diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e85121a..cc5aa34 100644
--- a/.github/workflows/pytest.yml
+++ b/.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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5cdffb9..d4b0fd9 100644
--- a/.pre-commit-config.yaml
+++ b/.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
diff --git a/docker-compose.yml b/docker-compose.yml
index e3ef8df..d20153a 100644
--- a/docker-compose.yml
+++ b/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:
diff --git a/docs/debugging.md b/docs/debugging.md
new file mode 100644
index 0000000..4ef6968
--- /dev/null
+++ b/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
diff --git a/docs/develop.md b/docs/develop.md
index cf19234..57d2b7f 100644
--- a/docs/develop.md
+++ b/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.
+```
+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
diff --git a/exporter-scripts/entrypoint.sh b/exporter-scripts/entrypoint.sh
index 2bf9ecb..81f2ab4 100755
--- a/exporter-scripts/entrypoint.sh
+++ b/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"
diff --git a/exporter-scripts/scheduled-script.sh b/exporter-scripts/scheduled-script.sh
index b7baed4..6faa7be 100755
--- a/exporter-scripts/scheduled-script.sh
+++ b/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 $ret_code"
diff --git a/pyproject.toml b/pyproject.toml
index 05283fd..7ee53db 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,12 +5,14 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
-    "pandas",
+    "pandas==2.2.3",
     #"pyarrow>=22.0",
     "pika>=1.3.2",
     "pre-commit>=4.5.0",
+    "snakemake==9.14.5",
     # need to be compatible with PIXL, which currently pins 2.9.10 (arguably it shouldn't)
     "psycopg2-binary>=2.9.10",
+    "stablehash==0.3.0",
     # trick for making a "relative" path, works inside or outside container image
     "core @ file:///${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
diff --git a/src/controller.py b/src/controller.py
index 861a7d7..ccaf776 100644
--- a/src/controller.py
+++ b/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:
diff --git a/src/csv_writer.py b/src/csv_writer.py
index 6025cc3..47b128f 100644
--- a/src/csv_writer.py
+++ b/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.
     """
diff --git a/src/exporter/ftps.py b/src/exporter/ftps.py
index 431732d..e7dd141 100644
--- a/src/exporter/ftps.py
+++ b/src/exporter/ftps.py
@@ -8,11 +8,8 @@
 
 from locations import WAVEFORM_PSEUDONYMISED_PARQUET
 
-logging.basicConfig(format="%(levelname)s:%(asctime)s: %(message)s")
-logger = logging.getLogger(__name__)
 
