sl-shared-assets 1.0.0__py3-none-any.whl

sl_shared_assets/data_classes/session_data.pyi

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+from pathlib import Path
+from dataclasses import field, dataclass
+
+from _typeshed import Incomplete
+from ataraxis_data_structures import YamlConfig
+
+from .configuration_data import get_system_configuration_data as get_system_configuration_data
+
+_valid_session_types: Incomplete
+
+@dataclass()
+class ProjectConfiguration(YamlConfig):
+    """Stores the project-specific configuration parameters that do not change between different animals and runtime
+    sessions.
+
+    An instance of this class is generated and saved as a .yaml file in the 'configuration' directory of each project
+    when it is created. After that, the stored data is reused for every runtime (training or experiment session) carried
+    out for each animal of the project. Additionally, a copy of the most actual configuration file is saved inside each
+    runtime session's 'raw_data' folder, providing seamless integration between the managed data and various Sun lab
+    (sl-) libraries.
+
+    Notes:
+        Together with SessionData, this class forms the entry point for all interactions with the data acquired in the
+        Sun lab. The fields of this class are used to flexibly configure the runtime behavior of major data acquisition
+        (sl-experiment) and processing (sl-forgery) libraries, adapting them for any project in the lab.
+    """
+
+    project_name: str = ...
+    surgery_sheet_id: str = ...
+    water_log_sheet_id: str = ...
+    @classmethod
+    def load(cls, configuration_path: Path) -> ProjectConfiguration:
+        """Loads the project configuration parameters from the specified project_configuration.yaml file.
+
+        This method is called during each interaction with any runtime session's data, including the creation of a new
+        session.
+
+        Args:
+            configuration_path: The path to the project_configuration.yaml file from which to load the data.
+
+        Returns:
+            The initialized ProjectConfiguration instance that stores the configuration data for the target project.
+
+        Raise:
+            FileNotFoundError: If the specified configuration file does not exist or is not a valid YAML file.
+        """
+    def save(self, path: Path) -> None:
+        """Saves class instance data to disk as a project_configuration.yaml file.
+
+        This method is automatically called from the 'sl_experiment' library when a new project is created. After this
+        method's runtime, all future project initialization calls will use the load() method to reuse configuration data
+        saved to the .yaml file created by this method.
+
+        Args:
+            path: The path to the .yaml file to save the data to.
+        """
+    def _verify_data(self) -> None:
+        """Verifies the user-modified data loaded from the project_configuration.yaml file.
+
+        Since this class is explicitly designed to be modified by the user, this verification step is carried out to
+        ensure that the loaded data matches expectations. This reduces the potential for user errors to impact the
+        runtime behavior of the libraries using this class. This internal method is automatically called by the load()
+        method.
+
+        Raises:
+            ValueError: If the loaded data does not match expected formats or values.
+        """
+
+@dataclass()
+class RawData:
+    """Stores the paths to the directories and files that make up the 'raw_data' session-specific directory.
+
+    The raw_data directory stores the data acquired during the session runtime before and after preprocessing. Since
+    preprocessing does not alter the data, any data in that folder is considered 'raw'.
+
+    Notes:
+        Sun lab data management strategy primarily relies on keeping multiple redundant copies of the raw_data for
+        each acquired session. Typically, one copy is stored on the lab's processing server and the other is stored on
+        the NAS.
+    """
+
+    raw_data_path: Path = ...
+    camera_data_path: Path = ...
+    mesoscope_data_path: Path = ...
+    behavior_data_path: Path = ...
+    zaber_positions_path: Path = ...
+    session_descriptor_path: Path = ...
+    hardware_state_path: Path = ...
+    surgery_metadata_path: Path = ...
+    project_configuration_path: Path = ...
+    session_data_path: Path = ...
+    experiment_configuration_path: Path = ...
+    mesoscope_positions_path: Path = ...
+    window_screenshot_path: Path = ...
+    system_configuration_path: Path = ...
+    checksum_path: Path = ...
