rcb1409 · Oct 1, 2026 · Oct 1, 2026 · Oct 1, 2026 · Oct 5, 2026 · Oct 5, 2026
diff --git a/Dockerfile b/Dockerfile
@@ -37,5 +37,5 @@ HEALTHCHECK --interval=30s --timeout=5s --start-period=20s --retries=3 \
   CMD python -c "import urllib.request,sys; sys.exit(0 if urllib.request.urlopen('http://127.0.0.1:5000/ping', timeout=4).status==200 else 1)"
 
 # 1 worker, as on the old server (~160 MB each). --timeout matches the timer client's
-# 600 s wait, so a long autofill or peroxide check isn't killed halfway.
+# 600 s wait, so a long peroxide check isn't killed halfway.
 CMD ["gunicorn", "-w", "1", "-b", "0.0.0.0:5000", "--timeout", "600", "--access-logfile", "-", "app:app"]
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 Unified server for the DDOM Lab's custom ELN (eLabFTW) tooling. Consolidates the
 former `eln_web_backend`, `eln_packages_backend`, and `eln_packages_common`
 repositories into one Flask application: the web interface, the eLab API
-wrapper, and the automations (autofill, label generation, RDKit images,
+wrapper, and the automations (label generation, RDKit images,
 peroxide-former Slack reminders) all live here and run through the server.
 
 To install an eLabFTW instance, follow the eLabFTW installation instructions at https://doc.elabftw.net/docs/category/installation/ 
@@ -21,7 +21,6 @@ To install an eLabFTW instance, follow the eLabFTW installation instructions at
   - Generating custom labels
   - Performing 'batch actions' (above actions taken on multiple items at once)
 - ELN Automations
-  - Autofilling Resource information from CAS (hazards, molecular weight, RDKit image, SMILES, etc.)
   - Reminders to check peroxide formers with formatted list of peroxide formers
 
 
@@ -30,8 +29,8 @@ To install an eLabFTW instance, follow the eLabFTW installation instructions at
 | Directory | Contents |
 |---|---|
 | `app.py` | Flask entry point; registers blueprints (gunicorn target `app:app`) |
-| `eln_common/` | eLab API wrapper (`Resource_Manager`, `config`, `fill_info`) — formerly `eln_packages_common` |
-| `automations/` | autofill, label generation, RDKit images, peroxide checks, Slack bot — formerly `eln_packages_backend` |
+| `eln_common/` | eLab API wrapper (`Resource_Manager`, `config`, `pubchem`, `compound_import`, `add_bottle`...) — formerly `eln_packages_common` |
+| `automations/` | label generation, RDKit images, peroxide checks, Slack bot — formerly `eln_packages_backend` |
 | `web/` | Flask blueprints: `interface` (the UI routes) and `automation_api` (`/api/...`) |
 | `static/` | Web UI pages and label templates |
 | `scripts/` | One-off maintenance scripts (inventory dumps, compound linking) |
@@ -42,7 +41,7 @@ To install an eLabFTW instance, follow the eLabFTW installation instructions at
 
 Server settings live in `config.yaml` at the repo root (relative paths resolve
 from there): the instance URLs (`eln_url`, `eln_web_url` — required),
-`printer_path`, `auto_upload_labels`, and the team-specific status/category
+`printer_path`, and the team-specific status/category
 IDs (`status_open`, `status_empty`, `chemical_categories`,
 `label_date_categories`). The ID settings can also be set from dropdowns at
 `/settings_interface`, which reads your team's actual lists from the eLabFTW
@@ -70,21 +69,15 @@ The Slack bot token is also server-side: set `slack_bot_token` in `secrets.yaml`
 
 ## Automation API
 
-- `POST /api/autofill` — PubChem info fill, RDKit image (and, legacy, label upload).
-  Optional JSON body: `{"id": 123}` for one item, or
-  `{"start": 0, "end": null, "size": 5, "force": false, "info": true, "label": true, "image": true}`
-  (defaults shown, autofills the 5 most recently modified Resources with IDs between 0 and `null` (infinity)). Errors are reported to the Slack error channel, like the old `main.py`.
 - `POST /api/check_peroxides` — checks the inventory against the class A–D
   peroxide-former lists and sends Slack reminders. Returns match counts.
 
