Complete pipeline migration from R to Python - #2

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Commits on Nov 28, 2025

Fix extraction bugs: handle None max_row and filter Excel errors

pmayd
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claude
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d121f76
Update validation tracking: 2024 Sultanah Bahiyah fixed

pmayd
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claude
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3f1ba18
Add patient_id normalization for transfer patients

pmayd
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426cae4
Add unit tests for patient cleaning preprocessing functions

pmayd
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2355603
Fix extraction to filter numeric zero patient IDs (0, 0.0)

pmayd
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989715b
Update validation tracking: investigation complete
pmayd
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0ba9d6e
Add comprehensive R vs Python validation test suite

pmayd
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228ebfc
Refactor R validation tests and fix HbA1c exceeds default value

pmayd
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f763c7b
Add patient-level exceptions for R extraction errors

pmayd
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0475663
Add file-specific column exceptions and identify R Unicode bug

pmayd
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c696630
Clarify Unicode character handling difference between R and Python

pmayd
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2ed8ee0
Treat null and empty string as equivalent in R vs Python validation

pmayd
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218886b
Add exceptions for Kantha Bopha II Hospital tracker R extraction errors

pmayd
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a9a74db
Implement province validation in Python to match R behavior

pmayd
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f2e8d4e
Remove Kantha Bopha II province validation exception

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c727c32
Revert: Keep province exception - R validation is still broken

pmayd
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63d9f38
Implement sex synonym mapping to match R behavior

pmayd
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71b86c1
Implement BMI calculation to match R pipeline

pmayd
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68b48b1
Complete migration of R data transformation functions

pmayd
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55ad1ca
Fix extract tests to use numeric values in column A

pmayd
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0eccaf9
update exceptions for end to end tests
pmayd
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42f4abb
add a delete parameter to ingest_Data
pmayd
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dc91f18
Add exception for 2017 Mandalay tracker missing status values

pmayd
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5ec67b8
Add exception for 2019 CDA tracker missing status value

pmayd
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7ed5e36
Update required column test to alert when exceptions are fixed

pmayd
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97d34de
Add exception for 2019 Preah Kossamak tracker missing status

pmayd
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d88ef45
Add exception for 2019 Vietnam National Children's Hospital tracker

pmayd
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870c505
Fix header merge bug causing status column loss in 2021 Kantha Bopha tracker

pmayd
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622d500
new limits for fbg, hba1c, bmi, age
pmayd
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87a7169
Fix validation error for rows with missing patient_id

pmayd
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c96611b
Improve worker log file naming with timestamp and PID

pmayd
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9c3f236
Fix patient_id normalization to handle hyphens before removing transfer suffix

pmayd
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52283fd
Add exception for missing status in 2021 Mandalay tracker

pmayd
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1948d13
Add exception for missing status in 2021 Preah Kossamak tracker

pmayd
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dbb94a4
Add exceptions for missing status in 2022 Chiang Mai tracker

pmayd
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52fa688
Add exception for missing status in 2022 Chulalongkorn tracker

pmayd
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3fe851a
Add exception for missing status in 2022 Kantha Bopha tracker

pmayd
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6d43474
Add exception for missing status in 2022 Likas tracker

pmayd
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60147ca
Add exception for missing status in 2022 Mandalay tracker

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c4975ce
Add exception for missing status in 2022 Penang tracker

pmayd
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f38d5b5
Add exception for missing status in 2022 Putrajaya DC tracker

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118c580
Add exception for missing status in 2022 Sarawak DC tracker

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a47cdc1
Add exception for missing status in 2022 Surat Thani tracker

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e28c695
Add exception for missing status in 2022 Udon Thani tracker

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e5e050b
Add exception for missing status in 2023 Mahosot tracker

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6371894
Add exception for missing status in 2023 Nakornping tracker

pmayd
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43d84d8
Add exception for missing status in 2023 Surat Thani tracker

pmayd
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59507bb

Commits on Dec 8, 2025

Commits on Dec 9, 2025

ruff check
pmayd
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f391249

Commits on Dec 27, 2025

fix header merge forward-fill for group headers like observations_category

Michael Aydinbas
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a9ce967
use Excel merge metadata for header forward-fill instead of heuristics

