jpomop 0.0.1__tar.gz

jpomop-0.0.1/.github/workflows/ci.yml

@@ -0,0 +1,21 @@
+name: ci
+on:
+  push:
+    branches: [main]
+  pull_request:
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.12", "3.13"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+      - run: uv venv --python ${{ matrix.python }}
+      - run: uv pip install -e ".[dev]"
+      - run: uv run --no-sync ruff check src tests
+      - run: uv run --no-sync ruff format --check src tests
+      - run: uv run --no-sync mypy src
+      - run: uv run --no-sync pytest -q

jpomop-0.0.1/.gitignore

@@ -0,0 +1,17 @@
+__pycache__/
+*.py[cod]
+.venv/
+dist/
+build/
+*.egg-info/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.coverage
+htmlcov/
+# code masters, Athena vocabularies and real data are never committed
+masters/
+athena/
+*.duckdb
+*.parquet
+*.pdf

jpomop-0.0.1/LICENSE

@@ -0,0 +1,202 @@
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+
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+   Copyright 2026 Koji Miyazawa
+
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+

jpomop-0.0.1/LICENSE-DATA

@@ -0,0 +1,6 @@
+Mapping tables and other data files created by the jpomop project are licensed
+under the Creative Commons Attribution 4.0 International licence (CC BY 4.0).
+https://creativecommons.org/licenses/by/4.0/
+
+This does not apply to third-party files that users download themselves
+(code masters, OMOP vocabularies from Athena), which remain under their own terms.

jpomop-0.0.1/PKG-INFO

@@ -0,0 +1,121 @@
+Metadata-Version: 2.5
+Name: jpomop
+Version: 0.0.1
+Summary: Convert Japanese DPC inpatient data to the OMOP Common Data Model v5.4
+Author: Koji Miyazawa
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: LICENSE-DATA
+Requires-Python: >=3.12
+Requires-Dist: click>=8.1
+Requires-Dist: duckdb>=1.0
+Requires-Dist: pyarrow>=16
+Requires-Dist: pyyaml>=6
+Provides-Extra: dev
+Requires-Dist: hypothesis>=6; extra == 'dev'
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: openpyxl>=3.1; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: types-pyyaml; extra == 'dev'
+Provides-Extra: vocab
+Requires-Dist: openpyxl>=3.1; extra == 'vocab'
+Description-Content-Type: text/markdown
+
+# jpomop
+
+jpomop converts Japanese DPC inpatient data to the OMOP Common Data Model v5.4.
+It reads two DPC files: Form 1 (様式1) and the EF file (入院EF統合ファイル).
+
+I wrote jpomop using the public DPC specification from the Ministry of Health, Labour and Welfare.
+This repository has no hospital data or code masters.
+
+## Status
+
+jpomop is in early development.
+It can read and check the two files and write eight CDM tables.
+I tested it with synthetic data and the examples in the specification.
+I have not tried it with real hospital data or measured mapping rates with a full Athena vocabulary yet.
+
+I plan to release v0.1 at the end of November 2026.
+
+## Try it
+
+```sh
+pip install jpomop
+jpomop synth --n 100 --out synth/
+jpomop validate --yoshiki1 synth/yoshiki1.txt --ef synth/ef.txt
+jpomop convert --yoshiki1 synth/yoshiki1.txt --ef synth/ef.txt --out cdm.duckdb
+jpomop report --cdm cdm.duckdb
+```
+
+`synth` makes fake data for 100 patients, and you can change the number with `--n`.
+
+`validate` checks the files against the FY2026 specification and lists the problems it finds.
+
+Without `--vocab`, the concept IDs for diagnoses and drugs are 0.
+The original codes stay in the source value columns.
+To map diagnoses and drugs, build a vocabulary first:
+
+```sh
+jpomop vocab build --athena athena/ --drug-master y_ALL20261001.csv \
+    --kimura rxnorm_mapping.tsv --out vocab.duckdb
+jpomop convert ... --vocab vocab.duckdb
+```
+
+You need the following three sources, and you must download them yourself.
+
+- Athena vocabularies: ICD10, SNOMED, RxNorm and RxNorm Extension (https://athena.ohdsi.org)
+- The drug master (医薬品マスター, `y_*.csv`) (https://www.hpdx.or.jp/seikyushiharai/tensuhyo/kihonmasta/kihonmasta_04.html)
+- The drug mapping table by Kimura et al. 2025, CC BY 4.0 (https://doi.org/10.17632/y3756v8237.1)
+
+## Walkthrough
+
+[examples/walkthrough_en.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_en.ipynb) runs every step on 100 invented patients.
+It shows the input files, the checks and each CDM table for one patient.
+A Japanese version is in [examples/walkthrough_ja.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_ja.ipynb).
+
+## How each part is converted
+
+| DPC | CDM table | Notes |
+|---|---|---|
+| Form 1, one form per stay | `person`, `visit_occurrence`, `observation_period` | Patient IDs are hashed. Some form types are counted but not converted. See below. |
+| EF, ward code for each day | `visit_detail` | One row for each run of days on the same ward. |
+| Form 1, diagnoses (ICD-10) | `condition_occurrence` | Form 1 has no date for each diagnosis, so the start date is the admission date. Suspected diagnoses (modifier 8002) are left out and counted. |
+| EF, codes that start with 6 | `drug_exposure` | Mapped through the NHI drug price code. Drugs that patients bring from home are left out. |
+| EF, codes that start with 1 | `procedure_occurrence` | The concept ID is 0 for now. The DPC code stays as the source value. Room and meal charges are left out. |
+| Form 1, discharge outcome 6 or 7 | `death` | The death date is the discharge date. |
+
+Form 1 has several form types, and jpomop uses the form for the whole stay.
+It uses the day-90 interim form only when the stay has no whole-stay form yet.
+It counts the ward-group forms and the readmission forms, but it does not convert them.
+These forms cover the same days as the whole-stay forms (specification p42 and p125).
+
+## Code masters are not included
+
+The code masters (基本マスター) come from 医療情報基盤・診療報酬審査支払機構.
+The website terms say that its documents may not be used or copied without permission.
+So this repository does not include the masters.
+Please download them from https://www.hpdx.or.jp/seikyushiharai/tensuhyo/kihonmasta/index.html.
+
+## Sources
+
+Each field in the specification files shows the document, the version and the page.
+See [PROVENANCE.md](https://github.com/kojikojikojikoji/jpomop/blob/main/PROVENANCE.md).
+
+## Licence
+
+The code uses the Apache-2.0 licence.
+Mapping tables made by this project use CC BY 4.0. See [LICENSE-DATA](LICENSE-DATA).
+
+---
+
+## 日本語
+
+厚生労働省が公開している DPC 調査の仕様（様式1・入院EF統合ファイル）だけを元に、DPC データを OMOP CDM v5.4 へ変換する Python のプログラムです。病院の実データとマスターは含みません。動作の確認には、このリポジトリで作る架空データと、仕様書の記載例だけを使っています。
+
+読み込み・仕様の確認・8つの表への変換までできています。病院の実データでの確認と、Athena の語彙一式での変換率の測定はこれからです。
+
+架空の患者 100 人のデータで最初から最後まで動かした例を、[examples/walkthrough_ja.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_ja.ipynb) に置いています。
+
+マスターは、医療情報基盤・診療報酬審査支払機構のサイトから各自でダウンロードしてください。

