Log check results

ISI-MIP · Jan 4, 2024 · 29b601c · 29b601c
1 parent 8b2e47a
commit 29b601c
Showing 1 changed file with 57 additions and 55 deletions.
diff --git a/isimip_publisher/utils/validation.py b/isimip_publisher/utils/validation.py
@@ -1,8 +1,10 @@
 import json
+import logging
 from pathlib import Path
 
 from isimip_utils.checksum import get_checksum
 
+logger = logging.getLogger(__name__)
 
 def validate_datasets(schema, path, datasets):
     if not datasets:
@@ -20,73 +22,73 @@ def validate_datasets(schema, path, datasets):
 
 def check_datasets(datasets, db_datasets):
     if len(datasets) != len(db_datasets):
-        raise RuntimeError(f'Length mismatch {len(datasets)} != {len(db_datasets)}')
+        logger.error(f'Length mismatch {len(datasets)} != {len(db_datasets)}')
 
     for dataset, db_dataset in zip(datasets, db_datasets):
         for file, db_file in zip(dataset.files, db_dataset.files):
             # check the actual file
             file_path = Path(file.abspath)
-            if not file_path.is_file():
-                raise RuntimeError(f'{file_path} does not exist')
+            if file_path.is_file():
+                # compute the checksum
+                computed_checksum = get_checksum(file.abspath, file.checksum_type)
+
+                # check file checksum consitency
+                if computed_checksum != db_file.checksum:
+                    logger.error(f'Checksum mismatch {file.checksum} != {computed_checksum} for file {db_file.id}')
+
+                # check file path consitency
+                if file.path != db_file.path:
+                    logger.error(f'Path mismatch {file.path} != {db_file.path} for file {db_file.id}')
+
+                # check file uuid consitency
+                if file.uuid:
+                    if str(file.uuid) != db_file.id:
+                        logger.error(f'UUID mismatch {file.uuid} != {db_file.id} for file {db_file.id}')
+
+                # check file specifiers consitency
+                if file.specifiers != db_file.specifiers:
+                    logger.error(f'Specifier mismatch {file.specifiers} != {db_file.specifiers}'
+                                  ' for file {db_file.id}')
+            else:
+                logger.error(f'{file_path} does not exist')
 
             # check the json file
-            if not file_path.with_suffix('.json').is_file():
-                raise RuntimeError(f'{file_path} does not exist')
-
-            # compute the checksum
-            computed_checksum = get_checksum(file.abspath, file.checksum_type)
-
-            # check file checksum consitency
-            if computed_checksum != db_file.checksum:
-                raise RuntimeError(f'Checksum mismatch {file.checksum} != {computed_checksum} for file {db_file.id}')
-
-            # check file path consitency
-            if file.path != db_file.path:
-                raise RuntimeError(f'Path mismatch {file.path} != {db_file.path} for file {db_file.id}')
-
-            # check file uuid consitency
-            if file.uuid:
-                if str(file.uuid) != db_file.id:
-                    raise RuntimeError(f'UUID mismatch {file.uuid} != {db_file.id} for file {db_file.id}')
-
-            # check file specifiers consitency
-            if file.specifiers != db_file.specifiers:
-                raise RuntimeError(f'Specifier mismatch {file.specifiers} != {db_file.specifiers}'
-                                    ' for file {db_file.id}')
-
-            # open json file
-            metadata = json.loads(file_path.with_suffix('.json').read_text())
-
-            # check json checksum consitency
-            if metadata.get('checksum') != db_file.checksum:
-                raise RuntimeError('Checksum mismatch {} != {} for file {}'.format(
-                    metadata.get('checksum'), computed_checksum, db_file.id
-                ))
-
-            # check json path consitency
-            if metadata.get('path') != db_file.path:
-                raise RuntimeError('Path mismatch {} != {} for file {}'.format(
-                    metadata.get('path'), db_file.path, db_file.id
-                ))
-
-            # check json uuid consitency
-            if metadata.get('id'):
-                if metadata.get('id') != db_file.id:
-                    raise RuntimeError('UUID mismatch {} != {} for file {}'.format(
-                        metadata.get('id'), db_file.id, db_file.id
+            if file_path.with_suffix('.json').is_file():
+                # open json file
+                metadata = json.loads(file_path.with_suffix('.json').read_text())
+
+                # check json checksum consitency
+                if metadata.get('checksum') != db_file.checksum:
+                    logger.error('Checksum mismatch {} != {} for file {}'.format(
+                        metadata.get('checksum'), computed_checksum, db_file.id
                     ))
 
-            # check json specifiers consitency
-            if metadata.get('specifiers') != db_file.specifiers:
-                raise RuntimeError('Specifier mismatch {} != {} for file {}'.format(
-                    metadata.get('specifiers'), db_file.specifiers, db_file.id
-                ))
+                # check json path consitency
+                if metadata.get('path') != db_file.path:
+                    logger.error('Path mismatch {} != {} for file {}'.format(
+                        metadata.get('path'), db_file.path, db_file.id
+                    ))
+
+                # check json uuid consitency
+                if metadata.get('id'):
+                    if metadata.get('id') != db_file.id:
+                        logger.error('UUID mismatch {} != {} for file {}'.format(
+                            metadata.get('id'), db_file.id, db_file.id
+                        ))
+
+                # check json specifiers consitency
+                if metadata.get('specifiers') != db_file.specifiers:
+                    logger.error('Specifier mismatch {} != {} for file {}'.format(
+                        metadata.get('specifiers'), db_file.specifiers, db_file.id
+                    ))
+            else:
+                logger.error(f'{file_path} does not exist')
 
         # check dataset
         if dataset.path != db_dataset.path:
-            raise RuntimeError(f'Path mismatch {dataset.path} != {db_dataset.path} for dataset {db_dataset.id}')
+            logger.error(f'Path mismatch {dataset.path} != {db_dataset.path} for dataset {db_dataset.id}')
 
         # check if the specifiers match
         if dataset.specifiers != db_dataset.specifiers:
-            raise RuntimeError(f'Specifier mismatch {dataset.specifiers} != {db_dataset.specifiers}'
-                                ' for dataset {db_dataset.id}')
+            logger.error(f'Specifier mismatch {dataset.specifiers} != {db_dataset.specifiers}'
+                          ' for dataset {db_dataset.id}')