Write outout files to an agreed location, to be copied elsewhere by another service.

src/ibex_bluesky_core/callbacks/_file_logger.py

@@ -4,6 +4,7 @@
 import logging
 import os
 from pathlib import Path
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 
 from bluesky.callbacks import CallbackBase
 from event_model.documents.event import Event
@@ -38,7 +39,9 @@
 class HumanReadableFileCallback(CallbackBase):
     """Outputs bluesky runs to human-readable output files in the specified directory path."""
 
-    def __init__(self, fields: list[str], *, output_dir: Path | None, postfix: str = "") -> None:
+    def __init__(
+        self, fields: list[str], *, output_dir: Path | None = None, postfix: str = ""
+    ) -> None:
         """Output human-readable output files of bluesky runs.
 
         If fields are given, just output those, otherwise output all hinted signals.
@@ -67,6 +70,7 @@ def start(self, doc: RunStart) -> None:
         self.current_start_document = doc[UID]
 
         rb_num = _get_rb_num(doc)
+        rb_num_str = rb_num if rb_num == "Unknown RB" else f"RB{rb_num}"
 
         # motors is a tuple, we need to convert to a list to join the two below
         motors = list(doc.get(MOTORS, []))
@@ -75,7 +79,8 @@ def start(self, doc: RunStart) -> None:
 
         self.filename = (
             self.output_dir
-            / f"{rb_num}"
+            / rb_num_str
+            / "bluesky_scans"
             / f"{get_instrument()}{'_' + '_'.join(motors) if motors else ''}_"
             f"{formatted_time}Z{self.postfix}.txt"
         )
@@ -150,4 +155,6 @@ def stop(self, doc: RunStop) -> RunStop | None:
         """Clear descriptors."""
         logger.info("Stopping run, clearing descriptors, filename=%s", self.filename)
         self.descriptors.clear()
+        if self.filename is not None:
+            os.chmod(self.filename, S_IRUSR | S_IRGRP | S_IROTH)
         return super().stop(doc)

src/ibex_bluesky_core/callbacks/_fitting.py

@@ -6,6 +6,7 @@
 import warnings
 from itertools import zip_longest
 from pathlib import Path
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 
 import lmfit
 import numpy as np
@@ -172,8 +173,9 @@ def start(self, doc: RunStart) -> None:
         file = f"{get_instrument()}_{self.x}_{self.y}_{title_format_datetime}Z{self.postfix}.txt"
 
         rb_num = _get_rb_num(doc)
+        rb_num_str = rb_num if rb_num == "Unknown RB" else f"RB{rb_num}"
 
-        self.filename = self.output_dir / f"{rb_num}" / file
+        self.filename = self.output_dir / f"{rb_num_str}" / "bluesky_scans" / file
 
     def event(self, doc: Event) -> Event:
         """Start collecting, y, x, and yerr data.
@@ -237,6 +239,7 @@ def stop(self, doc: RunStop) -> None:
                 self.write_fields_table_uncertainty()
 
             logger.info("Fitting information successfully written to: %s", self.filename.resolve())
+        os.chmod(self.filename, S_IRUSR | S_IRGRP | S_IROTH)
 
     def write_fields_table(self) -> None:
         """Write collected run info to the fitting file."""

src/ibex_bluesky_core/callbacks/_plotting.py

@@ -4,6 +4,7 @@
 import os
 import threading
 from pathlib import Path
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 from typing import Any
 
 import matplotlib
@@ -227,9 +228,12 @@ def __init__(
         self.filename = None
 
     def start(self, doc: RunStart) -> None:
+        rb_num = _get_rb_num(doc)
+        rb_num_str = rb_num if rb_num == "Unknown RB" else f"RB{rb_num}"
         self.filename = (
             self.output_dir
-            / f"{_get_rb_num(doc)}"
+            / f"{rb_num_str}"
+            / "bluesky_scans"
             / f"{get_instrument()}_{self.x}_{self.y}_{format_time(doc)}Z{self.postfix}.png"
         )
 
