DuckCDM

DuckCDM — DuckDB-powered OMOP CDM engine. OMOP data. Simpler. Faster. Everywhere.

DuckCDM runs the OHDSI analytics stack on a single DuckDB file (or a folder of Parquet files): OHDSI SqlRender, Circe and Achilles, plus an ATLAS 3.0-compatible WebAPI that serves the ATLAS 3.0 user interface. Pure Python — no Java, no PostgreSQL, no Docker.

pip install "duckcdm[server]"
duckcdm serve EUNOMIA=cdm.duckdb --achilles     # ATLAS 3.0 at http://127.0.0.1:8080/, API at /WebAPI

Python API

from duckcdm.sqlrender import render, translate
sql = render("SELECT TOP 10 * FROM @cdm.person {@adult}?{WHERE year_of_birth < 2000};", cdm="main", adult=True)
translate(sql, "duckdb")   # SELECT  * FROM main.person WHERE year_of_birth < 2000 LIMIT 10;

from duckcdm.circe import build_cohort_query
sql = build_cohort_query(open("cohort.json").read(), cdm_schema="main", target_table="main.cohort", cohort_id=1)
duck = translate(render(sql), "duckdb")

import duckdb
from duckcdm.achilles import run_achilles
run_achilles(duckdb.connect("cdm.duckdb"), cdm_schema="main", results_schema="results")

Command line

duckcdm serve EUNOMIA=cdm.duckdb --achilles   # ATLAS 3.0 + WebAPI; build Achilles results if missing
duckcdm views /data/cdm_parquet cdm.duckdb    # Parquet folder (one sub-folder per table) -> OMOP views
duckcdm views /data/cdm_parquet cdm.duckdb --materialize   # ... or native DuckDB tables (much faster)
duckcdm achilles cdm.duckdb                   # Achilles results for the data-source reports only
duckcdm cohort cohort.json duckdb --cdm main --results main --cohort-id 1
duckcdm translate query.sql postgresql -p cdm=main
duckcdm dialects

serve and achilles accept --memory-limit 8GB --threads 4 for shared servers.

Server (duckcdm serve)

• One DuckDB file is one WebAPI source (CDM, Vocabulary and Results daimons). The results schema (results) and the cohort result tables are created when missing.
• Concept sets and cohort definitions are stored in duckcdm_store.duckdb next to the first database.
• The ATLAS 3.0 UI is served from / with a relative API URL, so it also works behind a reverse proxy under a path prefix.
• No login of its own. For multi-user deployments run it behind an authenticating reverse proxy with --gateway: requests are accepted only from the proxy's network (--gateway-ip), only when the proxy's marker header is present (--gateway-marker, default X-Auth-Method=parent_gateway), and only for user ids (from X-Auth-User-ID / User-ID / X-Auth-Subject) listed in --allow-users FILE (re-read on change).
• Data-source reports appear after Achilles results are built (--achilles or duckcdm achilles).
• Not yet implemented: characterization, incidence rates, pathways, version history, tags.

Equivalence with the Java originals

SqlRender — tests/equiv/: 2,009 strings from the SqlRender R tests, 763 Circe/WebAPI SQL files (× 16 dialects, render and split) and 3,000 synthetic conditionals, run through the Java original (tests/java, run with the JDK 22+ source launcher) and this port:

python3 tests/equiv/build_corpus.py <clones dir> cases.tsv
python3 tests/equiv/run_java.py cases.tsv java.out 24
PYTHONPATH=src python3 tests/equiv/py_harness.py cases.tsv py.out 32
python3 tests/equiv/diff.py cases.tsv java.out py.out

Circe — tests/equiv/circe_corpus.py (PhenotypeLibrary cohorts × 3 option sets, their concept sets, circe test JSON, random cohorts) through tests/java_circe/CirceHarness.java (needs Jackson 2.11, commons-lang3, standardized-analysis-utils and semver4j jars) and tests/equiv/py_circe_harness.py, compared with tests/equiv/circe_diff.py.

End to end — tests/e2e/run_phenotypes.py generates, translates and executes all 1,104 PhenotypeLibrary cohorts on DuckDB (Eunomia: 1,104/1,104 succeed).

Known differences: only the message text of Java-internal exceptions (EmptyStack, ArrayIndexOutOfBounds) differs — the exceptions occur at the same inputs. Characters outside the BMP (emoji) count as two UTF-16 units in Java, so positions may differ for them.

License

Apache 2.0. Includes material from OHDSI SqlRender, circe-be, WebAPI, Atlas3, Achilles and CommonDataModel (all Apache 2.0); see NOTICE and third_party/.