From a21ce7ff3f3224b26305a4625ba586048a19b458 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 11 Dec 2025 20:15:03 +0000 Subject: [PATCH 01/19] First go at FTPS upload. Works! --- .dockerignore | 3 --- Dockerfile | 11 +++++++---- config/.gitignore | 2 -- docker-compose.yml | 6 +++--- pyproject.toml | 1 + settings.env.EXAMPLE | 5 +++++ src/exporter/__init__.py | 0 src/exporter/ftps.py | 29 +++++++++++++++++++++++++++++ src/settings.py | 10 ++++++++-- 9 files changed, 53 insertions(+), 14 deletions(-) delete mode 100644 .dockerignore delete mode 100644 config/.gitignore create mode 100644 src/exporter/__init__.py create mode 100644 src/exporter/ftps.py diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index c1fb6ad..0000000 --- a/.dockerignore +++ /dev/null @@ -1,3 +0,0 @@ -.venv -# secrets -config diff --git a/Dockerfile b/Dockerfile index ecae0ad..2a74d15 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,13 @@ -FROM python:3.14-slim-bookworm +FROM python:3.12-slim-bookworm LABEL authors="Stephen Thompson, Jeremy Stein" COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ -WORKDIR /app ARG UVCACHE=/root/.cache/uv -COPY pyproject.toml uv.lock* /app/ +COPY PIXL /PIXL +WORKDIR /PIXL +RUN --mount=type=cache,target=${UVCACHE} uv pip install --system pixl_core/ +WORKDIR /app +COPY waveform-controller/pyproject.toml waveform-controller/uv.lock /app/ RUN --mount=type=cache,target=${UVCACHE} uv pip install --system . -COPY . /app/ +COPY waveform-controller/. /app/ RUN --mount=type=cache,target=${UVCACHE} uv pip install --system . CMD ["emap-extract-waveform"] diff --git a/config/.gitignore b/config/.gitignore deleted file mode 100644 index a5f977a..0000000 --- a/config/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -# secrets go here, do not put in git -* diff --git a/docker-compose.yml b/docker-compose.yml index a49869c..75af4ee 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,8 +1,8 @@ services: waveform-controller: build: - context: . - dockerfile: Dockerfile + context: .. + dockerfile: waveform-controller/Dockerfile args: HTTP_PROXY: ${HTTP_PROXY} http_proxy: ${http_proxy} @@ -10,6 +10,6 @@ services: https_proxy: ${https_proxy} # ideally we'd use docker secrets but it's not enabled currently env_file: - - ./config/settings.env + - ../config/settings.env volumes: - ../waveform-export:/app/waveform-export diff --git a/pyproject.toml b/pyproject.toml index ab7df2f..5840a7c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,3 +13,4 @@ dependencies = [ [project.scripts] emap-extract-waveform = "controller:receiver" +emap-send-ftps = "exporter.ftps:do_upload" diff --git a/settings.env.EXAMPLE b/settings.env.EXAMPLE index 35027b6..c15ad9e 100644 --- a/settings.env.EXAMPLE +++ b/settings.env.EXAMPLE @@ -11,3 +11,8 @@ RABBITMQ_PASSWORD="my_pw" RABBITMQ_HOST="localhost" RABBITMQ_PORT=5672 RABBITMQ_QUEUE="waveform" + +FTPS_HOST=myftps.example.com +FTPS_PORT=990 +FTPS_USERNAME=my_username +FTPS_PASSWORD=my_password diff --git a/src/exporter/__init__.py b/src/exporter/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py new file mode 100644 index 0000000..ada4b22 --- /dev/null +++ b/src/exporter/ftps.py @@ -0,0 +1,29 @@ +import os +from typing import BinaryIO + +from core.uploader._ftps import _connect_to_ftp +import settings +import argparse + + +def do_upload(): + parser = argparse.ArgumentParser() + parser.add_argument("file_to_upload", type=str, help="file to upload") + args = parser.parse_args() + do_upload_inner(args.file_to_upload) + + +def do_upload_inner(file_to_upload): + ftp = _connect_to_ftp(settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME, settings.FTPS_PASSWORD) + project_dir = "foobar_waveform" + # ftp.mkd(project_dir) + ftp.cwd(project_dir) + remote_filename = os.path.basename(file_to_upload) + command = f"STOR {remote_filename}" + # BinaryIO + print("PWD: " + ftp.pwd()) + with open(file_to_upload, 'rb') as file_to_upload_fh: + ftp.storbinary(command, file_to_upload_fh) + ftp.dir() + print("Done dir") + ftp.quit() diff --git a/src/settings.py b/src/settings.py index 2ec92c9..75cea8f 100644 --- a/src/settings.py +++ b/src/settings.py @@ -1,10 +1,11 @@ import os -def get_from_env(env_var, setting_name=None): +def get_from_env(env_var, *, default_value=None, setting_name=None): if setting_name is None: setting_name = env_var - globals()[setting_name] = os.environ.get(env_var) + value_from_env = os.environ.get(env_var) + globals()[setting_name] = value_from_env if value_from_env is not None else default_value # read env vars into settings variables @@ -19,3 +20,8 @@ def get_from_env(env_var, setting_name=None): get_from_env("RABBITMQ_HOST") get_from_env("RABBITMQ_PORT") get_from_env("RABBITMQ_QUEUE") + +get_from_env("FTPS_HOST") +get_from_env("FTPS_PORT", default_value=990) +get_from_env("FTPS_USERNAME") +get_from_env("FTPS_PASSWORD") From 210556be5a508eb1e4c2b09c638e97a9f79ba8cd Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Fri, 12 Dec 2025 11:49:20 +0000 Subject: [PATCH 02/19] Document that settings should live outside of any repo so they don't end up in the docker image --- .gitignore | 3 +++ README.md | 3 ++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 0635af1..f368298 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,6 @@ wheels/ # IDEs .idea/ + +# settings file (should not be in the source tree anyway, but just in case) +settings.env \ No newline at end of file diff --git a/README.md b/README.md index 7de37b2..954f528 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,8 @@ Configuration, copy the configuration file to the config directory and edit as necessary. Remove the comment telling you not to put secrets in it. ``` -cp settings.env.EXAMPLE config/settings.env +mkdir ../config +cp settings.env.EXAMPLE ../config/settings.env ``` If it doesn't already exist you should create a directory named `waveform-export` in the parent directory to store the saved waveform From 1cf2e8ca8b7d7ef8edfa06e89070860b5e4808f1 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Fri, 12 Dec 2025 12:12:45 +0000 Subject: [PATCH 03/19] Control the PIXL install from our pyproject so the dependencies are all evaluated together. --- .python-version | 2 +- Dockerfile | 4 +- pyproject.toml | 5 +- uv.lock | 1622 +++++++++++++++++++++++++++++++++++++++++++---- 4 files changed, 1497 insertions(+), 136 deletions(-) diff --git a/.python-version b/.python-version index 2c07333..24ee5b1 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.11 +3.13 diff --git a/Dockerfile b/Dockerfile index 2a74d15..985f910 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,8 @@ -FROM python:3.12-slim-bookworm +FROM python:3.13-slim-bookworm LABEL authors="Stephen Thompson, Jeremy Stein" COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ ARG UVCACHE=/root/.cache/uv COPY PIXL /PIXL -WORKDIR /PIXL -RUN --mount=type=cache,target=${UVCACHE} uv pip install --system pixl_core/ WORKDIR /app COPY waveform-controller/pyproject.toml waveform-controller/uv.lock /app/ RUN --mount=type=cache,target=${UVCACHE} uv pip install --system . diff --git a/pyproject.toml b/pyproject.toml index 5840a7c..e066f78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,8 +7,11 @@ requires-python = ">=3.11" dependencies = [ "pika>=1.3.2", "pre-commit>=4.5.0", - "psycopg2-binary>=2.9.11", + # need to be compatible with PIXL, which currently pins 2.9.10 (arguably it shouldn't) + "psycopg2-binary>=2.9.10", "pytest>=9.0.2", + # trick for making a "relative" path, works inside or outside container image + "core @ file:///${PROJECT_ROOT}/../PIXL/pixl_core", ] [project.scripts] diff --git 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Make FTPS upload more usable and check that file to be uploaded is really under the right dir --- README.md | 10 ++++++++++ docker-compose.yml | 2 +- src/exporter/ftps.py | 29 ++++++++++++++++++++--------- src/locations.py | 5 +++++ 4 files changed, 36 insertions(+), 10 deletions(-) create mode 100644 src/locations.py diff --git a/README.md b/README.md index 954f528..0184d18 100644 --- a/README.md +++ b/README.md @@ -68,5 +68,15 @@ Each row of the csv will contain `csn, mrn, units, samplingRate, observationTime, waveformData` +## Perform an export + +Exported files must be under the WAVEFORM_PSEUDONYMISED directory. +Files passed in must be given relative to this directory: +``` +docker compose run waveform-controller emap-send-ftps my_pseudonymised_file.parquet +``` + +In future, this will be run on a schedule. + # Developing See [developing docs](docs/develop.md) diff --git a/docker-compose.yml b/docker-compose.yml index 75af4ee..eda6c13 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -12,4 +12,4 @@ services: env_file: - ../config/settings.env volumes: - - ../waveform-export:/app/waveform-export + - ../waveform-export:/waveform-export diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py index ada4b22..b42c1c9 100644 --- a/src/exporter/ftps.py +++ b/src/exporter/ftps.py @@ -1,29 +1,40 @@ import os +from pathlib import Path from typing import BinaryIO -from core.uploader._ftps import _connect_to_ftp +from core.uploader._ftps import _connect_to_ftp, _create_and_set_as_cwd import settings import argparse +from locations import WAVEFORM_PSEUDONYMISED def do_upload(): parser = argparse.ArgumentParser() - parser.add_argument("file_to_upload", type=str, help="file to upload") + parser.add_argument("file_to_upload", type=Path, help="file to upload relative to pseudonymised folder") args = parser.parse_args() do_upload_inner(args.file_to_upload) -def do_upload_inner(file_to_upload): +def do_upload_inner(rel_file_to_upload: Path): + # Absolute paths override the base path, so disallow that (abspath1 / abspath2 == abspath2) + if rel_file_to_upload.is_absolute(): + raise ValueError("File must be relative to pseudonymised folder") + WAVEFORM_PSEUDONYMISED.mkdir(parents=False, exist_ok=True) + file_to_upload = (WAVEFORM_PSEUDONYMISED / rel_file_to_upload).resolve(strict=True) + # Check that even after evaluating ".." and symlinks, the file is still under the "safe" directory + # for upload. + if not file_to_upload.is_relative_to(WAVEFORM_PSEUDONYMISED): + raise ValueError(f"File {file_to_upload} must be under {WAVEFORM_PSEUDONYMISED}. " + f"If this is unexpected, maybe you are using symlinks or '..' in the path?") + if not file_to_upload.exists(): + raise ValueError(f"File {file_to_upload} does not exist") ftp = _connect_to_ftp(settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME, settings.FTPS_PASSWORD) - project_dir = "foobar_waveform" - # ftp.mkd(project_dir) - ftp.cwd(project_dir) + remote_project_dir = "waveform-export" + _create_and_set_as_cwd(ftp, remote_project_dir) remote_filename = os.path.basename(file_to_upload) command = f"STOR {remote_filename}" - # BinaryIO - print("PWD: " + ftp.pwd()) with open(file_to_upload, 'rb') as file_to_upload_fh: ftp.storbinary(command, file_to_upload_fh) + print("Directory listing: ") ftp.dir() - print("Done dir") ftp.quit() diff --git a/src/locations.py b/src/locations.py new file mode 100644 index 0000000..a6a99db --- /dev/null +++ b/src/locations.py @@ -0,0 +1,5 @@ +from pathlib import Path + +WAVEFORM_EXPORT_BASE = Path('/waveform-export') +WAVEFORM_ORIGINAL = WAVEFORM_EXPORT_BASE / 'original' +WAVEFORM_PSEUDONYMISED = WAVEFORM_EXPORT_BASE / 'pseudonymised' From b64b299971bb9dd69c59e4e88722b79c36c06e6f Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Fri, 12 Dec 2025 18:05:07 +0000 Subject: [PATCH 05/19] Convert CSV into parquet with the appropriate decimal array type. --- docker-compose.yml | 15 +++++++++ hasher.env.EXAMPLE | 4 +++ pyproject.toml | 3 ++ src/csv_writer.py | 6 ++-- src/locations.py | 3 +- src/pseudon/__init__.py | 0 src/pseudon/pseudon.py | 67 +++++++++++++++++++++++++++++++++++++++++ uv.lock | 2 ++ 8 files changed, 96 insertions(+), 4 deletions(-) create mode 100644 hasher.env.EXAMPLE create mode 100644 src/pseudon/__init__.py create mode 100644 src/pseudon/pseudon.py diff --git a/docker-compose.yml b/docker-compose.yml index eda6c13..233b0aa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -13,3 +13,18 @@ services: - ../config/settings.env volumes: - ../waveform-export:/waveform-export + waveform-hasher: + build: + context: ../PIXL + dockerfile: ./docker/pixl-python/Dockerfile + target: hasher_api + args: + PIXL_PACKAGE_DIR: hasher + HTTP_PROXY: ${HTTP_PROXY} + http_proxy: ${http_proxy} + HTTPS_PROXY: ${HTTPS_PROXY} + https_proxy: ${https_proxy} + ports: + - "127.0.0.1:${HASHER_API_PORT}:8000" + env_file: + - ../config/hasher.env diff --git a/hasher.env.EXAMPLE b/hasher.env.EXAMPLE new file mode 100644 index 0000000..c6a453d --- /dev/null +++ b/hasher.env.EXAMPLE @@ -0,0 +1,4 @@ +HASHER_API_AZ_CLIENT_ID= +HASHER_API_AZ_CLIENT_PASSWORD= +HASHER_API_AZ_TENANT_ID= +HASHER_API_AZ_KEY_VAULT_NAME= \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index e066f78..b41fc66 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,8 @@ description = "Add your description here" readme = "README.md" requires-python = ">=3.11" dependencies = [ + "pandas", + #"pyarrow>=22.0", "pika>=1.3.2", "pre-commit>=4.5.0", # need to be compatible with PIXL, which currently pins 2.9.10 (arguably it shouldn't) @@ -16,4 +18,5 @@ dependencies = [ [project.scripts] emap-extract-waveform = "controller:receiver" +emap-csv-pseudon = "pseudon.pseudon:main" emap-send-ftps = "exporter.ftps:do_upload" diff --git a/src/csv_writer.py b/src/csv_writer.py index d99a9e1..f501cc2 100644 --- a/src/csv_writer.py +++ b/src/csv_writer.py @@ -2,6 +2,7 @@ import csv from datetime import datetime +from locations import WAVEFORM_ORIGINAL_CSV from pathlib import Path @@ -31,10 +32,9 @@ def write_frame(waveform_message: dict, csn: str, mrn: str) -> bool: observation_datetime = datetime.fromtimestamp(observationTime) units = waveform_message.get("unit", "") - out_path = "waveform-export/" - Path(out_path).mkdir(exist_ok=True) + WAVEFORM_ORIGINAL_CSV.mkdir(exist_ok=True, parents=False) - filename = out_path + create_file_name( + filename = WAVEFORM_ORIGINAL_CSV / create_file_name( sourceStreamId, observation_datetime, csn, units ) with open(filename, "a") as fileout: diff --git a/src/locations.py b/src/locations.py index a6a99db..62e23fa 100644 --- a/src/locations.py +++ b/src/locations.py @@ -1,5 +1,6 @@ from pathlib import Path WAVEFORM_EXPORT_BASE = Path('/waveform-export') -WAVEFORM_ORIGINAL = WAVEFORM_EXPORT_BASE / 'original' +WAVEFORM_ORIGINAL_CSV = WAVEFORM_EXPORT_BASE / 'original-csv' +WAVEFORM_ORIGINAL_PARQUET = WAVEFORM_EXPORT_BASE / 'original-parquet' WAVEFORM_PSEUDONYMISED = WAVEFORM_EXPORT_BASE / 'pseudonymised' diff --git a/src/pseudon/__init__.py b/src/pseudon/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py new file mode 100644 index 0000000..7aeda7e --- /dev/null +++ b/src/pseudon/pseudon.py @@ -0,0 +1,67 @@ +import argparse +from pathlib import Path +from decimal import Decimal + +from locations import WAVEFORM_ORIGINAL_CSV, WAVEFORM_ORIGINAL_PARQUET, WAVEFORM_PSEUDONYMISED +from pyarrow import timestamp + + +def