+    telomere_path: Path = ...
+    ubiquitin_path: Path = ...
+    verified_bin_path: Path = ...
+    def resolve_paths(self, root_directory_path: Path) -> None:
+        """Resolves all paths managed by the class instance based on the input root directory path.
+
+        This method is called each time the class is instantiated to regenerate the managed path hierarchy on any
+        machine that instantiates the class.
+
+        Args:
+            root_directory_path: The path to the top-level directory of the local hierarchy. Depending on the managed
+                hierarchy, this has to point to a directory under the main /session, /animal, or /project directory of
+                the managed session.
+        """
+    def make_directories(self) -> None:
+        """Ensures that all major subdirectories and the root directory exist, creating any missing directories."""
+
+@dataclass()
+class ProcessedData:
+    """Stores the paths to the directories and files that make up the 'processed_data' session-specific directory.
+
+    The processed_data directory stores the data generated by various processing pipelines from the raw data (contents
+    of the raw_data directory). Processed data represents an intermediate step between raw data and the dataset used in
+    the data analysis, but is not itself designed to be analyzed.
+    """
+
+    processed_data_path: Path = ...
+    camera_data_path: Path = ...
+    mesoscope_data_path: Path = ...
+    behavior_data_path: Path = ...
+    job_logs_path: Path = ...
+    single_day_suite2p_bin_path: Path = ...
+    multi_day_suite2p_bin_path: Path = ...
+    behavior_bin_path: Path = ...
+    dlc_bin_path: Path = ...
+    def resolve_paths(self, root_directory_path: Path) -> None:
+        """Resolves all paths managed by the class instance based on the input root directory path.
+
+        This method is called each time the class is instantiated to regenerate the managed path hierarchy on any
+        machine that instantiates the class.
+
+        Args:
+            root_directory_path: The path to the top-level directory of the local hierarchy. Depending on the managed
+                hierarchy, this has to point to a directory under the main /session, /animal, or /project directory of
+                the managed session.
+        """
+    def make_directories(self) -> None:
+        """Ensures that all major subdirectories and the root directory exist, creating any missing directories."""
+
+@dataclass
+class SessionData(YamlConfig):
+    """Stores and manages the data layout of a single training or experiment session acquired in the Sun lab.
+
+    The primary purpose of this class is to maintain the session data structure across all supported destinations and
+    during all processing stages. It generates the paths used by all other classes from all Sun lab libraries that
+    interact with the session's data from the point of its creation and until the data is integrated into an
+    analysis dataset.
+
+    When necessary, the class can be used to either generate a new session or load the layout of an already existing
+    session. When the class is used to create a new session, it generates the new session's name using the current
+    UTC timestamp, accurate to microseconds. This ensures that each session name is unique and preserves the overall
+    session order.
+
+    Notes:
+        This class is specifically designed for working with the data from a single session, performed by a single
+        animal under the specific experiment. The class is used to manage both raw and processed data. It follows the
+        data through acquisition, preprocessing and processing stages of the Sun lab data workflow. Together with
+        ProjectConfiguration class, this class serves as an entry point for all interactions with the managed session's
+        data.
+    """
+
+    project_name: str
+    animal_id: str
+    session_name: str
+    session_type: str
+    acquisition_system: str
+    experiment_name: str | None
+    raw_data: RawData = field(default_factory=Incomplete)
+    processed_data: ProcessedData = field(default_factory=Incomplete)
+    def __post_init__(self) -> None:
+        """Ensures raw_data and processed_data are always instances of RawData and ProcessedData."""
+    @classmethod
+    def create(
+        cls,
+        project_name: str,
+        animal_id: str,
+        session_type: str,
+        experiment_name: str | None = None,
+        session_name: str | None = None,
+    ) -> SessionData:
+        """Creates a new SessionData object and generates the new session's data structure on the local PC.
+
+        This method is intended to be called exclusively by the sl-experiment library to create new training or
+        experiment sessions and generate the session data directory tree.
