sl-shared-assets 3.1.3__py3-none-any.whl → 4.0.1__py3-none-any.whl

sl_shared_assets/__init__.py

@@ -11,6 +11,7 @@ from .tools import (
     ProjectManifest,
     resolve_p53_marker,
     transfer_directory,
+    generate_project_manifest,
     calculate_directory_checksum,
 )
 from .server import Job, Server, JupyterJob, ServerCredentials
@@ -30,6 +31,7 @@ from .data_classes import (
     ExperimentState,
     ExperimentTrial,
     MesoscopeCameras,
+    TrackerFileNames,
     ProcessingTracker,
     AcquisitionSystems,
     MesoscopePositions,
@@ -42,6 +44,8 @@ from .data_classes import (
     MesoscopeSystemConfiguration,
     MesoscopeExperimentDescriptor,
     MesoscopeExperimentConfiguration,
+    generate_manager_id,
+    get_processing_tracker,
     get_system_configuration_data,
     set_system_configuration_file,
 )
@@ -86,9 +90,13 @@ __all__ = [
     "SessionTypes",
     "AcquisitionSystems",
     "WindowCheckingDescriptor",
+    "get_processing_tracker",
+    "generate_manager_id",
+    "TrackerFileNames",
     # Tools package
     "ProjectManifest",
     "resolve_p53_marker",
     "transfer_directory",
     "calculate_directory_checksum",
+    "generate_project_manifest",
 ]

sl_shared_assets/__init__.pyi

@@ -2,6 +2,7 @@ from .tools import (
     ProjectManifest as ProjectManifest,
     resolve_p53_marker as resolve_p53_marker,
     transfer_directory as transfer_directory,
+    generate_project_manifest as generate_project_manifest,
     calculate_directory_checksum as calculate_directory_checksum,
 )
 from .server import (
@@ -26,6 +27,7 @@ from .data_classes import (
     ExperimentState as ExperimentState,
     ExperimentTrial as ExperimentTrial,
     MesoscopeCameras as MesoscopeCameras,
+    TrackerFileNames as TrackerFileNames,
     ProcessingTracker as ProcessingTracker,
     AcquisitionSystems as AcquisitionSystems,
     MesoscopePositions as MesoscopePositions,
@@ -38,6 +40,8 @@ from .data_classes import (
     MesoscopeSystemConfiguration as MesoscopeSystemConfiguration,
     MesoscopeExperimentDescriptor as MesoscopeExperimentDescriptor,
     MesoscopeExperimentConfiguration as MesoscopeExperimentConfiguration,
+    generate_manager_id as generate_manager_id,
+    get_processing_tracker as get_processing_tracker,
     get_system_configuration_data as get_system_configuration_data,
     set_system_configuration_file as set_system_configuration_file,
 )
@@ -76,8 +80,12 @@ __all__ = [
     "SessionTypes",
     "AcquisitionSystems",
     "WindowCheckingDescriptor",
+    "get_processing_tracker",
+    "generate_manager_id",
+    "TrackerFileNames",
     "ProjectManifest",
     "resolve_p53_marker",
     "transfer_directory",
     "calculate_directory_checksum",
+    "generate_project_manifest",
 ]

sl_shared_assets/cli.py

@@ -7,7 +7,7 @@ from ataraxis_base_utilities import LogLevel, console, ensure_directory_exists
 
 from .tools import ascend_tyche_data, resolve_p53_marker, verify_session_checksum, generate_project_manifest
 from .server import Server, JupyterJob, generate_server_credentials
-from .data_classes import SessionData, ProcessingTracker
+from .data_classes import SessionData, TrackerFileNames, get_processing_tracker
 
 
 @click.command()
@@ -18,6 +18,19 @@ from .data_classes import SessionData, ProcessingTracker
     required=True,
     help="The absolute path to the session directory whose raw data needs to be verified for potential corruption.",
 )
+@click.option(
+    "-id",
+    "--manager_id",
+    type=int,
+    required=True,
+    default=0,
+    show_default=True,
+    help=(
+        "The xxHash-64 hash value that represents the unique identifier for the process that manages this runtime. "
+        "This is primarily used when calling this CLI on remote compute servers to ensure that only a single process "
+        "can execute the CLI at a time."
+    ),
+)
 @click.option(
     "-c",
     "--create_processed_directories",
@@ -54,7 +67,11 @@ from .data_classes import SessionData, ProcessingTracker
     ),
 )
 def verify_session_integrity(
-    session_path: Path, create_processed_directories: bool, processed_data_root: Path | None, update_manifest: bool
+    session_path: Path,
+    manager_id: int,
+    create_processed_directories: bool,
+    processed_data_root: Path | None,
+    update_manifest: bool,
 ) -> None:
     """Checks the integrity of the target session's raw data (contents of the raw_data directory).
 