Michael Aydinbas
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claude
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4b1c6ab
fix openpyxl warning filter to match submodules

Michael Aydinbas
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0cffe77
perf: replace Excel merge metadata with synonym validation (6.6x faster)

Michael Aydinbas
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7c91db1
fix: convert height from cm to m before BMI calculation

Michael Aydinbas
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424f9e7

Commits on Dec 28, 2025

fix: date parsing truncated dd-Mon-yyyy format (11 chars) to 10

Michael Aydinbas
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claude
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a812ecc
test: add R extraction error exceptions for Mandalay trackers

Michael Aydinbas
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58700fd
test: add R extraction error exception for NPH tracker

Michael Aydinbas
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7018884
fix: calculate age/t1d_diagnosis_age from DOB, handle Excel errors

Michael Aydinbas
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1a8c7b8

Commits on Feb 20, 2026

Initial plan
Copilot
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a5b9948
feat: add BigQuery loading and GCS integration modules

Copilot
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pmayd
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1b7998d
refactor: address code review feedback

Copilot
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pmayd
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b2ccea1
Fix all 63 ruff linting errors in a4d-python

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Copilot
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ac2fa23

Commits on Feb 24, 2026

Merge pull request #3 from CorrelAid/copilot/plan-data-migration-steps
pmayd
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7e06dbc
Initial plan
Copilot
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580b186
Add Dockerfile, .dockerignore, deploy.sh, and cloud-run config for serverless GCP deployment

Copilot
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pmayd
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4eac0a8
Deploy Python pipeline as Cloud Run Job: fix Dockerfile, add run-pipeline CLI command, update deploy.sh

Copilot
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pmayd
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b57b483
Fix PR diff: sync migration branch files, leaving only the 4 new deployment files

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pmayd
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c488a8c

Commits on Feb 25, 2026

Merge branch 'migration' of https://github.com/CorrelAid/a4d into copilot/setup-serverless-pipeline
Copilot
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f3910a2
Upgrade Python from 3.11 to 3.13 in Dockerfile and CI workflow

Copilot
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pmayd
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e6241f8
Remove unused duckdb dependency and upgrade to Python 3.14

Copilot
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pmayd
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ac1181f
Merge pull request #4 from CorrelAid/copilot/setup-serverless-pipeline
pmayd
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ef6a1b9
Initial plan
Copilot
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38595b4
Fix patient pipeline: stale column names, Python version, product ingestion skip

Copilot
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pmayd
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f5db33c
Remove longitudinal data table creation and all related code

Copilot
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pmayd
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72c7be9
Merge pull request #5 from CorrelAid/copilot/finalize-patient-data-migration
pmayd
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8d188e6
Finalize patient pipeline: fix bugs, remove stale code, add CLI tests
Michael Aydinbas
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7fb63fa

Commits on Feb 26, 2026

format code
Michael Aydinbas
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cccaea8
Add clean output, CLI step output, and setup guide
Michael Aydinbas
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0a7c3c5
rename just commands, fix error in tests, fix max_workers not working for run-local
Michael Aydinbas
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7f88230

Commits on Feb 27, 2026

Improve CLI UX, GCS performance, and GCP setup
Michael Aydinbas
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b0085ce

Commits on Feb 28, 2026

Add backup-bq and fix logs-job in justfile
Michael Aydinbas
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a119270

