np_codeocean 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

np_codeocean/metadata/core.py

@@ -1,331 +1,333 @@
-"""Convenience functions for:
-- Adding neuropixels rig to dynamic routing session directory.
-- Updating neuropixels rig from dynamic routing session directory.
-"""
-
-import datetime
-import logging
-import pathlib
-import typing
-
-from aind_data_schema.core import rig, session
-
-from np_codeocean.metadata import common, np, rigs, storage, update, utils
-from np_codeocean.metadata.model_templates import behavior_box, neuropixels_rig
-
-logger = logging.getLogger(__name__)
-
-
-SESSION_MODEL_GLOB_PATTERN = "*session.json"
-
-
-def scrape_session_model_path(session_directory: pathlib.Path) -> pathlib.Path:
-    """Scrapes aind-metadata session json from dynamic routing session
-    directory.
-    """
-    matches = list(session_directory.glob(SESSION_MODEL_GLOB_PATTERN))
-    logger.debug("Scraped session model paths: %s" % matches)
-    return matches[0]
-
-
-def update_session_from_rig(
-    session_source: pathlib.Path,
-    rig_source: pathlib.Path,
-    output_path: pathlib.Path,
-) -> pathlib.Path:
-    """Convenience function that updates the `rig_id` of a session model at
-     `session_source`. Uses the `rig_id` of `rig_source`.
-
-    Notes
-    -----
-    - Overwrites the session model at `output_path`.
-    """
-    session_model = session.Session.model_validate_json(session_source.read_text())
-    rig_model = rig.Rig.model_validate_json(rig_source.read_text().replace('NP.2','NP2'))
-    session_model.rig_id = rig_model.rig_id
-    return utils.save_aind_model(session_model, output_path)
-
-
-def copy_or_init_rig(
-    storage_directory: pathlib.Path,
-    extracted_session_datetime: datetime.datetime,
-    extracted_rig_name: str,
-    output_path: pathlib.Path,
-) -> pathlib.Path:
-    try:
-        rig_model_path = storage.get_item(
-            storage_directory, extracted_session_datetime, extracted_rig_name
-        )
-        # validate that existing model is of the correct current
-        #  aind-data-schema metadata format
-        assert rig_model_path is not None
-        rig.Rig.model_validate_json(rig_model_path.read_text())
-
-        return rigs.copy_rig(
-            extracted_rig_name,
-            output_path,
-            extracted_session_datetime,
-            storage_directory,
-        )
-    except Exception:
-        logger.error("Failed to copy rig.", exc_info=True)
-        rig_model = neuropixels_rig.init(
-            extracted_rig_name,  # type: ignore
-            modification_date=datetime.date.today(),
-        )
-        rig_model.write_standard_file(output_path.parent)
-        return output_path
-
-
-def add_np_rig_to_session_dir(
-    session_dir: pathlib.Path,
-    session_datetime: datetime.datetime,
-    rig_model_dir: typing.Optional[pathlib.Path] = None,
-) -> None:
-    """Direct support for the dynamic routing task. Adds an `aind-data-schema`
-     `rig.json` to a dynamic routing session directory. The `aind-data-schema`
-     `session.json` in `session_dir` will be updated with the `rig_id` of the
-      added `rig.json`.
-
-    Notes
-    -----
-    - An aind metadata session json must exist and be ending with filename
-    session.json (pattern: `*session.json`) in `session_dir`.
-    - If `rig_model_dir` is not provided, will attempt to get default from
-     np-config. You will need to be onprem for `np-config` to work.
-    """
-    scraped_session_model_path = scrape_session_model_path(session_dir)
-    logger.debug("Scraped session model path: %s" % scraped_session_model_path)
-    scraped_session = session.Session.model_validate_json(
-        scraped_session_model_path.read_text()
-    )
-    scraped_rig_id = scraped_session.rig_id
-    logger.info("Scraped rig id: %s" % scraped_rig_id)
-    _, rig_name, _ = scraped_rig_id.split("_")
-    logger.info("Parsed rig name: %s" % rig_name)
-    rig_model_path = session_dir / "rig.json"
-
-    if not rig_model_dir:
-        logger.debug("Getting storage directory from np-config.")