@@ -73,14 +90,15 @@ def verify_session_integrity(
 
     # Runs the verification process
     verify_session_checksum(
-        session,
+        session_path=session,
+        manager_id=manager_id,
         create_processed_data_directory=create_processed_directories,
         processed_data_root=processed_data_root,
         update_manifest=update_manifest,
     )
 
     # Checks the outcome of the verification process
-    tracker = ProcessingTracker(file_path=session_data.raw_data.integrity_verification_tracker_path)
+    tracker = get_processing_tracker(root=session_data.raw_data.raw_data_path, file_name=TrackerFileNames.INTEGRITY)
     if tracker.is_complete:
         # noinspection PyTypeChecker
         console.echo(message=f"Session {session.stem} raw data integrity: Verified.", level=LogLevel.SUCCESS)
@@ -448,11 +466,7 @@ def start_jupyter_server(
     is_flag=True,
     show_default=True,
     default=False,
-    help=(
-        "Determines whether the command should create or remove the dataset integration marker. Do not enable this "
-        "flag unless you know what you are doing. It is only safe to enable this flag if the session is not currently "
-        "being integrated into any datasets."
-    ),
+    help="Determines whether the command should create or remove the dataset integration marker.",
 )
 @click.option(
     "-um",

sl_shared_assets/cli.pyi

@@ -13,11 +13,16 @@ from .server import (
 )
 from .data_classes import (
     SessionData as SessionData,
-    ProcessingTracker as ProcessingTracker,
+    TrackerFileNames as TrackerFileNames,
+    get_processing_tracker as get_processing_tracker,
 )
 
 def verify_session_integrity(
-    session_path: Path, create_processed_directories: bool, processed_data_root: Path | None, update_manifest: bool
+    session_path: Path,
+    manager_id: int,
+    create_processed_directories: bool,
+    processed_data_root: Path | None,
+    update_manifest: bool,
 ) -> None:
     """Checks the integrity of the target session's raw data (contents of the raw_data directory).
 

sl_shared_assets/data_classes/__init__.py

@@ -12,7 +12,16 @@ from .runtime_data import (
     WindowCheckingDescriptor,
     MesoscopeExperimentDescriptor,
 )
-from .session_data import RawData, SessionData, SessionTypes, ProcessedData, ProcessingTracker
+from .session_data import (
+    RawData,
+    SessionData,
+    SessionTypes,
+    ProcessedData,
+    TrackerFileNames,
+    ProcessingTracker,
+    generate_manager_id,
+    get_processing_tracker,
+)
 from .surgery_data import (
     DrugData,
     ImplantData,
@@ -65,4 +74,7 @@ __all__ = [
     "AcquisitionSystems",
     "SessionTypes",
     "WindowCheckingDescriptor",
+    "get_processing_tracker",
+    "generate_manager_id",
+    "TrackerFileNames",
 ]

sl_shared_assets/data_classes/__init__.pyi

@@ -12,7 +12,10 @@ from .session_data import (
     SessionData as SessionData,
     SessionTypes as SessionTypes,
     ProcessedData as ProcessedData,
+    TrackerFileNames as TrackerFileNames,
     ProcessingTracker as ProcessingTracker,
+    generate_manager_id as generate_manager_id,
+    get_processing_tracker as get_processing_tracker,
 )
 from .surgery_data import (
     DrugData as DrugData,
@@ -66,4 +69,7 @@ __all__ = [
     "AcquisitionSystems",
     "SessionTypes",
     "WindowCheckingDescriptor",
+    "get_processing_tracker",
+    "generate_manager_id",
+    "TrackerFileNames",
 ]

sl_shared_assets/data_classes/configuration_data.py

@@ -560,7 +560,7 @@ def get_system_configuration_data() -> MesoscopeSystemConfiguration:
     app_dir = Path(appdirs.user_data_dir(appname="sun_lab_data", appauthor="sun_lab"))
     path_file = app_dir.joinpath("configuration_path.txt")
 
-    # If the cache file or the Sun lab data directory do not exist, aborts with an error
+    # If the cache file or the Sun lab data directory does not exist, aborts with an error
     if not path_file.exists():
         message = (
             "Unable to resolve the path to the local system configuration file, as local machine does not have the "

