Skip to content

CLAUDE.md

Latest commit

 

History

History
69 lines (56 loc) · 7.75 KB

CLAUDE.md

File metadata and controls

69 lines (56 loc) · 7.75 KB
Raw

CLAUDE.md

Project Overview

cpp2sqlite is a C++ tool that generates SQLite databases containing Swiss Healthcare Public Domain Drug Information. It aggregates data from multiple Swiss health authority sources (Swissmedic, BAG, Refdata, etc.) into SQLite databases used by AmiKo and other applications.

Build

cd scripts && source steps_public1.source && ./download.sh
source steps_public2.source && ./download.sh
cd ../build && cmake .. && make -j9

Note: BOOST_BIND_GLOBAL_PLACEHOLDERS is defined in CMakeLists.txt to suppress Boost bind placeholder deprecation warnings (the project doesn't use boost::bind directly, but Boost headers trigger the warning internally).

Key Executables

  • cpp2sqlite - Main tool, generates amiko_db SQLite databases
  • pharma - Generates pharma.csv
  • sai - Processes SAI (Refdata structured article information)
  • zurrose - Processes Zur Rose data

All use BAG FHIR ndjson by default since 01.06.2026 (flagFHIR=true); pass --no-fhir to fall back to the legacy BAG XML. The --fhir flag still works as an explicit opt-in.

FHIR NDJSON Parsing

  • Source: src/bagFHIR.cpp / src/bagFHIR.hpp
  • Input: downloads/fhir-sl-{de,fr,it}.ndjson from https://epl.bag.admin.ch/static/fhir/foph-sl-export-latest-{de,fr,it}.ndjson (per-language NDJSON)
  • Each line is a FHIR Bundle with entries: MedicinalProductDefinition, RegulatedAuthorization, PackagedProductDefinition, Ingredient, ClinicalUseDefinition
  • Prices (EFP/PP) and reimbursement data are in RegulatedAuthorization extensions under reimbursementSL > productPrice
  • Legal status codes map to categories: A (756005022001), B (756005022003), C (756005022005), D (756005022007, 756005022008), E (756005022009)
  • When --fhir is active, all price lookups (including from Refdata and Swissmedic) must use BAGFHIR::getPricesAndFlags() instead of BAG::getPricesAndFlags(), since BAG::parseXML() is not called and its prepList is empty

Indikationscode (BAG XXXXX.NN)

  • Mandatory on SL prescriptions and invoices from 2026-07-01 (BAG Rundschreiben 2026-02-19); insurers may reject non-compliant invoices from 2027-01-01
  • Source: src/bagFHIR.cpp collectBundleIndC() — bundle-scoped pass over each NDJSON line (one Bundle per line)
  • Preferred source (BAG SL FHIR export >= v2.0.5): the explicit indicationCode sub-extension carried on each limitation (RegulatedAuthorization.indication[].extension[regulatedAuthorization-limitation].extension[indicationCode].valueString, e.g. 20403.01). The BAG changelog states the limitation code (ClinicalUseDefinition.id) and the indication code are independent fields, so XXXXX.NN must NOT be reconstructed from the CUD id suffix. The limitation text is resolved via the sibling limitationIndication reference (e.g. ClinicalUseDefinition/CYRAMZA.01) into that CUD's text. Verified on the live DE feed: 718 / 6'775 bundles carry the explicit field.
  • Fallback (older feeds without the extension): XXXXX from RegulatedAuthorization.extension[reimbursementSL].extension[FOPHDossierNumber].valueIdentifier.value; .NN is the trailing all-digit segment of each ClinicalUseDefinition.id (e.g. CYRAMZA.01); only type == "indication" CUDs are picked up. The feed ships type as a plain string and indication as a single object — both shapes are handled.
  • CUD text comes from indication.diseaseSymptomProcedure.concept.text, with fallback indication.extension[url == "limitationText"].valueString
  • Stored on BAG::Preparation.indicationCodes (and copied onto every Pack) as IndicationCode {code, cudId, text}
  • BAGFHIR::getIndCByRegnr(regnr, &codes, &text) returns the joined columns the schema expects: comma-joined codes + newline-joined code: text lines, deduped by code, in bundle order. Mirrors rust2xml ≥ 3.1.12 (INDIKATIONSCODE / INDIKATIONSCODE_TEXT XML elements). The function walks the entire prepList and merges IndicationCodes from every prep that shares the queried Swissmedic regnr, deduped by code — required because the same 5-digit Swissmedic regnr typically spans multiple FHIR bundles (only one of which carries the type=indication ClinicalUseDefinitions). An earlier early-return on the first matching prep with empty indicationCodes silently dropped IndC for ~80% of regnrs.
  • Schema/binding: Sql::useIndC is set from flagFHIR in openDB(). When true, the amikodb schema gains two trailing TEXT columns (indikationscode, indikationscode_text) and insertRow binds positions 19/20. Non-FHIR builds emit the legacy 19-column schema, so apps reading by column index keep working.
  • iOS consumer: generikacc/Generika/IndCSection.swift (issue zdavatz/generikacc#102) — guarded by AmikoDBManager isIndcColumnAvailable so older DB snapshots don't break the app

