Fix for epa-airpollutantemission-level1

[shourya116]

Summary

Fixes and stabilizes the EPA_AirPollutantEmission_Level1 import pipeline across all historical observation periods (2008–2020) and source categories (point, nonpoint, onroad, nonroad, and tribal sources).

This update resolves:

1. Pandas 2.x Type Mismatch & Silent Dropping: 767,314 nonpoint/area source observations for 2017 and 2020 were silently dropped due to invalid .loc string assignment on float64 columns and broad exception swallowing.
2. Consolidation Memory Surges (OOM Exit Code 50002): Intermediate file aggregation previously accumulated large raw DataFrames in memory, causing VM kernel OOM kills.
3. 2017 Point Source Regression (replacement_point_17): An errant 'total emissions': 'observation' mapping dropped all 108,057 point observations for EPA regions 1–5 in 2017 during regularized column subsetting, triggering validation failure.
4. Code Review & Standards Compliance: Corrected county FIPS code formatting (5-digit zero-padding), sanitized SCC codes, deduplicated manifest.json node MCF declarations, restored standard VM resource limits, quoted DuckDB date literals in date freshness validation, and retained operational configuration artifacts.

---

Root Cause & Incident Breakdown

1. Pandas 2.x Incompatible Assignment:
   • Raw 2017 and 2020 nonpoint CSVs contained empty emissions type code columns loaded as float64.
   • The substring check 'point' in file_path evaluated to True for ..._nonpoint/... paths, executing df.loc[:, 'emissions type code'] = ''. In Pandas 2.x, assigning a string to a float64 Series via .loc raises TypeError: Invalid value '' for dtype 'float64'.
   • _national_emissions() caught this exception and returned an empty DataFrame, silently omitting 767,314 nonpoint records.
2. Intermediate Consolidation Memory Surges:
   • Writing un-aggregated intermediate CSVs and concatenating all files in a single pass caused memory consumption to balloon past container limits.
3. Erroneous 2017 Point Mapping in config.py:
   • replacement_point_17 mapped 'total emissions': 'observation'. Because point_12345.csv already used standard 'total emissions', re-mapping to 'observation' caused the column to be dropped when filtered against df_columns, converting all observations to NaN and failing check_deleted_records_percent (108,057 deleted records).

---

Key Changes

1. Data Ingestion & Transformation (process.py, config.py)

• Precise File Routing & Safe Assignment: Distinguish point vs. nonpoint files using 'point_' in os.path.basename(file_path) and use direct column assignment (df['emissions type code'] = '').
• Fixed Column Mappings:
  • Removed erroneous 'total emissions': 'observation' mapping from replacement_point_17 in config.py.
  • Removed unused drop_tribes from config.py.
  • Fixed replacement_20 column mappings to retain raw columns matching df_columns.
  • Unconditionally regularize point files for 2017 (Regions 1–5) and 2020 (Regions 1–10).
  • Explicit survey year matching with ValueError fallback for unsupported years.
• Pre-Aggregation & Precision Storage:
  • Pre-aggregate emission observations by (geo_Id, year, Measurement_Method, SV) within each worker task before writing intermediate files.
  • Serialize intermediate chunks as binary pickle (.pkl) files rather than CSVs to preserve exact 64-bit IEEE float precision and eliminate text serialization overhead.
  • Batch-consolidate intermediate files in chunks of 10 with explicit gc.collect() to guarantee flat memory usage (< 2 GB peak).
• Data Normalization & Sanitization:
  • County FIPS codes coerced to numeric and zero-padded to 5 digits (zfill(5)), ensuring valid Data Commons geoId/XXXXX resolution (e.g., geoId/01001).
  • Stripped trailing .0 from float-parsed SCC strings and deduplicated key 4 in replace_source_metadata.
• Exception Logging Contract:
  • Cleaned up exception handling: helper methods log via logging.exception() and re-raise, while main(argv) handles top-level termination cleanly via logging.fatal(..., exc_info=True) without unreachable raise statements.

2. Import Manifest & Validation Config (manifest.json, validation_config.json)

• manifest.json:
  • Sized Cloud Batch resources to standard operational sizing (cpu: 8, memory: 128, disk: 300) and bounded MAX_WORKERS to 8.
  • Correctly omitted node_mcf under import_inputs to prevent duplicate ingestion of pre-existing canonical StatVars.
  • Retained operational configuration artifacts (manifest.json, validation_config.json) in source_files for provenance tracking.
• validation_config.json:
  • Enforced check_deleted_records_percent with a 0.1% threshold.
  • Quoted date literals in check_date_freshness (max_date >= '2020' AND min_date <= '2008'), completely preventing DuckDB VARCHAR vs INTEGER_LITERAL Binder Error / CONFIG_ERROR.