-The `/add_resource` UI route also triggers an autofill of the new item in
-the background, so info/images appear immediately after creation.
-
 Label printing (`/print`) generates the PDF on the fly from the item's current
-data. Attaching a `label.pdf` upload to each resource during autofill is a
-legacy feature, disabled by default; set `auto_upload_labels: true` in
-`config.yaml` to re-enable it (the `label` flag in the autofill body is
-ignored unless it is set).
+data.
+
+There is no autofill any more (removed 2026-10): chemical details live on the
+compound each resource is linked to, instead of being copied from PubChem into
+every resource's fields.
 
 ## Running the server
 
@@ -141,9 +134,8 @@ The PTH tracker is a separate project (https://github.com/ddomlab/pth_analysis).
 
 The systemd timers (in `client/`) execute the automated actions. They can be automatically installed with the `install.sh` script in `client/`
 
-This installs `eln-autofill.timer` (every 10 minutes — adjust `OnCalendar` to
-taste, including excluding backup windows) and `eln-peroxide-check.timer`
-(May 1 and Nov 1). The key is stored at `/etc/eln-client/api_key`; the server
+This installs `eln-peroxide-check.timer` (May 1 and Nov 1), and removes the old
+`eln-autofill.timer` from hosts that still have it. The key is stored at `/etc/eln-client/api_key`; the server
 URL is set via `ELN_SERVER_URL` in the `.service` files.
 Pass it at install time to skip editing them; with the Docker deploy on the same
 host that's the local port:

diff --git a/automations/autofill.py b/automations/autofill.py
diff --git a/automations/image_generator.py b/automations/image_generator.py
@@ -7,8 +7,8 @@
 
 def generate_image(smiles: str) -> str:
     mol = Chem.MolFromSmiles(smiles)
-    # the basename becomes the uploaded file's real_name, which autofill checks
-    # for, so it must stay "RDKitImage.png"
+    # the basename becomes the uploaded file's real_name; existing resources
+    # carry their structure image as "RDKitImage.png", so keep the name
     filename = str(Path(tempfile.gettempdir()) / "RDKitImage.png")
     Draw.MolToFile(mol, filename)
     return filename
diff --git a/automations/labels/generate_label.py b/automations/labels/generate_label.py
@@ -37,6 +37,13 @@ def add_item(self, id: int):
             )
         )
 
+    def pdf(self) -> bytes:
+        """The labels added so far as PDF data, without writing a file (so two people
+        printing at the same time can't get each other's labels)."""
+        data = self.label_writer.write_labels(self.records, target=None)
+        self.records = []
+        return data
+
     # generates pdf for all labels in records
     def write_labels(self, target: str | None = None):
         self.label_writer.write_labels(self.records, target=target or self.path)

diff --git a/automations/routine_checks.yaml b/automations/routine_checks.yaml
@@ -0,0 +1,23 @@
+# Routine checks on opened bottles, kept as steps on each bottle's ELN page.
+#
+# A bottle with one of these tags gets the step when it is marked open in the
+# Resource Manager app, due `every_months` later. Scanning it with "Tested" ticks
+# the step and adds the next one; "Mark Empty" closes it. The tags come from the
+# bottle's compound when the bottle is added (see eln_common/bottle_tags.py).
+#
+# Intervals: common lab-safety practice for peroxide formers (test after opening).
+# Change them here; the app reads this file when it starts.
+
+checks:
+  - tag: "Peroxide former: A"
+    step: "Test for peroxides (class A)"
+    every_months: 3
+  - tag: "Peroxide former: B"
+    step: "Test for peroxides (class B)"
+    every_months: 6
+  - tag: "Peroxide former: C"
+    step: "Test for peroxides (class C)"
+    every_months: 6
+  - tag: "Peroxide former: D"
+    step: "Test for peroxides (class D)"
+    every_months: 12
diff --git a/client/eln-autofill.service b/client/eln-autofill.service
diff --git a/client/eln-autofill.timer b/client/eln-autofill.timer
diff --git a/client/eln_timer_client.py b/client/eln_timer_client.py
@@ -6,7 +6,6 @@
 to be run by the systemd timers in this directory (replacing the old cron jobs),
 but can be run by hand:
 
