Establish consistent path names

.vscode/settings.json

@@ -6,12 +6,12 @@
     "python.analysis.typeCheckingMode": "off",
     "workbench.colorCustomizations": {
         "commandCenter.border": "#e7e7e799",
-        "panel.border": "#d56eb0",
-        "sash.hoverBorder": "#d56eb0",
-        "titleBar.activeBackground": "#ca469a",
+        "panel.border": "#ee2590",
+        "sash.hoverBorder": "#ee2590",
+        "titleBar.activeBackground": "#d01076",
         "titleBar.activeForeground": "#e7e7e7",
-        "titleBar.inactiveBackground": "#ca469a99",
+        "titleBar.inactiveBackground": "#d0107699",
         "titleBar.inactiveForeground": "#e7e7e799"
     },
-    "peacock.color": "#ca469a"
+    "peacock.color": "#d01076"
 }

README.md

@@ -57,7 +57,7 @@ pip install aind_session
 datetime.datetime(2023, 12, 13, 13, 43, 40)
 >>> session.raw_data_asset.id
 '16d46411-540a-4122-b47f-8cb2a15d593a'
->>> session.raw_data_folder.as_posix()
+>>> session.raw_data_dir.as_posix()
 's3://aind-ephys-data/ecephys_676909_2023-12-13_13-43-40'
 
 # Additional functionality in namespace extensions:

src/aind_session/extensions/ecephys.py

@@ -48,19 +48,19 @@ def sorted_data_asset(self) -> codeocean.data_asset.DataAsset:
         return asset
 
     @npc_io.cached_property
-    def sorted_data_folder(self) -> upath.UPath:
+    def sorted_data_dir(self) -> upath.UPath:
         """Path to the sorted data associated with the session, likely in an S3
         bucket.
 
         - uses latest sorted data asset to get path (existence is checked)
-        - if no sorted data asset is found, checks for a data folder in S3
+        - if no sorted data asset is found, checks for a data dir in S3
         - raises `FileNotFoundError` if no sorted data assets are available to link
           to the session
 
         Examples:
             >>> from aind_session import Session
             >>> session = Session('ecephys_676909_2023-12-13_13-43-40')
-            >>> session.ecephys.sorted_data_folder.as_posix()
+            >>> session.ecephys.sorted_data_dir.as_posix()
             's3://codeocean-s3datasetsbucket-1u41qdg42ur9/a2a54575-b5ca-4cf0-acd0-2933e18bcb2d'
         """
         try:
@@ -73,15 +73,15 @@ def sorted_data_folder(self) -> upath.UPath:
             logger.debug(
                 f"Using asset {self.sorted_data_asset.id} to find sorted data path for {self._session.id}"
             )
-            sorted_data_folder = (
-                aind_session.utils.codeocean_utils.get_data_asset_source_folder(
+            sorted_data_dir = (
+                aind_session.utils.codeocean_utils.get_data_asset_source_dir(
                     self.sorted_data_asset
                 )
             )
             logger.debug(
-                f"Sorted data path found for {self._session.id}: {sorted_data_folder}"
+                f"Sorted data path found for {self._session.id}: {sorted_data_dir}"
             )
-            return sorted_data_folder
+            return sorted_data_dir
 
     @staticmethod
     def is_sorted_data_asset(asset_id: str | codeocean.data_asset.DataAsset) -> bool:

src/aind_session/extensions/metadata.py

@@ -36,43 +36,43 @@ def __getattr__(self, name: str) -> dict[str, Any]:
             >>> content = getattr(session.metadata, 'metadata.nd')
         """
         try:
-            _ = self.json_paths
+            _ = self.json_files
         except FileNotFoundError:
             raise AttributeError(
-                f"No raw data folder found for {self._session.id}"
+                f"No raw data dir found for {self._session.id}"
             ) from None
         try:
-            path = next(p for p in self.json_paths if p.stem == str(name))
+            path = next(p for p in self.json_files if p.stem == str(name))
         except StopIteration:
             raise AttributeError(
-                f"No {name}.json found in cached view of {self.json_folder.as_posix()}. Available files: {[p.name for p in self.json_paths]}"
+                f"No {name}.json found in cached view of {self.json_dir.as_posix()}. Available files: {[p.name for p in self.json_files]}"
             ) from None
         else:
             logger.debug(f"Using contents of metadata json at {path.as_posix()}")
         return json.loads(path.read_text())
 