main(): + arg_parser = argparse.ArgumentParser() + arg_parser.add_argument('--csv', type=Path) + args = arg_parser.parse_args() + csv_to_parquets(args.csv) + + +# convert CSV data (with full identifiers) to two versions in parquet format: +# - full identifiers (intended for debugging, NOT to be exported to DSH) +# - pseudonymised identifiers (for export to DSH) +def csv_to_parquets(csv_path: Path): + import pandas as pd + import pyarrow as pa + import pyarrow.parquet as pq + + WAVEFORM_ORIGINAL_PARQUET.mkdir(parents=False, exist_ok=True) + # Read the CSV with two string columns and one array numeric column + # Assume col1, col2 are strings, col3 is array of numbers in string format, e.g. "[1,2,3]" + df = pd.read_csv(csv_path, + dtype={'csn': str, 'mrn': str, 'stream': str, 'units': str, + 'timestamp': float, 'location': str, 'values': str}, + keep_default_na=True, + na_values=["", "NaN", "nan", "None"]) + + def parse_array(x): + # Not sure if this is the most efficient way. Might be able to do something with DecimalArray? + # return [pa.decimal128(i) for i in x.replace(' ', '').split(',')] + return [Decimal(i) for i in x.strip().strip('[]').replace(' ', '').split(',')] + + df['values'] = df['values'].apply(parse_array) + + # Convert pandas DataFrame to pyarrow Table with proper types + schema = pa.schema([ + ('csn', pa.string()), + ('mrn', pa.string()), + ('stream', pa.string()), + ('units', pa.string()), + ('timestamp', pa.float64()), + ('location', pa.string()), + # decimal32 can have a maximum of 9 significant digits. + # We can go to 64 if needed but let's try and keep it compact. + # But they're not exposed?? Use 128 instead. + ('values', pa.list_(pa.decimal128(9,4))), + ]) + table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) + + pq.write_table( + table, + str(WAVEFORM_ORIGINAL_PARQUET / (csv_path.stem + '.parquet')), + # valid values: {‘NONE’, ‘SNAPPY’, ‘GZIP’, ‘BROTLI’, ‘LZ4’, ‘ZSTD’} + compression='zstd', + use_dictionary=True, + write_statistics=True, # enable indexes/statistics + flavor='spark' + ) + + +def call_hasher(identifier: str): + return thingy(identifier) diff --git a/uv.lock b/uv.lock index 070d2e8..b553409 100644 --- a/uv.lock +++ b/uv.lock @@ -1479,6 +1479,7 @@ version = "0.1.0" source = { virtual = "." } dependencies = [ { name = "core" }, + { name = "pandas" }, { name = "pika" }, { name = "pre-commit" }, { name = "psycopg2-binary" }, @@ -1488,6 +1489,7 @@ dependencies = [ [package.metadata] requires-dist = [ { name = "core", directory = "../PIXL/pixl_core" }, + { name = "pandas" }, { name = "pika", specifier = ">=1.3.2" }, { name = "pre-commit", specifier = ">=4.5.0" }, { name = "psycopg2-binary", specifier = ">=2.9.10" }, From 9edb4ff421b17763c2d15aa2dcb4caf75c6ff71c Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Tue, 16 Dec 2025 18:03:44 +0000 Subject: [PATCH 06/19] Make separate exporter container that runs cron to anonymise and export files at the end of each (eg) day --- Dockerfile | 11 ++++++++++- README.md | 4 +++- .../controller.env.EXAMPLE | 0 config.EXAMPLE/exporter.env.EXAMPLE | 2 ++ .../hasher.env.EXAMPLE | 0 docker-compose.yml | 18 +++++++++++++++++- exporter-scripts/entrypoint.sh | 16 ++++++++++++++++ exporter-scripts/scheduled-script.sh | 5 +++++ 8 files changed, 53 insertions(+), 3 deletions(-) rename settings.env.EXAMPLE => config.EXAMPLE/controller.env.EXAMPLE (100%) create mode 100644 config.EXAMPLE/exporter.env.EXAMPLE rename hasher.env.EXAMPLE => config.EXAMPLE/hasher.env.EXAMPLE (100%) create mode 100755 exporter-scripts/entrypoint.sh create mode 100755 exporter-scripts/scheduled-script.sh diff --git a/Dockerfile b/Dockerfile index 985f910..8a41606 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,11 @@ -FROM python:3.13-slim-bookworm +FROM python:3.13-slim-bookworm AS waveform_base LABEL authors="Stephen Thompson, Jeremy Stein" +# Cron is really small. For the sake of not having to reinstall it all the time, +# put it on both images even though we only need it on exporter. +RUN export DEBIAN_FRONTEND=noninteractive && \ + apt-get update && \ + apt-get install --yes --no-install-recommends cron && \ + apt-get autoremove --yes && apt-get clean --yes && rm -rf /var/lib/apt/lists/* COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ ARG UVCACHE=/root/.cache/uv COPY PIXL /PIXL @@ -8,4 +14,7 @@ COPY waveform-controller/pyproject.toml waveform-controller/uv.lock /app/ RUN --mount=type=cache,target=${UVCACHE} uv pip install --system . COPY waveform-controller/. /app/ RUN --mount=type=cache,target=${UVCACHE} uv pip install --system . +FROM waveform_base AS waveform_controller CMD ["emap-extract-waveform"] +FROM waveform_base AS waveform_exporter +ENTRYPOINT ["/app/exporter-scripts/entrypoint.sh"] diff --git a/README.md b/README.md index 0184d18..81f6cff 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,9 @@ as necessary. Remove the comment telling you not to put secrets in it. ``` mkdir ../config -cp settings.env.EXAMPLE ../config/settings.env +cp config.EXAMPLE/controller.env.EXAMPLE ../config/controller.env +cp config.EXAMPLE/exporter.env.EXAMPLE ../config/settings.env +cp config.EXAMPLE/hasher.env.EXAMPLE ../config/hasher.env ``` If it doesn't already exist you should create a directory named `waveform-export` in the parent directory to store the saved waveform diff --git a/settings.env.EXAMPLE b/config.EXAMPLE/controller.env.EXAMPLE similarity index 100% rename from settings.env.EXAMPLE rename to config.EXAMPLE/controller.env.EXAMPLE diff --git a/config.EXAMPLE/exporter.env.EXAMPLE b/config.EXAMPLE/exporter.env.EXAMPLE new file mode 100644 index 0000000..1917427 --- /dev/null +++ b/config.EXAMPLE/exporter.env.EXAMPLE @@ -0,0 +1,2 @@ +# When does the exporter run +EXPORTER_CRON_SCHEDULE="14 5 * * * *" diff --git a/hasher.env.EXAMPLE b/config.EXAMPLE/hasher.env.EXAMPLE similarity index 100% rename from hasher.env.EXAMPLE rename to config.EXAMPLE/hasher.env.EXAMPLE diff --git a/docker-compose.yml b/docker-compose.yml index 233b0aa..619abfa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -3,6 +3,7 @@ services: build: context: .. dockerfile: waveform-controller/Dockerfile + target: waveform_controller args: HTTP_PROXY: ${HTTP_PROXY} http_proxy: ${http_proxy} @@ -10,7 +11,22 @@ services: https_proxy: ${https_proxy} # ideally we'd use docker secrets but it's not enabled currently env_file: - - ../config/settings.env + - ../config/controller.env + volumes: + - ../waveform-export:/waveform-export + waveform-exporter: + build: + context: .. + dockerfile: waveform-controller/Dockerfile + target: waveform_exporter + args: + HTTP_PROXY: ${HTTP_PROXY} + http_proxy: ${http_proxy} + HTTPS_PROXY: ${HTTPS_PROXY} + https_proxy: ${https_proxy} + # ideally we'd use docker secrets but it's not enabled currently + env_file: + - ../config/exporter.env volumes: - ../waveform-export:/waveform-export waveform-hasher: diff --git a/exporter-scripts/entrypoint.sh b/exporter-scripts/entrypoint.sh new file mode 100755 index 0000000..60e5b72 --- /dev/null +++ b/exporter-scripts/entrypoint.