+
+        Notes:
+            To load an already existing session data structure, use the load() method instead.
+
+            This method automatically dumps the data of the created SessionData instance into the session_data.yaml file
+            inside the root raw_data directory of the created hierarchy. It also finds and dumps other configuration
+            files, such as project_configuration.yaml, experiment_configuration.yaml, and system_configuration.yaml into
+            the same raw_data directory. This ensures that if the session's runtime is interrupted unexpectedly, the
+            acquired data can still be processed.
+
+        Args:
+            project_name: The name of the project for which the data is acquired.
+            animal_id: The ID code of the animal for which the data is acquired.
+            session_type: The type of the session. Primarily, this determines how to read the session_descriptor.yaml
+                file. Valid options are 'Lick training', 'Run training', 'Window checking', or 'Experiment'.
+            experiment_name: The name of the experiment executed during managed session. This optional argument is only
+                used for 'Experiment' session types. It is used to find the experiment configuration .YAML file.
+            session_name: An optional session_name override. Generally, this argument should not be provided for most
+                sessions. When provided, the method uses this name instead of generating a new timestamp-based name.
+                This is only used during the 'ascension' runtime to convert old data structures to the modern
+                lab standards.
+
+        Returns:
+            An initialized SessionData instance that stores the layout of the newly created session's data.
+        """
+    @classmethod
+    def load(
+        cls, session_path: Path, processed_data_root: Path | None = None, make_processed_data_directory: bool = False
+    ) -> SessionData:
+        """Loads the SessionData instance from the target session's session_data.yaml file.
+
+        This method is used to load the data layout information of an already existing session. Primarily, this is used
+        when preprocessing or processing session data. Due to how SessionData is stored and used in the lab, this
+        method always loads the data layout from the session_data.yaml file stored inside the raw_data session
+        subfolder. Currently, all interactions with Sun lab data require access to the 'raw_data' folder.
+
+        Notes:
+            To create a new session, use the create() method instead.
+
+        Args:
+            session_path: The path to the root directory of an existing session, e.g.: root/project/animal/session.
+            processed_data_root: If processed data is kept on a drive different from the one that stores raw data,
+                provide the path to the root project directory (directory that stores all Sun lab projects) on that
+                drive. The method will automatically resolve the project/animal/session/processed_data hierarchy using
+                this root path. If raw and processed data are kept on the same drive, keep this set to None.
+            make_processed_data_directory: Determines whether this method should create processed_data directory if it
+                does not exist.
+
+        Returns:
+            An initialized SessionData instance for the session whose data is stored at the provided path.
+
+        Raises:
+            FileNotFoundError: If the 'session_data.yaml' file is not found under the session_path/raw_data/ subfolder.
+
+        """
+    def _save(self) -> None:
+        """Saves the instance data to the 'raw_data' directory of the managed session as a 'session_data.yaml' file.
+
+        This is used to save the data stored in the instance to disk, so that it can be reused during preprocessing or
+        data processing. The method is intended to only be used by the SessionData instance itself during its
+        create() method runtime.
+        """

sl_shared_assets/data_classes/surgery_data.py

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+"""This module provides classes to store animal surgery data. This is used to store the data extracted from the Sun lab
+surgery log, so that subject (animal) surgery data is always kept together with training and experiment data."""
+
+from dataclasses import dataclass
+
+from ataraxis_data_structures import YamlConfig
+
+
+@dataclass()
+class SubjectData:
+    """Stores the ID information of the surgical intervention's subject (animal)."""
+
+    id: int
+    """Stores the unique ID (name) of the subject. Assumes all animals are given a numeric ID, rather than a string 
+    name."""
+    ear_punch: str
+    """Stores the ear tag location of the subject."""
+    sex: str
+    """Stores the gender of the subject."""
+    genotype: str
+    """Stores the genotype of the subject."""
+    date_of_birth_us: int
+    """Stores the date of birth of the subject as the number of microseconds elapsed since UTC epoch onset."""