-        rig_model_dir = np.get_rig_storage_directory()
-
-    current_model_path = copy_or_init_rig(
-        rig_model_dir,
-        session_datetime,
-        rig_name,
-        rig_model_path,
-    )
-
-    logger.info("Current model path: %s" % current_model_path)
-    settings_sources = list(session_dir.glob("**/settings.xml"))
-    logger.info("Scraped open ephys settings: %s" % settings_sources)
-
-    updated_model_path = update.update_rig(
-        rig_model_path,
-        modification_date=session_datetime.date(),
-        open_ephys_settings_sources=settings_sources,
-        output_path=rig_model_path,
-    )
-
-    update_session_from_rig(
-        scraped_session_model_path,
-        updated_model_path,
-        scraped_session_model_path,
-    )
-
-    storage.update_item(
-        rig_model_dir,
-        updated_model_path,
-        session_datetime,
-        rig_name,
-    )
-
-
-def update_neuropixels_rig_from_dynamic_routing_session_dir(
-    rig_source: pathlib.Path,
-    session_dir: pathlib.Path,
-    output_path: pathlib.Path = pathlib.Path("rig.json"),
-    modification_date: typing.Optional[datetime.date] = None,
-    mvr_mapping: dict[str, str] = common.DEFAULT_MVR_MAPPING,
-) -> pathlib.Path:
-    """Scrapes dynamic routing session directory for various rig
-    configuration/settings and updates `rig_source`.
-
-    Notes
-    -----
-    - Will likely be depreciated in the future.
-    """
-    try:
-        task_source = next(session_dir.glob("**/Dynamic*.hdf5"))
-        logger.debug("Scraped task source: %s" % task_source)
-    except StopIteration:
-        task_source = None
-
-    # sync
-    try:
-        sync_source = next(session_dir.glob("**/sync.yml"))
-        logger.debug("Scraped sync source: %s" % sync_source)
-    except StopIteration:
-        sync_source = None
-
-    # mvr
-    try:
-        mvr_source = next(session_dir.glob("**/mvr.ini"))
-        logger.debug("Scraped mvr source: %s" % mvr_source)
-    except StopIteration:
-        mvr_source = None
-
-    # open ephys
-    settings_sources = list(session_dir.glob("**/settings.xml"))
-    logger.debug("Scraped open ephys settings: %s" % settings_sources)
-
-    return update.update_rig(
-        rig_source,
-        task_source=task_source,
-        sync_source=sync_source,
-        mvr_source=mvr_source,
-        mvr_mapping=mvr_mapping,
-        open_ephys_settings_sources=settings_sources,
-        output_path=output_path,
-        modification_date=modification_date,
-        reward_calibration_date=modification_date,
-        sound_calibration_date=modification_date,
-    )
-
-
-def extract_rig_name(task_source: pathlib.Path) -> str | None:
-    """Extracts rig_name from task_source.
-
-    >>> extract_rig_name(
-    ...     pathlib.Path("examples") / "neuropixels-rig-task.hdf5"
-    ... )
-    'NP2'
-    >>> extract_rig_name(
-    ...     pathlib.Path("examples") / "behavior-box-task-0.hdf5"
-    ... )
-    'D6'
-    >>> extract_rig_name(
-    ...     pathlib.Path("examples") / "behavior-box-task-1.hdf5"
-    ... )
-    'B2'
-
-    Notes
-    -----
-    - If extracted `computerName` is not found or is not bytes, will use
-     `rigName`.
-    """
-    computer_name = utils.extract_hdf5_value(
-        utils.load_hdf5(task_source),
-        [
-            "computerName",
-        ],
-    )
-    logger.debug("Extracted computerName: %s" % computer_name)
-    rig_name = utils.extract_hdf5_value(
-        utils.load_hdf5(task_source),
-        [
-            "rigName",
-        ],
-    )
-    logger.debug("Extracted rigName: %s" % rig_name)
-
-    if isinstance(computer_name, bytes):
-        decoded = computer_name.decode("utf8")
-        if decoded.lower().startswith("beh"):
-            postfixed = decoded.split(".")[1]
-            split = postfixed.split("-")
-            return split[0] + split[1][-1]
-        else:
-            return decoded
-
-    if isinstance(rig_name, bytes):
-        return rig_name.decode("utf-8")
-
-    return None
-
-
-def extract_session_datetime(
-    task_source: pathlib.Path,
-) -> datetime.datetime:
-    """
-    >>> extract_session_datetime(
-    ...     pathlib.Path("examples") / "behavior-box-task-0.hdf5"
-    ... )
-    datetime.datetime(2024, 5, 1, 0, 0)
-    >>> extract_session_datetime(
-    ...     pathlib.Path("examples") / "behavior-box-task-1.hdf5"
-    ... )
-    datetime.datetime(2023, 9, 8, 0, 0)
-    """
-    start_time_str = utils.extract_hdf5_value(
-        utils.load_hdf5(task_source),
-        [
-            "startTime",
-        ],
-    )
-    if not start_time_str:
-        raise Exception("Could not extract start time from task source.")
