diff --git a/bin/slurm_calibrate.sh b/bin/slurm_calibrate.sh
index 5786f7ce5737ed6a3be7a2d33658a1e359d5d331..98c45daedcaf5631efc55fc3ffd2c31f7d6c9143 100755
--- a/bin/slurm_calibrate.sh
+++ b/bin/slurm_calibrate.sh
@@ -26,6 +26,9 @@ echo "hostname: $(hostname)"
export CAL_NOTEBOOK_NAME="$notebook"
+# This is created by calibrate.py in CAL_WORKING_DIR
+setup_logger="setup-logging-nb.py"
+
# make sure we use agg backend
export MPLBACKEND=AGG
@@ -40,13 +43,12 @@ then
sleep 15
fi
-echo "Running notebook"
if [ "$caltype" == "CORRECT" ]
then
- # calparrot stores and repeats calcat queries
- ${python_path} -m calparrot -- ${python_path} -m princess ${nb_path} --save
+ # calparrot stores and repeats calcat queries
+ ${python_path} -m calparrot -- ${python_path} -m princess ${nb_path} --save --run-before "$setup_logger"
else
- ${python_path} -m princess ${nb_path} --save
+ ${python_path} -m princess ${nb_path} --save --run-before "$setup_logger"
fi
# stop the cluster if requested
diff --git a/notebooks/test/test-logging.ipynb b/notebooks/test/test-logging.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..f09b1109e399582ea24e76c9a22d05a0c9873a93
--- /dev/null
+++ b/notebooks/test/test-logging.ipynb
@@ -0,0 +1,125 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "98e38fec",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "in_folder = \"./\" # input folder\n",
+ "out_folder = \"./\" # output folder"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "7fbce574",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import logging\n",
+ "import warnings\n",
+ "\n",
+ "from cal_tools.warnings import CalibrationWarning"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "1bf72c57",
+ "metadata": {},
+ "source": [
+ "## WARNINGS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c0d290a1",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "class TestCalWarning(CalibrationWarning):\n",
+ " \"\"\"Base class for custom user warnings\"\"\"\n",
+ " pass\n",
+ "\n",
+ "\n",
+ "if 1 < 2:\n",
+ " warnings.warn('This inequality is true!', TestCalWarning)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6a4d4f01",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "warnings.warn('This user warning will be ignored', UserWarning)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "9b79ea47",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# This wont be logged\n",
+ "logging.warning(\"This is a warning message using logging standard library. It wont be logged\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "2b22e2e0",
+ "metadata": {},
+ "source": [
+ "## ERRORS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0f3bfeb7",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# This wont be logged\n",
+ "logging.error(\"Logging some (ERROR) without failing the notebook. It wont be logged\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c3b87719",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from cal_tools.exceptions import CalibrationError\n",
+ "\n",
+ "raise CalibrationError('Testing Calibration Failure!')"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": ".venv",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.9"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/src/cal_tools/exceptions.py b/src/cal_tools/exceptions.py
new file mode 100644
index 0000000000000000000000000000000000000000..5dbcbca65f8d7a81a4193df6821ca041d2df53ac
--- /dev/null
+++ b/src/cal_tools/exceptions.py
@@ -0,0 +1,2 @@
+class CalibrationError(Exception):
+ pass
diff --git a/src/cal_tools/warnings.py b/src/cal_tools/warnings.py
new file mode 100644
index 0000000000000000000000000000000000000000..d54686ba0fe5fc61e33d14df1b81b4bd4bb52668
--- /dev/null
+++ b/src/cal_tools/warnings.py