@@ -245,3 +249,4 @@ def stop(self, doc: RunStop) -> None:
 
         self.filename.parent.mkdir(parents=True, exist_ok=True)
         self.ax.figure.savefig(self.filename, format="png")  # pyright: ignore [reportAttributeAccessIssue]
+        os.chmod(self.filename, S_IRUSR | S_IRGRP | S_IROTH)

src/ibex_bluesky_core/callbacks/_utils.py

@@ -33,11 +33,7 @@ def get_instrument() -> str:
 
 def get_default_output_path() -> Path:
     output_dir_env = os.environ.get(OUTPUT_DIR_ENV_VAR)
-    return (
-        Path("//isis.cclrc.ac.uk/inst$") / node() / "user" / "bluesky_scans"
-        if output_dir_env is None
-        else Path(output_dir_env)
-    )
+    return Path("C:/Data") if output_dir_env is None else Path(output_dir_env)
 
 
 def format_time(doc: Event | RunStart | RunStop) -> str:

tests/callbacks/fitting/test_fit_logging_callback.py

@@ -2,6 +2,7 @@
 import os
 from pathlib import Path
 from platform import node
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 from unittest.mock import MagicMock, mock_open, patch
 
 import pytest
@@ -30,6 +31,7 @@ def test_after_fitting_callback_writes_to_file_successfully_no_y_uncertainty(
     with (
         patch("ibex_bluesky_core.callbacks._fitting.open", m),
         patch("ibex_bluesky_core.callbacks._fitting.os.makedirs"),
+        patch("os.chmod"),
     ):
         with patch("time.time", MagicMock(return_value=time)):
             RE(
@@ -39,7 +41,10 @@ def test_after_fitting_callback_writes_to_file_successfully_no_y_uncertainty(
             )
 
     assert m.call_args_list[0].args == (
-        filepath / "0" / f"{node()}_motor_invariant_2024-10-04_13-43-43Z{postfix}.txt",
+        (
+            filepath / "RB0" / "bluesky_scans" / f"{node()}_motor_invariant_2024-10-04_13-43-43"
+            f"Z{postfix}.txt"
+        ),
         "w",
     )  # type: ignore
 
@@ -68,6 +73,7 @@ def test_fitting_callback_handles_no_rb_number_save(
     with (
         patch("ibex_bluesky_core.callbacks._fitting.open", m),
         patch("ibex_bluesky_core.callbacks._fitting.os.makedirs"),
+        patch("os.chmod"),
     ):
         with patch("time.time", MagicMock(return_value=time)):
             RE(
@@ -76,7 +82,12 @@ def test_fitting_callback_handles_no_rb_number_save(
             )
 
     assert m.call_args_list[0].args == (
-        filepath / "Unknown RB" / f"{node()}_motor_invariant_2024-10-04_13-43-43Z{postfix}.txt",
+        (
+            filepath
+            / "Unknown RB"
+            / "bluesky_scans"
+            / f"{node()}_motor_invariant_2024-10-04_13-43-43Z{postfix}.txt"
+        ),
         "w",
     )  # type: ignore
 
@@ -100,6 +111,7 @@ def test_after_fitting_callback_writes_to_file_successfully_with_y_uncertainty(
     with (
         patch("ibex_bluesky_core.callbacks._fitting.open", m),
         patch("ibex_bluesky_core.callbacks._fitting.os.makedirs"),
+        patch("os.chmod"),
     ):
         with patch("time.time", MagicMock(return_value=time)):
             RE(
@@ -109,7 +121,10 @@ def test_after_fitting_callback_writes_to_file_successfully_with_y_uncertainty(
             )
 
     assert m.call_args_list[0].args == (
-        filepath / "0" / f"{node()}_motor_invariant_2024-10-04_13-43-43Z{postfix}.txt",
+        (
+            filepath / "RB0" / "bluesky_scans" / f"{node()}_motor_invariant_2024-10-04_13-43-43"
+            f"Z{postfix}.txt"
+        ),
         "w",
     )  # type: ignore
 
