diff --git a/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.failed-write-location.md b/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.failed-write-location.md new file mode 100644 index 0000000..87d4d66 --- /dev/null +++ b/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.failed-write-location.md @@ -0,0 +1,50 @@ +2026-06-30T14:54:03-07:00 | shell_command | command=initialize\ AGENT_ACTION_LOG.md\ in\ sandbox | reason=create required action log before any inspection +2026-06-30T14:54:03-07:00 | outcome | exit_status=0 | created action log +2026-06-30T14:54:18-07:00 | shell_command | command=sed\ -n\ \'1\,240p\'\ AGENT_INSTRUCTIONS.md\ \&\&\ sed\ -n\ \'1\,240p\'\ MANIFEST.json | reason=read sandbox instructions and manifest +2026-06-30T14:54:18-07:00 | outcome | exit_status=0 | read AGENT_INSTRUCTIONS.md and MANIFEST.json +2026-06-30T14:54:28-07:00 | shell_command | command=find\ skills\ -maxdepth\ 4\ -type\ f\ \|\ sort\ \&\&\ find\ data\ -maxdepth\ 6\ -type\ f\ \|\ sort | reason=list sandbox-local skills and exemplar files +2026-06-30T14:54:28-07:00 | outcome | exit_status=0 | listed sandbox skills and data files +2026-06-30T14:54:38-07:00 | shell_command | command=sed\ -n\ \'1\,260p\'\ skills/essdive_sm_curator/SKILL.md\ \&\&\ sed\ -n\ \'1\,260p\'\ skills/essdive_sm_harmonizer/SKILL.md\ \&\&\ sed\ -n\ \'1\,260p\'\ skills/essdive_sm_harmonizer/soilmoisture_harmonization_general_insights.md | reason=read sandbox-local curator and harmonizer skill instructions +2026-06-30T14:54:38-07:00 | outcome | exit_status=0 | read skill instructions and harmonization insights +2026-06-30T14:54:44-07:00 | shell_command | command=sed\ -n\ \'261\,520p\'\ skills/essdive_sm_harmonizer/SKILL.md | reason=read remaining harmonizer skill instructions +2026-06-30T14:54:44-07:00 | outcome | exit_status=0 | read remaining harmonizer skill instructions +2026-06-30T14:54:50-07:00 | shell_command | command=sed\ -n\ \'521\,760p\'\ skills/essdive_sm_harmonizer/SKILL.md | reason=read final harmonizer skill instructions +2026-06-30T14:54:50-07:00 | outcome | exit_status=0 | read final harmonizer skill instructions +2026-06-30T14:55:01-07:00 | shell_command | command=python\ -c\ \'import\ json\;\ p=\"data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json\"\;\ data=json.load\(open\(p\)\)\;\ print\(type\(data\).__name__\,\ len\(data\)\)\;\ \[print\(e.get\(\"index\"\)\,\ e.get\(\"dataset_identifier\"\)\,\ e.get\(\"data_payload_files\"\)\,\ e.get\(\"location_metadata_files\"\)\)\ for\ e\ in\ data\]\' | reason=inspect fold-local mapping entries for schema examples and exemplar identifiers +2026-06-30T14:55:01-07:00 | outcome | exit_status=0 | inspected fold-local mapping summary +2026-06-30T14:55:10-07:00 | shell_command | command=find\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831\'\ -maxdepth\ 4\ -type\ f\ \|\ sort | reason=list files in allowed held-out raw package only +2026-06-30T14:55:10-07:00 | outcome | exit_status=0 | listed held-out raw package files +2026-06-30T14:55:18-07:00 | shell_command | command=find\ data/external\ -maxdepth\ 3\ -type\ f\ \|\ sort | reason=check sandbox-local cached ESS-DIVE metadata availability +2026-06-30T14:55:18-07:00 | outcome | exit_status=0 | checked sandbox-local cached metadata +2026-06-30T14:55:31-07:00 | shell_command | command=sed\ -n\ \'1\,220p\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/README.txt\'\ \&\&\ python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"flmd.csv\"\,\"df_data_dd.csv\"\,\"df_meta_dd.csv\"\,\"df_meta.csv\"\,\"df_data.csv\"\]\;\\nfor\ f\ in\ files:\\n\ \ \ \ p=base/f\;\ print\(\"\\n###\"\,\ f\)\;\ df=pd.read_csv\(p\,\ nrows=8\)\;\ print\(\"shape_sample\"\,\ df.shape\)\;\ print\(\"columns\"\,\ list\(df.columns\)\)\;\ print\(df.head\(8\).to_string\(index=False\)\)\' | reason=read README and preview raw CSV/dictionary files for held-out package +2026-06-30T14:55:31-07:00 | outcome | exit_status=1 | previewed README and raw CSV/dictionary files +2026-06-30T14:55:43-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"flmd.csv\"\,\"df_data_dd.csv\"\,\"df_meta_dd.csv\"\,\"df_meta.csv\"\,\"df_data.csv\"\]\;\ \[\ \(print\(\"\\n###\"\,\ f\)\,\ \(lambda\ df:\ \(print\(\"sample_shape\"\,\ df.shape\)\,\ print\(\"columns\"\,\ list\(df.columns\)\)\,\ print\(df.head\(8\).to_string\(index=False\)\)\)\)\(pd.read_csv\(base/f\,\ nrows=8\)\)\)\ for\ f\ in\ files\ \]\' | reason=preview held-out raw CSV and data dictionary files after prior quoting failure +2026-06-30T14:55:44-07:00 | outcome | exit_status=0 | previewed held-out raw CSV and dictionary files +2026-06-30T14:55:57-07:00 | shell_command | command=sed\ -n\ \'1\,260p\'\ data/gold/expert_code/harmonize_sm/common.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_03.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_05.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_10.py | reason=read sandbox exemplar harmonizer code patterns for common helpers and similar soil moisture/potential datasets +2026-06-30T14:55:57-07:00 | outcome | exit_status=0 | read exemplar harmonizer code patterns +2026-06-30T14:56:11-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\\nprint\(\"df_data_dd\"\)\;\ print\(pd.read_csv\(base/\"df_data_dd.csv\"\).to_string\(index=False\)\)\;\\nprint\(\"\\ndf_meta_dd\"\)\;\ print\(pd.read_csv\(base/\"df_meta_dd.csv\"\).to_string\(index=False\)\)\;\\nmeta=pd.read_csv\(base/\"df_meta.csv\"\)\;\ data=pd.read_csv\(base/\"df_data.csv\"\)\;\\nprint\(\"\\nrow_counts\"\,\ len\(meta\)\,\ len\(data\)\)\;\ print\(\"sites\"\,\ sorted\(meta\[\"site\"\].dropna\(\).unique\(\).tolist\(\)\)\)\;\ print\(\"date_min_max\"\,\ meta\[\"datetime\"\].min\(\)\,\ meta\[\"datetime\"\].max\(\)\)\;\ print\(\"data_nonnull\"\,\ data\[\[\"swc\"\,\"swp\"\,\"ET\"\]\].notna\(\).sum\(\).to_dict\(\)\)\;\ print\(\"duplicate_site_date\"\,\ int\(meta.duplicated\(\[\"site\"\,\"datetime\"\]\).sum\(\)\)\)\' | reason=read full data dictionaries and basic row alignment stats for held-out package +2026-06-30T14:56:11-07:00 | outcome | exit_status=1 | inspected dictionaries and held-out row alignment +2026-06-30T14:56:29-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ print\(\"df_data_dd\"\)\;\ print\(pd.read_csv\(base/\"df_data_dd.csv\"\).to_string\(index=False\)\)\;\ print\(\"\\ndf_meta_dd\"\)\;\ print\(pd.read_csv\(base/\"df_meta_dd.csv\"\).to_string\(index=False\)\)\;\ meta=pd.read_csv\(base/\"df_meta.csv\"\)\;\ data=pd.read_csv\(base/\"df_data.csv\"\)\;\ print\(\"\\nrow_counts\"\,\ len\(meta\)\,\ len\(data\)\)\;\ print\(\"sites\"\,\ sorted\(meta\[\"site\"\].dropna\(\).unique\(\).tolist\(\)\)\)\;\ print\(\"date_min_max\"\,\ meta\[\"datetime\"\].min\(\)\,\ meta\[\"datetime\"\].max\(\)\)\;\ print\(\"data_nonnull\"\,\ data\[\[\"swc\"\,\"swp\"\,\"ET\"\]\].notna\(\).sum\(\).to_dict\(\)\)\;\ print\(\"duplicate_site_date\"\,\ int\(meta.duplicated\(\[\"site\"\,\"datetime\"\]\).sum\(\)\)\)\' | reason=read full data dictionaries and basic row alignment stats for held-out package +2026-06-30T14:56:29-07:00 | outcome | exit_status=0 | inspected dictionaries and held-out row alignment +2026-06-30T14:56:50-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\;\ p=\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive_b924ba040ecefee_20250707T154402200/data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv\'\"\;\ df=pd.read_csv\(p\)\;\ print\(\"columns\"\,\ list\(df.columns\)\)\;\ print\(\"rows\"\,\ len\(df\)\)\;\ sites=\[\"ph1\"\,\"ph2\"\,\"sg5\"\,\"tb\"\,\"PHS1\"\,\"PHS2\"\,\"SG-EHS5\"\,\"TB\"\]\;\ mask=df.astype\(str\).apply\(lambda\ col:\ col.str.contains\(\"ph1\|ph2\|sg5\|tb\|PHS1\|PHS2\|SG-EHS5\|TB\"\,\ case=False\,\ na=False\)\).any\(axis=1\)\;\ print\(df.loc\[mask\].head\(40\).to_string\(index=False\)\)\' | reason=read shared raw location-reference CSV allowed by sandbox mapping entry 0 to resolve held-out site coordinates +2026-06-30T14:56:50-07:00 | outcome | exit_status=0 | inspected shared location-reference rows for held-out site abbreviations +2026-06-30T14:57:02-07:00 | shell_command | command=rg\ -n\ --ignore-case\ \'ph1\|ph2\|sg5\|tb\|pumphouse\|snodgrass\|taylor\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/README.txt\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/methods.py\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/DAE_train.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/DAE_predict.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/ET_train.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/ET_predict.ipynb\' | reason=search held-out raw documentation/code for site abbreviation meanings +2026-06-30T14:57:02-07:00 | outcome | exit_status=0 | searched held-out files for site abbreviation meanings +2026-06-30T14:57:15-07:00 | shell_command | command=python\ -c\ \'import\ json\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"DAE_train.ipynb\"\,\"DAE_predict.ipynb\"\,\"ET_train.ipynb\"\,\"ET_predict.ipynb\"\]\;\\nfor\ fn\ in\ files:\ nb=json.load\(open\(base/fn\)\)\;\\n\ for\ i\,c\ in\ enumerate\(nb.get\(\"cells\"\,\[\]\)\):\\n\ \ src=\"\".join\(c.get\(\"source\"\,\[\]\)\)\;\\n\ \ if\ \"if\ site\ in\ \[\\\\\'ph1\\\\\'\,\ \\\\\'ph2\\\\\'\,\ \\\\\'sg5\\\\\'\]\"\ in\ src\ or\ \"if\ site\ in\ \[\\\\\'tb\\\\\'\]\"\ in\ src:\ print\(\"###\"\,\ fn\,\ \"cell\"\,\ i\)\;\ print\(src\[:3000\]\)\' | reason=extract held-out notebook code cells that define site-specific behavior +2026-06-30T14:57:15-07:00 | outcome | exit_status=1 | extracted relevant notebook code cells +2026-06-30T14:57:28-07:00 | shell_command | command=python\ -c\ \'import\ json\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"DAE_train.ipynb\"\,\"DAE_predict.ipynb\"\,\"ET_train.ipynb\"\,\"ET_predict.ipynb\"\]\;\ \[\(print\(\"###\"\,\ fn\,\ \"cell\"\,\ i\)\,\ print\(src\[:3000\]\)\)\ for\ fn\ in\ files\ for\ i\,c\ in\ enumerate\(json.load\(open\(base/fn\)\).get\(\"cells\"\,\ \[\]\)\)\ for\ src\ in\ \[\"\".join\(c.get\(\"source\"\,\ \[\]\)\)\]\ if\ \(\"if\ site\ in\"\ in\ src\ and\ \(\"ph1\"\ in\ src\ or\ \"tb\"\ in\ src\)\)\]\' | reason=extract held-out notebook code cells that define site-specific behavior after prior quoting failure +2026-06-30T14:57:28-07:00 | outcome | exit_status=0 | extracted relevant notebook code cells +2026-06-30T14:57:41-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\;\ df=pd.read_csv\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive_b924ba040ecefee_20250707T154402200/data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv\'\"\)\;\ cols=\[\"Location_ID\"\,\"Location_Name\"\,\"Location_Alias\"\,\"Geographic_Region\"\,\"Parent_Location_ID\"\,\"Latitude\"\,\"Longitude\"\,\"Variables_Measured\"\,\"Description\"\]\;\ mask=df\[\"Location_ID\"\].astype\(str\).str.contains\(\"TB\|TBA\|TAYLOR\|Taylor\|tb\"\,\ case=False\,\ na=False\)\ \|\ df\[\"Location_Name\"\].astype\(str\).str.contains\(\"Taylor\|TB\|TBA\|tower\"\,\ case=False\,\ na=False\)\ \|\ df\[\"Location_Alias\"\].astype\(str\).str.contains\(\"\^tb\$\|TB\|TBA\"\,\ case=False\,\ na=False\)\;\ print\(df.loc\[mask\,\ cols\].head\(120\).to_string\(index=False\)\)\' | reason=search shared location-reference CSV for possible tb site coordinate match +2026-06-30T14:57:42-07:00 | outcome | exit_status=0 | searched shared location-reference for tb candidates +2026-06-30T14:58:19-07:00 | shell_command | command=mkdir\ -p\ agent_outputs | reason=create sandbox output directory +2026-06-30T14:58:19-07:00 | outcome | exit_status=0 | created agent_outputs directory if absent +2026-06-30T14:58:30-07:00 | shell_command | command=printf\ \'%s\ \|\ output_file_modify\ \|\ paths=%s\ \|\ reason=%s\\n\'\ \"2026-06-30T14:58:30-07:00\"\ \"agent_outputs/harmonize_heldout.py\,\ agent_outputs/mapping.json\,\ agent_outputs/mapping_notes.md\"\ \"prepare\ to\ create\ pilot\ harmonization\ script\ and\ mapping\ documentation\"\ \>\>\ AGENT_ACTION_LOG.md | reason=log upcoming output file creation before apply_patch edits +2026-06-30T14:58:30-07:00 | output_file_modify | paths=agent_outputs/harmonize_heldout.py, agent_outputs/mapping.json, agent_outputs/mapping_notes.md | reason=prepare to create pilot harmonization script and mapping documentation +2026-06-30T14:58:30-07:00 | outcome | exit_status=0 | logged upcoming output file creation +2026-06-30T14:59:30-07:00 | shell_command | command=printf\ \'%s\ \|\ output_file_modify\ \|\ paths=%s\ \|\ reason=%s\\n\'\ \"2026-06-30T14:59:30-07:00\"\ \"agent_outputs/harmonize_heldout.py\,\ agent_outputs/mapping.json\,\ agent_outputs/mapping_notes.md\"\ \"created\ pilot\ harmonization\ script\ and\ mapping\ documentation\ via\ apply_patch\"\ \>\>\ AGENT_ACTION_LOG.md | reason=log completed output file creation after apply_patch edits +2026-06-30T14:59:30-07:00 | output_file_modify | paths=agent_outputs/harmonize_heldout.py, agent_outputs/mapping.json, agent_outputs/mapping_notes.md | reason=created pilot harmonization script and mapping documentation via apply_patch +2026-06-30T14:59:30-07:00 | outcome | exit_status=0 | logged completed output file creation +2026-06-30T14:59:37-07:00 | shell_command | command=python\ agent_outputs/harmonize_heldout.py | reason=run pilot harmonization script to generate output CSVs +2026-06-30T14:59:37-07:00 | output_file_modify | paths=agent_outputs/heldout_harmonized.csv, agent_outputs/heldout_locations.csv | reason=script is expected to write generated output CSVs +2026-06-30T14:59:37-07:00 | outcome | exit_status=2 | ran pilot harmonization script +2026-06-30T14:59:53-07:00 | violation | paths=/scratch/jmc/data-harmonization-eval/agent_outputs/harmonize_heldout.py, /scratch/jmc/data-harmonization-eval/agent_outputs/mapping.json, /scratch/jmc/data-harmonization-eval/agent_outputs/mapping_notes.md | reason=apply_patch created output files outside the fold sandbox; stopping immediately per anti-leak rule diff --git a/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.md b/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.md new file mode 100644 index 0000000..edb2242 --- /dev/null +++ b/evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.md @@ -0,0 +1,40 @@ +# Agent Action Log + +- 2026-06-30T15:10:01-07:00 | command | mkdir -p /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs and create AGENT_ACTION_LOG.md | reason: initialize required log and output directory before inspection +- 2026-06-30T15:10:01-07:00 | exit_status=0 | outcome: log initialized and output directory ensured +- 2026-06-30T15:10:13-07:00 | list | find /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4 -maxdepth 3 -mindepth 1 -print | reason: discover fold-local files and sandbox-local skill paths +- 2026-06-30T15:10:13-07:00 | exit_status=0 | outcome: listed fold-local paths at maxdepth 3 +- 2026-06-30T15:10:25-07:00 | read | cat /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/AGENT_INSTRUCTIONS.md /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/MANIFEST.json /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/skills/essdive_sm_curator/SKILL.md /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/skills/essdive_sm_harmonizer/SKILL.md | reason: read fold-local task manifest, agent instructions, and required sandbox-local skill instructions +- 2026-06-30T15:10:25-07:00 | exit_status=0 | outcome: read requested fold-local instruction files +- 2026-06-30T15:10:37-07:00 | list | find /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/data/processed /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/data/gold/expert_code/harmonize_sm /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/skills/essdive_sm_harmonizer -maxdepth 4 -type f -print | reason: identify allowed fold-local exemplar mapping, expert code, and harmonizer reference files +- 2026-06-30T15:10:37-07:00 | exit_status=0 | outcome: listed allowed fold-local exemplar files +- 2026-06-30T15:10:52-07:00 | read/list | python - <<'PY' summarize fold-local processed mapping and list raw held-out package files | reason: inspect allowed mapping schema/examples and raw held-out package contents +- 2026-06-30T15:10:53-07:00 | exit_status=0 | outcome: summarized mapping entries and listed raw held-out files +- 2026-06-30T15:11:09-07:00 | read | python - <<'PY' read README, data dictionaries, CSV headers/previews, and fold-local harmonizer insights | reason: inspect raw held-out tabular files and local harmonizer reference guidance +- 2026-06-30T15:11:09-07:00 | exit_status=0 | outcome: inspected raw README/dictionaries/previews and harmonizer insights +- 2026-06-30T15:11:29-07:00 | read/list | python - <<'PY' read mapping entry 0 and list/read shared raw East Taylor reference location package previews | reason: resolve held-out site codes against allowed shared raw East Taylor location reference +- 2026-06-30T15:11:30-07:00 | exit_status=0 | outcome: inspected allowed shared raw East Taylor reference package +- 2026-06-30T15:11:54-07:00 | read | python - <<'PY' summarize held-out rows/site codes, reference location matches, and read selected allowed exemplar code | reason: derive site/location mapping and inspect allowed expert code patterns for harmonization script +- 2026-06-30T15:11:54-07:00 | exit_status=0 | outcome: summarized site matches and selected exemplar code +- 2026-06-30T15:12:08-07:00 | read/search | rg -n "ph1|ph2|sg5|tb|site|df_meta|df_data" /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package | reason: inspect raw package code/notebooks for site-code interpretation and data provenance +- 2026-06-30T15:12:08-07:00 | exit_status=0 | outcome: searched raw package files for site-code and dataframe references +- 2026-06-30T15:12:24-07:00 | read | python - <<'PY' extract raw notebook code cells and methods snippets mentioning site codes/data loading | reason: inspect held-out raw code in a controlled way for site code provenance +- 2026-06-30T15:12:24-07:00 | exit_status=0 | outcome: extracted controlled raw code snippets for site/data interpretation +- 2026-06-30T15:12:50-07:00 | read | python - <<'PY' compute held-out date interval summaries and exact site/location candidates | reason: infer time-series interval and document location resolution quality +- 2026-06-30T15:12:50-07:00 | exit_status=0 | outcome: computed interval summary and location candidate matches +- 2026-06-30T15:14:58-07:00 | command/write | python - <<'PY' create curator_bundle.json, harmonize_heldout.py, mapping.json, and mapping_notes.md under agent_outputs | reason: produce required curator and harmonizer artifacts in allowed output directory +- 2026-06-30T15:14:58-07:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/curator_bundle.json | reason: phase 1 curator bundle created +- 2026-06-30T15:14:58-07:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/harmonize_heldout.py | reason: phase 2 harmonization script created +- 2026-06-30T15:14:58-07:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/mapping.json | reason: phase 2 mapping entry created +- 2026-06-30T15:14:58-07:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/mapping_notes.md | reason: phase 2 mapping notes created +- 2026-06-30T15:14:58-07:00 | exit_status=0 | outcome: generated required JSON/script/notes artifacts except runtime CSV +- 2026-06-30T15:15:09-07:00 | command | python /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/harmonize_heldout.py | reason: run generated harmonization script to create heldout_harmonized.csv if safe +- 2026-06-30T22:15:09.796062+00:00 | read | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/curator_bundle.json | reason: load curator bundle generated in phase 1 +- 2026-06-30T22:15:09.796940+00:00 | read | /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data.csv | reason: read held-out raw measurement payload df_data.csv +- 2026-06-30T22:15:09.804592+00:00 | read | /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta.csv | reason: read held-out raw row-aligned metadata df_meta.csv +- 2026-06-30T22:15:09.823147+00:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv | reason: write harmonized held-out target-schema CSV +- 2026-06-30T22:15:09.829678+00:00 | exit_status=0 | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv | reason: wrote 1001 harmonized rows +- 2026-06-30T15:15:09-07:00 | write | /scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv | reason: harmonization script produced runtime CSV +- 2026-06-30T15:15:09-07:00 | exit_status=0 | outcome: harmonization script completed successfully +- 2026-06-30T15:15:27-07:00 | read/list | python - <<'PY' verify agent_outputs contents, harmonized CSV schema, and action log forbidden-path scan | reason: final verification of created files, output schema, and log safety +- 2026-06-30T15:15:27-07:00 | exit_status=0 | outcome: verified outputs and scanned action log for forbidden patterns diff --git a/evaluations/fold-03-holdout-4/AGENT_INSTRUCTIONS.md b/evaluations/fold-03-holdout-4/AGENT_INSTRUCTIONS.md new file mode 100644 index 0000000..9a9dbfb --- /dev/null +++ b/evaluations/fold-03-holdout-4/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-6c7085e9c544cc6-20250424T164534831` diff --git a/evaluations/fold-03-holdout-4/EVALUATION.md b/evaluations/fold-03-holdout-4/EVALUATION.md new file mode 100644 index 0000000..c5f9454 --- /dev/null +++ b/evaluations/fold-03-holdout-4/EVALUATION.md @@ -0,0 +1,173 @@ +# Fold 03 Holdout 4 Agent Evaluation + +## Scope + +This directory records one sandboxed sub-agent attempt on fold 03, where dataset +index 4 was held out: + +- Dataset: `ess-dive-6c7085e9c544cc6-20250424T164534831` +- Sandbox: `.runs/fold-03-holdout-4` +- Tracked artifact copy: `evaluations/fold-03-holdout-4` +- Successful agent trace: `AGENT_ACTION_LOG.md` +- Failed earlier trace retained for audit: `AGENT_ACTION_LOG.failed-write-location.md` + +The successful agent was instructed to use the fold-local Skill 1 curator and +Skill 2 harmonizer materials, write only under the fold sandbox, and log each +read/list/command/write action before performing it. + +## Anti-Leakage Audit + +The successful trace was scanned for direct evidence of forbidden access to: + +- root gold data: `/scratch/jmc/data-harmonization-eval/data/gold` +- root processed data: `/scratch/jmc/data-harmonization-eval/data/processed` +- other fold sandboxes +- the held-out expert module name: `dataset_04.py` +- explicit `violation` markers + +Command: + +```bash +rg -n '(/scratch/jmc/data-harmonization-eval/data/gold|/scratch/jmc/data-harmonization-eval/data/processed|/scratch/jmc/data-harmonization-eval/.runs/fold-(01|02|04|05|06|07|08|09|10|11|12|13)|dataset_04\.py|violation)' evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.md +``` + +Result: no matches. The trace therefore passes this targeted path audit. + +The first attempt failed the operational audit because it wrote to root +`agent_outputs/`; that trace is preserved separately in +`AGENT_ACTION_LOG.failed-write-location.md`. The successful retry wrote artifacts +under the fold sandbox only. + +## Output Equivalence Against Gold + +The gold comparison used the current expert module for dataset 4. Running that +module required an evaluation-only compatibility shim for `add_loc_qc`, because +NumPy 2 raises a dtype promotion error when mixing string QC flags and `np.nan`. +The shim affected only the location-QC side output after the harmonized table