snakemake pipeline

.github/workflows/pytest.yml

@@ -3,23 +3,43 @@ name: Run pytest
 on: 
   push:
     branches: [main, dev]
-    pull_request:
-      branches: [main, dev]
-      types: ["opened", "reopened", "synchronize", "ready_for_review", "draft"]
+  pull_request:
+    branches: [main, dev]
   workflow_dispatch:
 
 jobs:
   build:
     name: Run pytest
     runs-on: ubuntu-latest
+    env:
+      PROJECT_ROOT: ${{ github.workspace }}/waveform-controller
 
     steps:
       - uses: actions/checkout@v5
+        with:
+          path: waveform-controller
+      - name: Checkout PIXL dependency
+        uses: actions/checkout@v5
+        with:
+          repository: SAFEHR-data/PIXL
+          ref: main
+          path: PIXL
+
       - name: Install uv
         uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.26"
+          python-version: "3.13"
+          enable-cache: true
+
+      - name: Make a venv
+        working-directory: waveform-controller
+        run: uv venv
 
-      - name: Install dependencies
-        run: uv sync --locked --all-extras --dev
+      - name: Install with dependencies
+        working-directory: waveform-controller
+        run: uv pip install '.[dev]'
 
       - name: Run the tests
+        working-directory: waveform-controller
         run: uv run pytest tests

.pre-commit-config.yaml

@@ -4,6 +4,17 @@ repos:
     hooks:
       - id: detect-secrets
         args: [--exclude-secrets=(^my_pw$)|(^inform$)]
+  # Formats docstrings to comply with PEP257.
+  # Use --black to keep output compatible with ruff-format.
+  - repo: https://github.com/PyCQA/docformatter
+    rev: 06907d0
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args:
+          - --in-place
+          - --black
+          - --config=pyproject.toml
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.8.2
     hooks:
@@ -25,14 +36,6 @@ repos:
             "types-pika"
           ]
         files: src/
-  # ----------
-  # Formats docstrings to comply with PEP257
-  - repo: https://github.com/PyCQA/docformatter
-    rev: 06907d0
-    hooks:
-      - id: docformatter
-        additional_dependencies: [tomli]
-        args: [--config=pyproject.toml]
   # a collection of sanity checks: check for merge conflicts, check the end of
   # lines, check for DOS vs unix stuff, and a newline at the end of files.
   - repo: https://github.com/pre-commit/pre-commit-hooks

docker-compose.yml

@@ -30,6 +30,10 @@ services:
       - ../config/exporter.env
     volumes:
       - ../waveform-export:/waveform-export
+      # because we're launching through cron in the container, which starts
+      # processes with a clean environment, also mount in the config file so
+      # it can be read in by snakemake later
+      - ../config/exporter.env:/config/exporter.env:ro
     restart: unless-stopped
   waveform-hasher:
     build:

docs/debugging.md

@@ -0,0 +1,128 @@
+# About
+This is a brief guide to inspecting the state of the waveform data pipeline.
+Eg, looking for intermediate data or error messages if something
+is not coming through as expected.
+
+# Start here
+
+It is helpful to refer to the pipeline diagram at
+https://github.com/SAFEHR-data/emap/blob/develop/docs/technical_overview/waveforms/pipeline.md
+to get an overview and find the right place to look.
+
+First, let's see what data is present in the `waveform-export` directory.
+
+Are there recent files in `ftps-logs`? 
+
+> [!NOTE]
+> The timestamps that are part of the file names are based on when the data is from, not when they were processed by us!
+
+> [!TIP]
+> Use `ls -latr` to see the latest files in a directory.
+
+If the relevant `*.uploaded.json` marker file is present, this means the FTPS
+upload to the DSH happened without an error.
+The file contents are upload stats in JSON format.
+Uploads will also generate email notifications from the DSH. 
+
+If the marker file is not present, let's check the
+other end of our pipeline: are there recent files in `original-csv`? 
+If not then you need to look at the `waveform-controller` logs,
+or failing that further upstream, at the Rabbitmq server (see later section).
+
+If files in `original-csv` are present, then the error is somewhere inside our pipeline,
+and you should check the logs in `snakemake-logs` (see later section).
+
+Parquets that are a direct translation from the CSV are found in `original-parquet`.
+
+Parquets that have been pseudonymised are found in `pseudonymised`.
+
+
+# Logging summary
+
+Logs are found in:
+* Docker container logs
+* Snakemake top-level logs
+* Snakemake job-level logs
+
+> [!CAUTION]
+> Always be aware that logs may contain sensitive information. The only
+> files considered safe for upload to the DSH are those in the `pseudonymised`
+> directory.
+
+## Docker logs
+
+### `waveform-controller` container
+```docker compose logs -t waveform-controller```
+Shows the `waveform-controller` service logs. Useful for:
+- Emap connectivity
+- RabbitMQ connectivity
+- patient correlation query errors (search for "unmatched")
+- CSV output failures
+
+This log is not very chatty if everything is going well.
+
+### `waveform-exporter` container
+```docker compose logs -t waveform-exporter```
+Shows the output from the cron-triggered script `scheduled-script.sh`.
+Useful for high-level pipeline failures before Snakemake starts, or
+Snakemake startup failures (eg. when snakemake already running)
+
+## Snakemake logs
+
+Written to the mounted volume under `waveform-export/snakemake-logs/`.
+These logs describe pipeline orchestration and per-rule execution.
+
+### `snakemake-outer-log*.log`
+Top-level Snakemake run logs, including:
+- recently written CSVs that were temporarily excluded from processing (search "File too new")
+- job summaries and Snakemake DAG resolution
+- more detailed errors when Snakemake itself fails
+
+Unlike data files, the timestamps in these file names are when the snakemake
+pipeline was invoked.
+
+### `{date}.{hashed_csn}.{stream_id}.{units}.log`
+Job-level log for the `csv_to_parquet` rule. Contains:
+- CSV -> parquet info
+- pseudonymisation steps
+
+## FTPS logs and marker files
+
+Produced under `waveform-export/ftps-logs/`.
+
+### `{date}.{hashed_csn}.{stream_id}.{units}.ftps.log`
+Job-level FTPS upload logs. Useful for:
+- connection/authentication errors
+- transfer failures
+
+### `{date}.{hashed_csn}.{stream_id}.{units}.ftps.uploaded.json`
+Upload marker file (aka sentinel) written after a successful transfer.
+It contains, in JSON format:
+- `uploaded_file` (the uploaded file path)
+- `upload_time_secs` (time to upload in seconds using monotonic clock)
+- `start_timestamp` and `end_timestamp` (wall clock UTC start and end timestamp)
+
+Example paths:
+- `waveform-export/snakemake-logs/snakemake-outer-log20260122T173201.log`
+- `waveform-export/snakemake-logs/2025-06-04.acbc4701.52912.mL.log`
+- `waveform-export/ftps-logs/2025-06-04.8bea0824.52912.mL.ftps.log`
+- `waveform-export/ftps-logs/2025-06-04.8bea0824.52912.mL.ftps.uploaded.json`
+
+# Rabbitmq (part of Emap)
+
+If the `waveform-controller` service appears to be up and running but is
+not generating data, you could check the `waveform_export` queue
+in the rabbitmq server, which is part of Emap.
+
+If there are no messages present, it's possible that the waveform reader (also 
+part of Emap) is not generating them.
+
+# Waveform reader (part of Emap)
+This receives HL7 data on a TCP port from the Capsule server.
+It writes received messages
+to the docker host directory `waveform-saved-messages`, so look
+there for recent messages.
+
+Useful commands, to be run from the emap venv (see Emap repo for more details):
+* `emap docker ps` check for container up status (`waveform-reader`)
+* `emap docker logs waveform-reader` see if HL7 messages are being received, check for errors

docs/develop.md

@@ -73,7 +73,20 @@ git push
 
 ## Testing
 
-No tests yet.
+Even though we are largely running in docker, you may wish to let your IDE have access to a venv for running tests in.
+
+Create the venv in the parent of the repo root and activate it (example for macOS/Linux shown, Windows can differ).
+```
+uv venv --python=3.13
+source .venv/bin/activate
+```
+
+From the repo root, install the software and its deps:
+```
+uv pip install -e '.[dev]'
+```
+
+
 ### API tests
 
 from PROJECT_ROOT directory

exporter-scripts/entrypoint.sh

@@ -3,6 +3,8 @@
 # (can't use -u because need to check for potentially unset var)
 set -eo pipefail
 
+CRON_OUTPUT_FILE="/var/log/cron_output.log"
+touch "$CRON_OUTPUT_FILE"
 # Set up cron schedule according to the environment variable
 if [ -z "$EXPORTER_CRON_SCHEDULE" ]; then
   echo "You must set EXPORTER_CRON_SCHEDULE when running this container"
@@ -12,8 +14,9 @@ set -x
 cat <<EOF | crontab -
 PATH=/usr/local/bin:/usr/bin:/bin
 SHELL=/usr/bin/bash
-$EXPORTER_CRON_SCHEDULE /app/exporter-scripts/scheduled-script.sh
+$EXPORTER_CRON_SCHEDULE /app/exporter-scripts/scheduled-script.sh >> "$CRON_OUTPUT_FILE" 2>&1
 EOF
 