-
-    logger.debug("Extracted start time bytes: %s" % start_time_str)
-    date_str, _ = start_time_str.decode("utf8").split("_")
-    logger.debug("Date string: %s" % date_str)
-    return datetime.datetime.strptime(date_str, "%Y%m%d")
-
-
-def copy_task_rig(
-    task_source: pathlib.Path,
-    output_path: pathlib.Path,
-    storage_directory: typing.Optional[pathlib.Path] = None,
-) -> pathlib.Path | None:
-    """Extracts rig_name from task_source and copies the associated `rig.json`
-     to output_path.
-
-    >>> storage_directory = pathlib.Path("examples") / "rig-directory"
-    >>> task_source = pathlib.Path("examples") / "neuropixels-rig-task.hdf5"
-    >>> copy_task_rig(
-    ...     task_source,
-    ...     pathlib.Path("rig.json"),
-    ...     storage_directory,
-    ... )
-    PosixPath('rig.json')
-
-    >>> task_source = pathlib.Path("examples") / "behavior-box-task-0.hdf5"
-    >>> copy_task_rig(
-    ...     task_source,
-    ...     pathlib.Path("rig.json"),
-    ...     storage_directory,
-    ... )
-    PosixPath('rig.json')
-
-    Notes
-    -----
-    - If `storage_directory` is not provided, will attempt to get default from
-     np-config.
-    """
-    # storage_directory optional is legacy behavior
-    # TODO: remove the optional so we can remove this safeguard
-    if not storage_directory:
-        raise Exception("Storage directory must be provided.")
-
-    extracted_rig_name = extract_rig_name(task_source)
-    logger.debug("Extracted rig name: %s" % extracted_rig_name)
-    if not extracted_rig_name:
-        raise Exception("Could not extract rig name from task source: %s" % task_source)
-
-    if rigs.is_behavior_box(extracted_rig_name):
-        rig_model = behavior_box.init(
-            extracted_rig_name,
-            modification_date=datetime.date.today(),
-        )
-        rig_model.write_standard_file(output_path.parent)
-        return output_path
-
-    extracted_session_datetime = extract_session_datetime(task_source)
-
-    # if grabbing latest rig model fails, return a new one
-    return copy_or_init_rig(
-        storage_directory,
-        extracted_session_datetime,
-        extracted_rig_name,
-        output_path,
-    )
+"""Convenience functions for:
+- Adding neuropixels rig to dynamic routing session directory.
+- Updating neuropixels rig from dynamic routing session directory.
+"""
+
+import datetime
+import logging
+import pathlib
+import typing
+
+from aind_data_schema.core import rig, session
+
+from np_codeocean.metadata import common, np, rigs, storage, update, utils
+from np_codeocean.metadata.model_templates import behavior_box, neuropixels_rig
+
+logger = logging.getLogger(__name__)
+
+
+SESSION_MODEL_GLOB_PATTERN = "*session.json"
+
+
+def scrape_session_model_path(session_directory: pathlib.Path) -> pathlib.Path:
+    """Scrapes aind-metadata session json from dynamic routing session
+    directory.
+    """
+    matches = list(session_directory.glob(SESSION_MODEL_GLOB_PATTERN))
+    logger.debug("Scraped session model paths: %s" % matches)
+    return matches[0]
+
+
+def update_session_from_rig(
+    session_source: pathlib.Path,
+    rig_source: pathlib.Path,
+    output_path: pathlib.Path,
+) -> pathlib.Path:
+    """Convenience function that updates the `rig_id` of a session model at
+     `session_source`. Uses the `rig_id` of `rig_source`.
+
+    Notes
+    -----
+    - Overwrites the session model at `output_path`.
+    """
+    session_model = session.Session.model_validate_json(session_source.read_text())
+    rig_model = rig.Rig.model_validate_json(
+        rig_source.read_text().replace("NP.2", "NP2")
+    )
+    session_model.rig_id = rig_model.rig_id
+    return utils.save_aind_model(session_model, output_path)
+
+
+def copy_or_init_rig(
+    storage_directory: pathlib.Path,
+    extracted_session_datetime: datetime.datetime,
+    extracted_rig_name: str,
+    output_path: pathlib.Path,
+) -> pathlib.Path:
+    try:
+        rig_model_path = storage.get_item(
+            storage_directory, extracted_session_datetime, extracted_rig_name
+        )
+        # validate that existing model is of the correct current
+        #  aind-data-schema metadata format
+        assert rig_model_path is not None
+        rig.Rig.model_validate_json(rig_model_path.read_text())
+
+        return rigs.copy_rig(
+            extracted_rig_name,
+            output_path,
+            extracted_session_datetime,
+            storage_directory,
+        )
+    except Exception:
+        logger.error("Failed to copy rig.", exc_info=True)
+        rig_model = neuropixels_rig.init(
+            extracted_rig_name,  # type: ignore
+            modification_date=datetime.date.today(),
+        )
+        rig_model.write_standard_file(output_path.parent)
+        return output_path
+
+
+def add_np_rig_to_session_dir(
+    session_dir: pathlib.Path,
+    session_datetime: datetime.datetime,
+    rig_model_dir: typing.Optional[pathlib.Path] = None,
+) -> None:
+    """Direct support for the dynamic routing task. Adds an `aind-data-schema`
+     `rig.json` to a dynamic routing session directory. The `aind-data-schema`
+     `session.json` in `session_dir` will be updated with the `rig_id` of the
+      added `rig.json`.