     @property
-    def json_folder(self) -> upath.UPath:
-        """Parent folder containing metadata json files"""
-        path = self._session.raw_data_folder  # may raise FileNotFoundError
+    def json_dir(self) -> upath.UPath:
+        """Parent dir containing metadata json files"""
+        path = self._session.raw_data_dir  # may raise FileNotFoundError
         logger.debug(
-            f"Using {path.as_posix()} as parent folder for metadata json files"
+            f"Using {path.as_posix()} as parent dir for metadata json files"
         )
         return path
 
     @npc_io.cached_property
-    def json_paths(self) -> tuple[upath.UPath, ...]:
+    def json_files(self) -> tuple[upath.UPath, ...]:
         """All available metadata jsons in the raw data folder.
 
         Examples:
             >>> from aind_session import Session
             >>> session = Session('ecephys_676909_2023-12-13_13-43-40')
-            >>> [path.name for path in session.metadata.json_paths]
+            >>> [path.name for path in session.metadata.json_files]
             ['data_description.json', 'metadata.nd.json', 'procedures.json', 'processing.json', 'rig.json', 'session.json', 'subject.json']
         """
         return tuple(
             sorted(
-                (path for path in self.json_folder.iterdir() if path.suffix == ".json"),
+                (path for path in self.json_dir.iterdir() if path.suffix == ".json"),
                 key=lambda p: p.name,
             )
         )

src/aind_session/session.py

@@ -32,23 +32,23 @@ class Session:
         datetime.datetime(2023, 12, 13, 13, 43, 40)
         >>> session.raw_data_asset.id
         '16d46411-540a-4122-b47f-8cb2a15d593a'
-        >>> session.raw_data_folder.as_posix()
+        >>> session.raw_data_dir.as_posix()
         's3://aind-ephys-data/ecephys_676909_2023-12-13_13-43-40'
 
         # Should be able to handle all platforms:
         >>> session = Session('multiplane-ophys_741863_2024-08-13_09-26-41')
-        >>> session.raw_data_folder.as_posix()
+        >>> session.raw_data_dir.as_posix()
         's3://aind-private-data-prod-o5171v/multiplane-ophys_741863_2024-08-13_09-26-41'
 
         >>> session = Session('behavior_717121_2024-06-16_11-39-34')
-        >>> session.raw_data_folder.as_posix()
+        >>> session.raw_data_dir.as_posix()
         's3://aind-private-data-prod-o5171v/behavior_717121_2024-06-16_11-39-34'
 
         >>> session = Session('SmartSPIM_698260_2024-07-20_21-47-21')
-        >>> session.raw_data_folder.as_posix()
+        >>> session.raw_data_dir.as_posix()
         Traceback (most recent call last):
         ...
-        FileNotFoundError: No raw data asset in CodeOcean and no folder in known data buckets on S3 for SmartSPIM_698260_2024-07-20_21-47-21
+        FileNotFoundError: No raw data asset in CodeOcean and no dir in known data buckets on S3 for SmartSPIM_698260_2024-07-20_21-47-21
 
         # Additional functionality for modalities added by extensions:
         >>> session = Session('ecephys_676909_2023-12-13_13-43-40')
@@ -109,36 +109,36 @@ def raw_data_asset(self) -> codeocean.data_asset.DataAsset:
         return asset
 
     @npc_io.cached_property
-    def raw_data_folder(self) -> upath.UPath:
+    def raw_data_dir(self) -> upath.UPath:
         """Path to the raw data associated with the session, likely in an S3
         bucket.
 
         - uses latest raw data asset to get path (existence is checked)
-        - if no raw data asset is found, checks for a data folder in S3
+        - if no raw data asset is found, checks for a data dir in S3
         - raises `FileNotFoundError` if no raw data assets are available to link
           to the session
         """
         try:
             _ = self.raw_data_asset
         except LookupError:
             with contextlib.suppress(FileNotFoundError):
-                path = aind_session.utils.get_source_folder_by_name(self.id)
+                path = aind_session.utils.get_source_dir_by_name(self.id)
                 logger.debug(
-                    f"No raw data asset uploaded for {self.id}, but data folder found: {path}"
+                    f"No raw data asset uploaded for {self.id}, but data dir found: {path}"
                 )
                 return path
             raise FileNotFoundError(
-                f"No raw data asset in CodeOcean and no folder in known data buckets on S3 for {self.id}"
+                f"No raw data asset in CodeOcean and no dir in known data buckets on S3 for {self.id}"
             ) from None
         else:
             logger.debug(
                 f"Using asset {self.raw_data_asset.id} to find raw data path for {self.id}"
             )
-            raw_data_folder = aind_session.utils.get_data_asset_source_folder(
+            raw_data_dir = aind_session.utils.get_data_asset_source_dir(
                 self.raw_data_asset
             )
-            logger.debug(f"Raw data folder found for {self.id}: {raw_data_folder}")
-            return raw_data_folder
+            logger.debug(f"Raw data dir found for {self.id}: {raw_data_dir}")
+            return raw_data_dir
 