Commits on Mar 1, 2026

Audit and update docs: remove obsolete files, update to reflect current state
Michael Aydinbas
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945d230
Move all GCP resources to asia-southeast2 (Jakarta) for data residency
Michael Aydinbas
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fc5973f
Fix uv not found in Docker and update justfile region to Jakarta
Michael Aydinbas
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aa70d9e
Fix Docker build: add UV_PYTHON_DOWNLOADS and copy README.md
Michael Aydinbas
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767b433
Fix Docker build: split uv sync to avoid editable install before src/ exists
Michael Aydinbas
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2012fe6
Add gcloud command to list images in Artifact Registry after docker-push
Michael Aydinbas
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6b22d19
Add local Docker test instructions and docker-smoke just command
Michael Aydinbas
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81b77bf
Add --provenance=false to docker-build to suppress attestation manifests
Michael Aydinbas
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dce1dd7
Add git-SHA tagging strategy and rollback command to justfile
Michael Aydinbas
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92f9ac6
Add docker-list command to justfile
Michael Aydinbas
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40293dc
Reorder and group justfile into logical sections
Michael Aydinbas
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7236446
Fix E402: move warnings.filterwarnings after imports in cli.py
Michael Aydinbas
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9e8089d
Fix ty type errors: PolarsDataType annotation and tqdm isinstance check
Michael Aydinbas
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f96d4e0
Update Cloud Run Job spec: bump to 8 vCPU / 8 GiB, add jobs list command
Michael Aydinbas
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657e3f6
Code cleanup: remove unused imports, fix forward reference, reformat
Michael Aydinbas
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80ee1e3
Add --platform=linux/amd64 to docker-build for Cloud Run compatibility
Michael Aydinbas
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3a6faae
Fix CI test failures by excluding slow and integration tests
Michael Aydinbas
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8824cc3
Fix reference_data path resolution in Docker/Cloud Run
Michael Aydinbas
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b2c91a6
Switch parallel processing from ProcessPoolExecutor to ThreadPoolExecutor
Michael Aydinbas
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bfa8c85
Update SETUP.md: fix BigQuery IAM grant command
Michael Aydinbas
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fb078ff
Restore clean console output for parallel pipeline runs
Michael Aydinbas
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113890f
Revert to ProcessPoolExecutor; add docker-clean command
Michael Aydinbas
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c306479
Fix GCS upload: timestamped prefix, upload only tables and logs
Michael Aydinbas
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38efab6
Fix BigQuery loading: delete-before-recreate and update logs clustering
Michael Aydinbas
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5560b38
Add clinic_data_static table creation
Michael Aydinbas
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c18fb70
Add error_code classification to pipeline logs
Michael Aydinbas
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7e345dd
Fix CLI test runner for CI environment
Michael Aydinbas
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f4fb7b5

Commits on Mar 13, 2026

add new command to see resources of cloud job; add script dependencies
Michael Aydinbas
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a99473a
Promote Python pipeline to root; archive R code
Michael Aydinbas
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24125ae
Update clinic_data.xlsx from Google Drive
Michael Aydinbas
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76631d4

Commits on Mar 29, 2026

docs: add product data pipeline feature proposal
Michael Aydinbas
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8f4b8bc

Commits on Apr 1, 2026

Persist data quality errors to table_errors.parquet and BigQuery
Michael Aydinbas
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2069a4d
add new error log table combining all errors in a single parquet file and preparing for BigQuery upload
Michael Aydinbas
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faa3c28

Commits on May 4, 2026

refactor(patient): extract shared tracker helpers
Ali88-hub
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56f2192
feat(patient): typo-rescue + multi-insulin CSV
Ali88-hub
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b810120
feat(clean): shared utilities + product extraction layer
Ali88-hub
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9608bca
feat(product): cleaning pipeline + table aggregation
Ali88-hub
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1151155
feat(state): incremental processing via tracker_metadata
Ali88-hub
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fdc8c8c
feat(pipeline): product orchestration + CLI integration
Ali88-hub
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85891e7
feat(validate): source-vs-output reconciliation
Ali88-hub
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c485bc2

Commits on May 5, 2026

refactor(bigquery): drop pandas from tracker_metadata read

Ali88-hub
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claude
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9e95796
chore: drop redundant utf-8 encoding and Windows path shims

Ali88-hub
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27cfe26
chore(justfile): drop Windows compatibility shims

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9a30cc9

Commits on May 7, 2026

feat(cli): --skip-patient flag for run-pipeline

Ali88-hub
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3070ea6
feat(product): propagate clinic_id from tracker folder to product output

Ali88-hub
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b9a67ac
docs(readme): align with dual patient + product pipeline

Ali88-hub
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2daae89

Commits on May 10, 2026

fix(product): null end-of-block residue in product_entry_date

Ali88-hub
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523a2d6

Commits on May 28, 2026

chore: fix readme casing

Ali88-hub
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e2f25fa
docs(product): bump schema column count 19 -> 20

Ali88-hub
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840daa3
feat(reference): add 226 product->category mappings to Stock_Summary