3. Unit Tests (process_test.py)

• Comprehensive test coverage expanded to 13 unit test suites (all passing hermetically in CI in 1.74s):
  • 2017 / 2020 nonpoint float64 NaN handling.
  • Point file column regularization and preservation of total emissions for 2017 Regions 1–5 (point_12345.csv) and 2020 Regions 1–10.
  • 2014 tribal schema variants.
  • County FIPS 5-digit zero-padding and SCC string sanitization.
  • Intermediate output directory initialization and corrupt pickle detection.
  • Worker exception bubbling and end-to-end multi-year pipeline execution.
  • Unhandled survey cycle validation.

---

Verification & Artifacts

• Latest Head Commit: 23a89dcf11302c1828312a60bda27c9d52163627 (23a89dcf)
  • Latest Feature Commit: a1ca509663d77be5da24ae5806c7fe098679a8e2 (a1ca5096)
• Latest Cloud Batch Run:
  • Job ID: epa-airpollutantemission-level1-shouryasingh-20260922-192749
  • Job UID: epa-airpollutantem-1b3ef5bf-e17f-41130
  • Project: datcom-infosys-dev (Location: us-west4)
  • Machine Type: n2-highmem-64 (32 vCPUs, 512 GiB RAM, 300 GB disk)
  • Status: SUCCEEDED (Exit Code: 0, Total Duration: 5,738.49s / ~1h 35m)
  • Cloud Batch Console Details
  • Cloud Batch Console Logs
• GCS Staging Output:
  • Path: gs://datcom-import-test/scripts/us_epa/national_emissions_inventory/EPA_AirPollutantEmission_Level1/2026_09_22T12_30_45_790197_07_00
  • Cloud Storage Console Browser
  • Status: ImportStatus.STAGING

Differ & Validation Summary

Metric / Rule	Result	Description
Total Observations	3,041,170	Matches baseline observation count (100% data recovery)
Added Observations	0	No unexpected additions
Deleted Observations	0	0.00% deleted (threshold: 0.1%)
Modified Observations	98,560	Expected due to 5-digit county FIPS zero-padding and SCC string sanitization
Schema Diffs	0	No unexpected schema mutations
check_deleted_records_percent	PASSED	0 deleted observations (threshold: 0.1%)
check_empty_import	PASSED	3.04M observations
check_missing_refs_count	PASSED	0 missing references (threshold: 0)
check_lint_error_count	PASSED	0 lint errors (threshold: 0)
check_date_freshness	PASSED	min_date <= '2008' AND max_date >= '2020'

• Unit Tests:

  • python3 -m unittest scripts/us_epa/national_emissions_inventory/process_test.py
  • Ran 13 tests in 1.742s — OK.

• References:

  • Buganizer Issue: b/542470230
  • CRA Document: https://paste.googleplex.com/5757637107515392
  • Postmortem Report: https://paste.googleplex.com/5957668808818688

[google-cla]

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[gemini-code-assist]

Code Review

This pull request increases the resource limits (CPU, memory, and disk) in the manifest configuration and refactors pandas DataFrame operations in process.py to avoid using .loc for simple column assignments and to replace deprecated inplace=True usage. Feedback is provided to remove a redundant .replace('', np.nan) call on the observation column, as empty strings are already converted to NaN earlier in the processing pipeline.

[abhishekjaisw]

Review scope

• Target: PR #2148 (4fc4609467faf6425589b232ce6e674c6677ec2d)
• Reviewed:
  • scripts/us_epa/national_emissions_inventory/manifest.json
  • scripts/us_epa/national_emissions_inventory/process.py
  • scripts/us_epa/national_emissions_inventory/validation_config.json
• Skipped: None

Summary of Findings

1. [P1] CI Test Suite Failure (data-pull-request-py) & Missing Regression Tests for 2017/2020 Nonpoint & Tribal Fixes (process.py:144, process_test.py)
   • Running ./run_tests.sh -p scripts/us_epa/national_emissions_inventory (executed by GitHub CI data-pull-request-py) fails with ImportError: attempted relative import with no known parent package at process_test.py:20 (from .process import *) because scripts/us_epa/national_emissions_inventory/ lacks an __init__.py.
   • Furthermore, PR #2148 modifies _regularize_columns to fix the silent drop of 767,314 observations across 2017/2020 nonpoint, point_, and 2014 tribes files, but adds zero unit tests or test fixtures for these branches.
2. [P2] Missing Date Freshness Validation Rule in validation_config.json (Outdated Branch / Already Fixed DuckDB Differ Issue) (validation_config.json:9)
   • validation_config.json omits date freshness validation because SQL_VALIDATOR previously failed on empty differ_df (Need a DataFrame with at least one column). However, this framework bug was already fixed on master in commits 3315fc4b (Aug 14, 2026) and 4d856505 (Aug 31, 2026) in tools/import_validation/validator.py:62-63 and runner.py:194. Rebasing PR #2148 onto master enables re-adding the SQL_VALIDATOR date freshness check (MAX(MaxDate) >= 2020 and MIN(MaxDate) >= 2014).
3. [P2] Exception Tracebacks Discarded in logging.fatal Catch Blocks (process.py:239)
   • Passing only {e} to logging.fatal(...) discards the Python stack trace (exc_info), obscuring line numbers and call stacks during Cloud Batch failures.
4. [P3] Operational Configs in source_files & Google CLA Check (manifest.json:25)
   • Consider adding "validation_config.json" to "source_files" in manifest.json so validation configs are archived in GCS. Additionally, please resolve the failing cla/google check on GitHub before merge.

