Merge pull request #25 from SAFEHR-data/jeremy/pseudon

jeremyestein · web-flow · commit 166b0905c79a · 2025-12-23T14:31:25.000+01:00
Pseudonymisation and FTPS
diff --git a/.dockerignore b/.dockerignore
diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,6 @@ wheels/
 
 # IDEs
 .idea/
+
+# settings files (should not be in the source tree anyway, but just in case)
+*.env
diff --git 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/.python-version b/.python-version
@@ -1 +1 @@
-3.11
+3.13
diff --git a/Dockerfile b/Dockerfile
@@ -1,10 +1,20 @@
-FROM python:3.14-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/
-WORKDIR /app
 ARG UVCACHE=/root/.cache/uv
-COPY pyproject.toml uv.lock* /app/
+COPY PIXL /PIXL
+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 .
+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
@@ -35,23 +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
 ```
-cp settings.env.EXAMPLE config/settings.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 with docker
+Build and start the controller and exporter with docker
 ```
-cd ../waveform-controller
+cd waveform-controller
 docker compose build
 docker compose up -d
 ```
@@ -67,5 +86,22 @@ 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 --entrypoint "" waveform-exporter emap-send-ftps my_pseudonymised_file.parquet
+```
+
 # Developing
 See [developing docs](docs/develop.md)
diff --git 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/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
@@ -0,0 +1,8 @@
+# This is an EXAMPLE file, do not put real secrets in here.
+# 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
+FTPS_PORT=990
+FTPS_USERNAME=
+FTPS_PASSWORD=
diff --git a/config.EXAMPLE/hasher.env.EXAMPLE b/config.EXAMPLE/hasher.env.EXAMPLE
@@ -0,0 +1,6 @@
+# This is an EXAMPLE file, do not put real secrets in here.
+# 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=
+HASHER_API_AZ_KEY_VAULT_NAME=
diff --git a/config/.gitignore b/config/.gitignore
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,15 +1,46 @@
 services:
   waveform-controller:
     build:
-      context: .
-      dockerfile: Dockerfile
+      context: ..
+      dockerfile: waveform-controller/Dockerfile
+      target: waveform_controller
       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/settings.env
+     - ../config/controller.env
     volumes:
-      - ../waveform-export:/app/waveform-export
+      - ../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:
+    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/exporter-scripts/entrypoint.sh b/exporter-scripts/entrypoint.sh
@@ -0,0 +1,19 @@
+#!/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 "$EXPORTER_CRON_SCHEDULE" ]; then
+  echo "You must set EXPORTER_CRON_SCHEDULE when running this container"
+  exit 1
+fi
+set -x
+cat <<EOF | crontab -
+PATH=/usr/local/bin:/usr/bin:/bin
+SHELL=/usr/bin/bash
+$EXPORTER_CRON_SCHEDULE /app/exporter-scripts/scheduled-script.sh
+EOF
+
+# cron scheduler is PID 1 in this container
+exec cron -f
diff --git a/exporter-scripts/scheduled-script.sh b/exporter-scripts/scheduled-script.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# Run by the cron scheduler
+# Probably want snakemake instead...
+emap-csv-pseudon --help
+emap-send-ftps --help
diff --git a/pyproject.toml b/pyproject.toml
@@ -5,13 +5,23 @@ 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",
-    "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",
+    # trick for making a "relative" path, works inside or outside container image
+    "core @ file:///${PROJECT_ROOT}/../PIXL/pixl_core",
 ]
 
 [project.optional-dependencies]
 dev = ["pytest>=9.0.2"]
 
 [project.scripts]
 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/controller.py b/src/controller.py
@@ -64,12 +64,17 @@ 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(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}")
+    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
@@ -2,7 +2,7 @@
 
 import csv
 from datetime import datetime
-from pathlib import Path
+from locations import WAVEFORM_ORIGINAL_CSV
 
 
 def create_file_name(
@@ -33,12 +33,19 @@ def write_frame(
     """
     observation_datetime = datetime.fromtimestamp(observation_timestamp)
 
-    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(
         source_stream_id, observation_datetime, csn, units
     )
+
+    # 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"
+            )
+
     with open(filename, "a") as fileout:
         wv_writer = csv.writer(fileout, delimiter=",")
         waveform_data = waveform_data.get("value", "")
diff --git a/src/exporter/__init__.py b/src/exporter/__init__.py
diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py
@@ -0,0 +1,64 @@
+import argparse
+import logging
+import os
+from pathlib import Path
+
+import settings
+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")
+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",
+    )
+    args = parser.parse_args()
+    do_upload_inner(args.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_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_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")
+    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: ")
+    ftp.dir()
+    ftp.quit()
diff --git a/src/locations.py b/src/locations.py
@@ -0,0 +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"
diff --git a/src/pseudon/__init__.py b/src/pseudon/__init__.py
diff --git a/src/pseudon/hashing.py b/src/pseudon/hashing.py
@@ -0,0 +1,15 @@
+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
diff --git a/src/settings.py b/src/settings.py
diff --git a/uv.lock b/uv.lock

-Original file line number
+Diff line change
 # IDEs
 .idea/
++
 +# settings files (should not be in the source tree anyway, but just in case)
 +*.env
Original file line number	Diff line number	Diff line change
`@@ -20,6 +20,7 @@ repos:`
`20`	`20`	`args: [--config-file=pyproject.toml]`
`21`	`21`	`additional_dependencies:`
`22`	`22`	`[`
	`23`	`+ "pandas-stubs",`
`23`	`24`	`"types-psycopg2",`
`24`	`25`	`"types-pika"`
`25`	`26`	`]`