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +# Set up cron schedule according to the environment variable +if [ -z "$EXPORTER_CRON_SCHEDULE" ]; then + echo "You must set EXPORTER_CRON_SCHEDULE when running this container" + exit 1 +fi +set -x +cat <> /emap.viascript 2>> /emap.viascript2 \ No newline at end of file From 129f8a62169e90bb1df6dfb41db7504d693550df Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 10:57:55 +0000 Subject: [PATCH 07/19] Write a toy hasher so we can develop the rest of the pipeline in the meantime. Couple of other fixes. --- README.md | 2 +- __init__.py | 0 exporter-scripts/scheduled-script.sh | 5 +-- src/csv_writer.py | 6 ++++ src/exporter/ftps.py | 10 +++--- src/locations.py | 2 +- src/pseudon/hashing.py | 16 +++++++++ src/pseudon/pseudon.py | 50 ++++++++++++++++++++-------- 8 files changed, 68 insertions(+), 23 deletions(-) create mode 100644 __init__.py create mode 100644 src/pseudon/hashing.py diff --git a/README.md b/README.md index 81f6cff..5583f0f 100644 --- a/README.md +++ b/README.md @@ -72,7 +72,7 @@ Each row of the csv will contain ## Perform an export -Exported files must be under the WAVEFORM_PSEUDONYMISED directory. +Exported files must be under the WAVEFORM_PSEUDONYMISED_PARQUET directory. Files passed in must be given relative to this directory: ``` docker compose run waveform-controller emap-send-ftps my_pseudonymised_file.parquet diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/exporter-scripts/scheduled-script.sh b/exporter-scripts/scheduled-script.sh index ca97dc4..f8b99f6 100755 --- a/exporter-scripts/scheduled-script.sh +++ b/exporter-scripts/scheduled-script.sh @@ -1,5 +1,6 @@ #!/bin/bash # Run by the cron scheduler -# Exact script TBD... -emap-send-ftps --help >> /emap.viascript 2>> /emap.viascript2 \ No newline at end of file +# Probably want snakemake instead... +emap-csv-pseudon --help +emap-send-ftps --help \ No newline at end of file diff --git a/src/csv_writer.py b/src/csv_writer.py index f501cc2..8a9bb61 100644 --- a/src/csv_writer.py +++ b/src/csv_writer.py @@ -37,6 +37,12 @@ def write_frame(waveform_message: dict, csn: str, mrn: str) -> bool: filename = WAVEFORM_ORIGINAL_CSV / create_file_name( sourceStreamId, observation_datetime, csn, units ) + + # write header if is new file + if not filename.exists(): + with open(filename, "w") as fileout: + fileout.write("csn,mrn,sourceStreamId,units,samplingRate,timestamp,location,values\n") + with open(filename, "a") as fileout: wv_writer = csv.writer(fileout, delimiter=",") waveform_data = waveform_message.get("numericValues", "") diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py index b42c1c9..77cfbbd 100644 --- a/src/exporter/ftps.py +++ b/src/exporter/ftps.py @@ -5,7 +5,7 @@ from core.uploader._ftps import _connect_to_ftp, _create_and_set_as_cwd import settings import argparse -from locations import WAVEFORM_PSEUDONYMISED +from locations import WAVEFORM_PSEUDONYMISED_PARQUET def do_upload(): @@ -19,12 +19,12 @@ def do_upload_inner(rel_file_to_upload: Path): # Absolute paths override the base path, so disallow that (abspath1 / abspath2 == abspath2) if rel_file_to_upload.is_absolute(): raise ValueError("File must be relative to pseudonymised folder") - WAVEFORM_PSEUDONYMISED.mkdir(parents=False, exist_ok=True) - file_to_upload = (WAVEFORM_PSEUDONYMISED / rel_file_to_upload).resolve(strict=True) + WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True) + file_to_upload = (WAVEFORM_PSEUDONYMISED_PARQUET / rel_file_to_upload).resolve(strict=True) # Check that even after evaluating ".." and symlinks, the file is still under the "safe" directory # for upload. - if not file_to_upload.is_relative_to(WAVEFORM_PSEUDONYMISED): - raise ValueError(f"File {file_to_upload} must be under {WAVEFORM_PSEUDONYMISED}. " + if not file_to_upload.is_relative_to(WAVEFORM_PSEUDONYMISED_PARQUET): + raise ValueError(f"File {file_to_upload} must be under {WAVEFORM_PSEUDONYMISED_PARQUET}. " f"If this is unexpected, maybe you are using symlinks or '..' in the path?") if not file_to_upload.exists(): raise ValueError(f"File {file_to_upload} does not exist") diff --git a/src/locations.py b/src/locations.py index 62e23fa..0b32857 100644 --- a/src/locations.py +++ b/src/locations.py @@ -3,4 +3,4 @@ WAVEFORM_EXPORT_BASE = Path('/waveform-export') WAVEFORM_ORIGINAL_CSV = WAVEFORM_EXPORT_BASE / 'original-csv' WAVEFORM_ORIGINAL_PARQUET = WAVEFORM_EXPORT_BASE / 'original-parquet' -WAVEFORM_PSEUDONYMISED = WAVEFORM_EXPORT_BASE / 'pseudonymised' +WAVEFORM_PSEUDONYMISED_PARQUET = WAVEFORM_EXPORT_BASE / 'pseudonymised' diff --git a/src/pseudon/hashing.py b/src/pseudon/hashing.py new file mode 100644 index 0000000..9e5f412 --- /dev/null +++ b/src/pseudon/hashing.py @@ -0,0 +1,16 @@ + +from functools import lru_cache + + +@lru_cache +def do_hash(type_prefix, value: str): + """ + Stub implementation of deidentification function for testing purposes. + + Not that I think this will happen in practice, but we'd want the CSN "1234" to hash to a different + value than the MRN "1234", so prefix each value with its type. + """ + SALT = "waveform-exporter" + full_value_to_hash = f"{SALT}:{type_prefix}:{value}" + hash_str = f"{hash(full_value_to_hash) & 0xFFFFFFFF:08x}" + return hash_str diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py index 7aeda7e..7d98203 100644 --- a/src/pseudon/pseudon.py +++ b/src/pseudon/pseudon.py @@ -1,9 +1,14 @@ import argparse -from pathlib import Path +import functools from decimal import Decimal +from pathlib import Path + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +from locations import WAVEFORM_ORIGINAL_CSV, WAVEFORM_ORIGINAL_PARQUET, WAVEFORM_PSEUDONYMISED_PARQUET -from locations import WAVEFORM_ORIGINAL_CSV, WAVEFORM_ORIGINAL_PARQUET, WAVEFORM_PSEUDONYMISED -from pyarrow import timestamp +from .hashing import do_hash def main(): @@ -17,18 +22,17 @@ def main(): # - full identifiers (intended for debugging, NOT to be exported to DSH) # - pseudonymised identifiers (for export to DSH) def csv_to_parquets(csv_path: Path): - import pandas as pd - import pyarrow as pa - import pyarrow.parquet as pq WAVEFORM_ORIGINAL_PARQUET.mkdir(parents=False, exist_ok=True) + WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True) # Read the CSV with two string columns and one array numeric column # Assume col1, col2 are strings, col3 is array of numbers in string format, e.g. "[1,2,3]" - df = pd.read_csv(csv_path, - dtype={'csn': str, 'mrn': str, 'stream': str, 'units': str, + df = pd.read_csv(str(csv_path), + dtype={'csn': str, 'mrn': str, 'sourceStreamId': str, 'units': str, + 'samplingRate': int, 'timestamp': float, 'location': str, 'values': str}, - keep_default_na=True, - na_values=["", "NaN", "nan", "None"]) + header=0 # Explicitly specify that the first line is always the header + ) def parse_array(x): # Not sure if this is the most efficient way. Might be able to do something with DecimalArray? @@ -41,8 +45,9 @@ def parse_array(x): schema = pa.schema([ ('csn', pa.string()), ('mrn', pa.string()), - ('stream', pa.string()), + ('sourceStreamId', pa.string()), ('units', pa.string()), + ('samplingRate', pa.int32()), ('timestamp', pa.float64()), ('location', pa.string()), # decimal32 can have a maximum of 9 significant digits. @@ -52,9 +57,10 @@ def parse_array(x): ]) table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) + original_parquet_path = WAVEFORM_ORIGINAL_PARQUET / (csv_path.stem + '.parquet') pq.write_table( table, - str(WAVEFORM_ORIGINAL_PARQUET / (csv_path.stem + '.parquet')), + str(original_parquet_path), # valid values: {‘NONE’, ‘SNAPPY’, ‘GZIP’, ‘BROTLI’, ‘LZ4’, ‘ZSTD’} compression='zstd', use_dictionary=True, @@ -62,6 +68,22 @@ def parse_array(x): flavor='spark' ) + df = pseudonymise_relevant_columns(df) + pseudon_table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) + + # XXX: The file path itself contains an identifier (the CSN). Need to fix. + pseudon_parquet_path = WAVEFORM_PSEUDONYMISED_PARQUET / (csv_path.stem + '.parquet') + pq.write_table( + pseudon_table, + str(pseudon_parquet_path), + compression='zstd', + use_dictionary=True, + write_statistics=True, # enable indexes/statistics + flavor='spark' + ) + +def pseudonymise_relevant_columns(df: pd.DataFrame): + for col in ['csn', 'mrn', 'location']: + df[col] = df[col].apply(functools.partial(do_hash, col)) + return df -def call_hasher(identifier: str): - return thingy(identifier) From e0d64a43adaf848998124ae0edd54e34b3c29949 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 12:27:43 +0000 Subject: [PATCH 08/19] Consistently use Python-style variable names --- src/csv_writer.py | 2 +- src/pseudon/pseudon.py | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/csv_writer.py b/src/csv_writer.py index 65ad45e..a865b25 100644 --- a/src/csv_writer.py +++ b/src/csv_writer.py @@ -43,7 +43,7 @@ def write_frame( # write header if is new file if not filename.exists(): with open(filename, "w") as fileout: - fileout.write("csn,mrn,sourceStreamId,units,samplingRate,timestamp,location,values\n") + fileout.write("csn,mrn,source_stream_id,units,sampling_rate,timestamp,location,values\n") with open(filename, "a") as fileout: wv_writer = csv.writer(fileout, delimiter=",") diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py index 7d98203..9a67eae 100644 --- a/src/pseudon/pseudon.py +++ b/src/pseudon/pseudon.py @@ -28,8 +28,8 @@ def csv_to_parquets(csv_path: Path): # Read the CSV with two string columns and one array numeric column # Assume col1, col2 are strings, col3 is array of numbers in string format, e.g. "[1,2,3]" df = pd.read_csv(str(csv_path), - dtype={'csn': str, 'mrn': str, 'sourceStreamId': str, 'units': str, - 'samplingRate': int, + dtype={'csn': str, 'mrn': str, 'source_stream_id': str, 'units': str, + 'sampling_rate': int, 'timestamp': float, 'location': str, 'values': str}, header=0 # Explicitly specify that the first line is always the header ) @@ -45,9 +45,9 @@ def parse_array(x): schema = pa.schema([ ('csn', pa.string()), ('mrn', pa.string()), - ('sourceStreamId', pa.string()), + ('source_stream_id', pa.string()), ('units', pa.string()), - ('samplingRate', pa.int32()), + ('sampling_rate', pa.int32()), ('timestamp', pa.float64()), ('location', pa.string()), # decimal32 can have a maximum of 9 significant digits. From 7f7dd8ad9423ffaeaa3a1ef2811e8f4a382f7e8a Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 13:00:18 +0000 Subject: [PATCH 09/19] Move config around to reflect recent container changes --- config.EXAMPLE/controller.env.EXAMPLE | 7 +------ config.EXAMPLE/exporter.env.EXAMPLE | 6 ++++++ config.EXAMPLE/hasher.env.EXAMPLE | 4 +++- 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/config.EXAMPLE/controller.env.EXAMPLE b/config.EXAMPLE/controller.env.EXAMPLE index 3020e19..08ba2dc 100644 --- a/config.EXAMPLE/controller.env.EXAMPLE +++ b/config.EXAMPLE/controller.env.EXAMPLE @@ -1,5 +1,5 @@ # This is an EXAMPLE file, do not put real secrets in here. -# Copy it to ./config/settings.env and then DELETE THIS COMMENT. +# Copy it to ./config/*.env and then DELETE THIS COMMENT. UDS_DBNAME="fakeuds" UDS_USERNAME="inform_user" UDS_PASSWORD="inform" @@ -13,8 +13,3 @@ RABBITMQ_PASSWORD="my_pw" RABBITMQ_HOST="localhost" RABBITMQ_PORT=5672 RABBITMQ_QUEUE="waveform" - -FTPS_HOST=myftps.example.com -FTPS_PORT=990 -FTPS_USERNAME=my_username -FTPS_PASSWORD=my_password diff --git a/config.EXAMPLE/exporter.env.EXAMPLE b/config.EXAMPLE/exporter.env.EXAMPLE index 1917427..721a8cf 100644 --- a/config.EXAMPLE/exporter.env.EXAMPLE +++ b/config.EXAMPLE/exporter.env.EXAMPLE @@ -1,2 +1,8 @@ +# This is an EXAMPLE file, do not put real secrets in here. +# Copy it to ./config/*.env and then DELETE THIS COMMENT. # When does the exporter run EXPORTER_CRON_SCHEDULE="14 5 * * * *" +FTPS_HOST=myftps.example.com +FTPS_PORT=990 +FTPS_USERNAME=my_username +FTPS_PASSWORD=my_password diff --git a/config.EXAMPLE/hasher.env.EXAMPLE b/config.EXAMPLE/hasher.env.EXAMPLE index c6a453d..c326850 100644 --- a/config.EXAMPLE/hasher.env.EXAMPLE +++ b/config.EXAMPLE/hasher.env.EXAMPLE @@ -1,4 +1,6 @@ +# This is an EXAMPLE file, do not put real secrets in here. +# Copy it to ./config/*.env and then DELETE THIS COMMENT. HASHER_API_AZ_CLIENT_ID= HASHER_API_AZ_CLIENT_PASSWORD= HASHER_API_AZ_TENANT_ID= -HASHER_API_AZ_KEY_VAULT_NAME= \ No newline at end of file +HASHER_API_AZ_KEY_VAULT_NAME= From f6b1a67a44cd53ac5d8f48fcbd7ce48454c70037 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 13:58:06 +0000 Subject: [PATCH 10/19] Make log message more useful --- src/controller.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/controller.py b/src/controller.py index 15a7e60..06cd392 100644 --- a/src/controller.py +++ b/src/controller.py @@ -66,10 +66,11 @@ def waveform_callback(ch, method_frame, _header_frame, body): matched_mrn = emap_db.get_row(location_string, observation_time) except ValueError as e: lookup_success = False - logger.error(f"Ambiguous or non existent match: {e}") + logger.error("Ambiguous or non existent match for location %s, obs time %s", + location_string, observation_time, exc_info=True) matched_mrn = ("unmatched_mrn", "unmatched_nhs", "unmatched_csn") except ConnectionError as e: - logger.error(f"Database error, will try again: {e}") + logger.error("Database error, will try again", exc_info=True) reject_message(ch, method_frame.delivery_tag, True) return From 00167a958ffb53cbe3c3739cd48b473201ec0eb7 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 14:10:08 +0000 Subject: [PATCH 11/19] many env files now --- .gitignore | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index f368298..3eaa234 100644 --- a/.gitignore +++ b/.gitignore @@ -12,5 +12,5 @@ wheels/ # IDEs .idea/ -# settings file (should not be in the source tree anyway, but just in case) -settings.env \ No newline at end of file +# settings files (should not be in the source tree anyway, but just in case) +*.env \ No newline at end of file From 4ef9683b66336ad0e2803023168b505acf2f75aa Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 15:03:06 +0000 Subject: [PATCH 12/19] Document manual pipeline calls --- README.md | 15 +++++++++++---- src/exporter/ftps.py | 5 +++++ src/pseudon/pseudon.py | 6 ++---- 3 files changed, 18 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 5583f0f..750dd9f 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,7 @@ messages. mkdir ../waveform-export ``` -Build and start the controller with docker +Build and start the controller and exporter with docker ``` cd ../waveform-controller docker compose build @@ -70,15 +70,22 @@ Each row of the csv will contain `csn, mrn, units, samplingRate, observationTime, waveformData` +## Perform a parquet conversion (including de-id) +At the time of writing, the cron pipeline is not set up. This section shows +how to perform an ad-hoc de-id. +``` +docker compose run waveform-controller emap-csv-pseudon --csv /waveform-export/original-csv/my_original_csv.csv +``` + ## Perform an export +At the time of writing, the cron pipeline is not set up. This section shows +how to perform an ad-hoc FTPS upload. Exported files must be under the WAVEFORM_PSEUDONYMISED_PARQUET directory. Files passed in must be given relative to this directory: ``` -docker compose run waveform-controller emap-send-ftps my_pseudonymised_file.parquet +docker compose run --entrypoint "" waveform-exporter emap-send-ftps my_pseudonymised_file.parquet ``` -In future, this will be run on a schedule. - # Developing See [developing docs](docs/develop.md) diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py