+
+    Notes
+    -----
+    - An aind metadata session json must exist and be ending with filename
+    session.json (pattern: `*session.json`) in `session_dir`.
+    - If `rig_model_dir` is not provided, will attempt to get default from
+     np-config. You will need to be onprem for `np-config` to work.
+    """
+    scraped_session_model_path = scrape_session_model_path(session_dir)
+    logger.debug("Scraped session model path: %s" % scraped_session_model_path)
+    scraped_session = session.Session.model_validate_json(
+        scraped_session_model_path.read_text()
+    )
+    scraped_rig_id = scraped_session.rig_id
+    logger.info("Scraped rig id: %s" % scraped_rig_id)
+    _, rig_name, _ = scraped_rig_id.split("_")
+    logger.info("Parsed rig name: %s" % rig_name)
+    rig_model_path = session_dir / "rig.json"
+
+    if not rig_model_dir:
+        logger.debug("Getting storage directory from np-config.")
+        rig_model_dir = np.get_rig_storage_directory()
+
+    current_model_path = copy_or_init_rig(
+        rig_model_dir,
+        session_datetime,
+        rig_name,
+        rig_model_path,
+    )
+
+    logger.info("Current model path: %s" % current_model_path)
+    settings_sources = list(session_dir.glob("**/settings.xml"))
+    logger.info("Scraped open ephys settings: %s" % settings_sources)
+
+    updated_model_path = update.update_rig(
+        rig_model_path,
+        modification_date=session_datetime.date(),
+        open_ephys_settings_sources=settings_sources,
+        output_path=rig_model_path,
+    )
+
+    update_session_from_rig(
+        scraped_session_model_path,
+        updated_model_path,
+        scraped_session_model_path,
+    )
+
+    storage.update_item(
+        rig_model_dir,
+        updated_model_path,
+        session_datetime,
+        rig_name,
+    )
+
+
+def update_neuropixels_rig_from_dynamic_routing_session_dir(
+    rig_source: pathlib.Path,
+    session_dir: pathlib.Path,
+    output_path: pathlib.Path = pathlib.Path("rig.json"),
+    modification_date: typing.Optional[datetime.date] = None,
+    mvr_mapping: dict[str, str] = common.DEFAULT_MVR_MAPPING,
+) -> pathlib.Path:
+    """Scrapes dynamic routing session directory for various rig
+    configuration/settings and updates `rig_source`.
+
+    Notes
+    -----
+    - Will likely be depreciated in the future.
+    """
+    try:
+        task_source = next(session_dir.glob("**/Dynamic*.hdf5"))
+        logger.debug("Scraped task source: %s" % task_source)
+    except StopIteration:
+        task_source = None
+
+    # sync
+    try:
+        sync_source = next(session_dir.glob("**/sync.yml"))
+        logger.debug("Scraped sync source: %s" % sync_source)
+    except StopIteration:
+        sync_source = None
+
+    # mvr
+    try:
+        mvr_source = next(session_dir.glob("**/mvr.ini"))
+        logger.debug("Scraped mvr source: %s" % mvr_source)
+    except StopIteration:
+        mvr_source = None
+
+    # open ephys
+    settings_sources = list(session_dir.glob("**/settings.xml"))
+    logger.debug("Scraped open ephys settings: %s" % settings_sources)
+
+    return update.update_rig(
+        rig_source,
+        task_source=task_source,
+        sync_source=sync_source,
+        mvr_source=mvr_source,
+        mvr_mapping=mvr_mapping,
+        open_ephys_settings_sources=settings_sources,
+        output_path=output_path,
+        modification_date=modification_date,
+        reward_calibration_date=modification_date,
+        sound_calibration_date=modification_date,
+    )
+
+
+def extract_rig_name(task_source: pathlib.Path) -> str | None:
+    """Extracts rig_name from task_source.