Ali88-hub
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b309fcb

Commits on May 29, 2026

docs(migration): add dashboard evaluation and product parity reports

Ali88-hub
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7b60b16

Commits on Aug 8, 2026

Chart wayfinder map for closing out the R-to-Python migration
Michael Aydinbas
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f917703
Record execution-override and daily-routine notes on the wayfinder map
Michael Aydinbas
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1b43e92
Clarify cloud routine has no GCP creds or real tracker data
Michael Aydinbas
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c425988
Bring product pytest suite to parity with patient (ticket 8)
Michael Aydinbas
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6b9a095
Merge migration into product-pipeline, resolve conflicts
Michael Aydinbas
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2322166
Fix repo-wide ruff violations blocking PR CI
Michael Aydinbas
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f90eaa6
Fix the 2 remaining ty diagnostics blocking CI
Michael Aydinbas
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acb748e

Commits on Aug 9, 2026

Fix CI: disable Typer's forced terminal styling in tests
Michael Aydinbas
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b970cf6
Merge pull request #6 from CorrelAid/product-pipeline
pmayd
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7713fea
Close wayfinder ticket 7: pipeline completeness audit
Michael Aydinbas
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7417faf
Close wayfinder ticket 8: pytest-suite parity decision
Michael Aydinbas
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530470c
Record PDF contents on wayfinder ticket 2
Michael Aydinbas
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18c1e8b
Resequence wayfinder ticket 2 to after the merge, not before
Michael Aydinbas
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aabc472
Close wayfinder ticket 3: PR #6 conflicts resolved, mergeable
Michael Aydinbas
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87bebda
Close wayfinder ticket 4: CI fixed via Typer force-terminal escape hatch
Michael Aydinbas
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4c26084
Record PR #6 merged into migration on wayfinder map
Michael Aydinbas
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9a343bb
Add production-run verification script comparing live tables to backup snapshot
Michael Aydinbas
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29e2286
Fix verify_production_run.py crashing on tables without clinic_id
Michael Aydinbas
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b304068
Close wayfinder ticket 5: real GCP production run executed and verified
Michael Aydinbas
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7e38fb2
Redraw wayfinder destination to include rollout readiness
Michael Aydinbas
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50e55dd
Add wayfinder tickets 12 and 13: retire R, audit dependencies before rollout
Michael Aydinbas
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c31660d
Remove tools/LogViewerA4D (R Shiny log viewer), out of ticket-12 sequence
Michael Aydinbas
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cd5d7e9
Audit and update dependencies before rollout (ticket 13)
Michael Aydinbas
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c4721ad
Close ticket 13 on the wayfinder map, unblocking ticket 10
Michael Aydinbas
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9a36dfd
Fix O(n^2) find_data_start_row on read-only worksheets (ticket 10)
Michael Aydinbas
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97479f8
Close ticket 10 (performance profiling), spawn ticket 14 (product bug)
Michael Aydinbas
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da8b590
Fix product cleaning crash on pre-product-tracking tracker years (ticket 14)
Michael Aydinbas
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1242dc4
Close ticket 2 (comparison-doc strategy), spawn ticket 15 to build/run it
Michael Aydinbas
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9eeb12d
Add combined patient+product run summary; soft-fail patient arm
Michael Aydinbas
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33694b4
Close ticket 11 (combined run summary), spawn ticket 16 (log-analyzer drill-down)
Michael Aydinbas
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6de3551
Restructure CLI into process-first command groups (run/create/upload/download)
Michael Aydinbas
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0e05590
Rename download trackers --destination to --data-root for consistency
Michael Aydinbas
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daf0a61
Fix product-patient link validation joining against the wrong patient table
Michael Aydinbas
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2958f06
Condense product table-stage error logging; add dataset overview and pre-upload preview
Michael Aydinbas
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5c762b6
Give run product parity with run patient's console output; drop per-file success noise
Michael Aydinbas
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05a4eb3

Commits on Aug 11, 2026

Build R/Python output comparison script; find product row-alignment bug (ticket 15)
Michael Aydinbas
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296fa86
Fix compare-outputs just recipe quoting; add a legend explaining each measure
Michael Aydinbas
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3f5ebde
Add ID/categorical overlap checks, raw-stage comparison, year grouping
Michael Aydinbas
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512c6a1
Add Excel detail export, --only-mismatches flag; rename overlap to divergence
Michael Aydinbas
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ac4090e
Drop HTML output; add row-key divergence check; consistent naming
Michael Aydinbas
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9fd16bb
Add row_key_overlap sheet to the Excel export
Michael Aydinbas
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a96ffc4
Update wayfinder map with tool-hardening work done after ticket 15 closed
Michael Aydinbas
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6307be8
Fix product row-alignment key with ordinal position, not equi-join