@@ -0,0 +1,2 @@
+class CalibrationWarning(UserWarning):
+ pass
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index 5d2b63c6f4d00a2e717bd86cd95c37e5b56b2a0c..61f35e0a85fcd83b313d237ebbb4602d0efec48a 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -675,6 +675,12 @@ def run(argv=None):
cal_work_dir / "pycalib-run-nb.sh"
)
+ # Copy the setup logger handler
+ shutil.copy2(
+ os.path.join(PKG_DIR, "setup_logging.py"),
+ cal_work_dir / "setup-logging-nb.py"
+ )
+
if nb_details.user_venv:
print("Using specified venv:", nb_details.user_venv)
python_exe = str(nb_details.user_venv / 'bin' / 'python')
diff --git a/src/xfel_calibrate/notebooks.py b/src/xfel_calibrate/notebooks.py
index 5ac28ac12340e67410fe62750fd86e95ac8b8efd..97769638974ee8bd60545b4f70699c0cd979bbf4 100644
--- a/src/xfel_calibrate/notebooks.py
+++ b/src/xfel_calibrate/notebooks.py
@@ -360,6 +360,14 @@ notebooks = {
"cluster cores": 1
},
},
+ "TEST-LOGGING": {
+ "notebook": "notebooks/test/test-logging.ipynb",
+ "concurrency": {
+ "parameter": None,
+ "default concurrency": None,
+ "cluster cores": 1,
+ },
+ },
},
"TEST-RAISES-ERRORS": {
"TEST-BAD-KEY": {
diff --git a/src/xfel_calibrate/setup_logging.py b/src/xfel_calibrate/setup_logging.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9237517c50870e9d492672939d1799611004256
--- /dev/null
+++ b/src/xfel_calibrate/setup_logging.py
@@ -0,0 +1,94 @@
+import json
+import os
+import sys
+import warnings
+from datetime import datetime
+from typing import Any, Type
+
+import IPython
+
+from cal_tools.warnings import CalibrationWarning
+
+JOB_ID = os.getenv('SLURM_JOB_ID', 'local')
+
+
+def get_class_hierarchy(cls: Type) -> str:
+ """Get the full class hierarchy of a class."""
+ return ".".join(c.__name__ for c in cls.__mro__ if c != object)
+
+
+def get_log_info(
+ message: str,
+ log_type: Type[Exception] | Type[Warning]
+) -> dict:
+ """Create a dictionary with log information."""
+ return {
+ "timestamp": datetime.now().isoformat(),
+ "message": message,
+ "class": get_class_hierarchy(log_type),
+ }
+
+
+def log_error(
+ exc_type: Type[Exception],
+ exc_value: Exception,
+ exc_traceback: Any
+) -> None:
+ """Log error information to file."""
+ try:
+ error_info = get_log_info(str(exc_value), exc_type)
+
+ with open(f"errors_{JOB_ID}.log", "a") as log_file:
+ log_file.write(json.dumps(error_info) + "\n")
+
+ except Exception as e:
+ sys.stdout.write(f"Logging failed: {e}\n")
+
+
+original_showwarning = warnings.showwarning
+
+
+def handle_warning(
+ message: Warning, category: Type[Warning],
+ # these are needed for `warnings.showwarning`
+ filename=None, lineno=None,
+ file=None, line=None,
+) -> None:
+ """Log and display warnings."""
+ try:
+ if issubclass(category, CalibrationWarning):
+ warning_info = get_log_info(str(message), category)
+
+ with open(f"warnings_{JOB_ID}.log", "a") as log_file:
+ log_file.write(json.dumps(warning_info) + "\n")
+
+ except Exception as e:
+ sys.stderr.write(f"Warning logging failed: {e}\n")
+ finally:
+ # Ensure warning is displayed in notebook.
+ original_showwarning(message, category, filename, lineno, file, line)
+
+
+# Get IPython shell
+shell = IPython.get_ipython()
+
+# Store original handlers
+original_showtraceback = shell.showtraceback
+
+
+# Custom exception handler for IPython
+def custom_showtraceback(*args, **kwargs):
+ etype, value, tb = sys.exc_info()
+ log_error(etype, value, tb)
+ original_showtraceback(*args, **kwargs)
+ if not args and not kwargs:
+ return etype, value, tb
+
+
+# Install handlers
+shell.showtraceback = custom_showtraceback
+warnings.showwarning = handle_warning
+
+# Ignore all warnings globally, except CalibrationWarning
+warnings.filterwarnings("ignore")
+warnings.simplefilter("default", CalibrationWarning)