-
-def do_upload():
+def do_upload_cli():
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "file_to_upload",
@@ -20,19 +17,20 @@ def do_upload():
         help="file to upload relative to pseudonymised folder",
     )
     args = parser.parse_args()
-    do_upload_inner(args.file_to_upload)
+    do_upload(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():
+def do_upload(abs_file_to_upload: Path):
+    """We need to ensure that a user cannot accidentally ask for a file to be uploaded
+    unless it's under the correct directory that we know contains pseudonymised data."""
+    logger = logging.getLogger(__name__)
+    # Keep things simple, paths must be absolute
+    if not abs_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.
+    # Even an absolute path may contain a ".." or a symlink. Fully resolve so we
+    # know what we are dealing with.
+    file_to_upload = abs_file_to_upload.resolve()
+    # Check 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}. "
diff --git a/src/locations.py b/src/locations.py
index bfc8b1a..ff37838 100644
--- a/src/locations.py
+++ b/src/locations.py
@@ -4,3 +4,15 @@
 WAVEFORM_ORIGINAL_CSV = WAVEFORM_EXPORT_BASE / "original-csv"
 WAVEFORM_ORIGINAL_PARQUET = WAVEFORM_EXPORT_BASE / "original-parquet"
 WAVEFORM_PSEUDONYMISED_PARQUET = WAVEFORM_EXPORT_BASE / "pseudonymised"
+WAVEFORM_SNAKEMAKE_LOGS = WAVEFORM_EXPORT_BASE / "snakemake-logs"
+WAVEFORM_FTPS_LOGS = WAVEFORM_EXPORT_BASE / "ftps-logs"
+
+
+# file patterns
+FILE_STEM_PATTERN = "{date}.{csn}.{stream_id}.{units}"
+FILE_STEM_PATTERN_HASHED = "{date}.{hashed_csn}.{stream_id}.{units}"
+CSV_PATTERN = WAVEFORM_ORIGINAL_CSV / (FILE_STEM_PATTERN + ".csv")
+ORIGINAL_PARQUET_PATTERN = WAVEFORM_ORIGINAL_PARQUET / (FILE_STEM_PATTERN + ".parquet")
+PSEUDONYMISED_PARQUET_PATTERN = WAVEFORM_PSEUDONYMISED_PARQUET / (
+    FILE_STEM_PATTERN_HASHED + ".parquet"
+)
diff --git a/src/pipeline/Snakefile b/src/pipeline/Snakefile
new file mode 100644
index 0000000..89bc22b
--- /dev/null
+++ b/src/pipeline/Snakefile
@@ -0,0 +1,163 @@
+import os
+import sys
+import time
+from datetime import datetime, timedelta, timezone
+from snakemake.io import glob_wildcards
+from exporter.ftps import do_upload
+from locations import (
+    WAVEFORM_EXPORT_BASE,
+    WAVEFORM_ORIGINAL_CSV,
+    WAVEFORM_ORIGINAL_PARQUET,
+    WAVEFORM_SNAKEMAKE_LOGS,
+    WAVEFORM_PSEUDONYMISED_PARQUET,
+    WAVEFORM_FTPS_LOGS,
+    FILE_STEM_PATTERN,
+    FILE_STEM_PATTERN_HASHED,
+    CSV_PATTERN,
+)
+from pathlib import Path
+from pseudon.hashing import do_hash
+from pseudon.pseudon import csv_to_parquets
+
+def get_file_age(file_path: Path) -> timedelta:
+    # need to use UTC to avoid DST issues
+    file_time_utc = datetime.fromtimestamp(file_path.stat().st_mtime, timezone.utc)
+    now_utc = datetime.now(timezone.utc)
+    return now_utc - file_time_utc
+
+def hash_csn(csn: str) -> str:
+    return do_hash("csn", csn)
+
+
+# How long before we assume that no more data will be written to the file, and
+# that we can process it.
+# In production we may wish to use something in the order of hours.
+# We may also wish to compare it to the latest modified time of *any* file,
+# to be sure that the data hasn't just stopped coming in altogether. (would not
+# protect against very out of order data though)
+# Also note that snakemake can detect and re-run if the file is subsequently updated,
+# so being very cautious here may not be necessary.
+CSV_WAIT_TIME = timedelta(minutes=5)
+
+# The problem here is that snakemake works "backwards" in that you have to define which
+# files you want to be produced, yet we don't know what output files we need until the
+# input files (original CSVs) are present.
+# Therefore, look at the input files and work out the eventual output files so they can
+# be fed into snakemake.
+
+def determine_eventual_outputs():
+    # Parse all CSVs using the basic file name pattern
+    before = time.perf_counter()
+    all_wc = glob_wildcards(CSV_PATTERN)
+
+    # all_wc.date, all_wc.csn, all_wc.streamId, all_wc.units are parallel lists
+    # e.g. all_wc.csn[0] corresponds to all_wc.date[0], etc.
+
+    # Build reverse lookup using named wildcards
+    _hash_to_csn: dict[str, str] = {}
+    for csn in all_wc.csn:
+        _hash_to_csn[hash_csn(csn)] = csn
