feat(OMNY): upload tomo PDF report to the samples web folder

Replaces the old, already-broken upload_last_pon.sh shell-out (and
assorted other dead/abandoned upload attempts left commented out in
flomni.py) with a direct HTTP upload: POSTs the just-written PDF,
base64-encoded, to omny-test.psi.ch/samples/upload.php with
filename="new.pdf" so the server assigns the number itself from its
own counter file -- the same counter newmeasurement.php
(TomoIDManager.register(), called via add_sample_database() just
before write_pdf_report()) already incremented and returned as
self.tomo_id. Runs in a background thread so a slow/unreachable host
never delays the calling tomo_scan(), and cross-checks the response
against the expected filename to flag a possible race with a
concurrent registration.

Added to TomoQueueMixin (OMNY_shared) rather than duplicated in both
LamNI and Flomni, following add_sample_database()'s existing pattern
of shared, setup-agnostic tomo-id/database logic.

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -2,7 +2,6 @@ import builtins
 import datetime
 import json
 import os
-import subprocess
 import time
 from pathlib import Path
 
@@ -2124,11 +2123,9 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
                 file.write(
                     f"\nAt-each-angle hook source ('{self.at_each_angle_hook}'):\n{hook_source}"
                 )
-        # upload_last_pon.sh no longer works and needs a rewrite -- disabled
-        # for now (mirrors Flomni, which already has this commented out).
-        # subprocess.run(
-        #     "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
-        # )
+        # Replaces the old upload_last_pon.sh script (broken, never rewritten --
+        # see git history) with a direct HTTP upload to the samples web folder.
+        self._upload_pdf_report_to_samples(user_target)
         # Same tolerance as write_to_scilog(): a session without scilog/logbook
         # configured (e.g. a dev/sim session) must not crash report generation
         # over the logbook upload -- the PDF itself is already written above.

csaxs_bec/bec_ipython_client/plugins/OMNY_shared/tomo_queue_mixin.py

@@ -39,6 +39,7 @@ import builtins
 import datetime
 import inspect
 import json
+import threading
 import uuid
 from typing import Callable
 
@@ -390,6 +391,82 @@ class TomoQueueMixin:
             user=user,
         )
 
+    # Only omny-test.psi.ch, not v1p0zyg2w9n2k9c1.myfritz.net (the host
+    # TomoIDManager.OMNY_URL registers measurements against, and the
+    # webpage generators mirror their own content to): only
+    # omny-test.psi.ch has the sample counter that actually matches
+    # self.tomo_id.
+    _SAMPLES_UPLOAD_HOSTS = ("https://omny-test.psi.ch",)
+
+    def _upload_pdf_report_to_samples(self, pdf_path: str) -> None:
+        """Upload a just-written PDF report to the OMNY samples web folder
+        (see _SAMPLES_UPLOAD_HOSTS). Identical for every setup that uses
+        ``self.tomo_id`` (set via add_sample_database() just before
+        write_pdf_report() calls this) -- shared here so LamNI/Flomni don't
+        each carry their own copy. Replaces the old, broken
+        upload_last_pon.sh script both used to shell out to.
+
+        POSTs to <host>/samples/upload.php with filename="new.pdf" so the
+        server assigns the number itself from its own counter file
+        (countersaver.txt) -- the same counter newmeasurement.php
+        (TomoIDManager.register()) already incremented and returned as
+        self.tomo_id. Any other filename would be saved under samples/png/
+        instead of directly in samples/, per upload.php's own branching, so
+        "new.pdf" is the only way to land the PDF at samples/<tomo_id>.pdf
+        (matching the <A HREF="%d.pdf"> link newmeasurement.php writes into
+        the samples listing).
+
+        Runs in a background daemon thread so a slow/unreachable host never
+        delays the calling tomo_scan().
+        """
+
+        def _run():
+            try:
+                import base64
+
+                import requests
+                import urllib3
+
+                urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+            except ImportError:
+                print("Could not upload PDF report: 'requests' library not installed.")
+                return
+
+            try:
+                with open(pdf_path, "rb") as f:
+                    filedata = base64.b64encode(f.read()).decode("ascii")
+            except OSError as exc:
+                print(f"Could not read PDF report for upload ({pdf_path}): {exc}")
+                return
+
+            expected_name = f"{self.tomo_id}.pdf"
+            for host in self._SAMPLES_UPLOAD_HOSTS:
+                url = f"{host}/samples/upload.php"
+                try:
+                    r = requests.post(
+                        url,
+                        data={"filename": "new.pdf", "filedata": filedata},
+                        timeout=20,
+                        verify=False,  # accept self-signed certs
+                        allow_redirects=False,  # SSRF hardening
+                    )
+                    if r.status_code != 200:
+                        print(f"PDF upload to {url} -> HTTP {r.status_code}: {r.text[:120]}")
+                        continue
+                    if expected_name not in r.text:
+                        print(
+                            f"PDF upload to {url} succeeded but the server-assigned "
+                            f"filename doesn't match tomo_id {self.tomo_id} (response: "
+                            f"{r.text[:120]!r}) -- a concurrent measurement "
+                            "registration may have raced this upload."
+                        )
+                    else:
+                        print(f"Uploaded PDF report to {url} as {expected_name}.")
+                except Exception as exc:
+                    print(f"PDF upload to {url} failed: {exc}")
+
+        threading.Thread(target=_run, name="PdfUpload", daemon=True).start()
+
     # ── command-job action registry / dispatch ──────────────────────────────
 
     def _validate_action_kwargs(self, action_name: str, kwargs: dict) -> None:

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -3,7 +3,6 @@ import datetime
 import json
 import os
 import random
-import subprocess
 import time
 from pathlib import Path
 
@@ -3817,16 +3816,9 @@ class Flomni(
                 file.write(
                     f"\nAt-each-angle hook source ('{self.at_each_angle_hook}'):\n{hook_source}"
                 )
-        # subprocess.run(
-        #     "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
-        # )
-        # status = subprocess.run(f"cp /tmp/spec-e20131-specES1.pdf {user_target}", shell=True)
-        # msg = bec.tomo_progress.tomo_progressMessage()
-        # logo_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "LamNI_logo.png")
-        # msg.add_file(logo_path).add_text("".join(content).replace("\n", "</p><p>")).add_tag(
-        #     ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "flOMNI", self.sample_name]
-        # )
-        # self.client.tomo_progress.send_tomo_progress_message("~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf").send()
+        # Replaces the old upload_last_pon.sh script (broken, never rewritten)
+        # with a direct HTTP upload to the samples web folder.
+        self._upload_pdf_report_to_samples(user_target)
         import csaxs_bec
 
         # Ensure this is a Path object, not a string