was +constructed; it did not alter the soil-moisture transformation being compared. + +Summary: + +| Metric | Agent | Gold | +| --- | ---: | ---: | +| Rows | 1001 | 552 | +| Columns | 9 | 9 | +| Schema exact match | yes | yes | +| Unique keyed rows recovered | 552 | 552 | +| Missing gold keyed rows | 0 | n/a | +| Extra keyed rows | 449 | n/a | + +Site counts: + +| site_id | Agent rows | Gold rows | +| --- | ---: | ---: | +| `ph1` | 275 | 275 | +| `ph2` | 148 | 148 | +| `sg5` | 129 | 129 | +| `tb` | 449 | 0 | + +For the 552 shared keyed rows, all checked target values matched gold: + +| Column | Matched rows | +| --- | ---: | +| `depth_m` | 552 / 552 | +| `interval_min` | 552 / 552 | +| `volumetric_water_content_m3_m3` | 552 / 552 | +| `gravimetric_water_content_gH2O_gs` | 552 / 552 | +| `water_potential_kPa` | 552 / 552 | +| `is_timeseries` | 552 / 552 | + +Interpretation: the agent recovered every gold observation and got the numeric +transformations right, but kept 449 `tb` rows that the gold expert drops. As a +full output submission, that is perfect recall and 552 / 1001 = 55.1% row +precision. After dropping `tb` and sorting, there were no observed cell-level +value differences in the target columns. + +Additional formatting/order differences: + +- Gold sorts by `datetime_UTC, site_id`; the agent leaves raw order. +- Gold stores timezone-aware UTC timestamps in the dataframe; the agent writes + ISO strings ending in `Z`. Parsed as UTC, the timestamps match. + +## JSON Mapping Match + +The generated `mapping.json` was compared to gold mapping entry 4 from +`data/gold/sm_data_harmonization_mapping.json`. + +Top-level exact matches: + +| Field | Match | +| --- | --- | +| `index` | yes | +| `dataset_identifier` | yes | +| `doi` | no | +| `archive_repository` | yes | +| `data_payload_files` | yes | +| `location_metadata_files` | no | +| `sensor_metadata_files` | yes | + +Mapping category coverage: + +- Gold categories present: 8 / 8 +- Extra agent category: `gravimetric_water_content` +- Missing gold categories: none + +Field-level exact matches across shared categories: + +| Field | Exact matches | +| --- | ---: | +| `destination_variable` | 8 / 8 | +| `source_pattern` | 5 / 8 | +| `source_files` | 4 / 8 | +| `transformation` | 0 / 8 | +| `unit_conversion` | 8 / 8 | +| Total | 25 / 40 | + +Important JSON differences: + +- Agent set `doi` to `null`; gold has `doi:10.15485/2561511`. +- Agent included an extra East Taylor reference file in + `location_metadata_files`; gold lists only `df_meta.csv`. +- Agent mapped `datetime.source_files` to `df_meta.csv`; gold JSON says + `df_data.csv`. The agent choice matches where the `datetime` field is actually + read from by both the gold code and the agent code, but it does not match the + gold JSON literally. +- Transformation prose did not match gold text literally. +- Agent included `gravimetric_water_content`, which is absent from the gold + mapping JSON even though the output schema contains + `gravimetric_water_content_gH2O_gs`. + +## Python Match + +The generated `harmonize_heldout.py` captured most of the gold expert +transformation: + +- Reads `df_data.csv` and `df_meta.csv`. +- Concatenates row-aligned data and metadata. +- Converts local `America/Denver` dates to UTC. +- Maps `site` to `site_id`. +- Sets `depth_m` to null. +- Sets `replicate` to `1`. +- Sets `is_timeseries` to `True`. +- Sets `interval_min` to `1440`. +- Maps `swc` to `volumetric_water_content_m3_m3`. +- Maps `swp` to `water_potential_kPa`. +- Sets `gravimetric_water_content_gH2O_gs` to null. + +Python misses relative to gold: + +- Did not drop rows where `site_id == "tb"`. +- Did not sort by `datetime_UTC, site_id`. +- Did not implement the gold module interface using `Context` and + `DatasetResult`. +- Did not emit the gold location side dataframe for `ph1`, `ph2`, and `sg5`. + +## Overall Assessment + +The successful sub-agent was strong on the executable transformation and weak +on the held-out curation details around row exclusion and location side output. +It appears to have obeyed the no-gold/no-other-fold constraint based on the +recorded trace and targeted path scan. The generated Python is close enough that +a small patch, dropping `tb` and sorting the output, would make the harmonized +target table match gold at the observed-value level. The generated JSON is +useful but only a moderate literal match to the held-out gold mapping. diff --git a/evaluations/fold-03-holdout-4/MANIFEST.json b/evaluations/fold-03-holdout-4/MANIFEST.json new file mode 100644 index 0000000..d58d586 --- /dev/null +++ b/evaluations/fold-03-holdout-4/MANIFEST.json @@ -0,0 +1,35 @@ +{ + "name": "fold-03-holdout-4", + "holdout_indices": [ + 4 + ], + "holdout_identifiers": [ + "ess-dive-6c7085e9c544cc6-20250424T164534831" + ], + "exemplar_indices": [ + 1, + 2, + 3, + 5, + 6, + 7, + 8, + 9, + 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-03-holdout-4/agent_outputs/curator_bundle.json b/evaluations/fold-03-holdout-4/agent_outputs/curator_bundle.json new file mode 100644 index 0000000..6146d02 --- /dev/null +++ b/evaluations/fold-03-holdout-4/agent_outputs/curator_bundle.json @@ -0,0 +1,145 @@ +{ + "package_id": "ess-dive-6c7085e9c544cc6-20250424T164534831", + "doi": null, + "doi_note": "DOI was not present in the allowed fold-local files or raw package files inspected; no network lookup was performed under the anti-leak constraints.", + "curator_decision": "INCLUDE", + "exclusion_reason": null, + "data_payload_files": [ + { + "filename": "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data.csv", + "columns": [ + "txmax", + "txmin", + "tomax", + "tomin", + "u", + "vpd", + "pa", + "precip", + "srad", + "nsrad", + "nlrad", + "rn", + "g", + "lai", + "swc", + "swp", + "xT", + "xu", + "h", + "ET" + ], + "row_count_estimate": 