+    # Apply all_wc to FILE_STEM_PATTERN_HASHED to generate the output stems
+    _all_outputs = []
+    for date, csn, stream_id, units in zip(all_wc.date, all_wc.csn, all_wc.stream_id, all_wc.units):
+        subs_dict = dict(
+            date = date,
+            csn = csn,
+            hashed_csn = hash_csn(csn),
+            stream_id = stream_id,
+            units = units
+        )
+        orig_file = Path(str(CSV_PATTERN).format(**subs_dict))
+        if csn == 'unmatched_csn':
+            print(f"Skipping file with unmatched CSN: {orig_file}")
+            continue
+        file_age = get_file_age(orig_file)
+        if file_age < CSV_WAIT_TIME:
+            print(f"File too new (age={file_age}): {orig_file}")
+            continue
+        final_stem = FILE_STEM_PATTERN_HASHED.format(**subs_dict)
+        final_output_file = WAVEFORM_FTPS_LOGS / (final_stem + ".ftps.uploaded.json")
+        _all_outputs.append(final_output_file)
+    after = time.perf_counter()
+    print(f"Calculated output files using newness threshold {CSV_WAIT_TIME} in {after - before} seconds")
+    return _all_outputs, _hash_to_csn
+
+
+all_outputs, hash_to_csn = determine_eventual_outputs()
+
+def configure_file_logging(log_file):
+    import logging
+    logging.basicConfig(
+        filename=log_file,
+        level=logging.INFO,
+        format='%(asctime)s - %(levelname)s - %(message)s',
+        force=True
+    )
+    print(f"Configured logging to use file {log_file}")
+    logger = logging.getLogger(__name__)
+    return logger
+
+
+rule all:
+    input:
+        all_outputs
+
+def input_file_maker(wc):
+    unhashed_csn = hash_to_csn[wc.hashed_csn]
+    # when using input functions, snakemake doesn't do its normal templating, you have to do it, hence the f-string
+    return WAVEFORM_ORIGINAL_CSV / f"{wc.date}.{unhashed_csn}.{wc.stream_id}.{wc.units}.csv"
+
+rule csv_to_parquet:
+    input:
+        input_file_maker
+    output:
+        # Do not specify the original parquet as an output, even though it is,
+        # because snakemake doesn't allow a different subset of wildcards to be used in each output file.
+        # WAVEFORM_ORIGINAL_PARQUET / (FILE_STEM_PATTERN + ".parquet"),
+        WAVEFORM_PSEUDONYMISED_PARQUET / (FILE_STEM_PATTERN_HASHED + ".parquet")
+    log:
+        # these do not get uploaded as they may contain identifiers
+        WAVEFORM_SNAKEMAKE_LOGS / (FILE_STEM_PATTERN_HASHED + ".log")
+    run:
+        logger = configure_file_logging(log[0])
+        original_csn = hash_to_csn[wildcards.hashed_csn]
+        logger.info("Running csv to parquets, csn %s -> %s", original_csn, wildcards.hashed_csn)
+        csv_to_parquets(
+            date_str=wildcards.date,
+            original_csn=original_csn,
+            hashed_csn=wildcards.hashed_csn,
+            variable_id=wildcards.stream_id,
+            units=wildcards.units)
+
+
+rule send_ftps:
+    input:
+        WAVEFORM_PSEUDONYMISED_PARQUET / (FILE_STEM_PATTERN_HASHED + ".parquet")
+    output:
+        # sentinel file
+        WAVEFORM_FTPS_LOGS / (FILE_STEM_PATTERN_HASHED + ".ftps.uploaded.json")
+    log:
+        WAVEFORM_FTPS_LOGS / (FILE_STEM_PATTERN_HASHED + ".ftps.log")
+    run:
+        from datetime import datetime
+        import json
+        import time
+        start_perf = time.perf_counter()
+        start_timestamp = datetime.now(timezone.utc).isoformat()
+        logger = configure_file_logging(log[0])
+        logger.info("Calling do_upload to upload file %s", input[0])
+        do_upload(Path(input[0]))
+        end_perf = time.perf_counter()
+        end_timestamp = datetime.now(timezone.utc).isoformat()
+        # now that we have success, create the sentinel file
+        with open(output[0], "w") as fh:
+            json.dump(
+                {
+                    "uploaded_file": str(input[0]),
+                    "upload_time_secs": end_perf - start_perf,
+                    "start_timestamp": start_timestamp,
+                    "end_timestamp": end_timestamp,
+                },
+                fh,
+                indent=0,
+            )
diff --git a/src/pseudon/hashing.py b/src/pseudon/hashing.py
index b4253d6..d7ac7b9 100644
--- a/src/pseudon/hashing.py
+++ b/src/pseudon/hashing.py
@@ -1,15 +1,17 @@
 from functools import lru_cache
+from stablehash import stablehash
 
