 'transformation': 'Compute (wet weight - dry weight) / dry weight for rows with both weights.', 'unit_conversion': 'g water per g dry soil from gram weights.'}}, + 'latitude': {'pattern_1': {'source_pattern': None, 'source_files': [DATASETS[26]['file']], 'destination_variable': 'latitude', 'transformation': 'No per-site coordinates in payload; package metadata only provides a bounding box, so exact row coordinates are unresolved.', 'unit_conversion': None}}, + 'longitude': {'pattern_1': {'source_pattern': None, 'source_files': [DATASETS[26]['file']], 'destination_variable': 'longitude', 'transformation': 'No per-site coordinates in payload; package metadata only provides a bounding box, so exact row coordinates are unresolved.', 'unit_conversion': None}}, + }, + }, + ] + + +def build_curator_bundle(df15: pd.DataFrame, loc15: pd.DataFrame, df26: pd.DataFrame, loc26: pd.DataFrame) -> dict: + return { + 'datasets': [ + { + 'package_id': DATASETS[15]['package_id'], + 'doi': DATASETS[15]['doi'], + 'title': DATASETS[15]['title'], + 'curator_decision': 'INCLUDE', + 'exclusion_reason': None, + 'data_payload_files': [{'filename': DATASETS[15]['file'], 'columns': ['GPS_id', 'Sample_id', 'id', 'Site', 'Easting_m', 'Northing_m', 'Elevation_m', 'TDR_T(C)_1', 'TDR_T(C)_2', 'TDR_T(C)_3', 'TDR_SM(VWC%)_1', 'TDR_SM(VWC%)_2', 'TDR_SM(VWC%)_3', 'TDR_EC(mS/m)_1', 'TDR_EC(mS/m)_2', 'TDR_EC(mS/m)_3'], 'row_count_estimate': 101, 'file_size_bytes': raw_path(15).stat().st_size, 'soil_moisture_columns': ['TDR_SM(VWC%)_1', 'TDR_SM(VWC%)_2', 'TDR_SM(VWC%)_3']}], + 'location_metadata_files': [{'filename': DATASETS[15]['file'], 'columns': ['GPS_id', 'Site', 'Easting_m', 'Northing_m', 'Elevation_m']}], + 'sensor_metadata_files': None, + 'readme_content': None, + 'location_resolution': {'source': 'data_payload', 'qc_flag_recommendation': None, 'site_coordinates_preview': loc15[['site_id', 'latitude', 'longitude']].head(10).to_dict(orient='records'), 'site_coordinate_count': int(loc15['site_id'].nunique())}, + 'time_series_inference': {'is_timeseries': False, 'interval_min': None, 'reasoning': 'One spatial survey with repeated TDR readings per point; no row-level time sequence.'}, + 'experimental_context': {'manipulation_detected': False, 'manipulation_type': None, 'has_control_data': None, 'recommendation': 'include_all'}, + 'similar_dataset_reference': {'index': 9, 'reason': 'Discrete VWC survey with UTM coordinates and replicate VWC columns.'}, + 'open_questions': ['Row-level dates are absent; the harmonizer assigns package temporalCoverage startDate 2019-07-02 as the nominal survey date.'], + 'harmonized_rows': int(len(df15)), + }, + { + 'package_id': DATASETS[26]['package_id'], + 'doi': DATASETS[26]['doi'], + 'title': DATASETS[26]['title'], + 'curator_decision': 'INCLUDE', + 'exclusion_reason': None, + 'data_payload_files': [{'filename': DATASETS[26]['file'], 'columns': ['Unnamed: 0', 'SampleSiteCode', 'SampleID', 'Soil Wet Weight (g)', 'Soil Dry Weight (g)', 'Lab #', 'SiteID', 'Whole sample wt, g', '>2mm portion wt, g', 'SAND', 'SILT', 'CLAY', 'IGSN', 'Top sample depth_cm', 'Bottom sample depth_cm', 'Collection date', 'BD_tot g/cm3', '<2mm portion wt, g', 'BD_2mm g/cm3', 'BD_wet g/cm3', 'water content %vol', 'mineral density g/cm3', 'sand density g/cm3', 'silt density g/cm3', 'clay density g/cm3'], 'row_count_estimate': 586, 'file_size_bytes': raw_path(26).stat().st_size, 'soil_moisture_columns': ['water content %vol', 'Soil Wet Weight (g)', 'Soil Dry Weight (g)']}], + 'location_metadata_files': None, + 'sensor_metadata_files': None, + 'readme_content': None, + 'location_resolution': {'source': 'package_metadata_bbox_only', 'qc_flag_recommendation': 'g2', 'site_coordinates': [], 'site_coordinate_count': 0}, + 'time_series_inference': {'is_timeseries': False, 'interval_min': None, 'reasoning': 'Discrete soil-core collection dates; no repeated sensor time series per site/depth.'}, + 'experimental_context': {'manipulation_detected': False, 'manipulation_type': None, 'has_control_data': None, 'recommendation': 'include_all'}, + 'similar_dataset_reference': {'index': 18, 'reason': 'Discrete lab soil-water-content sampling with dated samples and depth ranges.'