@@ -203,3 +218,35 @@ def test_error_thrown_if_no_y_err_data_in_event(RE: run_engine.RunEngine):
                 }
             }
         )
+
+
+def test_file_set_readonly_after_written(
+    RE: run_engine.RunEngine,
+):
+    invariant = soft_signal_rw(float, 0.5, name="invariant")
+    mot = soft_signal_rw(float, name="motor")
+
+    filepath = Path("C:\\") / "instrument" / "var" / "logs"
+    postfix = "fit1"
+    m = mock_open()
+
+    lf = LiveFit(Linear.fit(), y="invariant", x="motor", update_every=50)
+    lfl = LiveFitLogger(lf, y="invariant", x="motor", postfix=postfix, output_dir=filepath)
+    with (
+        patch("ibex_bluesky_core.callbacks._fitting.open", m),
+        patch("ibex_bluesky_core.callbacks._fitting.os.makedirs"),
+        patch("os.chmod") as mock_chmod,
+    ):
+        with patch("time.time", MagicMock(return_value=time)):
+            RE(
+                scan([invariant], mot, -1, 1, 3),
+                [lf, lfl],  # pyright: ignore until https://github.com/bluesky/bluesky/issues/1938
+            )
+
+    fit_filepath = (
+        filepath
+        / "Unknown RB"
+        / "bluesky_scans"
+        / f"{node()}_motor_invariant_2024-10-04_13-43-43Z{postfix}.txt"
+    )
+    mock_chmod.assert_called_with(fit_filepath, S_IRUSR | S_IRGRP | S_IROTH)

tests/callbacks/test_plotting_callback.py

@@ -1,3 +1,4 @@
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 from typing import Any
 from unittest.mock import MagicMock, patch
 
@@ -82,32 +83,58 @@ def test_errorbars_created_if_yerr_is_given():
 
 
 def test_png_saved_on_run_stop():
-    ax = MagicMock(spec=Axes)
-    ax.figure = MagicMock(spec=Figure)
-    s = PlotPNGSaver(x="x", y="y", ax=ax, postfix="123", output_dir="")
-
-    s.start(
-        {
-            "uid": "0",
-            RB: 1234,  # pyright: ignore reportArgumentType
-            "time": 123456789,
-        }
-    )
-
-    s.stop(
-        {
-            "time": 234567891,
-            "uid": "2",
-            "exit_status": "success",
-            "run_start": "",
-        }
-    )
+    with patch("os.chmod"):
+        ax = MagicMock(spec=Axes)
+        ax.figure = MagicMock(spec=Figure)
+        s = PlotPNGSaver(x="x", y="y", ax=ax, postfix="123", output_dir="")
+
+        s.start(
+            {
+                "uid": "0",
+                RB: 1234,  # pyright: ignore reportArgumentType
+                "time": 123456789,
+            }
+        )
+
+        s.stop(
+            {
+                "time": 234567891,
+                "uid": "2",
+                "exit_status": "success",
+                "run_start": "",
+            }
+        )
 
     assert ax.figure.savefig.call_count == 1
     assert ax.figure.savefig.call_args.kwargs["format"] == "png"
     assert "x_y_1973-11-29_21-33-09Z123.png" in ax.figure.savefig.call_args.args[0].name
 
 
+def test_file_readonly_on_stop():
+    with patch("os.chmod") as mock_chmod:
+        ax = MagicMock(spec=Axes)
+        ax.figure = MagicMock(spec=Figure)
+        s = PlotPNGSaver(x="x", y="y", ax=ax, postfix="123", output_dir="")
+
+        s.start(
+            {
+                "uid": "0",
+                RB: 1234,  # pyright: ignore reportArgumentType
+                "time": 123456789,
+            }
+        )
+        directory = s.filename
+        s.stop(
+            {
+                "time": 234567891,
+                "uid": "2",
+                "exit_status": "success",
+                "run_start": "",
+            }
+        )
+    mock_chmod.assert_called_with(directory, S_IRUSR | S_IRGRP | S_IROTH)
+
+
 def test_errorbars_not_created_if_no_yerr():
     _, ax = plt.subplots()
     ax.errorbar = MagicMock()

tests/callbacks/test_utils.py

@@ -14,4 +14,4 @@ def test_default_output_location_with_env_var():
 @pytest.mark.skipif(os.name != "nt", reason="Windows only")
 def test_default_output_location_without_env_var():
     with patch("ibex_bluesky_core.callbacks._utils.os.environ.get", return_value=None):
-        assert str(get_default_output_path()).startswith(r"\\isis.cclrc.ac.uk")
+        assert str(get_default_output_path()) == r"C:\Data"