1001, + "file_size_mb": 0.109, + "column_preview": "txmax,txmin,tomax,tomin,u,vpd,pa,precip,srad,nsrad,nlrad,rn,g,lai,swc,swp,xT,xu,h,ET\n295.05,283.55,301.29,276.87,1.52,1194,70402,0,284.87,227.45,-99.84,127.61,4.42,2.26,0.165,-145.67,3.75,3.75,0.24,3.38", + "classification_reasoning": "Machine-readable daily meteorological, vegetation, and soil data. Data dictionary defines swc as 24-hour average depth-averaged soil water content in m3/m3 and swp as soil water potential in kPa." + } + ], + "location_metadata_files": [ + { + "filename": "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta.csv", + "columns": [ + "site", + "datetime", + "year", + "doy" + ], + "content_preview": "site,datetime,year,doy\nsg5,2022-07-22,2022,203\ntb,2022-10-15,2022,288", + "classification_reasoning": "Row-aligned site/date metadata for df_data.csv." + }, + { + "filename": "data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv", + "source_package_id": "ess-dive_b924ba040ecefee_20250707T154402200", + "columns": [ + "Location_ID", + "Location_Name", + "Location_Alias", + "Latitude", + "Longitude", + "Variables_Measured" + ], + "content_preview": "Used as allowed shared location-reference package from mapping index 0." + } + ], + "sensor_metadata_files": null, + "documentation_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/README.txt", + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data_dd.csv", + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta_dd.csv", + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/flmd.csv" + ], + "readme_content": "README describes notebooks for DAE observation repair and ET prediction neural networks. It states df_data.csv has one variable per column and one data instance per row; df_meta.csv has rows for sites used to collect df_data.", + "location_resolution": { + "source": "varadharajan_lookup_partial", + "qc_flag_recommendation": "g1 for matched East Taylor reference sites; g2 for unresolved tb if no operator-approved match is available", + "site_coordinates": [ + { + "site_id": "ph1", + "matched_reference_id": "ER-PHS1", + "latitude": 38.92, + "longitude": -106.95, + "qc_flag": "g1", + "confidence": "moderate", + "reason": "ph1 appears to correspond to Pumphouse sensor tower 1; reference site measures WC/WP." + }, + { + "site_id": "ph2", + "matched_reference_id": "ER-PHS2", + "latitude": 38.922583, + "longitude": -106.947288, + "qc_flag": "g1", + "confidence": "moderate", + "reason": "ph2 appears to correspond to Pumphouse sensor tower 2; reference site measures WC/WP." + }, + { + "site_id": "sg5", + "matched_reference_id": "SG-EHS5", + "latitude": 38.92625, + "longitude": -106.98, + "qc_flag": "g1", + "confidence": "moderate", + "reason": "sg5 appears to correspond to Snodgrass tower 5; reference site measures WC/WP." + }, + { + "site_id": "tb", + "matched_reference_id": null, + "latitude": null, + "longitude": null, + "qc_flag": "g2", + "confidence": "low", + "reason": "Only weak literal candidate WC-TBA1/TB1 was found; it is an ERT profile and was not used automatically." + } + ] + }, + "time_series_inference": { + "is_timeseries": true, + "interval_min": 1440.0, + "reasoning": "Each site has many dated daily records; data dictionary defines swc as a 24-hour average. Dates are irregular with gaps, but median within-site interval is 1 day." + }, + "experimental_context": { + "manipulation_detected": false, + "manipulation_type": null, + "has_control_data": null, + "recommendation": "include_all" + }, + "similar_dataset_reference": { + "index": 26, + "reason": "Uses the fold-local reference location dataset at mapping index 0 for site-coordinate lookup when package files do not provide coordinates." + }, + "harmonization_plan": { + "join_strategy": "Concatenate df_meta columns to df_data by row order after verifying equal row counts.", + "datetime": "Parse df_meta.datetime as a date in America/Denver and convert to UTC ISO-8601.", + "site_id": "Use df_meta.site as reported.", + "depth_m": "Set to NaN because source defines swc as depth-averaged but gives no depth interval.", + "replicate": "Set to 1; no replicate field is provided.", + "volumetric_water_content_m3_m3": "Use df_data.swc directly; source units are m3/m3.", + "water_potential_kPa": "Use df_data.swp directly; source units are kPa.", + "gravimetric_water_content_gH2O_gs": "Set to NaN; not reported." + }, + "open_questions": [ + "Package DOI is unknown from allowed local evidence.", + "Depth is only described as depth-averaged; no depth interval is documented in allowed files.", + "Site abbreviation tb was not confidently resolved to a coordinate in the allowed East Taylor reference package.", + "The package contains neural-network code and ET predictions, but df_data.csv appears to contain observed/direct predictor variables; ET was not harmonized because it is derived and outside the target schema." + ] +} diff --git a/evaluations/fold-03-holdout-4/agent_outputs/harmonize_heldout.py b/evaluations/fold-03-holdout-4/agent_outputs/harmonize_heldout.py new file mode 100644 index 0000000..e0d0a64 --- /dev/null +++ b/evaluations/fold-03-holdout-4/agent_outputs/harmonize_heldout.py @@ -0,0 +1,95 @@ +#!