}, + 'open_questions': ['Exact per-site coordinates are not in the payload; package metadata provides only a bounding box.', 'Depth is represented as the midpoint of reported ranges, corresponding to qc_flag d1 in mapping notes.'], + 'harmonized_rows': int(len(df26)), + }, + ] + } + + +def write_json(path: Path, obj: object, reason: str) -> None: + log_action('write', str(path), reason) + path.write_text(json.dumps(obj, indent=2) + '\n', encoding='utf-8') + + +def write_csv(path: Path, df: pd.DataFrame, reason: str) -> None: + log_action('write', str(path), reason) + df.to_csv(path, index=False) + + +def write_text(path: Path, text: str, reason: str) -> None: + log_action('write', str(path), reason) + path.write_text(text, encoding='utf-8') + + +def main() -> None: + log_action('command', 'harmonize_heldout.py main', 'generate all held-out benchmark outputs') + OUT_DIR.mkdir(parents=True, exist_ok=True) + df15, loc15 = harmonize_dataset_15() + df26, loc26 = harmonize_dataset_26() + heldout = pd.concat([df15, df26], ignore_index=True) + + write_csv(OUT_DIR / 'heldout_harmonized_dataset_15.csv', df15, 'write optional per-dataset harmonized rows for held-out index 15') + write_csv(OUT_DIR / 'heldout_harmonized_dataset_26.csv', df26, 'write optional per-dataset harmonized rows for held-out index 26') + write_csv(OUT_DIR / 'heldout_harmonized.csv', heldout, 'write concatenated held-out target-schema harmonized rows') + write_json(OUT_DIR / 'mapping.json', build_mapping(), 'write held-out mapping entries') + write_json(OUT_DIR / 'curator_bundle.json', build_curator_bundle(df15, loc15, df26, loc26), 'write curator decisions and structured inputs') + + notes = f'''# Held-out Mapping Notes\n\n## Dataset 15\n\n- Included: direct TDR volumetric water-content measurements.\n- Rows: {len(df15)} long-format VWC readings from 101 survey points and up to three replicate TDR columns.\n- Date handling: the CSV lacks row-level dates; package temporal coverage starts on 2019-07-02, so all rows use 2019-07-02 local midnight converted to UTC.\n- Depth handling: package metadata states the TDR survey was at 25 cm, mapped to depth_m = 0.25.\n- Site handling: GPS_id is used as point-level site_id; coordinates are embedded as EPSG:32613 Easting/Northing in the payload.\n\n## Dataset 26\n\n- Included: soil-core volumetric water content and computable gravimetric water content from wet/dry weights.\n- Rows: {len(df26)} rows with at least one moisture measurement; rows containing only texture/bulk-density fields were excluded from the target moisture table.\n- Depth handling: reported top and bottom sample depths are converted to midpoint depth in meters; this is a depth-range approximation (qc d1 conceptually, but qc_flag is not part of the target CSV schema).\n- Location handling: no per-site coordinates are present in the payload; package metadata has only a bounding box, so exact site coordinates would be g2 if a location table were emitted.\n\n## Output Schema\n\nThe concatenated CSV contains exactly these columns: {', '.join(TARGET_COLUMNS)}.\n''' + write_text(OUT_DIR / 'mapping_notes.md', notes, 'write harmonization decisions and unresolved assumptions') + + summary = {'dataset_15_rows': int(len(df15)), 'dataset_26_rows': int(len(df26)), 'heldout_rows': int(len(heldout)), 'columns': TARGET_COLUMNS} + print(json.dumps(summary, indent=2)) + + +if __name__ == '__main__': + main() diff --git a/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv b/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv new file mode 100644 index 0000000..0bcc3a4 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized.csv @@ -0,0 +1,712 @@ +datetime_UTC,site_id,depth_m,replicate,is_timeseries,interval_min,volumetric_water_content_m3_m3,gravimetric_water_content_gH2O_gs,water_potential_kPa +2019-07-02T06:00:00Z,ss01,0.25,1.0,False,,0.0,, +2019-07-02T06:00:00Z,ss02,0.25,1.0,False,,0.10099999999999999,, +2019-07-02T06:00:00Z,ss03,0.25,1.0,False,,0.195,, +2019-07-02T06:00:00Z,ss04,0.25,1.0,False,,0.13,, +2019-07-02T06:00:00Z,ss05,0.25,1.0,False,,0.13699999999999998,, +2019-07-02T06:00:00Z,ss06,0.25,1.0,False,,0.318,, 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a/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv b/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv new file mode 100644 index 0000000..b2b7ab6 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/agent_outputs/heldout_harmonized_dataset_15.csv @@ -0,0 +1,287 @@ +datetime_UTC,site_id,depth_m,replicate,is_timeseries,interval_min,volumetric_water_content_m3_m3,gravimetric_water_content_gH2O_gs,water_potential_kPa +2019-07-02T06:00:00Z,ss01,0.25,1,False,,0.0,, +2019-07-02T06:00:00Z,ss02,0.25,1,False,,0.10099999999999999,, +2019-07-02T06:00:00Z,ss03,0.25,1,False,,0.195,, +2019-07-02T06:00:00Z,ss04,0.25,1,False,,0.13,, +2019-07-02T06:00:00Z,ss05,0.25,1,False,,0.13699999999999998,, +2019-07-02T06:00:00Z,ss06,0.25,1,False,,0.318,, +2019-07-02T06:00:00Z,ss07,0.25,1,False,,0.174,, +2019-07-02T06:00:00Z,ss08,0.25,1,False,,0.166,, +2019-07-02T06:00:00Z,ss09,0.25,1,False,,0.033,, +2019-07-02T06:00:00Z,ss10,0.25,1,False,,0.09,, 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"sensor_metadata_files": null, + "harmonization_mappings": { + "datetime": { + "pattern_1": { + "source_pattern": "package temporalCoverage startDate; filename date TDR_survey_ER_20190701.csv", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "datetime_UTC", + "transformation": "Assign nominal survey date from package temporal coverage start (2019-07-02) and convert local America/Denver date to UTC.", + "unit_conversion": null + } + }, + "site_id": { + "pattern_1": { + "source_pattern": "GPS_id", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "site_id", + "transformation": "Use GPS_id as the point-level site identifier because each row has separate coordinates.", + "unit_conversion": null + } + }, + "depth": { + "pattern_1": { + "source_pattern": "package description reports TDR at 25 cm", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "depth_m", + "transformation": "Assign constant sampling depth 0.25 m.", + "unit_conversion": "Divide reported 25 cm depth by 100 to convert to m." + } + }, + "replicate": { + "pattern_1": { + "source_pattern": "TDR_SM(VWC%)_1, TDR_SM(VWC%)_2, TDR_SM(VWC%)_3", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "replicate", + "transformation": "Parse trailing integer from repeated TDR VWC columns after wide-to-long reshape.", + "unit_conversion": null + } + }, + "volumetric_water_content": { + "pattern_1": { + "source_pattern": "TDR_SM(VWC%)_i", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "volumetric_water_content_m3_m3", + "transformation": "Reshape replicate VWC percent columns to long rows and drop missing readings.", + "unit_conversion": "Divide by 100 to convert percent VWC to m3/m3." + } + }, + "latitude": { + "pattern_1": { + "source_pattern": "Northing_m", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "latitude", + "transformation": "Reproject EPSG:32613 northing/easting to WGS84 latitude for location metadata.", + "unit_conversion": "EPSG:32613 to EPSG:4326." + } + }, + "longitude": { + "pattern_1": { + "source_pattern": "Easting_m", + "source_files": [ + "TDR_survey_ER_20190701.csv" + ], + "destination_variable": "longitude", + "transformation": "Reproject EPSG:32613 easting/northing to WGS84 longitude for location metadata.", + "unit_conversion": "EPSG:32613 to EPSG:4326." + } + } + } + }, + { + "index": 26, + "dataset_identifier": "ess-dive-f782da867133296-20230504T211008637996", + "doi": "doi:10.15485/1671826", + "archive_repository": "ESS-DIVE", + "data_payload_files": [ + "ER18_soil_physical.csv" + ], + "location_metadata_files": null, + "sensor_metadata_files": null, + "harmonization_mappings": { + "datetime": { + "pattern_1": { + "source_pattern": "Collection date", + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "datetime_UTC", + "transformation": "Parse collection date as local America/Denver date and convert to UTC.", + "unit_conversion": null + } + }, + "site_id": { + "pattern_1": { + "source_pattern": "SampleSiteCode", + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "site_id", + "transformation": "Direct column mapping.", + "unit_conversion": null + } + }, + "depth": { + "pattern_1": { + "source_pattern": "Top sample depth_cm, Bottom sample depth_cm", + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "depth_m", + "transformation": "Use