Positive findings

• scripts/us_epa/national_emissions_inventory/process.py:139-155 - Precise filename/path disambiguation and direct column assignment ✓
  • Finding: Good - Replaced broad "point" in file_path checks with "point_" in os.path.basename(file_path) or "facility_process" in file_path and explicit "nonpoint" branches, avoiding substring collisions with nonpoint files, and replaced .loc[:, col] = "" with direct column assignment (df["emissions type code"] = "") to prevent Pandas 2.x float64 dtype errors.
• scripts/us_epa/national_emissions_inventory/process.py:314 - Eager evaluation of ThreadPoolExecutor.map ✓
  • Finding: Good - Wrapped executor.map(...) in list(...) so worker thread exceptions and SystemExit from logging.fatal propagate immediately to the main thread rather than silently dropping failed files.
• scripts/us_epa/national_emissions_inventory/manifest.json:21-29 - Scaled Cloud Batch compute resources and registered node_mcf ✓
  • Finding: Good - Increased memory to 512 GiB and CPU to 32 to eliminate OOM kills (exit code 50002) during multi-year DataFrame concatenation, and explicitly wired node_mcf and validation_config_file.

Coverage

File	Status	Result
scripts/us_epa/national_emissions_inventory/manifest.json	Reviewed	One P3 finding
scripts/us_epa/national_emissions_inventory/process.py	Reviewed	One P1 finding, one P2 finding
scripts/us_epa/national_emissions_inventory/validation_config.json	Reviewed	One P2 finding

Verification and limitations

• Checks run:
  • ./run_tests.sh -p scripts/us_epa/national_emissions_inventory (Reproduced CI failure: ImportError: attempted relative import with no known parent package in process_test.py)
  • PYTHONPATH=. .env/bin/python3 -m unittest scripts/us_epa/national_emissions_inventory/process_test.py (Passed: 1 test in 0.575s)
  • Inspected GCS prod (2025_12_31T16_03_29_040514_08_00) and dev (2026_09_06T07_23_45_163580_07_00) summary_report.csv and validation_output.csv.
• Checks not run: None
• Limitations: None

[shourya116]

Changed Implemented as per feedback

[abhishekjaisw]

Code Review Summary for PR #2148 (EPA_AirPollutantEmission_Level1)

Root Cause & Data Transformation Fixes (Verified):

• Fix in _regularize_columns ('point_' in os.path.basename(file_path) and direct column assignment df['emissions type code'] = '') resolves the Pandas 2.x float64 TypeError that dropped 2017/2020 nonpoint observations.
• RegularizeColumnsTest in process_test.py (5 unit tests passing) covers nonpoint, point, and 2014 tribal schema variants.
• "node_mcf": "gcs_output/output_files/national_emissions.mcf" in manifest.json is valid and should be kept (unlike PR Added validation configuration for EPA_airqualityindex #2147), as it resolves 8 Existence_MissingReference_variableMeasured warnings present in the baseline run (report.json).
• Cloud Batch run (2026_09_07T06_25_07_719529_07_00) ran after the latest commit (15b2958b) and confirmed check_date_freshness passed.

Action Items Before Merge:

1. [P2] Sanitize PR Description URLs (from PR Added validation configuration for EPA_airqualityindex #2147 review): Replace internal https://pantheon.corp.google.com/... links (with corp query params) in the PR description with gs://datcom-import-test/scripts/us_epa/national_emissions_inventory/EPA_AirPollutantEmission_Level1/2026_09_07T06_25_07_719529_07_00 or clean https://console.cloud.google.com/... links.
2. [P2] process.py (logging.fatal + raise): Remove unreachable raise / sys.exit(1) after logging.fatal() across 6 exception blocks (lines 242–246, 263–267, 337–341, 344–345, 432–436, 458–461), avoid calling logging.fatal() inside ThreadPoolExecutor worker threads (_national_emissions, _process_file) so exceptions propagate cleanly via list(executor.map(...)), and remove commented-out imports (# import shutil, # import tempfile).
3. [P2] validation_config.json (DELETED_RECORDS_PERCENT): Update the description of check_deleted_records_percent to explicitly state the 0.1% threshold and deletion rationale (and fix the typo in Postmortem Section 5.3 from (10%) to (0.1%)).
4. [P2] CRA Paste & Postmortem Sync: Update both documents to reference head commit 15b2958b68aa936fe242d820ee50f3f01661d8d1, reflect that check_date_freshness (SQL_VALIDATOR) is active and passing, and update the unit test count in Section 5.4 to 5 tests.
5. [P3] Formatting & CI: Remove the 3 extra trailing blank lines at EOF in manifest.json, resolve the cla/google check, and trigger /gcbrun.