index 77cfbbd..aeca9e9 100644 --- a/src/exporter/ftps.py +++ b/src/exporter/ftps.py @@ -1,3 +1,4 @@ +import logging import os from pathlib import Path from typing import BinaryIO @@ -7,6 +8,8 @@ import argparse from locations import WAVEFORM_PSEUDONYMISED_PARQUET +logging.basicConfig(format="%(levelname)s:%(asctime)s: %(message)s") +logger = logging.getLogger(__name__) def do_upload(): parser = argparse.ArgumentParser() @@ -28,11 +31,13 @@ def do_upload_inner(rel_file_to_upload: Path): f"If this is unexpected, maybe you are using symlinks or '..' in the path?") if not file_to_upload.exists(): raise ValueError(f"File {file_to_upload} does not exist") + logger.info("Connecting to FTPS server %s:%s, with username %s", settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME) ftp = _connect_to_ftp(settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME, settings.FTPS_PASSWORD) remote_project_dir = "waveform-export" _create_and_set_as_cwd(ftp, remote_project_dir) remote_filename = os.path.basename(file_to_upload) command = f"STOR {remote_filename}" + logger.info("Uploading file %s", file_to_upload) with open(file_to_upload, 'rb') as file_to_upload_fh: ftp.storbinary(command, file_to_upload_fh) print("Directory listing: ") diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py index 9a67eae..8220270 100644 --- a/src/pseudon/pseudon.py +++ b/src/pseudon/pseudon.py @@ -25,13 +25,11 @@ def csv_to_parquets(csv_path: Path): WAVEFORM_ORIGINAL_PARQUET.mkdir(parents=False, exist_ok=True) WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True) - # Read the CSV with two string columns and one array numeric column - # Assume col1, col2 are strings, col3 is array of numbers in string format, e.g. "[1,2,3]" df = pd.read_csv(str(csv_path), dtype={'csn': str, 'mrn': str, 'source_stream_id': str, 'units': str, 'sampling_rate': int, 'timestamp': float, 'location': str, 'values': str}, - header=0 # Explicitly specify that the first line is always the header + header=0 # the first line is always the header ) def parse_array(x): @@ -71,7 +69,7 @@ def parse_array(x): df = pseudonymise_relevant_columns(df) pseudon_table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) - # XXX: The file path itself contains an identifier (the CSN). Need to fix. + # XXX: The file path itself contains an identifier (the CSN). See issue #26. pseudon_parquet_path = WAVEFORM_PSEUDONYMISED_PARQUET / (csv_path.stem + '.parquet') pq.write_table( pseudon_table, From 32ccc74d583158474b3efba7ed597482e311212f Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 18:10:38 +0000 Subject: [PATCH 13/19] Fix all but one linting error --- .gitignore | 2 +- config.EXAMPLE/exporter.env.EXAMPLE | 4 +- exporter-scripts/scheduled-script.sh | 2 +- src/controller.py | 12 +++-- src/csv_writer.py | 5 +- src/exporter/ftps.py | 34 ++++++++++--- src/locations.py | 8 +-- src/pseudon/hashing.py | 9 ++-- src/pseudon/pseudon.py | 73 ++++++++++++++++------------ src/settings.py | 4 +- 10 files changed, 93 insertions(+), 60 deletions(-) diff --git a/.gitignore b/.gitignore index 3eaa234..be3f5ce 100644 --- a/.gitignore +++ b/.gitignore @@ -13,4 +13,4 @@ wheels/ .idea/ # settings files (should not be in the source tree anyway, but just in case) -*.env \ No newline at end of file +*.env diff --git a/config.EXAMPLE/exporter.env.EXAMPLE b/config.EXAMPLE/exporter.env.EXAMPLE index 721a8cf..e3c45d5 100644 --- a/config.EXAMPLE/exporter.env.EXAMPLE +++ b/config.EXAMPLE/exporter.env.EXAMPLE @@ -4,5 +4,5 @@ EXPORTER_CRON_SCHEDULE="14 5 * * * *" FTPS_HOST=myftps.example.com FTPS_PORT=990 -FTPS_USERNAME=my_username -FTPS_PASSWORD=my_password +FTPS_USERNAME= +FTPS_PASSWORD= diff --git a/exporter-scripts/scheduled-script.sh b/exporter-scripts/scheduled-script.sh index f8b99f6..b7baed4 100755 --- a/exporter-scripts/scheduled-script.sh +++ b/exporter-scripts/scheduled-script.sh @@ -3,4 +3,4 @@ # Run by the cron scheduler # Probably want snakemake instead... emap-csv-pseudon --help -emap-send-ftps --help \ No newline at end of file +emap-send-ftps --help diff --git a/src/controller.py b/src/controller.py index 06cd392..861a7d7 100644 --- a/src/controller.py +++ b/src/controller.py @@ -64,12 +64,16 @@ def waveform_callback(ch, method_frame, _header_frame, body): lookup_success = True try: matched_mrn = emap_db.get_row(location_string, observation_time) - except ValueError as e: + except ValueError: lookup_success = False - logger.error("Ambiguous or non existent match for location %s, obs time %s", - location_string, observation_time, exc_info=True) + logger.error( + "Ambiguous or non existent match for location %s, obs time %s", + location_string, + observation_time, + exc_info=True, + ) matched_mrn = ("unmatched_mrn", "unmatched_nhs", "unmatched_csn") - except ConnectionError as e: + except ConnectionError: logger.error("Database error, will try again", exc_info=True) reject_message(ch, method_frame.delivery_tag, True) return diff --git a/src/csv_writer.py b/src/csv_writer.py index a865b25..6025cc3 100644 --- a/src/csv_writer.py +++ b/src/csv_writer.py @@ -3,7 +3,6 @@ import csv from datetime import datetime from locations import WAVEFORM_ORIGINAL_CSV -from pathlib import Path def create_file_name( @@ -43,7 +42,9 @@ def write_frame( # write header if is new file if not filename.exists(): with open(filename, "w") as fileout: - fileout.write("csn,mrn,source_stream_id,units,sampling_rate,timestamp,location,values\n") + fileout.write( + "csn,mrn,source_stream_id,units,sampling_rate,timestamp,location,values\n" + ) with open(filename, "a") as fileout: wv_writer = csv.writer(fileout, delimiter=",") diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py index aeca9e9..a9fdddd 100644 --- a/src/exporter/ftps.py +++ b/src/exporter/ftps.py @@ -1,7 +1,6 @@ import logging import os from pathlib import Path -from typing import BinaryIO from core.uploader._ftps import _connect_to_ftp, _create_and_set_as_cwd import settings @@ -11,9 +10,14 @@ logging.basicConfig(format="%(levelname)s:%(asctime)s: %(message)s") logger = logging.getLogger(__name__) + def do_upload(): parser = argparse.ArgumentParser() - parser.add_argument("file_to_upload", type=Path, help="file to upload relative to pseudonymised folder") + parser.add_argument( + "file_to_upload", + type=Path, + help="file to upload relative to pseudonymised folder", + ) args = parser.parse_args() do_upload_inner(args.file_to_upload) @@ -23,22 +27,36 @@ def do_upload_inner(rel_file_to_upload: Path): if rel_file_to_upload.is_absolute(): raise ValueError("File must be relative to pseudonymised folder") WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True) - file_to_upload = (WAVEFORM_PSEUDONYMISED_PARQUET / rel_file_to_upload).resolve(strict=True) + file_to_upload = (WAVEFORM_PSEUDONYMISED_PARQUET / rel_file_to_upload).resolve( + strict=True + ) # Check that even after evaluating ".." and symlinks, the file is still under the "safe" directory # for upload. if not file_to_upload.is_relative_to(WAVEFORM_PSEUDONYMISED_PARQUET): - raise ValueError(f"File {file_to_upload} must be under {WAVEFORM_PSEUDONYMISED_PARQUET}. " - f"If this is unexpected, maybe you are using symlinks or '..' in the path?") + raise ValueError( + f"File {file_to_upload} must be under {WAVEFORM_PSEUDONYMISED_PARQUET}. " + f"If this is unexpected, maybe you are using symlinks or '..' in the path?" + ) if not file_to_upload.exists(): raise ValueError(f"File {file_to_upload} does not exist") - logger.info("Connecting to FTPS server %s:%s, with