-# cron scheduler is PID 1 in this container
-exec cron -f
+# run cron in background, and ensure that output goes to docker logs
+cron
+tail -f "$CRON_OUTPUT_FILE"

exporter-scripts/scheduled-script.sh

@@ -1,6 +1,32 @@
 #!/bin/bash
 
-# Run by the cron scheduler
-# Probably want snakemake instead...
-emap-csv-pseudon --help
-emap-send-ftps --help
+set -euo pipefail
+
+# This script is to be run by the cron scheduler, and its
+# output goes to the docker logs.
+# The snakemake output goes to its own log file as defined here.
+# These files will end up on Windows so be careful about disallowed characters in the names.
+date_str=$(date --utc +"%Y%m%dT%H%M%S")
+SNAKEMAKE_CORES="${SNAKEMAKE_CORES:-1}"
+# for temporarily making the pipeline not go all the way
+SNAKEMAKE_RULE_UNTIL="${SNAKEMAKE_RULE_UNTIL:-all}"
+
+# log file for the overall snakemake run (as opposed to per-job logs,
+# which are defined in the snakefile)
+outer_log_file="/waveform-export/snakemake-logs/snakemake-outer-log${date_str}.log"
+# snakemake has not run yet so will not create the log dir; do it manually
+mkdir -p "$(dirname "$outer_log_file")"
+echo "$0: invoking snakemake, cores=$SNAKEMAKE_CORES, logging to $outer_log_file"
+touch "$outer_log_file"
+# bring in envs from file because cron gives us a clean environment
+set -a
+source /config/exporter.env
+set +a
+set +e
+snakemake --snakefile /app/src/pipeline/Snakefile \
+  --cores "$SNAKEMAKE_CORES" \
+  --until "$SNAKEMAKE_RULE_UNTIL" \
+  >> "$outer_log_file" 2>&1
+ret_code=$?
+set -e
+echo "$0: snakemake exited with return code $ret_code"

pyproject.toml

@@ -5,12 +5,14 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
-    "pandas",
+    "pandas==2.2.3",
     #"pyarrow>=22.0",
     "pika>=1.3.2",
     "pre-commit>=4.5.0",
+    "snakemake==9.14.5",
     # need to be compatible with PIXL, which currently pins 2.9.10 (arguably it shouldn't)
     "psycopg2-binary>=2.9.10",
+    "stablehash==0.3.0",
     # trick for making a "relative" path, works inside or outside container image
     "core @ file:///${PROJECT_ROOT}/../PIXL/pixl_core",
 ]
@@ -20,8 +22,8 @@ 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"
+emap-csv-pseudon = "pseudon.pseudon:psudon_cli"
+emap-send-ftps = "exporter.ftps:do_upload_cli"
 
 [tool.mypy]
 ignore_missing_imports = true

src/controller.py

@@ -14,7 +14,6 @@
 logging.basicConfig(format="%(levelname)s:%(asctime)s: %(message)s")
 logger = logging.getLogger(__name__)
 
-
 emap_db = db.starDB()
 emap_db.init_query()
 emap_db.connect()
@@ -28,8 +27,8 @@ def __init__(self, ch, delivery_tag, body):
 
 
 def ack_message(ch, delivery_tag):
-    """Note that `ch` must be the same pika channel instance via which the
-    message being ACKed was retrieved (AMQP protocol constraint)."""
+    """Note that `ch` must be the same pika channel instance via which the message being
+    ACKed was retrieved (AMQP protocol constraint)."""
     if ch.is_open:
         ch.basic_ack(delivery_tag)
     else:

src/csv_writer.py

@@ -8,8 +8,8 @@
 def create_file_name(
     source_stream_id: str, observation_time: datetime, csn: str, units: str
 ) -> str:
-    """Create a unique file name based on the patient contact serial number
-    (csn) the date, and the source system."""
+    """Create a unique file name based on the patient contact serial number (csn) the
+    date, and the source system."""
     datestring = observation_time.strftime("%Y-%m-%d")
     units = units.replace("/", "p")
     units = units.replace("%", "percent")
@@ -26,8 +26,7 @@ def write_frame(
     csn: str,
     mrn: str,
 ) -> bool:
-    """Appends a frame of waveform data to a csv file (creates file if it
-    doesn't exist.
+    """Appends a frame of waveform data to a csv file (creates file if it doesn't exist.
 
     :return: True if write was successful.
     """