 
 @lru_cache
-def do_hash(type_prefix, value: str):
+def do_hash(type_prefix: str, 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.
+    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.
     """
+    # Full implementation of issue #6 must remove this code and call the real hasher!!
     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
+    full_hash = stablehash(full_value_to_hash).hexdigest()
+    tiny_hash = full_hash[:8]
+    return tiny_hash
diff --git a/src/pseudon/pseudon.py b/src/pseudon/pseudon.py
index 4f6094e..5f18c3f 100644
--- a/src/pseudon/pseudon.py
+++ b/src/pseudon/pseudon.py
@@ -1,27 +1,59 @@
 import argparse
 import functools
+import logging
 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_PARQUET, WAVEFORM_PSEUDONYMISED_PARQUET
 
+from locations import (
+    WAVEFORM_ORIGINAL_PARQUET,
+    WAVEFORM_PSEUDONYMISED_PARQUET,
+    CSV_PATTERN,
+    PSEUDONYMISED_PARQUET_PATTERN,
+)
 from .hashing import do_hash
 
 
-def main():
+def pseudon_cli():
     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):
+def csv_to_parquets(
+    *, date_str: str, original_csn: str, hashed_csn: str, variable_id: str, units: str
+) -> None:
+    """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)
+
+    This is a privacy-sensitive area of code. The two versions of the parquet file
+    have different names (hashed vs unhashed CSN). Unhashed CSNs must not appear in
+    the uploaded files.
+    It might have been more convenient (esp for CLI usage) to pass in the CSV path directly,
+    then parse out the sections here to generate both output file names,
+    but that is going to be lead to fragile assumptions that eg. element "1" is always the CSN.
+
+    Instead, pass in individual named components of the file path.
+    """
+    # will pick up the logger config defined in the snakemake job (ie. log to file)
+    logger = logging.getLogger(__name__)
+
+    csv_path = Path(
+        str(CSV_PATTERN).format(
+            date=date_str, csn=original_csn, stream_id=variable_id, units=units
+        )
+    )
+    # it's in the csv_path, but at least nowhere else!
+    del original_csn
+
+    logger.info("Turning CSV %s to parquets", csv_path)
     WAVEFORM_ORIGINAL_PARQUET.mkdir(parents=False, exist_ok=True)
     WAVEFORM_PSEUDONYMISED_PARQUET.mkdir(parents=False, exist_ok=True)
     df = pd.read_csv(
@@ -79,23 +111,44 @@ def parse_array(x):
         write_statistics=True,  # enable indexes/statistics
         flavor="spark",
     )
+    logger.info(
+        "Done turning CSV %s to original parquet %s", csv_path, original_parquet_path
+    )
 
