FileStore: cleanups and fixes

src/maggma/stores/file_store.py

@@ -5,7 +5,6 @@
 """
 
 import hashlib
-import fnmatch
 from pathlib import Path
 from datetime import datetime, timezone
 from typing import Dict, List, Optional, Union
@@ -36,10 +35,9 @@ class File(BaseModel):
 
     def __init__(self, *args, **kwargs):
         """
-        Overriding __init__ allows class methods
-        to function like a default_factory argument to the last_updated and hash
-        fields. Class methods cannot be used as default_factory methods because
-        they have not been defined on init.
+        Overriding __init__ allows class methods to function like a default_factory
+        argument to various fields. Class methods cannot be used as default_factory
+        methods because they have not been defined on init.
 
         See https://stackoverflow.com/questions/63051253/using-class-or-static-method-as-default-factory-in-dataclasses, except
         post_init is not supported in BaseModel at this time
@@ -94,30 +92,15 @@ def from_file(cls, path):
 
 class FileStore(JSONStore):
     """
-    A Store for files on disk. Provides a common access method consistent with other stores.
-
-    Each Item is a subdirectory of the Path used to instantiate the Store
-    that contains one or more files. For example,
-
-    <path passed to FileStore.__init__()>
-        calculation1/
-            input.in
-            output.out
-            logfile.log
-        calculation2/
-            input.in
-            output.out
-            logfile.log
-        calculation3/
-            input.in
-            output.out
-            logfile.log
-
-    The name of the subdirectory serves as the identifier for
-    each item, and each item contains a list of File objects which each
-    corresponds to a single file contained in the subdirectory. So the example
-    data above would result in 3 unique items with keys 'calculation1',
-    'calculation2', and 'calculation3'.
+    A Store for files on disk. Provides a common access method consistent with
+    other stores. Each Item in the Store represents one file. Files can be organized
+    into any type of directory structure.
+
+    A hash of the full path to each file is used to define a file_id that uniquely
+    identifies each item.
+
+    Any metadata added to the items is written to a .json file in the root directory
+    of the FileStore.
     """
 
     def __init__(
@@ -132,21 +115,21 @@ def __init__(
         """
         Initializes a FileStore
         Args:
-        path: parent directory containing all files and subdirectories to process
-        track_files: List of files or fnmatch patterns to be    tracked by the FileStore.
+            path: parent directory containing all files and subdirectories to process
+            track_files: List of glob patterns defining the files to be tracked by the FileStore.
                 Only files that match the pattern provided will be included in the
-                Directory for each directory or monitored for changes. If None
-                (default), all files are included.
-        max_depth: The maximum depth to look into subdirectories. 0 = no recursion,
+                Store or monitored for changes. If None (default), all files are included.
+            max_depth: The maximum depth to look into subdirectories. 0 = no recursion,
                 1 = include files 1 directory below the FileStore, etc.
                 None (default) will scan all files below
                 the FileStore root directory, regardless of depth.
-        read_only: If True (default), the .update() and .remove_docs
-                () methods are disabled, preventing any changes to the files on
+            read_only: If True (default), the .update() and .remove_docs()
+                methods are disabled, preventing any changes to the files on
                 disk. In addition, metadata cannot be written to disk.
-        json_name: Name of the .json file to which metadata is saved. If read_only
+            json_name: Name of the .json file to which metadata is saved. If read_only
                 is False, this file will be created in the root directory of the
                 FileStore.
+            kwargs: kwargs passed to JSONStore.__init__()
         """
 
         self.path = Path(path) if isinstance(path, str) else path
@@ -164,7 +147,7 @@ def __init__(
             file_writable=(not self.read_only),
             collection_name=self.collection_name,
             key=self.key,
-            **kwargs,
+            **self.kwargs,
         )
 
     @property
@@ -189,8 +172,7 @@ def read(self) -> List[File]:
                     if f.name == self.json_name:
                         continue
                     # filter based on depth
-                    depth = len(f.relative_to(self.path).parts)-1
-                    print(depth)
+                    depth = len(f.relative_to(self.path).parts) - 1
                     if self.max_depth is not None and depth <= self.max_depth:
                         file_list.append(File.from_file(f))
 
@@ -225,12 +207,6 @@ def update(self, docs: Union[List[Dict], Dict], key: Union[List, str, None] = No
                 "This Store is read-only. To enable file I/O, re-initialize the store with read_only=False."
             )
 
-        # warnings.warn(
-        #     "FileStore does not yet support file I/O. Therefore, adding a document "
-        #     "to the store only affects the underlying MemoryStore and not any "
-        #     "files on disk.",
-        #     UserWarning,
-        # )
         super().update(docs, key)
 
     def remove_docs(self, criteria: Dict):

src/maggma/stores/mongolike.py

@@ -895,7 +895,8 @@ def _find_free_port(address="0.0.0.0"):
     return s.getsockname()[1]  # Return the port number assigned.
 
 
-# Included for now to make it possible to serialize datetime objects. Probably maggma already has a solution to this somewhere.
+# Included for now to make it possible to serialize datetime objects. Probably
+# maggma already has a solution to this somewhere.
 def json_serial(obj):
     """JSON serializer for objects not serializable by default json code"""