Michael Aydinbas
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claude
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bcfc32e
Close ticket 17 (product row-alignment key fix), spawn ticket 18 for triage

Michael Aydinbas
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claude
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cc2ef67
Add run-over-run history/deltas to the R/Python comparison script

Michael Aydinbas
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claude
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7c90645
Give compare_outputs.py a per-run output directory, clean up scripts/

Michael Aydinbas
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claude
committed
5d62865
Update wayfinder map for compare_outputs.py's per-run-folder refinement

Michael Aydinbas
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claude
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d9a8357
Close ticket 18: root-cause product_category/entry_date mismatches, spawn tickets 20-23
Michael Aydinbas
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655369f
remove deprecated files
Michael Aydinbas
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9279386
Close ticket 20: normalize raw-stage product_entry_date representation
Michael Aydinbas
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7804b8f
Fold ticket 20's residual entry_date mismatches into ticket 22
Michael Aydinbas
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dfa6b55

Commits on Aug 12, 2026

Close ticket 22: fix blank-row extraction bug, normalize float/whitespace representation in raw product comparison
Michael Aydinbas
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1027218
Close ticket 21: root-cause remaining product cleaned-stage mismatches
Michael Aydinbas
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d9022ef
Silence loguru DEBUG spam in compare_outputs.py
Michael Aydinbas
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ed572ad
Spawn ticket 26: compare_columns' Column divergence was never triaged
Michael Aydinbas
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23e7204
Close ticket 23: patient raw-stage mismatches are the ticket-20 date artifact
Michael Aydinbas
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90c6275
new clinic data
Michael Aydinbas
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4eb6a40
Fix t1d_diagnosis_age bug, classify two more patient cleaned-stage divergences (ticket 28)
Michael Aydinbas
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3607ffe
Triage product/patient column-existence and dtype divergence (ticket 26)
Michael Aydinbas
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42562f0
Close ticket 24: triage residual raw-stage units_received/released/received_from mismatches

Michael Aydinbas
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claude
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28c5082
Close ticket 27: normalize patient raw-stage numeric/date columns, classify formula-error and Buddhist-era-typo mismatches
Michael Aydinbas
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dc074e9
Preserve source Excel formula errors through extraction, null and log them in cleaning
Michael Aydinbas
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bd341ba
Set triage decision bar, add comparison totals rollup, silence date-parser noise
Michael Aydinbas
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a042194
Ticket 33: diagnose red CI on migration (ruff format on markdown snippets)
Michael Aydinbas
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d41916a
Close ticket 33: exclude docs/migration from ruff, restoring green CI
Michael Aydinbas
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62445e2
Remove accidentally committed coverage.xml, gitignore it
Michael Aydinbas
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c185f71
Ticket 35: surface the 17 Polars 2.0 deprecation warnings
Michael Aydinbas
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91f8571
Close ticket 25: product_units_released cleaned-stage is row-order divergence
Michael Aydinbas
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702ab3c
Ticket 36: record the measured product_balance mechanism and open question
Michael Aydinbas
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8d2b3ca
Warn when the recomputed closing balance contradicts the tracker's own
Michael Aydinbas
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440a363

Commits on Aug 13, 2026

Ticket 36: triage the unowned product cleaned-stage mismatches
Michael Aydinbas
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edac02b
Ticket 29: triage the residual patient cleaned-stage mismatches
Michael Aydinbas
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6f5bbeb