+    weight_g: float
+    """Stores the weight of the subject pre-surgery, in grams."""
+    cage: int
+    """Stores the number of the cage used to house the subject after surgery."""
+    location_housed: str
+    """Stores the location used to house the subject after the surgery."""
+    status: str
+    """Stores the current status of the subject (alive / deceased)."""
+
+
+@dataclass()
+class ProcedureData:
+    """Stores the general information about the surgical intervention."""
+
+    surgery_start_us: int
+    """Stores the date and time when the surgery has started as microseconds elapsed since UTC epoch onset."""
+    surgery_end_us: int
+    """Stores the date and time when the surgery has ended as microseconds elapsed since UTC epoch onset."""
+    surgeon: str
+    """Stores the name or ID of the surgeon. If the intervention was carried out by multiple surgeons, all participating
+    surgeon names and IDs are stored as part of the same string."""
+    protocol: str
+    """Stores the experiment protocol number (ID) used during the surgery."""
+    surgery_notes: str
+    """Stores surgeon's notes taken during the surgery."""
+    post_op_notes: str
+    """Stores surgeon's notes taken during the post-surgery recovery period."""
+    surgery_quality: int = 0
+    """Stores the quality of the surgical intervention as a numeric level. 0 indicates unusable (bad) result, 1 
+    indicates usable result that is not good enough to be included in a publication, 2 indicates publication-grade 
+    result."""
+
+
+@dataclass
+class ImplantData:
+    """Stores the information about a single implantation performed during the surgical intervention.
+
+    Multiple ImplantData instances are used at the same time if the surgery involved multiple implants.
+    """
+
+    implant: str
+    """The descriptive name of the implant."""
+    implant_target: str
+    """The name of the brain region or cranium section targeted by the implant."""
+    implant_code: int
+    """The manufacturer code or internal reference code for the implant. This code is used to identify the implant in 
+    additional datasheets and lab ordering documents."""
+    implant_ap_coordinate_mm: float
+    """Stores implant's antero-posterior stereotactic coordinate, in millimeters, relative to bregma."""
+    implant_ml_coordinate_mm: float
+    """Stores implant's medial-lateral stereotactic coordinate, in millimeters, relative to bregma."""
+    implant_dv_coordinate_mm: float
+    """Stores implant's dorsal-ventral stereotactic coordinate, in millimeters, relative to bregma."""
+
+
+@dataclass
+class InjectionData:
+    """Stores the information about a single injection performed during surgical intervention.
+
+    Multiple InjectionData instances are used at the same time if the surgery involved multiple injections.
+    """
+
+    injection: str
+    """The descriptive name of the injection."""
+    injection_target: str
+    """The name of the brain region targeted by the injection."""
+    injection_volume_nl: float
+    """The volume of substance, in nanoliters, delivered during the injection."""
+    injection_code: int
+    """The manufacturer code or internal reference code for the injected substance. This code is used to identify the 
+    substance in additional datasheets and lab ordering documents."""
+    injection_ap_coordinate_mm: float
+    """Stores injection's antero-posterior stereotactic coordinate, in millimeters, relative to bregma."""
+    injection_ml_coordinate_mm: float
+    """Stores injection's medial-lateral stereotactic coordinate, in millimeters, relative to bregma."""
+    injection_dv_coordinate_mm: float
+    """Stores injection's dorsal-ventral stereotactic coordinate, in millimeters, relative to bregma."""
+
+
+@dataclass
+class DrugData:
+    """Stores the information about all drugs administered to the subject before, during, and immediately after the
+    surgical intervention.
+    """
+
+    lactated_ringers_solution_volume_ml: float
+    """Stores the volume of Lactated Ringer's Solution (LRS) administered during surgery, in ml."""
+    lactated_ringers_solution_code: int
+    """Stores the manufacturer code or internal reference code for Lactated Ringer's Solution (LRS). This code is used 
+    to identify the LRS batch in additional datasheets and lab ordering documents."""