sl_shared_assets/data_classes/runtime_data.py

@@ -87,9 +87,6 @@ class LickTrainingDescriptor(YamlConfig):
     """The ID of the experimenter running the session."""
     mouse_weight_g: float
     """The weight of the animal, in grams, at the beginning of the session."""
-    dispensed_water_volume_ml: float
-    """Stores the total water volume, in milliliters, dispensed during runtime. This excludes the water volume 
-    dispensed during the paused (idle) state."""
     minimum_reward_delay_s: int
     """Stores the minimum delay, in seconds, that can separate the delivery of two consecutive water rewards."""
     maximum_reward_delay_s: int
@@ -102,17 +99,23 @@ class LickTrainingDescriptor(YamlConfig):
     """Stores the maximum number of consecutive rewards that can be delivered without the animal consuming them. If 
     the animal receives this many rewards without licking (consuming) them, reward delivery is paused until the animal 
     consumes the rewards."""
+    dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during runtime. This excludes the water volume 
+    dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter replaces this field with their 
-    notes made during runtime."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
+    preferred_session_water_volume_ml: float = 0.0
+    """The volume of water, in milliliters, the animal should be receiving during the session runtime if its 
+    performance matches experimenter-specified threshold."""
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter replaces this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -123,8 +126,6 @@ class RunTrainingDescriptor(YamlConfig):
     """The ID of the experimenter running the session."""
     mouse_weight_g: float
     """The weight of the animal, in grams, at the beginning of the session."""
-    dispensed_water_volume_ml: float
-    """Stores the total water volume, in milliliters, dispensed during runtime."""
     final_run_speed_threshold_cm_s: float
     """Stores the final running speed threshold, in centimeters per second, that was active at the end of training."""
     final_run_duration_threshold_s: float
@@ -154,17 +155,23 @@ class RunTrainingDescriptor(YamlConfig):
     """Stores the maximum time, in seconds, the animal can dip below the running speed threshold to still receive the 
     reward. This allows animals that 'run' by taking a series of large steps, briefly dipping below speed threshold at 
     the end of each step, to still get water rewards."""
+    dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during runtime. This excludes the water volume 
+    dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
-    notes made during runtime."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
+    preferred_session_water_volume_ml: float = 0.0
+    """The volume of water, in milliliters, the animal should be receiving during the session runtime if its 
+    performance matches experimenter-specified threshold."""
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -175,23 +182,27 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     """The ID of the experimenter running the session."""
     mouse_weight_g: float
     """The weight of the animal, in grams, at the beginning of the session."""
-    dispensed_water_volume_ml: float
-    """Stores the total water volume, in milliliters, dispensed during runtime."""
     maximum_unconsumed_rewards: int = 1
     """Stores the maximum number of consecutive rewards that can be delivered without the animal consuming them. If 
     the animal receives this many rewards without licking (consuming) them, reward delivery is paused until the animal 
     consumes the rewards."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
-    notes made during runtime."""
+    dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during runtime. This excludes the water volume 
+    dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
+    preferred_session_water_volume_ml: float = 0.0
+    """The volume of water, in milliliters, the animal should be receiving during the session runtime if its 
+    performance matches experimenter-specified threshold."""
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -206,14 +217,14 @@ class WindowCheckingDescriptor(YamlConfig):
 
     experimenter: str
     """The ID of the experimenter running the session."""
-    experimenter_notes: str = "Replace this with your notes."
-    """The notes on the quality of the cranial window and animal's suitability for the target project."""
     surgery_quality: int = 0
     """The quality of the cranial window and surgical intervention on a scale from 0 (non-usable) to 
     3 (high-tier publication grade) inclusive."""
     incomplete: bool = True
     """Window checking sessions are always considered 'incomplete', as they do not contain the full range of 
     information collected as part of a 'standard' behavior training or experiment session."""
+    experimenter_notes: str = "Replace this with your notes."
+    """The notes on the quality of the cranial window and animal's suitability for the target project."""
 
 
 @dataclass()

sl_shared_assets/data_classes/runtime_data.pyi

@@ -49,16 +49,17 @@ class LickTrainingDescriptor(YamlConfig):
 
     experimenter: str
     mouse_weight_g: float
-    dispensed_water_volume_ml: float
     minimum_reward_delay_s: int
     maximum_reward_delay_s: int
     maximum_water_volume_ml: float
     maximum_training_time_m: int
     maximum_unconsumed_rewards: int = ...
+    dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
-    experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
+    preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class RunTrainingDescriptor(YamlConfig):
@@ -66,7 +67,6 @@ class RunTrainingDescriptor(YamlConfig):
 
     experimenter: str
     mouse_weight_g: float
-    dispensed_water_volume_ml: float
     final_run_speed_threshold_cm_s: float
     final_run_duration_threshold_s: float
     initial_run_speed_threshold_cm_s: float
@@ -78,10 +78,12 @@ class RunTrainingDescriptor(YamlConfig):
     maximum_training_time_m: int
     maximum_unconsumed_rewards: int = ...
     maximum_idle_time_s: float = ...
+    dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
-    experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
+    preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class MesoscopeExperimentDescriptor(YamlConfig):
@@ -89,12 +91,13 @@ class MesoscopeExperimentDescriptor(YamlConfig):
 
     experimenter: str
     mouse_weight_g: float
-    dispensed_water_volume_ml: float
     maximum_unconsumed_rewards: int = ...
-    experimenter_notes: str = ...
+    dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
     experimenter_given_water_volume_ml: float = ...
+    preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class WindowCheckingDescriptor(YamlConfig):
@@ -107,9 +110,9 @@ class WindowCheckingDescriptor(YamlConfig):
     """
 
     experimenter: str
-    experimenter_notes: str = ...
     surgery_quality: int = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class ZaberPositions(YamlConfig):