Commits on Aug 14, 2026

Ticket 29: one canonical status label, declared in config
Michael Aydinbas
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23f1859
Ticket 37: four date/header extraction bugs, and the 2022 header fixup
Michael Aydinbas
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14765f6
Ticket 38: the date path was sentinelling cells that recorded nothing
Michael Aydinbas
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f77d196
Add MR description for PR #2: pipeline overview, comparison harness, open items
Michael Aydinbas
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a9a5d41
MR description: add production Cloud Run Job section, point to SETUP.md
Michael Aydinbas
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1aa4d32
Fix stale paths and config drift in setup docs, CI triggers and backup-bq
Michael Aydinbas
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10bb0ae
Remove PLAN.md: the a4d-python-to-root migration it plans is done
Michael Aydinbas
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4fb2dab
Update wayfinder map: MR description is a session-end deliverable, CI/backup staleness fixes
Michael Aydinbas
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559dcda

Commits on Aug 15, 2026

Recover blank-header columns and flag trackers that change shape mid-year
Michael Aydinbas
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573c887
Record the glucose unit-confusion analysis sent to the medical advisor
Michael Aydinbas
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c998f0b
Merge source columns that share a canonical name instead of dropping them
Michael Aydinbas
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8b05cba

Commits on Aug 16, 2026

Resolve glucose readings recorded under the wrong unit's header
Michael Aydinbas
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9667df1

Commits on Aug 17, 2026

Stop inventing patient rows from a stray list of IDs, and compare floats as floats
Michael Aydinbas
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64ee13c
Refresh the MR description for ticket 43's fixes and the new frontier
Michael Aydinbas
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d50bfd5
Align patient rows on identity, breaking ties by content rather than position
Michael Aydinbas
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428c510
Refresh the MR description for the patient row-alignment fix and the new frontier
Michael Aydinbas
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52bfe27
Drop the dangling node left in the treasure map when a ticket closed
Michael Aydinbas
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b7326c1
Recover a number typed into a date-formatted cell, and name R's dropped rich-text space
Michael Aydinbas
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772a614
Propagate a merged header across its block, and stop recovery guessing inside it
Michael Aydinbas
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bc78cf6

Commits on Aug 18, 2026

Take the patient raw stage to zero unexplained differences
Michael Aydinbas
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324cfa8
Explain half the patient cleaned stage, starting with R reading dates year-first
Michael Aydinbas
committed
3142c6d
Refresh the MR description for round 4's three causes and the new frontier
Michael Aydinbas
committed
3604b6f

Commits on Aug 19, 2026

Read a bare year in a date cell as that year, not as an Excel serial
Michael Aydinbas
committed
623e88e
Stop filling an absent day from today, and keep a spaced blood pressure
Michael Aydinbas
committed
f16101e
Close round 6 of the patient cleaned-stage triage and open round 7
Michael Aydinbas
committed
a15d086
Refresh the MR description for round 6's two fixes and the new frontier
Michael Aydinbas
committed
21dceef
Explain the diagnosis ages R never derives, and stop reparsing rounded floats
Michael Aydinbas
committed
b019c3d
Close round 7 of the patient cleaned-stage triage and open round 8
Michael Aydinbas
committed
afba877
Refresh the MR description for round 7's two findings and the new frontier
Michael Aydinbas
committed
0cae88d
Stop publishing impossible heights, BMIs and ancient dates
Michael Aydinbas
committed
d365d8a
Read the dates R was silently inventing, and stop losing the ones it reads
Michael Aydinbas
committed
120ad0f
Correct the round 9 residual count from 94 to 96
Michael Aydinbas
committed
9e9957e

Commits on Aug 20, 2026

Read the measurement dates R could read and Python could not
Michael Aydinbas
committed
30da148
Record that R retires only when nothing still needs to read it
Michael Aydinbas
committed
f154ad3
Stop publishing a patient ID that no tracker contains
Michael Aydinbas
committed
b21169d
Name the rows that pair with nothing, instead of only counting them
Michael Aydinbas
committed
230f33e

Commits on Aug 21, 2026

Read the date a clinician wrote inside the note
Michael Aydinbas
committed
c281449
Read the mmol glucose column as the mg column's shadow, not its own reading
Michael Aydinbas
committed
1418694
Stop letting a classifier name a difference it never explained
Michael Aydinbas
committed
0661eec
Record the decision to convert Buddhist-era dates, and measure who it touches
Michael Aydinbas
committed
905b4bc
Carry the Buddhist-era decision onto the map
Michael Aydinbas
committed
a9d9d1f

Commits on Aug 22, 2026

Read a Thai clinic's date in the calendar it was written in
Michael Aydinbas
committed
1ff021c