username %s", settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME) - ftp = _connect_to_ftp(settings.FTPS_HOST, settings.FTPS_PORT, settings.FTPS_USERNAME, settings.FTPS_PASSWORD) + logger.info( + "Connecting to FTPS server %s:%s, with username %s", + settings.FTPS_HOST, + settings.FTPS_PORT, + settings.FTPS_USERNAME, + ) + ftp = _connect_to_ftp( + settings.FTPS_HOST, + settings.FTPS_PORT, + settings.FTPS_USERNAME, + settings.FTPS_PASSWORD, + ) remote_project_dir = "waveform-export" _create_and_set_as_cwd(ftp, remote_project_dir) remote_filename = os.path.basename(file_to_upload) command = f"STOR {remote_filename}" logger.info("Uploading file %s", file_to_upload) - with open(file_to_upload, 'rb') as file_to_upload_fh: + with open(file_to_upload, "rb") as file_to_upload_fh: ftp.storbinary(command, file_to_upload_fh) print("Directory listing: ") ftp.dir() diff --git a/src/locations.py b/src/locations.py index 0b32857..bfc8b1a 100644 --- a/src/locations.py +++ b/src/locations.py @@ -1,6 +1,6 @@ from pathlib import Path -WAVEFORM_EXPORT_BASE = Path('/waveform-export') -WAVEFORM_ORIGINAL_CSV = WAVEFORM_EXPORT_BASE / 'original-csv' -WAVEFORM_ORIGINAL_PARQUET = WAVEFORM_EXPORT_BASE / 'original-parquet' -WAVEFORM_PSEUDONYMISED_PARQUET = WAVEFORM_EXPORT_BASE / 'pseudonymised' +WAVEFORM_EXPORT_BASE = Path("/waveform-export") +WAVEFORM_ORIGINAL_CSV = WAVEFORM_EXPORT_BASE / "original-csv" +WAVEFORM_ORIGINAL_PARQUET = WAVEFORM_EXPORT_BASE / "original-parquet" +WAVEFORM_PSEUDONYMISED_PARQUET = WAVEFORM_EXPORT_BASE / "pseudonymised" diff --git a/src/pseudon/hashing.py b/src/pseudon/hashing.py index 9e5f412..b4253d6 100644 --- a/src/pseudon/hashing.py +++ b/src/pseudon/hashing.py @@ -1,14 +1,13 @@ - from functools import lru_cache @lru_cache def do_hash(type_prefix, value: str): - """ - Stub implementation of deidentification function for testing purposes. + """Stub implementation of deidentification function for testing purposes. - Not that I think this will happen in practice, but we'd want the CSN "1234" to hash to a different - value than the MRN "1234", so prefix each value with its type. + Not that I think this will happen in practice, but we'd want the CSN + "1234" to hash to a different value than the MRN "1234", so prefix + each value with its type. """ SALT = "waveform-exporter" full_value_to_hash = f"{SALT}:{type_prefix}:{value}" diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py index 8220270..ffac0c3 100644 --- a/src/pseudon/pseudon.py +++ b/src/pseudon/pseudon.py @@ -6,14 +6,14 @@ import pandas as pd import pyarrow as pa import pyarrow.parquet as pq -from locations import WAVEFORM_ORIGINAL_CSV, WAVEFORM_ORIGINAL_PARQUET, WAVEFORM_PSEUDONYMISED_PARQUET +from locations import WAVEFORM_ORIGINAL_PARQUET, WAVEFORM_PSEUDONYMISED_PARQUET from .hashing import do_hash def main(): arg_parser = argparse.ArgumentParser() - arg_parser.add_argument('--csv', type=Path) + arg_parser.add_argument("--csv", type=Path) args = arg_parser.parse_args() csv_to_parquets(args.csv) @@ -22,66 +22,75 @@ def main(): # - full identifiers (intended for debugging, NOT to be exported to DSH) # - pseudonymised identifiers (for export to DSH) def csv_to_parquets(csv_path: Path): - WAVEFORM_ORIGINAL_PARQUET.mkdir(parents=False, exist_ok=True) WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True) - df = pd.read_csv(str(csv_path), - dtype={'csn': str, 'mrn': str, 'source_stream_id': str, 'units': str, - 'sampling_rate': int, - 'timestamp': float, 'location': str, 'values': str}, - header=0 # the first line is always the header - ) + df = pd.read_csv( + str(csv_path), + dtype={ + "csn": str, + "mrn": str, + "source_stream_id": str, + "units": str, + "sampling_rate": int, + "timestamp": float, + "location": str, + "values": str, + }, + header=0, # the first line is always the header + ) def parse_array(x): # Not sure if this is the most efficient way. Might be able to do something with DecimalArray? # return [pa.decimal128(i) for i in x.replace(' ', '').split(',')] - return [Decimal(i) for i in x.strip().strip('[]').replace(' ', '').split(',')] + return [Decimal(i) for i in x.strip().strip("[]").replace(" ", "").split(",")] - df['values'] = df['values'].apply(parse_array) + df["values"] = df["values"].apply(parse_array) # Convert pandas DataFrame to pyarrow Table with proper types - schema = pa.schema([ - ('csn', pa.string()), - ('mrn', pa.string()), - ('source_stream_id', pa.string()), - ('units', pa.string()), - ('sampling_rate', pa.int32()), - ('timestamp', pa.float64()), - ('location', pa.string()), - # decimal32 can have a maximum of 9 significant digits. - # We can go to 64 if needed but let's try and keep it compact. - # But they're not exposed?? Use 128 instead. - ('values', pa.list_(pa.decimal128(9,4))), - ]) + schema = pa.schema( + [ + ("csn", pa.string()), + ("mrn", pa.string()), + ("source_stream_id", pa.string()), + ("units", pa.string()), + ("sampling_rate", pa.int32()), + ("timestamp", pa.float64()), + ("location", pa.string()), + # decimal32 can have a maximum of 9 significant digits. + # We can go to 64 if needed but let's try and keep it compact. + # But they're not exposed?? Use 128 instead. + ("values", pa.list_(pa.decimal128(9, 4))), + ] + ) table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) - original_parquet_path = WAVEFORM_ORIGINAL_PARQUET / (csv_path.stem + '.parquet') + original_parquet_path = WAVEFORM_ORIGINAL_PARQUET / (csv_path.stem + ".parquet") pq.write_table( table, str(original_parquet_path), # valid values: {‘NONE’, ‘SNAPPY’, ‘GZIP’, ‘BROTLI’, ‘LZ4’, ‘ZSTD’} - compression='zstd', + compression="zstd", use_dictionary=True, write_statistics=True, # enable indexes/statistics - flavor='spark' + flavor="spark", ) df = pseudonymise_relevant_columns(df) pseudon_table = pa.Table.from_pandas(df, schema=schema, preserve_index=True) # XXX: The file path itself contains an identifier (the CSN). See issue #26. - pseudon_parquet_path = WAVEFORM_PSEUDONYMISED_PARQUET / (csv_path.stem + '.parquet') + pseudon_parquet_path = WAVEFORM_PSEUDONYMISED_PARQUET / (csv_path.stem + ".parquet") pq.write_table( pseudon_table, str(pseudon_parquet_path), - compression='zstd', + compression="zstd", use_dictionary=True, write_statistics=True, # enable indexes/statistics - flavor='spark' + flavor="spark", ) + def pseudonymise_relevant_columns(df: pd.DataFrame): - for col in ['csn', 'mrn', 'location']: + for col in ["csn", "mrn", "location"]: df[col] = df[col].apply(functools.partial(do_hash, col)) return df - diff --git a/src/settings.py b/src/settings.py index 98f6e94..dfbebc1 100644 --- a/src/settings.py +++ b/src/settings.py @@ -5,7 +5,9 @@ def get_from_env(env_var, *, default_value=None, setting_name=None): if setting_name is None: setting_name = env_var value_from_env = os.environ.get(env_var) - globals()[setting_name] = value_from_env if value_from_env is not None else default_value + globals()[setting_name] = ( + value_from_env if value_from_env is not None else default_value + ) # read env vars into settings variables From b54d1fb6bacf9ecc766fd8a8e5c014773a89beac Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 18:34:06 +0000 Subject: [PATCH 14/19] Remove __init__.py that I had accidentally introduced at the top level, which was triggering a mypy warning --- __init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 __init__.py diff --git a/__init__.py b/__init__.py deleted file mode 100644 index e69de29..0000000 From 9b39a4791917d019ed9d79960dc87a55cdbb9350 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Thu, 