jpomop-0.0.1/PROVENANCE.md

@@ -0,0 +1,32 @@
+# Provenance
+
+jpomop is written from public documents only. This file lists each document, the version used, and when it was retrieved. Specification YAML files cite the page number for every field.
+
+No code, data, documents or other material from any employer or client of the author were used.
+
+## DPC specification
+
+| Document | Version | URL | Retrieved | SHA-256 |
+|---|---|---|---|---|
+| DPCの評価・検証等に係る調査（退院患者調査）実施説明資料 | FY2026, 2026-07-17 (244 pages) | https://www.mhlw.go.jp/content/12400000/001738680.pdf | 2026-10-12 | f1a099cb57c14251497863cc1fb46c9186c7febd3a7160dca73f9639383b1ed1 |
+
+Terms: the Ministry of Health, Labour and Welfare website allows reuse and modification with attribution (公共データ利用規約 第1.0版, https://www.mhlw.go.jp/chosakuken/index.html). jpomop does not copy the text of the specification. It records field names, lengths, types and page numbers only.
+
+The PDF itself is not committed.
+
+## Code masters (not redistributed)
+
+基本マスター from 医療情報基盤・診療報酬審査支払機構: https://www.hpdx.or.jp/seikyushiharai/tensuhyo/kihonmasta/index.html
+
+The site terms (https://www.hpdx.or.jp/riyo.html) prohibit reproduction without permission, so the masters are never committed. Users download them and build the vocabulary locally.
+
+Drug master layout: receipt code in field 3 and NHI price listing code (薬価基準収載医薬品コード) in field 32, checked against `y_ALL20261001.csv` (42 fields per row).
+
+## Third-party mapping tables (not redistributed)
+
+| Table | Licence | Where | Used for |
+|---|---|---|---|
+| Kimura E. et al. A dataset for mapping the Japanese drugs to RxNorm standard concepts. Data in Brief, 2025. doi:10.1016/j.dib.2025.111418 | CC BY 4.0 | https://doi.org/10.17632/y3756v8237.1 | NHI price listing code (`NHIDPLC`) to OMOP concept (`OSV_ID`) |
+| OMOP Standardized Vocabularies (ICD10, SNOMED, RxNorm, RxNorm Extension) | per vocabulary, see Athena | https://athena.ohdsi.org | ICD-10 to SNOMED (`Maps to`) |
+
+Users download both themselves; `jpomop vocab build` joins them locally.