     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")
+    hashed_path = Path(
+        str(PSEUDONYMISED_PARQUET_PATTERN).format(
+            date=date_str, hashed_csn=hashed_csn, stream_id=variable_id, units=units
+        )
+    )
     pq.write_table(
         pseudon_table,
-        str(pseudon_parquet_path),
+        str(hashed_path),
         compression="zstd",
         use_dictionary=True,
         write_statistics=True,  # enable indexes/statistics
         flavor="spark",
     )
+    logger.info(
+        "Done turning CSV %s to pseudonymised parquet %s", csv_path, hashed_path
+    )
+
+
+SAFE_COLUMNS = ["sampling_rate", "source_stream_id", "timestamp", "units", "values"]
 
 
 def pseudonymise_relevant_columns(df: pd.DataFrame):
-    for col in ["csn", "mrn", "location"]:
-        df[col] = df[col].apply(functools.partial(do_hash, col))
+    """ "csn", "mrn", "location" are examples of columns that must be pseudonymised.
+
+    However, it's safer to list which columns *don't* need to be pseudonymised. Eg. you
+    add a column but forget to consider whether it's sensitive, OR you rename one of the
+    known sensitive columns and forget that this will cause privacy to break. This means
+    that when you add a new column, you have to add it here if you don't want it to be
+    hashed.
+    """
+    for col in df.columns:
+        if col not in SAFE_COLUMNS:
+            df[col] = df[col].apply(functools.partial(do_hash, col))
     return df
diff --git a/tests/test_ftps.py b/tests/test_ftps.py
new file mode 100644
index 0000000..df0dc41
--- /dev/null
+++ b/tests/test_ftps.py
@@ -0,0 +1,55 @@
+from pathlib import Path
+from unittest.mock import Mock
+
+import pytest
+
+from src.exporter import ftps
+
+
+@pytest.mark.parametrize(
+    ["rel_path_to_try", "should_pass"],
+    [
+        # These will all be turned into abs paths in the test (test params are evaluated before fixtures
+        # so we can't know the tmp_path at this point)
+        ["sensitive/foobar.txt", False],
+        ["../sensitive/foobar.txt", False],
+        ["pseudonymised/../sensitive/foobar.txt", False],
+        ["pseudonymised/../../sensitive/foobar.txt", False],
+        ["pseudonymised/blah/../blah/foobar.txt", True],
+        ["pseudonymised/foobar.txt", True],
+        ["pseudonymised/../foobar.txt", False],
+        # weird cases
+        ["..", False],
+        ["", False],
+        ["/", False],
+    ],
+)
+def test_do_upload_input_paths(
+    monkeypatch, tmp_path: Path, rel_path_to_try: str, should_pass: bool
+):
+    fake_abs_root = tmp_path.absolute()
+    fake_waveform_pseudonymised_parquet = fake_abs_root / "pseudonymised"
+    monkeypatch.setattr(
+        ftps, "WAVEFORM_PSEUDONYMISED_PARQUET", fake_waveform_pseudonymised_parquet
+    )
+
+    ftp_mock = Mock()
+    connect_mock = Mock(return_value=ftp_mock)
+    monkeypatch.setattr(ftps, "_connect_to_ftp", connect_mock)
+
+    # do_upload expects file to already exist, but we are setting up a test, so we must create the dir here
+    # (and the file later)
+    fake_waveform_pseudonymised_parquet.mkdir()
+    path_to_try = fake_abs_root / rel_path_to_try
+    if should_pass:
+        # file needs to exist
+        path_to_try.parent.mkdir(parents=True, exist_ok=True)
+        path_to_try.write_text("blah")
+        ftps.do_upload(path_to_try)
+        assert connect_mock.called
+        ftp_mock.storbinary.assert_called_once()
+    else:
+        # Don't create upload file as it may be outside the pytest tmp_path. We expect things to fail before that point anyway
+        with pytest.raises(ValueError, match="must be under"):
+            ftps.do_upload(path_to_try)
+        connect_mock.assert_not_called()
diff --git a/uv.lock b/uv.lock
index 24c637b..716dfcd 100644
--- a/uv.lock
+++ b/uv.lock
@@ -54,6 +54,33 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/7f/9c/36c5c37947ebfb8c7f22e0eb6e4d188ee2d53aa3880f3f2744fb894f0cb1/anyio-4.12.0-py3-none-any.whl", hash = "sha256:dad2376a628f98eeca4881fc56cd06affd18f659b17a747d3ff0307ced94b1bb", size = 113362 },
 ]
 