18 Dec 2025 18:56:27 +0000 Subject: [PATCH 15/19] Ignore missing import errors --- .pre-commit-config.yaml | 1 + pyproject.toml | 3 +++ src/exporter/ftps.py | 5 +++-- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f202a2e..5cdffb9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,6 +20,7 @@ repos: args: [--config-file=pyproject.toml] additional_dependencies: [ + "pandas-stubs", "types-psycopg2", "types-pika" ] diff --git a/pyproject.toml b/pyproject.toml index e09f3e5..05283fd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,3 +22,6 @@ dev = ["pytest>=9.0.2"] emap-extract-waveform = "controller:receiver" emap-csv-pseudon = "pseudon.pseudon:main" emap-send-ftps = "exporter.ftps:do_upload" + +[tool.mypy] +ignore_missing_imports = true diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py index a9fdddd..431732d 100644 --- a/src/exporter/ftps.py +++ b/src/exporter/ftps.py @@ -1,10 +1,11 @@ +import argparse import logging import os from pathlib import Path -from core.uploader._ftps import _connect_to_ftp, _create_and_set_as_cwd import settings -import argparse +from core.uploader._ftps import _connect_to_ftp, _create_and_set_as_cwd + from locations import WAVEFORM_PSEUDONYMISED_PARQUET logging.basicConfig(format="%(levelname)s:%(asctime)s: %(message)s") From 48e2a8375a4436741be0b933839ed0d9c8ac3ace Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Tue, 23 Dec 2025 12:37:26 +0000 Subject: [PATCH 16/19] Example crontab timing value was invalid (too many fields) --- config.EXAMPLE/exporter.env.EXAMPLE | 2 +- exporter-scripts/entrypoint.sh | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/config.EXAMPLE/exporter.env.EXAMPLE b/config.EXAMPLE/exporter.env.EXAMPLE index e3c45d5..172aa90 100644 --- a/config.EXAMPLE/exporter.env.EXAMPLE +++ b/config.EXAMPLE/exporter.env.EXAMPLE @@ -1,7 +1,7 @@ # This is an EXAMPLE file, do not put real secrets in here. # Copy it to ./config/*.env and then DELETE THIS COMMENT. # When does the exporter run -EXPORTER_CRON_SCHEDULE="14 5 * * * *" +EXPORTER_CRON_SCHEDULE="14 5 * * *" FTPS_HOST=myftps.example.com FTPS_PORT=990 FTPS_USERNAME= diff --git a/exporter-scripts/entrypoint.sh b/exporter-scripts/entrypoint.sh index 60e5b72..2bf9ecb 100755 --- a/exporter-scripts/entrypoint.sh +++ b/exporter-scripts/entrypoint.sh @@ -1,5 +1,8 @@ #!/bin/bash +# (can't use -u because need to check for potentially unset var) +set -eo pipefail + # Set up cron schedule according to the environment variable if [ -z "$EXPORTER_CRON_SCHEDULE" ]; then echo "You must set EXPORTER_CRON_SCHEDULE when running this container" From 0ceaa394ea12bc411fa94e3775bff0ee8e9d582a Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Tue, 23 Dec 2025 12:43:10 +0000 Subject: [PATCH 17/19] Apply suggestions from code review Co-authored-by: Stephen Thompson --- config.EXAMPLE/controller.env.EXAMPLE | 2 +- config.EXAMPLE/exporter.env.EXAMPLE | 2 +- config.EXAMPLE/hasher.env.EXAMPLE | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config.EXAMPLE/controller.env.EXAMPLE b/config.EXAMPLE/controller.env.EXAMPLE index 08ba2dc..e055216 100644 --- a/config.EXAMPLE/controller.env.EXAMPLE +++ b/config.EXAMPLE/controller.env.EXAMPLE @@ -1,5 +1,5 @@ # This is an EXAMPLE file, do not put real secrets in here. -# Copy it to ./config/*.env and then DELETE THIS COMMENT. +# Copy it to ../config/controller.env and then DELETE THIS COMMENT. UDS_DBNAME="fakeuds" UDS_USERNAME="inform_user" UDS_PASSWORD="inform" diff --git a/config.EXAMPLE/exporter.env.EXAMPLE b/config.EXAMPLE/exporter.env.EXAMPLE index 172aa90..7be714c 100644 --- a/config.EXAMPLE/exporter.env.EXAMPLE +++ b/config.EXAMPLE/exporter.env.EXAMPLE @@ -1,5 +1,5 @@ # This is an EXAMPLE file, do not put real secrets in here. -# Copy it to ./config/*.env and then DELETE THIS COMMENT. +# Copy it to ../config/exporter.env and then DELETE THIS COMMENT. # When does the exporter run EXPORTER_CRON_SCHEDULE="14 5 * * *" FTPS_HOST=myftps.example.com diff --git a/config.EXAMPLE/hasher.env.EXAMPLE b/config.EXAMPLE/hasher.env.EXAMPLE index c326850..1cd6ad0 100644 --- a/config.EXAMPLE/hasher.env.EXAMPLE +++ b/config.EXAMPLE/hasher.env.EXAMPLE @@ -1,5 +1,5 @@ # This is an EXAMPLE file, do not put real secrets in here. -# Copy it to ./config/*.env and then DELETE THIS COMMENT. +# Copy it to ../config/hasher.env and then DELETE THIS COMMENT. HASHER_API_AZ_CLIENT_ID= HASHER_API_AZ_CLIENT_PASSWORD= HASHER_API_AZ_TENANT_ID= From dfcb84539521e7b32faf397576cea6cf381d5e1c Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Tue, 23 Dec 2025 13:01:50 +0000 Subject: [PATCH 18/19] Clarify pyarrow data type usage --- src/pseudon/pseudon.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py index ffac0c3..4f6094e 100644 --- a/src/pseudon/pseudon.py +++ b/src/pseudon/pseudon.py @@ -56,9 +56,14 @@ def parse_array(x): ("sampling_rate", pa.int32()), ("timestamp", pa.float64()), ("location", pa.string()), - # decimal32 can have a maximum of 9 significant digits. - # We can go to 64 if needed but let's try and keep it compact. - # But they're not exposed?? Use 128 instead. + # As per requirements, compactness is important here. + # decimal32 can have a maximum of 9 significant digits and should + # satisfy our needs, but it only exists in pyarrow >= 19. + # We are currently tied to 18.1 because of PIXL core. + # So for now, use decimal128 instead. + # Not yet tested whether the specified precision + # and scale cause it to be equivalent in size to decimal32. + # See issue #31. ("values", pa.list_(pa.decimal128(9, 4))), ] ) From b4c7405935a8d438e10a004aabf022cd565aa273 Mon Sep 17 00:00:00 2001 From: Jeremy Stein Date: Tue, 23 Dec 2025 13:21:43 +0000 Subject: [PATCH 19/19] Add mention of PIXL to readme --- README.md | 32 ++++++++++++++++++++++++-------- 1 file changed, 24 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 750dd9f..4743482 100644 --- a/README.md +++ b/README.md @@ -35,26 +35,42 @@ emap docker up -d ## 2 Install and deploy waveform controller using docker -Configuration, copy the configuration file to the config directory and edit -as necessary. Remove the comment telling you not to put secrets in it. +Create a root directory for your installation of the waveform-controller project, +separate to the Emap project root. +### Expected top-level dir structure ``` -mkdir ../config -cp config.EXAMPLE/controller.env.EXAMPLE ../config/controller.env -cp config.EXAMPLE/exporter.env.EXAMPLE ../config/settings.env -cp config.EXAMPLE/hasher.env.EXAMPLE ../config/hasher.env +├── PIXL +├── config +├── waveform-controller +└── waveform-export ``` + +### Instructions for achieving this structure + +Clone this repo (`waveform-controller`) and [PIXL](https://github.com/SAFEHR-data/PIXL), +both inside your root directory. + +Set up the config files as follows: +``` +mkdir config +cp waveform-controller/config.EXAMPLE/controller.env.EXAMPLE config/controller.env +cp waveform-controller/config.EXAMPLE/exporter.env.EXAMPLE config/settings.env +cp waveform-controller/config.EXAMPLE/hasher.env.EXAMPLE config/hasher.env +``` +From the new config files, remove the comments telling you not to put secrets in it, as instructed. + If it doesn't already exist you should create a directory named `waveform-export` in the parent directory to store the saved waveform messages. ``` -mkdir ../waveform-export +mkdir waveform-export ``` Build and start the controller and exporter with docker ``` -cd ../waveform-controller +cd waveform-controller docker compose build docker compose up -d ```