tests/callbacks/test_write_log_callback.py

@@ -3,6 +3,7 @@
 
 from pathlib import Path
 from platform import node
+from stat import S_IRGRP, S_IROTH, S_IRUSR
 from unittest.mock import call, mock_open, patch
 
 import pytest
@@ -32,7 +33,8 @@ def test_header_data_all_available_on_start(cb):
         cb.start(run_start)
         result = (
             save_path
-            / f"{run_start.get('rb_number', None)}"
+            / f"RB{run_start.get('rb_number', None)}"
+            / "bluesky_scans"
             / f"{node()}_block_2024-10-04_13-43-43Z.txt"
         )
 
@@ -54,11 +56,13 @@ def test_no_rb_number_folder(cb):
         patch("ibex_bluesky_core.callbacks._file_logger.os.makedirs") as mock_mkdir,
     ):
         cb.start(run_start)
-        result = save_path / "Unknown RB" / f"{node()}_block_2024-10-04_13-43-43Z.txt"
+        result = (
+            save_path / "Unknown RB" / "bluesky_scans" / f"{node()}_block_2024-10-04_13-43-43Z.txt"
+        )
         assert mock_mkdir.called
 
     mock_file.assert_called_with(result, "a", newline="\n", encoding="utf-8")
-    # time should have been renamed to start_time and converted to human readable
+    # time should have been renamed to start_time and converted to human-readable
     writelines_call_args = mock_file().writelines.call_args[0][0]
     assert "start_time: 2024-10-04_13-43-43\n" in writelines_call_args
     assert f"uid: {uid}\n" in writelines_call_args
@@ -75,7 +79,7 @@ def test_no_motors_doesnt_append_to_filename(cb):
         patch("ibex_bluesky_core.callbacks._file_logger.os.makedirs") as mock_mkdir,
     ):
         cb.start(run_start)
-        result = save_path / "Unknown RB" / f"{node()}_2024-10-04_13-43-43Z.txt"
+        result = save_path / "Unknown RB" / "bluesky_scans" / f"{node()}_2024-10-04_13-43-43Z.txt"
         assert mock_mkdir.called
 
     mock_file.assert_called_with(result, "a", newline="\n", encoding="utf-8")
@@ -202,7 +206,37 @@ def test_event_called_before_filename_specified_does_nothing():
 
 def test_stop_clears_descriptors(cb):
     cb.descriptors["test"] = EventDescriptor(uid="test", run_start="", time=0.1, data_keys={})
-
-    cb.stop(RunStop(uid="test", run_start="", time=0.1, exit_status="success"))
+    with patch("os.chmod"):
+        cb.stop(RunStop(uid="test", run_start="", time=0.1, exit_status="success"))
 
     assert not cb.descriptors
+
+
+def test_file_set_readonly_when_finished(cb):
+    time = 1728049423.5860472
+    start_uid = "test123start"
+    stop_uid = "test123stop"
+    scan_id = 1234
+    run_start = RunStart(
+        time=time,
+        uid=start_uid,
+        scan_id=scan_id,
+        rb_number="0",
+        detectors=["dae"],
+        motors=("block",),
+    )
+    run_stop = RunStop(time=time, run_start=start_uid, uid=stop_uid, exit_status="success")
+    with (
+        patch("ibex_bluesky_core.callbacks._file_logger.open", mock_open()),
+        patch("ibex_bluesky_core.callbacks._file_logger.os.makedirs"),
+        patch("ibex_bluesky_core.callbacks._file_logger.os.chmod") as mock_chmod,
+    ):
+        cb.start(run_start)
+        result = (
+            save_path
+            / f"RB{run_start.get('rb_number', None)}"
+            / "bluesky_scans"
+            / f"{node()}_block_2024-10-04_13-43-43Z.txt"
+        )
+        cb.stop(run_stop)
+    mock_chmod.assert_called_with(result, S_IRUSR | S_IRGRP | S_IROTH)