[ENH] Add function log_and_raise (#1238)

* add log_and_raise function

* use it in adni_json

clinica/iotools/converters/adni_to_bids/adni_json.py

@@ -5,17 +5,16 @@
 import pandas as pd
 
 from clinica.utils.exceptions import ClinicaXMLParserError
-from clinica.utils.stream import cprint
+from clinica.utils.stream import cprint, log_and_raise
 
 __all__ = ["create_json_metadata"]
 
 
 LOGGING_HEADER = "[ADNI JSON]"
 
 
-def _log_and_raise(message: str):
-    cprint(f"{LOGGING_HEADER} {message}", lvl="error")
-    raise ClinicaXMLParserError(f"{LOGGING_HEADER} {message}")
+def _log_and_raise_xml_parser_error(message: str):
+    log_and_raise(f"{LOGGING_HEADER} {message}", ClinicaXMLParserError)
 
 
 # Map from names of extracted metadata to their proper BIDS names.
@@ -65,7 +64,9 @@ def _read_xml_files(
 def _check_xml_tag(element_tag: str, expected_tag: str):
     """Check that the XML element tagged matches the expected tag."""
     if element_tag != expected_tag:
-        _log_and_raise(f"Bad tag: expected {expected_tag}, got {element_tag}")
+        _log_and_raise_xml_parser_error(
+            f"Bad tag: expected {expected_tag}, got {element_tag}"
+        )
 
 
 def _check_xml_nb_children(
@@ -78,13 +79,13 @@ def _check_xml_nb_children(
     nb_children = len(xml_el)
     if isinstance(expected_nb_children, int):
         if nb_children != expected_nb_children:
-            _log_and_raise(
+            _log_and_raise_xml_parser_error(
                 f"Bad number of children for <{xml_el.tag}>: "
                 f"got {nb_children} != {expected_nb_children}"
             )
     else:
         if nb_children not in expected_nb_children:
-            _log_and_raise(
+            _log_and_raise_xml_parser_error(
                 f"Bad number of children for <{xml_el.tag}>: "
                 f"got {nb_children}, not in {expected_nb_children}"
             )
@@ -112,8 +113,8 @@ def _parse_project(
     Check that the project identifier contains ADNI.
     """
     if len(root) != 1:
-        _log_and_raise(
-            "XML root should have only one child. " f"{len(root)} children found."
+        _log_and_raise_xml_parser_error(
+            "XML root should have only one child. " f"{len(root)} children found.",
         )
     project = _check_xml(root[0], "project", 4)
     _check_xml_project_identifier(project, "ADNI")
@@ -138,7 +139,7 @@ def _get_text(xml_element: xml.etree.ElementTree.Element, cast=None) -> str:
 def _check_derived_image_xml(derived: xml.etree.ElementTree.Element) -> None:
     """Perform sanity checks on derived images."""
     if len(derived) < 9:
-        _log_and_raise("Derived image does not have enough field.")
+        _log_and_raise_xml_parser_error("Derived image does not have enough field.")
     for idx, field, expected in zip(
         [2, 3, 4, 5, 6],
         ["imageType", "tissue", "hemisphere", "anatomicStructure", "registration"],
@@ -152,15 +153,17 @@ def _check_derived_image_xml(derived: xml.etree.ElementTree.Element) -> None:
         try:
             _validate_date_iso_format(image_create_date)
         except ValueError as e:
-            _log_and_raise(f"The creationDate for the derived image is not valid: {e}")
+            _log_and_raise_xml_parser_error(
+                f"The creationDate for the derived image is not valid: {e}"
+            )
 
 
 def _check_xml_field(
     xml_element: xml.etree.ElementTree.Element, field: str, expected_value: str
 ) -> None:
     """Check that the given field of the given XML element has the expected value."""
     if (found_value := _check_xml_and_get_text(xml_element, field)) != expected_value:
-        _log_and_raise(
+        _log_and_raise_xml_parser_error(
             f"The {field} for the derived image should be '{expected_value}'. "
             f"{found_value} was found instead."
         )
@@ -193,7 +196,7 @@ def _check_xml_project_identifier(
 ):
     """Check the project identifier."""
     if _check_xml_and_get_text(project[0], "projectIdentifier") != expected:
-        _log_and_raise(f"Not {expected} cohort")
+        _log_and_raise_xml_parser_error(f"Not {expected} cohort")
 
 
 def _get_original_image_metadata(original_image: xml.etree.ElementTree.Element) -> dict:
@@ -248,7 +251,9 @@ def _get_root_from_xml_path(xml_path: Path) -> xml.etree.ElementTree.Element:
         root = tree.getroot()
         return root
     except Exception as e:
-        _log_and_raise(f"Error parsing XML file {xml_path.name} :\n{e}")
+        _log_and_raise_xml_parser_error(
+            f"Error parsing XML file {xml_path.name} :\n{e}"
+        )
 
 
 def _parse_series(
@@ -294,13 +299,13 @@ def _check_image(img: xml.etree.ElementTree.Element):
         "imagingProtocol",  # for original image metadata
         "originalRelatedImage",  # for processed image
     }:
-        _log_and_raise(
+        _log_and_raise_xml_parser_error(
             f"Bad image tag <{img.tag}>. "
             "Should be either 'imagingProtocol' or 'originalRelatedImage'."
         )
     if len(img) not in {3, 4}:
-        _log_and_raise(
-            f"Image XML element has {len(img)} children. " "Expected either 3 or 4."
+        _log_and_raise_xml_parser_error(
+            f"Image XML element has {len(img)} children. " "Expected either 3 or 4.",
         )
 
 
@@ -361,7 +366,9 @@ def _check_modality(study: xml.etree.ElementTree.Element, expected_modality: str
     series = _parse_series(study)
     modality = _check_xml_and_get_text(series[1], "modality")
     if modality != expected_modality:
-        _log_and_raise(f"Unexpected modality {modality}, expected {expected_modality}.")
+        _log_and_raise_xml_parser_error(
+            f"Unexpected modality {modality}, expected {expected_modality}."
+        )
 
 
 def _parse_subject(
@@ -418,7 +425,9 @@ def _parse_xml_file(xml_path: Path) -> dict:
         **derived_image_metadata,
     }
     if "image_proc_id" not in scan_metadata and "image_orig_id" not in scan_metadata:
-        _log_and_raise(f"Scan metadata for subject {subject_id} has no image ID.")
+        _log_and_raise_xml_parser_error(
+            f"Scan metadata for subject {subject_id} has no image ID."
+        )
     return scan_metadata
 
 

clinica/utils/stream.py

@@ -1,6 +1,7 @@
 """This module handles stream and log redirection."""
 
 from enum import Enum
+from typing import Type
 
 
 class LoggingLevel(str, Enum):
@@ -38,3 +39,18 @@ def cprint(msg: str, lvl: str = "info") -> None:
         logger.critical(msg=msg)
     else:
         pass
+
+
+def log_and_raise(message: str, error_type: Type[Exception]):
+    """Log the error message using cprint and raise.
+
+    Parameters
+    ----------
+    message : str
+        The error message.
+
+    error_type : Exception
+        The error type to raise.
+    """
+    cprint(message, lvl="error")
+    raise error_type(message)