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d7/d8/05696357e0311f5b5c316d7b95f46c669dd9c15aaeecbb48c7d0aeb88c40/appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41", size = 13470 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/3b/00/2344469e2084fb287c2e0b57b72910309874c3245463acd6cf5e3db69324/appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128", size = 9566 },
+]
+
+[[package]]
+name = "argparse-dataclass"
+version = "2.0.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/1a/ff/a2e4e328075ddef2ac3c9431eb12247e4ba707a70324894f1e6b4f43c286/argparse_dataclass-2.0.0.tar.gz", hash = "sha256:09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f", size = 6395 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b3/66/e6c0a808950ba5a4042e2fcedd577fc7401536c7db063de4d7c36be06f84/argparse_dataclass-2.0.0-py3-none-any.whl", hash = "sha256:3ffc8852a88d9d98d1364b4441a712491320afb91fb56049afd8a51d74bb52d2", size = 8762 },
+]
+
+[[package]]
+name = "attrs"
+version = "25.4.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/6b/5c/685e6633917e101e5dcb62b9dd76946cbb57c26e133bae9e0cd36033c0a9/attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11", size = 934251 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373", size = 67615 },
+]
+
 [[package]]
 name = "azure-core"
 version = "1.37.0"
@@ -334,6 +361,33 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6", size = 25335 },
 ]
 
+[[package]]
+name = "conda-inject"
+version = "1.3.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pyyaml" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/b1/a8/8dc86113c65c949cc72d651461d6e4c544b3302a85ed14a5298829e6a419/conda_inject-1.3.2.tar.gz", hash = "sha256:0b8cde8c47998c118d8ff285a04977a3abcf734caf579c520fca469df1cd0aac", size = 3635 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/87/4c/fc30b69fb4062aee57e3ab7ff493647c4220144908f0839c619f912045bf/conda_inject-1.3.2-py3-none-any.whl", hash = "sha256:6e641b408980c2814e3e527008c30749117909a21ff47392f07ef807da93a564", size = 4133 },
+]
+
+[[package]]
+name = "configargparse"
+version = "1.7.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/85/4d/6c9ef746dfcc2a32e26f3860bb4a011c008c392b83eabdfb598d1a8bbe5d/configargparse-1.7.1.tar.gz", hash = "sha256:79c2ddae836a1e5914b71d58e4b9adbd9f7779d4e6351a637b7d2d9b6c46d3d9", size = 43958 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/31/28/d28211d29bcc3620b1fece85a65ce5bb22f18670a03cd28ea4b75ede270c/configargparse-1.7.1-py3-none-any.whl", hash = "sha256:8b586a31f9d873abd1ca527ffbe58863c99f36d896e2829779803125e83be4b6", size = 25607 },
+]
+
+[[package]]
+name = "connection-pool"
+version = "0.0.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/bd/df/c9b4e25dce00f6349fd28aadba7b6c3f7431cc8bd4308a158fbe57b6a22e/connection_pool-0.0.3.tar.gz", hash = "sha256:bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc", size = 3795 }
+
 [[package]]
 name = "core"
 version = "0.2.0rc0"
@@ -452,6 +506,24 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/33/6b/e0547afaf41bf2c42e52430072fa5658766e3d65bd4b03a563d1b6336f57/distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16", size = 469047 },
 ]
 