-    eln_timer_client.py autofill
     eln_timer_client.py check_peroxides
 
 Uses only the Python standard library, so it needs no environment to run.
@@ -25,8 +24,6 @@
 API_KEY_FILE = os.environ.get("ELN_API_KEY_FILE", "/etc/eln-client/api_key")
 
 TASKS = {
-    # autofill the 5 most recently created items
-    "autofill": {"size": 5, "info": True, "label": False, "image": True},
     "check_peroxides": {},
 }
 

diff --git a/client/install.sh b/client/install.sh
@@ -14,14 +14,13 @@ KEY_FILE=/etc/eln-client/api_key
 
 install -d /opt/eln-client
 install -m 755 "$SCRIPT_DIR/eln_timer_client.py" /opt/eln-client/
-install -m 644 "$SCRIPT_DIR"/eln-autofill.{service,timer} /etc/systemd/system/
 install -m 644 "$SCRIPT_DIR"/eln-peroxide-check.{service,timer} /etc/systemd/system/
 
 # optional: point the timers at a server other than the default in the .service files,
 # e.g. sudo ELN_SERVER_URL=http://127.0.0.1:5001 ./install.sh (the Docker deploy's local port)
 if [[ -n ${ELN_SERVER_URL:-} ]]; then
     sed -i "s|^Environment=ELN_SERVER_URL=.*|Environment=ELN_SERVER_URL=$ELN_SERVER_URL|" \
-        /etc/systemd/system/eln-autofill.service /etc/systemd/system/eln-peroxide-check.service
+        /etc/systemd/system/eln-peroxide-check.service
     echo "Timers will call $ELN_SERVER_URL"
 fi
 
@@ -42,12 +41,20 @@ if [[ ! -f $KEY_FILE ]]; then
     echo "Wrote $KEY_FILE"
 fi
 
+# autofill was removed (compounds now hold the chemical details): take its old
+# timer off hosts that still have it, so it stops calling a route that is gone
+if [[ -f /etc/systemd/system/eln-autofill.timer ]]; then
+    systemctl disable --now eln-autofill.timer || true
+    rm -f /etc/systemd/system/eln-autofill.service /etc/systemd/system/eln-autofill.timer
+    echo "Removed the old eln-autofill timer"
+fi
+
 systemctl daemon-reload
-systemctl enable --now eln-autofill.timer eln-peroxide-check.timer
+systemctl enable --now eln-peroxide-check.timer
 
 echo
 echo "Installed. Check status with:"
 echo "  systemctl list-timers 'eln-*'"
 echo "To point at a non-local server, edit ELN_SERVER_URL in"
-echo "  /etc/systemd/system/eln-autofill.service and eln-peroxide-check.service,"
+echo "  /etc/systemd/system/eln-peroxide-check.service,"
 echo "then: systemctl daemon-reload"
diff --git a/config-ex.yaml b/config-ex.yaml
@@ -14,12 +14,6 @@ eln_web_url: https://eln.ddomlab.org
 # Where generated label PDFs are written before printing/upload
 printer_path: /tmp/label.pdf
 
-# Legacy feature: /print used to fetch a label.pdf stored on each resource, so
-# autofill uploaded one to every new item. /print now generates labels on the
-# fly, making the uploads redundant; set this to true to keep attaching
-# label.pdf to resources anyway.
-auto_upload_labels: false
-
 ## Team-specific IDs ##########################################################
 # eLabFTW statuses and resource categories are per-team lists with arbitrary
 # IDs, so they must be mapped here for your instance. Two ways to find them:
@@ -33,13 +27,13 @@ auto_upload_labels: false
 status_open: 4
 # Status a resource gets when marked as empty
 status_empty: 5
-# Resource categories that get PubChem info + an RDKit structure image on autofill
+# Resource categories that hold chemicals
 chemical_categories: [2, 3]
 # Resource categories whose printed labels show a "Received" date
 label_date_categories: [2, 3, 4]
 
 ## Slack integration ##########################################################
-# Set to true to have the automations report to Slack (autofill errors,
+# Set to true to have the automations report to Slack (errors,
 # peroxide reminders). Requires slack_bot_token in secrets.yaml. When false
 # (the default), messages are written to the server log instead.
 slack_enabled: false