/usr/bin/env python3 +from __future__ import annotations + +from pathlib import Path +import json +import numpy as np +import pandas as pd + +FOLD_DIR = Path('/scratch/jmc/data-harmonization-eval/.runs/fold-03-holdout-4') +OUT_DIR = FOLD_DIR / 'agent_outputs' +LOG_PATH = FOLD_DIR / 'AGENT_ACTION_LOG.md' +CURATOR_BUNDLE_PATH = OUT_DIR / 'curator_bundle.json' +HELDOUT_CSV_PATH = OUT_DIR / 'heldout_harmonized.csv' +PACKAGE_ID = 'ess-dive-6c7085e9c544cc6-20250424T164534831' +RAW_DIR = Path('/h/jmc/ess-dive_wfsfa_soil_datasets') / PACKAGE_ID / 'Johnsen_Bi_2025_DAE_Manuscript_Data_Package' +DATA_PATH = RAW_DIR / 'df_data.csv' +META_PATH = RAW_DIR / 'df_meta.csv' + +TARGET_COLS = [ + '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 log_line(action: str, subject: str, reason: str) -> None: + ts = pd.Timestamp.now(tz='UTC').isoformat() + with LOG_PATH.open('a', encoding='utf-8') as fh: + fh.write(f'- {ts} | {action} | {subject} | reason: {reason}\n') + + +def ensure_harmonized_cols(df: pd.DataFrame) -> pd.DataFrame: + for col in TARGET_COLS: + if col not in df.columns: + df[col] = np.nan + return df[TARGET_COLS] + + +def parse_local_date_to_utc_iso(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') + dt = dt.dt.tz_convert('UTC') + return dt.dt.strftime('%Y-%m-%dT%H:%M:%SZ') + + +def harmonize() -> pd.DataFrame: + log_line('read', str(CURATOR_BUNDLE_PATH), 'load curator bundle generated in phase 1') + with CURATOR_BUNDLE_PATH.open('r', encoding='utf-8') as fh: + bundle = json.load(fh) + if bundle.get('package_id') != PACKAGE_ID: + raise ValueError(f'Unexpected package_id in curator bundle: {bundle.get("package_id")}') + + log_line('read', str(DATA_PATH), 'read held-out raw measurement payload df_data.csv') + ddf = pd.read_csv(DATA_PATH) + log_line('read', str(META_PATH), 'read held-out raw row-aligned metadata df_meta.csv') + mdf = pd.read_csv(META_PATH) + + if len(ddf) != len(mdf): + raise ValueError(f'Row count mismatch: df_data={len(ddf)} df_meta={len(mdf)}') + required_data = {'swc', 'swp'} + required_meta = {'site', 'datetime'} + missing_data = required_data.difference(ddf.columns) + missing_meta = required_meta.difference(mdf.columns) + if missing_data or missing_meta: + raise ValueError(f'Missing required columns: data={sorted(missing_data)} meta={sorted(missing_meta)}') + + x = pd.concat([mdf.reset_index(drop=True), ddf.reset_index(drop=True)], axis=1) + out = pd.DataFrame(index=x.index) + out['datetime_UTC'] = parse_local_date_to_utc_iso(x['datetime']) + out['site_id'] = x['site'].astype(str) + out['depth_m'] = np.nan + out['replicate'] = 1 + out['is_timeseries'] = True + out['interval_min'] = 1440.0 + out['volumetric_water_content_m3_m3'] = pd.to_numeric(x['swc'], errors='coerce') + out['gravimetric_water_content_gH2O_gs'] = np.nan + out['water_potential_kPa'] = pd.to_numeric(x['swp'], errors='coerce') + out = ensure_harmonized_cols(out) + out = out[out['datetime_UTC'].notna()].copy() + return out + + +if __name__ == '__main__': + OUT_DIR.mkdir(parents=True, exist_ok=True) + df = harmonize() + log_line('write', str(HELDOUT_CSV_PATH), 'write harmonized held-out target-schema CSV') + df.to_csv(HELDOUT_CSV_PATH, index=False) + log_line('exit_status=0', str(HELDOUT_CSV_PATH), f'wrote {len(df)} harmonized rows') + print(f'wrote {HELDOUT_CSV_PATH} rows={len(df)}') diff --git a/evaluations/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv b/evaluations/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv new file mode 100644 index 0000000..cb8bdc0 --- /dev/null +++ b/evaluations/fold-03-holdout-4/agent_outputs/heldout_harmonized.csv @@ -0,0 +1,1002 @@ +datetime_UTC,site_id,depth_m,replicate,is_timeseries,interval_min,volumetric_water_content_m3_m3,gravimetric_water_content_gH2O_gs,water_potential_kPa +2022-07-22T06:00:00Z,sg5,,1,True,1440.0,0.165,,-145.67 +2022-10-15T06:00:00Z,tb,,1,True,1440.0,0.113,,-725.39 +2021-05-26T06:00:00Z,tb,,1,True,1440.0,0.303,,-17.8 +2022-09-28T06:00:00Z,ph1,,1,True,1440.0,0.163,,-1383.33 +2022-10-22T06:00:00Z,sg5,,1,True,1440.0,0.168,,-127.1 +2022-07-09T06:00:00Z,ph1,,1,True,1440.0,0.233,,-65.73 +2021-07-11T06:00:00Z,tb,,1,True,1440.0,0.203,,-75.55 +2020-10-13T06:00:00Z,ph2,,1,True,1440.0,0.214,,-584.02 +2021-06-08T06:00:00Z,tb,,1,True,1440.0,0.257,,-33.01 +2020-09-25T06:00:00Z,ph2,,1,True,1440.0,0.236,,-175.39 +2022-10-07T06:00:00Z,ph1,,1,True,1440.0,0.18,,-505.03 +2022-05-11T06:00:00Z,tb,,1,True,1440.0,0.137,,-319.05 +2021-05-06T06:00:00Z,ph1,,1,True,1440.0,0.314,,-10.03 +2021-08-18T06:00:00Z,tb,,1,True,1440.0,0.111,,-773.72 +2021-09-27T06:00:00Z,ph1,,1,True,1440.0,0.149,,-4130.57 +2022-05-30T06:00:00Z,tb,,1,True,1440.0,0.117,,-614.39 +2021-05-29T06:00:00Z,ph1,,1,True,1440.0,0.305,,-12.01 +2020-07-08T06:00:00Z,ph1,,1,True,1440.0,0.212,,-127.9 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"ESS-DIVE", + "data_payload_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data.csv" + ], + "location_metadata_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta.csv", + "data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv" + ], + "sensor_metadata_files": null, + "harmonization_mappings": { + "datetime": { + "pattern_1": { + "source_pattern": "datetime", + "source_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta.csv" + ], + "destination_variable": "datetime_UTC", + "transformation": "Parse date in America/Denver timezone and convert to ISO-8601 UTC timestamp.", + "unit_conversion": null + } + }, + "site_id": { + "pattern_1": { + "source_pattern": "site", + "source_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_meta.csv" + ], + "destination_variable": "site_id", + "transformation": "Use reported site abbreviation as site_id.", + "unit_conversion": null + } + }, + "depth": { + "pattern_1": { + "source_pattern": "swc definition: 24-hour average depth-averaged soil water content", + "source_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data_dd.csv" + ], + "destination_variable": "depth_m", + "transformation": "No numeric depth or depth interval is reported; populate with null.", + "unit_conversion": null + } + }, + "replicate": { + "pattern_1": { + "source_pattern": null, + "source_files": null, + "destination_variable": "replicate", + "transformation": "No replicate field is provided; populate with 1.", + "unit_conversion": null + } + }, + "volumetric_water_content": { + "pattern_1": { + "source_pattern": "swc", + "source_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data.csv" + ], + "destination_variable": "volumetric_water_content_m3_m3", + "transformation": "Direct column mapping.", + "unit_conversion": "None; source units are m3/m3." + } + }, + "soil_water_potential": { + "pattern_1": { + "source_pattern": "swp", + "source_files": [ + "Johnsen_Bi_2025_DAE_Manuscript_Data_Package/df_data.csv" + ], + "destination_variable": "water_potential_kPa", + "transformation": "Direct column mapping.", + "unit_conversion": "None; source units are kPa." + } + }, + "gravimetric_water_content": { + "pattern_1": { + "source_pattern": null, + "source_files": null, + "destination_variable": "gravimetric_water_content_gH2O_gs", + "transformation": "Not reported; populate with null.", + "unit_conversion": null + } + }, + "latitude": { + "pattern_1": { + "source_pattern": "Location_ID/Latitude in reference package; partial matches ph1->ER-PHS1, ph2->ER-PHS2, sg5->SG-EHS5; tb unresolved", + "source_files": [ + "data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv" + ], + "destination_variable": "latitude", + "transformation": "Coordinates are not part of held-out harmonized CSV target schema; mapping notes document partial lookup and qc flags.", + "unit_conversion": null + } + }, + "longitude": { + "pattern_1": { + "source_pattern": "Location_ID/Longitude in reference package; partial matches ph1->ER-PHS1, ph2->ER-PHS2, sg5->SG-EHS5; tb unresolved", + "source_files": [ + "data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv" + ], + "destination_variable": "longitude", + "transformation": "Coordinates are not part of held-out harmonized CSV target schema; mapping notes document partial lookup and qc flags.", + "unit_conversion": null + } + } + } +} diff --git a/evaluations/fold-03-holdout-4/agent_outputs/mapping_notes.md b/evaluations/fold-03-holdout-4/agent_outputs/mapping_notes.md new file mode 100644 index 0000000..7f1d289 --- /dev/null +++ b/evaluations/fold-03-holdout-4/agent_outputs/mapping_notes.md @@ -0,0 +1,29 @@ +# Mapping Notes: ess-dive-6c7085e9c544cc6-20250424T164534831 + +Decision: INCLUDE (best effort). + +Evidence used from allowed files: +- `df_data_dd.csv` defines `swc` as 24-hour average depth-averaged soil water content in m3/m3. +- `df_data_dd.csv` defines `swp` as soil water potential in kPa. +- `df_meta.csv` is row-aligned metadata containing `site` and `datetime` for `df_data.csv`. +- Notebooks treat `swc` and `swp` as observed predictor variables with source units m3/m3 and kPa. + +Harmonization choices: +- `datetime_UTC`: parse `df_meta.datetime` as `%Y-%m-%d` in `America/Denver`, then convert to UTC. +- `site_id`: preserve `df_meta.site` (`ph1`, `ph2`, `sg5`, `tb`). +- `depth_m`: set to null. The source says depth-averaged but gives no depth or interval in allowed files. +- `replicate`: set to 1 because no replicate field is present. +- `is_timeseries`: set to true because each site has many dated daily observations. +- `interval_min`: set to 1440 based on the 24-hour-average definition and median within-site date interval. +- `volumetric_water_content_m3_m3`: direct mapping from `swc`. +- `water_potential_kPa`: direct mapping from `swp`. +- `gravimetric_water_content_gH2O_gs`: set to null; not reported. + +Location notes: +- Coordinates are not included in the target held-out harmonized CSV, but were reviewed for curation. +- Allowed reference package index 0 supports moderate-confidence matches: `ph1 -> ER-PHS1`, `ph2 -> ER-PHS2`, `sg5 -> SG-EHS5`; use `qc_flag=g1` if those locations are materialized elsewhere. +- `tb` was not confidently resolved. A weak literal candidate `WC-TBA1`/`TB1` exists, but it is described as an ERT profile, so it was not used automatically; use `qc_flag=g2` unless an operator approves a match. + +Open issues: +- DOI was not found in allowed local files; no network/API lookup was performed. +- The package includes neural-network code and derived ET modeling outputs. This mapping only harmonizes direct soil moisture variables (`swc`, `swp`) from `df_data.csv` and excludes `ET`. diff --git a/evaluations/fold-03-holdout-4/evaluation_metrics.json b/evaluations/fold-03-holdout-4/evaluation_metrics.json new file mode 100644 index 0000000..4146318 --- /dev/null +++ b/evaluations/fold-03-holdout-4/evaluation_metrics.json @@ -0,0 +1,67 @@ +{ + "fold": "fold-03-holdout-4", + "dataset_index": 4, + "dataset_identifier": "ess-dive-6c7085e9c544cc6-20250424T164534831", + "trace_forbidden_path_scan_matches": 0, + "agent_output": { + "rows": 1001, + "columns": 9, + "site_counts": { + "ph1": 275, + "ph2": 148, + "sg5": 129, + "tb": 449 + } + }, + "gold_output": { + "rows": 552, + "columns": 9, + "site_counts": { + "ph1": 275, + "ph2": 148, + "sg5": 129 + } + }, + "output_equivalence": { + "schema_equal": true, + "key_intersection": 552, + "agent_extra_keys": 449, + "agent_missing_gold_keys": 0, + "agent_extra_key_sites": { + "tb": 449 + }, + "shared_row_value_matches": { + "depth_m": "552/552", + "interval_min": "552/552", + "volumetric_water_content_m3_m3": "552/552", + "gravimetric_water_content_gH2O_gs": "552/552", + "water_potential_kPa": "552/552", + "is_timeseries": "552/552" + }, + "row_precision": 0.5514485514485514, + "gold_recall": 1.0 + }, + "json_mapping_equivalence": { + "top_level_exact_matches": "5/7", + "gold_mapping_categories_present": "8/8", + "extra_agent_categories": [ + "gravimetric_water_content" + ], + "missing_gold_categories": [], + "field_level_exact_matches": "25/40", + "field_exact_matches_by_name": { + "destination_variable": "8/8", + "source_pattern": "5/8", + "source_files": "4/8", + "transformation": "0/8", + "unit_conversion": "8/8" + } + }, + "python_equivalence": { + "core_transformation_matched": true, + "missed_drop_tb": true, + "missed_sort": true, + "missed_gold_context_api": true, + "missed_location_side_output": true + } +}