+[[package]]
+name = "docutils"
+version = "0.22.4"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/ae/b6/03bb70946330e88ffec97aefd3ea75ba575cb2e762061e0e62a213befee8/docutils-0.22.4.tar.gz", hash = "sha256:4db53b1fde9abecbb74d91230d32ab626d94f6badfc575d6db9194a49df29968", size = 2291750 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/02/10/5da547df7a391dcde17f59520a231527b8571e6f46fc8efb02ccb370ab12/docutils-0.22.4-py3-none-any.whl", hash = "sha256:d0013f540772d1420576855455d050a2180186c91c15779301ac2ccb3eeb68de", size = 633196 },
+]
+
+[[package]]
+name = "dpath"
+version = "2.2.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/b5/ce/e1fd64d36e4a5717bd5e6b2ad188f5eaa2e902fde871ea73a79875793fc9/dpath-2.2.0.tar.gz", hash = "sha256:34f7e630dc55ea3f219e555726f5da4b4b25f2200319c8e6902c394258dd6a3e", size = 28266 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/05/d1/8952806fbf9583004ab479d8f58a9496c3d35f6b6009ddd458bdd9978eaf/dpath-2.2.0-py3-none-any.whl", hash = "sha256:b330a375ded0a0d2ed404440f6c6a715deae5313af40bbb01c8a41d891900576", size = 17618 },
+]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.3.1"
@@ -478,6 +550,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/52/b3/7e4df40e585df024fac2f80d1a2d579c854ac37109675db2b0cc22c0bb9e/fastapi-0.115.6-py3-none-any.whl", hash = "sha256:e9240b29e36fa8f4bb7290316988e90c381e5092e0cbe84e7818cc3713bcf305", size = 94843 },
 ]
 
+[[package]]
+name = "fastjsonschema"
+version = "2.21.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/20/b5/23b216d9d985a956623b6bd12d4086b60f0059b27799f23016af04a74ea1/fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de", size = 374130 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/cb/a8/20d0723294217e47de6d9e2e40fd4a9d2f7c4b6ef974babd482a59743694/fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463", size = 24024 },
+]
+
 [[package]]
 name = "filelock"
 version = "3.20.0"
@@ -487,6 +568,30 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/76/91/7216b27286936c16f5b4d0c530087e4a54eead683e6b0b73dd0c64844af6/filelock-3.20.0-py3-none-any.whl", hash = "sha256:339b4732ffda5cd79b13f4e2711a31b0365ce445d95d243bb996273d072546a2", size = 16054 },
 ]
 
+[[package]]
+name = "gitdb"
+version = "4.0.12"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "smmap" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/72/94/63b0fc47eb32792c7ba1fe1b694daec9a63620db1e313033d18140c2320a/gitdb-4.0.12.tar.gz", hash = "sha256:5ef71f855d191a3326fcfbc0d5da835f26b13fbcba60c32c21091c349ffdb571", size = 394684 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/a0/61/5c78b91c3143ed5c14207f463aecfc8f9dbb5092fb2869baf37c273b2705/gitdb-4.0.12-py3-none-any.whl", hash = "sha256:67073e15955400952c6565cc3e707c554a4eea2e428946f7a4c162fab9bd9bcf", size = 62794 },
+]
+
+[[package]]
+name = "gitpython"
+version = "3.1.45"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "gitdb" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/9a/c8/dd58967d119baab745caec2f9d853297cec1989ec1d63f677d3880632b88/gitpython-3.1.45.tar.gz", hash = "sha256:85b0ee964ceddf211c41b9f27a49086010a190fd8132a24e21f362a4b36a791c", size = 215076 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/01/61/d4b89fec821f72385526e1b9d9a3a0385dda4a72b206d28049e2c7cd39b8/gitpython-3.1.45-py3-none-any.whl", hash = "sha256:8908cb2e02fb3b93b7eb0f2827125cb699869470432cc885f019b8fd0fccff77", size = 208168 },
+]
+
 [[package]]
 name = "greenlet"
 version = "3.3.0"
@@ -534,6 +639,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/4f/dc/041be1dff9f23dac5f48a43323cd0789cb798342011c19a248d9c9335536/greenlet-3.3.0-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:6c10513330af5b8ae16f023e8ddbfb486ab355d04467c4679c5cfe4659975dd9", size = 1676034 },
 ]
 
+[[package]]
+name = "humanfriendly"
+version = "10.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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