+    ketoprofen_volume_ml: float
+    """Stores the volume of ketoprofen diluted with saline administered during surgery, in ml."""
+    ketoprofen_code: int
+    """Stores the manufacturer code or internal reference code for ketoprofen. This code is used to identify the 
+    ketoprofen batch in additional datasheets and lab ordering documents."""
+    buprenorphine_volume_ml: float
+    """Stores the volume of buprenorphine diluted with saline administered during surgery, in ml."""
+    buprenorphine_code: int
+    """Stores the manufacturer code or internal reference code for buprenorphine. This code is used to identify the 
+    buprenorphine batch in additional datasheets and lab ordering documents."""
+    dexamethasone_volume_ml: float
+    """Stores the volume of dexamethasone diluted with saline administered during surgery, in ml."""
+    dexamethasone_code: int
+    """Stores the manufacturer code or internal reference code for dexamethasone. This code is used to identify the 
+    dexamethasone batch in additional datasheets and lab ordering documents."""
+
+
+@dataclass
+class SurgeryData(YamlConfig):
+    """Stores the data about a single animal surgical intervention.
+
+    This class aggregates other dataclass instances that store specific data about the surgical procedure. Primarily, it
+    is used to save the data as a .yaml file to every session's 'raw_data' directory of each animal used in every lab
+    project. This way, the surgery data is always stored alongside the behavior and brain activity data collected
+    during the session.
+    """
+
+    subject: SubjectData
+    """Stores the ID information about the subject (mouse)."""
+    procedure: ProcedureData
+    """Stores general data about the surgical intervention."""
+    drugs: DrugData
+    """Stores the data about the substances subcutaneously injected into the subject before, during and immediately 
+    after the surgical intervention."""
+    implants: list[ImplantData]
+    """Stores the data for all cranial and transcranial implants introduced to the subject during the surgical 
+    intervention."""
+    injections: list[InjectionData]
+    """Stores the data about all substances infused into the brain of the subject during the surgical intervention."""

sl_shared_assets/data_classes/surgery_data.pyi

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+from dataclasses import dataclass
+
+from ataraxis_data_structures import YamlConfig
+
+@dataclass()
+class SubjectData:
+    """Stores the ID information of the surgical intervention's subject (animal)."""
+
+    id: int
+    ear_punch: str
+    sex: str
+    genotype: str
+    date_of_birth_us: int
+    weight_g: float
+    cage: int
+    location_housed: str
+    status: str
+
+@dataclass()
+class ProcedureData:
+    """Stores the general information about the surgical intervention."""
+
+    surgery_start_us: int
+    surgery_end_us: int
+    surgeon: str
+    protocol: str
+    surgery_notes: str
+    post_op_notes: str
+    surgery_quality: int = ...
+
+@dataclass
+class ImplantData:
+    """Stores the information about a single implantation performed during the surgical intervention.
+
+    Multiple ImplantData instances are used at the same time if the surgery involved multiple implants.
+    """
+
+    implant: str
+    implant_target: str
+    implant_code: int
+    implant_ap_coordinate_mm: float
+    implant_ml_coordinate_mm: float
+    implant_dv_coordinate_mm: float
+
+@dataclass
+class InjectionData:
+    """Stores the information about a single injection performed during surgical intervention.
+
+    Multiple InjectionData instances are used at the same time if the surgery involved multiple injections.
+    """
+
+    injection: str
+    injection_target: str
+    injection_volume_nl: float
+    injection_code: int
+    injection_ap_coordinate_mm: float
+    injection_ml_coordinate_mm: float
+    injection_dv_coordinate_mm: float
+
+@dataclass
+class DrugData:
+    """Stores the information about all drugs administered to the subject before, during, and immediately after the
+    surgical intervention.
+    """
+
+    lactated_ringers_solution_volume_ml: float
+    lactated_ringers_solution_code: int
+    ketoprofen_volume_ml: float
+    ketoprofen_code: int
+    buprenorphine_volume_ml: float
+    buprenorphine_code: int
+    dexamethasone_volume_ml: float
+    dexamethasone_code: int
+
+@dataclass
+class SurgeryData(YamlConfig):
+    """Stores the data about a single animal surgical intervention.