midpoint of reported depth range.", + "unit_conversion": "Average top and bottom depths in cm, then divide by 100 to convert to m." + } + }, + "volumetric_water_content": { + "pattern_1": { + "source_pattern": "water content %vol", + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "volumetric_water_content_m3_m3", + "transformation": "Direct calculated volumetric water-content column from source data; rows without any moisture measure are excluded.", + "unit_conversion": "Divide by 100 to convert percent volumetric water content to m3/m3." + } + }, + "gravimetric_water_content": { + "pattern_1": { + "source_pattern": "Soil Wet Weight (g), Soil Dry Weight (g)", + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "gravimetric_water_content_gH2O_gs", + "transformation": "Compute (wet weight - dry weight) / dry weight for rows with both weights.", + "unit_conversion": "g water per g dry soil from gram weights." + } + }, + "latitude": { + "pattern_1": { + "source_pattern": null, + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "latitude", + "transformation": "No per-site coordinates in payload; package metadata only provides a bounding box, so exact row coordinates are unresolved.", + "unit_conversion": null + } + }, + "longitude": { + "pattern_1": { + "source_pattern": null, + "source_files": [ + "ER18_soil_physical.csv" + ], + "destination_variable": "longitude", + "transformation": "No per-site coordinates in payload; package metadata only provides a bounding box, so exact row coordinates are unresolved.", + "unit_conversion": null + } + } + } + } +] diff --git a/evaluations/fold-02-holdout-15-26/agent_outputs/mapping_notes.md b/evaluations/fold-02-holdout-15-26/agent_outputs/mapping_notes.md new file mode 100644 index 0000000..8e9fdd3 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/agent_outputs/mapping_notes.md @@ -0,0 +1,20 @@ +# Held-out Mapping Notes + +## Dataset 15 + +- Included: direct TDR volumetric water-content measurements. +- Rows: 286 long-format VWC readings from 101 survey points and up to three replicate TDR columns. +- Date handling: the CSV lacks row-level dates; package temporal coverage starts on 2019-07-02, so all rows use 2019-07-02 local midnight converted to UTC. +- Depth handling: package metadata states the TDR survey was at 25 cm, mapped to depth_m = 0.25. +- Site handling: GPS_id is used as point-level site_id; coordinates are embedded as EPSG:32613 Easting/Northing in the payload. + +## Dataset 26 + +- Included: soil-core volumetric water content and computable gravimetric water content from wet/dry weights. +- Rows: 425 rows with at least one moisture measurement; rows containing only texture/bulk-density fields were excluded from the target moisture table. +- Depth handling: reported top and bottom sample depths are converted to midpoint depth in meters; this is a depth-range approximation (qc d1 conceptually, but qc_flag is not part of the target CSV schema). +- Location handling: no per-site coordinates are present in the payload; package metadata has only a bounding box, so exact site coordinates would be g2 if a location table were emitted. + +## Output Schema + +The concatenated CSV contains exactly these 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. diff --git a/evaluations/fold-02-holdout-15-26/evaluation_metrics.json b/evaluations/fold-02-holdout-15-26/evaluation_metrics.json new file mode 100644 index 0000000..685cea2 --- /dev/null +++ b/evaluations/fold-02-holdout-15-26/evaluation_metrics.json @@ -0,0 +1,45 @@ +{ + "fold": "fold-02-holdout-15-26", + "dataset_indices": [ + 15, + 26 + ], + "trace_forbidden_path_scan_matches": 0, + "agent_output": { + "rows": 711, + "target_columns_present": 9, + "schema_equal": true, + "extra_columns": [ + "dataset_index" + ] + }, + "gold_output": { + "rows": 586, + "columns": 9 + }, + "output_equivalence": { + "key_includes_dataset_index": true, + "unique_agent_keys": 711, + "unique_gold_keys": 584, + "key_intersection": 0, + "agent_extra_keys": 711, + "agent_missing_gold_keys": 584, + "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": { + "note": "cluster mapping literal comparison not computed", + "heldout_indices": [ + 15, + 26 + ] + } +}