Zur Rose Artikelstamm (Exfact column)

  • Feed: artikel_vollstamm_zurrose.csv and artikel_stamm_zurrose.csv are downloaded via scripts/download_zr.sh (SFTP from ftp.zur-rose.ch).
  • Schema change (2026-05): a trailing column Exfact (V, index 21) was appended, growing the row from 21 to 22 semicolon-separated fields. All four column-count guards must match the new width — src/zur/stamm.cpp:69, src/zur/stamm.cpp:129, src/zur/voll.cpp:152, src/zur/voll.cpp:355. Note that voll.cpp::parseCSV (line 152) silently continues on mismatch instead of exiting, so a missed bump there empties the output DB without an error message.
  • Exfact is the Zur Rose ex-factory price and is wired into rosedb.exfprice as a fallback for the BAG EFP in voll.cpp::parseCSV (~line 304). BAG values stay canonical for SL-listed drugs; Zur Rose Exfact fills the long tail. In --fhir builds without BAG XML this lifts rosedb.exfprice population from 0/163858 to 163858/163858.

zurrose SQLite lifecycle (do not double-close)

VOLL::closeDB() calls sqlite3_finalize(statement) then sqlite3_close(db), so it must be called exactly once. Calling it twice double-frees both handles and corrupts the glibc heap — the failure surfaces as free(): invalid next size (fast) on process exit and, depending on arena state, may not reproduce on smaller workloads (atcdb hid it while fulldb crashed every run). src/zur/main.cpp previously had a stray second closeDB block right after the fulldb/atcdb branch; the single call inside the branch is the correct lifecycle.

ean13 is a separate git submodule

src/c2s/ean13 is a git submodule pointing at ywesee/BarcodeGenerator (separate org from zdavatz/cpp2sqlite). Fixes there require: commit + push inside the submodule on master, then bump the parent's submodule pointer in a parent commit. Consumers (and the build server) must run git submodule update after pulling the parent.

GCC 13+ header transitivity

GCC 13+ (and current libstdc++) no longer pulls many standard headers transitively. New code that uses standard types/streams must #include them explicitly or the Funtoo build server breaks:

  • <cstdint> for uint8_t / int32_t / etc. (tripped src/c2s/ean13/functii.cpp — fixed in ywesee/BarcodeGenerator c1f17da)
  • <fstream> for std::ofstream / std::ifstream (tripped src/sap/main.cpp, src/dru/main.cpp — fixed in 0203368, plus bagFHIR.cpp, c2s/peddose.cpp, c2s/sappinfo.cpp, c2s/refdata.cpp cleaned up preemptively)

If a new source file uses these (or <sstream>, <iomanip>, etc.) without an explicit include, it will compile locally on older toolchains and break on the build server.

Directory Structure

  • src/ - C++ source files
  • src/c2s/ - cpp2sqlite specific sources
  • src/pha/ - pharma specific sources
  • src/sai/ - SAI specific sources
  • src/zur/ - zurrose specific sources
  • scripts/ - Build and download scripts
  • input/ - Input data files (not in git)
  • downloads/ - Downloaded source files (not in git)
  • output/ - Generated databases and reports (not in git)