 
 if __name__ == "__main__":

src/aind_session/utils/codeocean_utils.py

@@ -127,34 +127,34 @@ def is_raw_data_asset(asset: str | uuid.UUID | codeocean.data_asset.DataAsset) -
         return False
 
 
-def get_data_asset_source_folder(
+def get_data_asset_source_dir(
     asset: str | uuid.UUID | codeocean.data_asset.DataAsset,
 ) -> upath.UPath:
-    """Get the source folder for a data asset.
+    """Get the source dir for a data asset.
 
     - the path is constructed from the asset's `source_bucket` metadata
     - otherwise, the path is constructed from the asset's ID and known S3
       buckets, and existence is checked
     - otherwse, the path is constructed from the asset's name and known S3
       buckets, and existence is checked
 
-    - raises `FileNotFoundError` if a folder is not found
+    - raises `FileNotFoundError` if a dir is not found
 
     Examples:
-        >>> get_data_asset_source_folder('83636983-f80d-42d6-a075-09b60c6abd5e').as_posix()
+        >>> get_data_asset_source_dir('83636983-f80d-42d6-a075-09b60c6abd5e').as_posix()
         's3://aind-ephys-data/ecephys_668759_2023-07-11_13-07-32'
     """
 
-    def get_folder_from_known_s3_locations(
+    def get_dir_from_known_s3_locations(
         asset: codeocean.data_asset.DataAsset,
     ) -> upath.UPath:
         for key in (asset.id, asset.name):
             with contextlib.suppress(FileNotFoundError):
-                return aind_session.utils.get_source_folder_by_name(
+                return aind_session.utils.get_source_dir_by_name(
                     key, ttl_hash=aind_session.utils.get_ttl_hash(10 * 60)
                 )
         raise FileNotFoundError(
-            f"No source folder found for {asset.id=} or {asset.name=} in known S3 buckets"
+            f"No source dir found for {asset.id=} or {asset.name=} in known S3 buckets"
         )
 
     asset = get_data_asset(asset)
@@ -182,7 +182,7 @@ def get_folder_from_known_s3_locations(
         logger.debug(
             f"No source_bucket metadata available for {asset.id}, {asset.name}"
         )
-    return get_folder_from_known_s3_locations(asset)
+    return get_dir_from_known_s3_locations(asset)
 
 
 @functools.cache

src/aind_session/utils/s3_utils.py

@@ -16,13 +16,13 @@
 
 
 @functools.cache
-def get_source_folder_by_name(name: str, ttl_hash: int | None = None) -> upath.UPath:
-    """Checks known S3 buckets for a folder with the given name.
+def get_source_dir_by_name(name: str, ttl_hash: int | None = None) -> upath.UPath:
+    """Checks known S3 buckets for a dir with the given name.
 
-    - raises `FileNotFoundError` if the folder is not found
+    - raises `FileNotFoundError` if the dir is not found
 
     Examples:
-        >>> get_source_folder_by_name('ecephys_676909_2023-12-13_13-43-40').as_posix()
+        >>> get_source_dir_by_name('ecephys_676909_2023-12-13_13-43-40').as_posix()
         's3://aind-ephys-data/ecephys_676909_2023-12-13_13-43-40'
     """
     del ttl_hash  # only used for functools.cache
@@ -32,7 +32,7 @@ def get_source_folder_by_name(name: str, ttl_hash: int | None = None) -> upath.U
         if path.exists():
             return path
     raise FileNotFoundError(
-        f"No folder named {name!r} found in known data buckets on S3"
+        f"No dir named {name!r} found in known data buckets on S3"
     )