+
+    >>> extract_rig_name(
+    ...     pathlib.Path("examples") / "neuropixels-rig-task.hdf5"
+    ... )
+    'NP2'
+    >>> extract_rig_name(
+    ...     pathlib.Path("examples") / "behavior-box-task-0.hdf5"
+    ... )
+    'D6'
+    >>> extract_rig_name(
+    ...     pathlib.Path("examples") / "behavior-box-task-1.hdf5"
+    ... )
+    'B2'
+
+    Notes
+    -----
+    - If extracted `computerName` is not found or is not bytes, will use
+     `rigName`.
+    """
+    computer_name = utils.extract_hdf5_value(
+        utils.load_hdf5(task_source),
+        [
+            "computerName",
+        ],
+    )
+    logger.debug("Extracted computerName: %s" % computer_name)
+    rig_name = utils.extract_hdf5_value(
+        utils.load_hdf5(task_source),
+        [
+            "rigName",
+        ],
+    )
+    logger.debug("Extracted rigName: %s" % rig_name)
+
+    if isinstance(computer_name, bytes):
+        decoded = computer_name.decode("utf8")
+        if decoded.lower().startswith("beh"):
+            postfixed = decoded.split(".")[1]
+            split = postfixed.split("-")
+            return split[0] + split[1][-1]
+        else:
+            return decoded
+
+    if isinstance(rig_name, bytes):
+        return rig_name.decode("utf-8")
+
+    return None
+
+
+def extract_session_datetime(
+    task_source: pathlib.Path,
+) -> datetime.datetime:
+    """
+    >>> extract_session_datetime(
+    ...     pathlib.Path("examples") / "behavior-box-task-0.hdf5"
+    ... )
+    datetime.datetime(2024, 5, 1, 0, 0)
+    >>> extract_session_datetime(
+    ...     pathlib.Path("examples") / "behavior-box-task-1.hdf5"
+    ... )
+    datetime.datetime(2023, 9, 8, 0, 0)
+    """
+    start_time_str = utils.extract_hdf5_value(
+        utils.load_hdf5(task_source),
+        [
+            "startTime",
+        ],
+    )
+    if not start_time_str:
+        raise Exception("Could not extract start time from task source.")
+
+    logger.debug("Extracted start time bytes: %s" % start_time_str)
+    date_str, _ = start_time_str.decode("utf8").split("_")
+    logger.debug("Date string: %s" % date_str)
+    return datetime.datetime.strptime(date_str, "%Y%m%d")
+
+
+def copy_task_rig(
+    task_source: pathlib.Path,
+    output_path: pathlib.Path,
+    storage_directory: typing.Optional[pathlib.Path] = None,
+) -> pathlib.Path | None:
+    """Extracts rig_name from task_source and copies the associated `rig.json`
+     to output_path.
+
+    >>> storage_directory = pathlib.Path("examples") / "rig-directory"
+    >>> task_source = pathlib.Path("examples") / "neuropixels-rig-task.hdf5"
+    >>> copy_task_rig(
+    ...     task_source,
+    ...     pathlib.Path("rig.json"),
+    ...     storage_directory,
+    ... )
+    PosixPath('rig.json')
+
+    >>> task_source = pathlib.Path("examples") / "behavior-box-task-0.hdf5"
+    >>> copy_task_rig(
+    ...     task_source,
+    ...     pathlib.Path("rig.json"),
+    ...     storage_directory,
+    ... )
+    PosixPath('rig.json')
+
+    Notes
+    -----
+    - If `storage_directory` is not provided, will attempt to get default from
+     np-config.
+    """
+    # storage_directory optional is legacy behavior
+    # TODO: remove the optional so we can remove this safeguard
+    if not storage_directory:
+        raise Exception("Storage directory must be provided.")
+
+    extracted_rig_name = extract_rig_name(task_source)
+    logger.debug("Extracted rig name: %s" % extracted_rig_name)
+    if not extracted_rig_name:
+        raise Exception("Could not extract rig name from task source: %s" % task_source)
+
+    if rigs.is_behavior_box(extracted_rig_name):
+        rig_model = behavior_box.init(
+            extracted_rig_name,
+            modification_date=datetime.date.today(),
+        )
+        rig_model.write_standard_file(output_path.parent)
+        return output_path
+
+    extracted_session_datetime = extract_session_datetime(task_source)
+
+    # if grabbing latest rig model fails, return a new one
+    return copy_or_init_rig(
+        storage_directory,
+        extracted_session_datetime,
+        extracted_rig_name,
+        output_path,
+    )