[shourya116]

All the latest review comments have been resolved and verified. Both the CRA review document and Postmortem report have also been updated and synced live.

Summary of Actions Taken

1. [P2] process.py Exception Handling & Cleanup:

   • Worker Thread Exception Propagation: Avoided calling logging.fatal() inside ThreadPoolExecutor worker threads (_national_emissions and _process_file). Errors are logged using logging.exception() and re-raised so exceptions propagate cleanly to list(executor.map(...)) on the main thread.
   • Unreachable Code Removal: Removed unreachable raise and sys.exit(1) statements after terminating logging.fatal() calls across 6 exception blocks (intermediate file reading loop, empty DataFrame check, input file discovery, and main execution handler).
   • Import Cleanup: Removed commented-out imports (# import shutil, # import tempfile).

2. [P2] validation_config.json Description Update:

   • Updated check_deleted_records_percent description to explicitly state the 0.1% threshold and deletion rationale:

     {
         "rule_id": "check_deleted_records_percent",
         "description": "Verifies that the percentage of deleted records does not exceed the 0.1% threshold, ensuring unintended observation drops (such as missing nonpoint sources which drop >20% of records) are caught while accommodating minor upstream EPA revisions.",
         "validator": "DELETED_RECORDS_PERCENT",
         "params": {
             "threshold": 0.1
         }
     }

   • Corrected the typo in Postmortem Section 5.3 from (10%) to (0.1%).

3. [P3] manifest.json Formatting:

   • Removed the 3 extra trailing blank lines at EOF.

4. [P2] CRA Paste & Postmortem Sync:

   • Head Commit Sync: Updated both documents to reference head commit 242f22800dcf60581dc309111b5388ddb77f974e.
   • Unit Tests: Updated unit test counts in both documents to reflect 5 passing tests (0.635s, OK).
   • Date Freshness Validation: Confirmed that check_date_freshness (SQL_VALIDATOR) is active and passing following the clean rebase with master's DuckDB empty-differ fix.
   • Updated Paste Links:
     • CRA Paste: https://paste.googleplex.com/6620650563829760
     • Postmortem Report: https://paste.googleplex.com/5957668808818688

5. Cloud Batch Verification Run (SUCCEEDED):

   • Ran end-to-end verification job epa-airpollutantemission-level1-shouryasingh-20260908-184507 on us-west4 using n2-highmem-64 (32 CPUs / 512 GiB RAM / 300 GB disk).
   • Status: SUCCEEDED (execution duration: 7,932s / ~2.2 hrs).
   • All 3,041,170 rows were successfully processed (all 767,314 missing nonpoint observations recovered).
   • All 5 validations passed:
     • check_deleted_records_percent: PASSED (0 deleted records, 0.0% vs 0.1% threshold)
     • check_empty_import: PASSED (3,041,634 nodes, 3,041,170 rows)
     • check_missing_refs_count: PASSED (0 missing references)
     • check_lint_error_count: PASSED (0 lint errors)
     • check_date_freshness: PASSED (MAX(MaxDate) >= 2020 AND MIN(MaxDate) >= 2008)
   • Cloud Batch Job: https://console.cloud.google.com/batch/jobsDetail/regions/us-west4/jobs/epa-airpollutantemission-level1-shouryasingh-20260908-184507/details?project=datcom-infosys-dev
   • GCS Output: gs://datcom-import-test/scripts/us_epa/national_emissions_inventory/EPA_AirPollutantEmission_Level1/2026_09_08T11_47_48_764425_07_00
   • GCS Console: https://console.cloud.google.com/storage/browser/datcom-import-test/scripts/us_epa/national_emissions_inventory/EPA_AirPollutantEmission_Level1/2026_09_08T11_47_48_764425_07_00?project=datcom-infosys-dev

6. Sanitized PR Description

[abhishekjaisw]

LGTM

[abhishekjaisw]

LGTM

[abhishekjaisw]

/gcbrun

[SandeepTuniki]

/gcbrun

[SandeepTuniki]

Thanks for the fixes! I've requested one change below.

[SandeepTuniki]

/gcbrun

[SandeepTuniki]

Thanks for the changes! Please fix the CI failures before merging.