+
+    This class aggregates other dataclass instances that store specific data about the surgical procedure. Primarily, it
+    is used to save the data as a .yaml file to every session's 'raw_data' directory of each animal used in every lab
+    project. This way, the surgery data is always stored alongside the behavior and brain activity data collected
+    during the session.
+    """
+
+    subject: SubjectData
+    procedure: ProcedureData
+    drugs: DrugData
+    implants: list[ImplantData]
+    injections: list[InjectionData]

sl_shared_assets/server/__init__.py

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+"""This package provides the classes and methods used by all Sun lab libraries to submit remote jobs to the BioHPC
+and other compute servers. This package is also used across all Sun lab members private code to interface with the
+shared server."""
+
+from .job import Job
+from .server import Server, ServerCredentials, generate_server_credentials
+
+__all__ = ["Server", "ServerCredentials", "generate_server_credentials", "Job"]

sl_shared_assets/server/__init__.pyi

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+from .job import Job as Job
+from .server import (
+    Server as Server,
+    ServerCredentials as ServerCredentials,
+    generate_server_credentials as generate_server_credentials,
+)
+
+__all__ = ["Server", "ServerCredentials", "generate_server_credentials", "Job"]

sl_shared_assets/server/job.py

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+"""This module provides the core Job class, used as the starting point for all SLURM-managed job executed on lab compute
+server(s). Specifically, the Job class acts as a wrapper around the SLURM configuration and specific logic of each
+job. During runtime, Server class interacts with input job objects to manage their transfer and execution on the
+remote servers."""
+
+# noinspection PyProtectedMember
+from pathlib import Path
+import datetime
+
+from simple_slurm import Slurm  # type: ignore
+
+
+class Job:
+    """Aggregates the data of a single SLURM-managed job to be executed on the Sun lab BioHPC cluster.
+
+    This class provides the API for constructing any server-side job in the Sun lab. Internally, it wraps an instance
+    of a Slurm class to package the job data into the format expected by the SLURM job manager. All jobs managed by this
+    class instance should be submitted to an initialized Server class 'submit_job' method to be executed on the server.
+
+    Notes:
+        The initialization method of the class contains the arguments for configuring the SLURM and Conda environments
+        used by the job. Do not submit additional SLURM or Conda commands via the 'add_command' method, as this may
+        produce unexpected behavior.
+
+        Each job can be conceptualized as a sequence of shell instructions to execute on the remote compute server. For
+        the lab, that means that the bulk of the command consists of calling various CLIs exposed by data processing or
+        analysis pipelines, installed in the Conda environment on the server. Other than that, the job contains commands
+        for activating the target conda environment and, in some cases, doing other preparatory or cleanup work. The
+        source code of a 'remote' job is typically identical to what a human operator would type in a 'local' terminal
+        to run the same job on their PC.
+
+        A key feature of server-side jobs is that they are executed on virtual machines managed by SLURM. Since the
+        server has a lot more compute and memory resources than likely needed by individual jobs, each job typically
+        requests a subset of these resources. Upon being executed, SLURM creates an isolated environment with the
+        requested resources and runs the job in that environment.
+
+        Since all jobs are expected to use the CLIs from python packages (pre)installed on the BioHPC server, make sure
+        that the target environment is installed and configured before submitting jobs to the server. See notes in
+        ReadMe to learn more about configuring server-side conda environments.
+
+    Args:
+        job_name: The descriptive name of the SLURM job to be created. Primarily, this name is used in terminal
+            printouts to identify the job to human operators.
+        output_log: The absolute path to the .txt file on the processing server, where to store the standard output
+            data of the job.
+        error_log: The absolute path to the .txt file on the processing server, where to store the standard error
+            data of the job.