jpomop-0.0.1/README.md

@@ -0,0 +1,97 @@
+# jpomop
+
+jpomop converts Japanese DPC inpatient data to the OMOP Common Data Model v5.4.
+It reads two DPC files: Form 1 (様式1) and the EF file (入院EF統合ファイル).
+
+I wrote jpomop using the public DPC specification from the Ministry of Health, Labour and Welfare.
+This repository has no hospital data or code masters.
+
+## Status
+
+jpomop is in early development.
+It can read and check the two files and write eight CDM tables.
+I tested it with synthetic data and the examples in the specification.
+I have not tried it with real hospital data or measured mapping rates with a full Athena vocabulary yet.
+
+I plan to release v0.1 at the end of November 2026.
+
+## Try it
+
+```sh
+pip install jpomop
+jpomop synth --n 100 --out synth/
+jpomop validate --yoshiki1 synth/yoshiki1.txt --ef synth/ef.txt
+jpomop convert --yoshiki1 synth/yoshiki1.txt --ef synth/ef.txt --out cdm.duckdb
+jpomop report --cdm cdm.duckdb
+```
+
+`synth` makes fake data for 100 patients, and you can change the number with `--n`.
+
+`validate` checks the files against the FY2026 specification and lists the problems it finds.
+
+Without `--vocab`, the concept IDs for diagnoses and drugs are 0.
+The original codes stay in the source value columns.
+To map diagnoses and drugs, build a vocabulary first:
+
+```sh
+jpomop vocab build --athena athena/ --drug-master y_ALL20261001.csv \
+    --kimura rxnorm_mapping.tsv --out vocab.duckdb
+jpomop convert ... --vocab vocab.duckdb
+```
+
+You need the following three sources, and you must download them yourself.
+
+- Athena vocabularies: ICD10, SNOMED, RxNorm and RxNorm Extension (https://athena.ohdsi.org)
+- The drug master (医薬品マスター, `y_*.csv`) (https://www.hpdx.or.jp/seikyushiharai/tensuhyo/kihonmasta/kihonmasta_04.html)
+- The drug mapping table by Kimura et al. 2025, CC BY 4.0 (https://doi.org/10.17632/y3756v8237.1)
+
+## Walkthrough
+
+[examples/walkthrough_en.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_en.ipynb) runs every step on 100 invented patients.
+It shows the input files, the checks and each CDM table for one patient.
+A Japanese version is in [examples/walkthrough_ja.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_ja.ipynb).
+
+## How each part is converted
+
+| DPC | CDM table | Notes |
+|---|---|---|
+| Form 1, one form per stay | `person`, `visit_occurrence`, `observation_period` | Patient IDs are hashed. Some form types are counted but not converted. See below. |
+| EF, ward code for each day | `visit_detail` | One row for each run of days on the same ward. |
+| Form 1, diagnoses (ICD-10) | `condition_occurrence` | Form 1 has no date for each diagnosis, so the start date is the admission date. Suspected diagnoses (modifier 8002) are left out and counted. |
+| EF, codes that start with 6 | `drug_exposure` | Mapped through the NHI drug price code. Drugs that patients bring from home are left out. |
+| EF, codes that start with 1 | `procedure_occurrence` | The concept ID is 0 for now. The DPC code stays as the source value. Room and meal charges are left out. |
+| Form 1, discharge outcome 6 or 7 | `death` | The death date is the discharge date. |
+
+Form 1 has several form types, and jpomop uses the form for the whole stay.
+It uses the day-90 interim form only when the stay has no whole-stay form yet.
+It counts the ward-group forms and the readmission forms, but it does not convert them.
+These forms cover the same days as the whole-stay forms (specification p42 and p125).
+
+## Code masters are not included
+
+The code masters (基本マスター) come from 医療情報基盤・診療報酬審査支払機構.
+The website terms say that its documents may not be used or copied without permission.
+So this repository does not include the masters.
+Please download them from https://www.hpdx.or.jp/seikyushiharai/tensuhyo/kihonmasta/index.html.
+
+## Sources
+
+Each field in the specification files shows the document, the version and the page.
+See [PROVENANCE.md](https://github.com/kojikojikojikoji/jpomop/blob/main/PROVENANCE.md).
+
+## Licence
+
+The code uses the Apache-2.0 licence.
+Mapping tables made by this project use CC BY 4.0. See [LICENSE-DATA](LICENSE-DATA).
+
+---
+
+## 日本語
+
+厚生労働省が公開している DPC 調査の仕様（様式1・入院EF統合ファイル）だけを元に、DPC データを OMOP CDM v5.4 へ変換する Python のプログラムです。病院の実データとマスターは含みません。動作の確認には、このリポジトリで作る架空データと、仕様書の記載例だけを使っています。
+
+読み込み・仕様の確認・8つの表への変換までできています。病院の実データでの確認と、Athena の語彙一式での変換率の測定はこれからです。
+
+架空の患者 100 人のデータで最初から最後まで動かした例を、[examples/walkthrough_ja.ipynb](https://github.com/kojikojikojikoji/jpomop/blob/main/examples/walkthrough_ja.ipynb) に置いています。
+
+マスターは、医療情報基盤・診療報酬審査支払機構のサイトから各自でダウンロードしてください。

jpomop-0.0.1/docs/adr/0000-template.md

@@ -0,0 +1,10 @@
+# NNNN. Title
+
+- Status: proposed | accepted | superseded by NNNN
+- Date: YYYY-MM-DD
+
+## Context
+
+## Decision
+
+## Consequences