minor bugfixes

h5rdmtoolbox/_cfg.py

@@ -32,7 +32,7 @@ def is_valid_logger_level(level: Union[str, int]):
     'expose_user_prop_to_attrs': True,
     'add_provenance': False,
     'ignore_set_std_attr_err': False,
-    'auto_create_h5tbx_version': True,  # automatically creates the group h5rdmtoolbox with the version attribute
+    'auto_create_h5tbx_version': False,  # automatically creates the group h5rdmtoolbox with the version attribute
     'uuid_name': 'uuid',  # attribute name used for UUIDs
     # if a standard attribute is defined and cannot be retrieved because the value is invalid, ignore it:
     'ignore_get_std_attr_err': False,

h5rdmtoolbox/_user.py

@@ -1,12 +1,11 @@
+import appdirs
+import importlib_resources
 import pathlib
 import shutil
 import time
 from itertools import count
 from typing import Tuple
 
-import appdirs
-import importlib_resources
-
 _filecounter = count()
 _dircounter = count()
 
@@ -89,16 +88,28 @@ def _get_dir(self, name: str) -> pathlib.Path:
 
         return self.user_dirs[name]
 
-    def clear_cache(self, delta_days: int):
+    def clear_cache(self, delta_days: int, utime: bool = False):
         """Clear the cache directory. The delta_days arguments will be used
-        to delete files older than delta_days days. This is only applied to files"""
+        to delete files older than delta_days days. This is only applied to files
+
+        Parameters
+        ----------
+        delta_days : int
+            The number of days to keep the files in the cache.
+        utime : bool
+            If True, the file access time will be used to determine the age of the file.
+            Otherwise, the file creation time will be used.
+        """
         if delta_days == 0:
             shutil.rmtree(self.user_dirs['cache'])
             return
         if self.user_dirs['cache'].exists():
             for f in self.user_dirs['cache'].iterdir():
                 # get the file creation time
-                fct = f.stat().st_ctime
+                if utime:
+                    fct = f.stat().st_atime
+                else:
+                    fct = f.stat().st_ctime
                 dt = _now - fct
                 if dt > delta_days * 86400:
                     f.unlink()

h5rdmtoolbox/database/hdfdb/filedb.py

@@ -2,8 +2,8 @@
 import pathlib
 from typing import Union, Generator, List
 
-from .objdb import ObjDB
 from .nonsearchable import NonInsertableDatabaseInterface
+from .objdb import ObjDB
 from .. import lazy
 from ..template import HDF5DBInterface
 
@@ -12,16 +12,14 @@ class FileDB(NonInsertableDatabaseInterface, HDF5DBInterface):
     """A database interface for an HDF5 file, where the filename is given."""
 
     def __init__(self, filename: Union[str, pathlib.Path]):
-        self.filename = pathlib.Path(filename)
+        self.filename: str = str(filename)
         self.find = self._instance_find  # allow `find` to be a static method and instance method
         self.find_one = self._instance_find_one  # allow `find_one` to be a static method and instance method
 
     @staticmethod
-    def find_one(file_or_filename, *args, **kwargs) -> lazy.LHDFObject:
+    def find_one(filename: Union[str, pathlib.Path], *args, **kwargs) -> lazy.LHDFObject:
         """Please refer to the docstring of the find_one method of the ObjDB class"""
-        if isinstance(file_or_filename, (h5py.Group, h5py.Dataset)):
-            return ObjDB(file_or_filename).find_one(*args, **kwargs)
-        with h5py.File(file_or_filename, 'r') as h5:
+        with h5py.File(str(filename), 'r') as h5:
             return ObjDB(h5).find_one(*args, **kwargs)
 
     def _instance_find(self, *args, **kwargs):
@@ -81,16 +79,15 @@ def find_one(self, *args, **kwargs) -> lazy.LHDFObject:
         contains the object, the first one is returned. If you want to find one per file,
         call find_one_per_file instead."""
         for filename in self.filenames:
-            with h5py.File(filename, 'r') as h5:
+            with h5py.File(filename, mode='r') as h5:
                 ret = ObjDB(h5).find_one(*args, **kwargs)
                 if ret:
                     return ret
-        return
 
     def find(self, *args, **kwargs) -> Generator[lazy.LHDFObject, None, None]:
-        all_results = []
+        """Call find on all the files"""
         for filename in self.filenames:
             with h5py.File(filename, 'r') as h5:
                 ret = ObjDB(h5).find(*args, **kwargs)
-                all_results.extend(ret)
-        return all_results
+                for r in ret:
+                    yield r

h5rdmtoolbox/database/hdfdb/objdb.py

@@ -158,7 +158,6 @@ def _h5find(h5obj: Union[h5py.Group, h5py.Dataset], qk, qv, recursive, objfilter
 