+        working_directory: The absolute path to the directory where temporary job files will be stored. During runtime,
+            classes from this library use that directory to store files such as the job's shell script. All such files
+            are automatically removed from the directory at the end of a non-errors runtime.
+        conda_environment: The name of the conda environment to activate on the server before running the job logic. The
+            environment should contain the necessary Python packages and CLIs to support running the job's logic.
+        cpus_to_use: The number of CPUs to use for the job.
+        ram_gb: The amount of RAM to allocate for the job, in Gigabytes.
+        time_limit: The maximum time limit for the job, in minutes. If the job is still running at the end of this time
+            period, it will be forcibly terminated. It is highly advised to always set adequate maximum runtime limits
+            to prevent jobs from hogging the server in case of runtime or algorithm errors.
+
+    Attributes:
+        remote_script_path: Stores the path to the script file relative to the root of the remote server that runs the
+            command.
+        job_id: Stores the unique job identifier assigned by the SLURM manager to this job, when it is accepted for
+            execution. This field initialized to None and is overwritten by the Server class that submits the job.
+        job_name: Stores the descriptive name of the SLURM job.
+        _command: Stores the managed SLURM command object.
+    """
+
+    def __init__(
+        self,
+        job_name: str,
+        output_log: Path,
+        error_log: Path,
+        working_directory: Path,
+        conda_environment: str,
+        cpus_to_use: int = 10,
+        ram_gb: int = 10,
+        time_limit: int = 60,
+    ) -> None:
+        # Resolves the paths to the remote (server-side) .sh script file. This is the path where the job script
+        # will be stored on the server, once it is transferred by the Server class instance.
+        self.remote_script_path = str(working_directory.joinpath(f"{job_name}.sh"))
+
+        # Defines additional arguments used by the Server class that executed the job.
+        self.job_id: str | None = None  # This is set by the Server that submits the job.
+        self.job_name: str = job_name  # Also stores the job name to support more informative terminal prints
+
+        # Builds the slurm command object filled with configuration information
+        self._command: Slurm = Slurm(
+            cpus_per_task=cpus_to_use,
+            job_name=job_name,
+            output=str(output_log),
+            error=str(error_log),
+            mem=f"{ram_gb}G",
+            time=datetime.timedelta(minutes=time_limit),
+        )
+
+        # Conda shell initialization commands
+        self._command.add_cmd("eval $(conda shell.bash hook)")
+        self._command.add_cmd("conda init bash")
+
+        # Activates the target conda environment for the command.
+        self._command.add_cmd(f"source activate {conda_environment}")  # Need to use old syntax for our server.
+
+    def __repr__(self) -> str:
+        """Returns the string representation of the Job instance."""
+        return f"Job(name={self.job_name}, id={self.job_id})"
+
+    def add_command(self, command: str) -> None:
+        """Adds the input command string to the end of the managed SLURM job command list.
+
+        This method is a wrapper around simple_slurm's 'add_cmd' method. It is used to iteratively build the shell
+        command sequence of the job.
+
+        Args:
+            command: The command string to add to the command list, e.g.: 'python main.py --input 1'.
+        """
+
+        self._command.add_cmd(command)
+
+    @property
+    def command_script(self) -> str:
+        """Translates the managed job data into a shell-script-writable string and returns it to caller.
+
+        This method is used by the Server class to translate the job into the format that can be submitted to and
+        executed on the remote compute server. Do not call this method manually unless you know what you are doing.
+        The returned string is safe to dump into a .sh (shell script) file and move to the BioHPC server for execution.
+        """
+
+        # Appends the command to clean up (remove) the temporary script file after processing runtime is over
+        self._command.add_cmd(f"rm -f {self.remote_script_path}")
+
+        # Translates the command to string format
+        script_content = str(self._command)
+
+        # Replaces escaped $ (/$) with $. This is essential, as without this correction, things like conda
+        # initialization would not work as expected.
+        fixed_script_content = script_content.replace("\\$", "$")
+
+        # Returns the script content to caller as a string
+        return fixed_script_content