     """
     found_objs = []
-
     if qk in query.value_operator:
         # user wants to compare qv to the value of the object
 
@@ -301,7 +300,7 @@ def _h5find(h5obj: Union[h5py.Group, h5py.Dataset], qk, qv, recursive, objfilter
                         if query.operator[ok](objattr, ov):
                             found_objs.append(hv)
                     except Exception as e:
-                        raise Exception(f'Error while filtering for "{qk}" with "{ok}" and "{ov}"') from e
+                        raise Exception(f'Error while filtering for "{qk}" with "{ok}" and "{ov}": {e}')
     return found_objs
 
 
@@ -420,8 +419,20 @@ def __init__(self, obj: Union[h5py.Dataset, h5py.Group]):
             self.src_obj = h5py.Dataset(obj.id)
         else:
             raise TypeError(f'Unexpected type: {type(obj)}')
+        self.find = self._instance_find  # allow `find` to be a static method and instance method
+        self.find_one = self._instance_find_one  # allow `find_one` to be a static method and instance method
+
+    @staticmethod
+    def find_one(obj: Union[h5py.Dataset, h5py.Group], *args, **kwargs) -> lazy.LHDFObject:
+        """Please refer to the docstring of the find_one method of the ObjDB class"""
+        return ObjDB(obj).find_one(*args, **kwargs)
+
+    @staticmethod
+    def find(obj: Union[h5py.Dataset, h5py.Group], *args, **kwargs) -> lazy.LHDFObject:
+        """Please refer to the docstring of the find_one method of the ObjDB class"""
+        return ObjDB(obj).find(*args, **kwargs)
 
-    def find_one(self,
+    def _instance_find_one(self,
                  flt: Union[Dict, str],
                  objfilter=None,
                  recursive: bool = True,
@@ -452,7 +463,7 @@ def find_one(self,
                 ignore_attribute_error=ignore_attribute_error)
         )
 
-    def find(self,
+    def _instance_find(self,
              flt: Union[Dict, str],
              objfilter=None,
              recursive: bool = True,

h5rdmtoolbox/database/hdfdb/query.py

@@ -1,3 +1,4 @@
+"""query module"""
 import logging
 import numpy as np
 import re
@@ -59,9 +60,12 @@ def _regex(value, pattern) -> bool:
         except UnicodeDecodeError:
             warnings.warn(f'could not decode {value}', UserWarning)
             return False
+
     if isinstance(value, bytes):
         value = value.decode()
 
+    value = str(value)
+
     match = re.search(pattern, value)
     if match is None:
         return False

h5rdmtoolbox/layout/core.py

@@ -66,7 +66,7 @@ class SpecificationResult:
 
     def __init__(self, target):
         self.target = target
-        self.target_name = target.name
+        self.target_name = target if isinstance(target, str) else target.name
         self.target_type = 'Dataset' if isinstance(target, h5py.Dataset) else 'Group'
         self.validation_flag = VALIDATION_FLAGS.UNCALLED.value
         self.res = []
@@ -575,13 +575,13 @@ def validate(self, filename_or_root_group: Union[str, pathlib.Path, h5py.Group])
         """Validate the layout by passing a filename or an opened root group"""
         self.reset()
 
-        if isinstance(filename_or_root_group, (str, pathlib.Path)):
-            with h5tbx.File(filename_or_root_group, mode='r') as h5:
-                return self.validate(h5)
+        # if isinstance(filename_or_root_group, (str, pathlib.Path)):
+        #     with h5tbx.File(filename_or_root_group, mode='r') as h5:
+        #         return self.validate(h5)
 
-        if isinstance(filename_or_root_group, h5py.Group):
-            if not filename_or_root_group.name == '/':
-                raise ValueError('If passing an HDF5 group, a root group must be passed')
+        # if isinstance(filename_or_root_group, h5py.Group):
+        #     if not filename_or_root_group.name == '/':
+        #         raise ValueError('If passing an HDF5 group, a root group must be passed')
 
         # first reset all specs (n_calls = 0, _n_fails = 0, failed = None)
         for spec in self.specifications: