sl-shared-assets 2.0.1__tar.gz → 3.0.0rc2__tar.gz

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 2.0.1
-Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
+Version: 3.0.0rc2
+Summary: Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/
 Author: Ivan Kondratyev, Kushaan Gupta, Natalie Yeung
@@ -681,7 +681,7 @@ License:                     GNU GENERAL PUBLIC LICENSE
         Public License instead of this License.  But first, please read
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
 License-File: LICENSE
-Keywords: acquisition,assets,data,processing,sunlab
+Keywords: acquisition,assets,data,processing,server,sunlab
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
@@ -697,7 +697,7 @@ Requires-Dist: ataraxis-time==3.0.0
 Requires-Dist: click==8.2.1
 Requires-Dist: filelock==3.18.0
 Requires-Dist: natsort==8.4.0
-Requires-Dist: numpy<2.3.0,>=2.0.2
+Requires-Dist: numpy==2.2.6
 Requires-Dist: paramiko==3.5.1
 Requires-Dist: polars==1.31.0
 Requires-Dist: pyarrow==20.0.0
@@ -725,7 +725,7 @@ Requires-Dist: appdirs==1.4.4; extra == 'condarun'
 Requires-Dist: click==8.2.1; extra == 'condarun'
 Requires-Dist: filelock==3.18.0; extra == 'condarun'
 Requires-Dist: natsort==8.4.0; extra == 'condarun'
-Requires-Dist: numpy<2.3.0,>=2.0.2; extra == 'condarun'
+Requires-Dist: numpy==2.2.6; extra == 'condarun'
 Requires-Dist: paramiko==3.5.1; extra == 'condarun'
 Requires-Dist: polars==1.31.0; extra == 'condarun'
 Requires-Dist: pyarrow==20.0.0; extra == 'condarun'
@@ -858,7 +858,6 @@ We use [semantic versioning](https://semver.org/) for this project. For the vers
 
 - Ivan Kondratyev ([Inkaros](https://github.com/Inkaros))
 - Kushaan Gupta ([kushaangupta](https://github.com/kushaangupta))
-- Yuantao Deng ([YuantaoDeng](https://github.com/YuantaoDeng))
 - Natalie Yeung
 
 ___

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/README.md

@@ -93,7 +93,6 @@ We use [semantic versioning](https://semver.org/) for this project. For the vers
 
 - Ivan Kondratyev ([Inkaros](https://github.com/Inkaros))
 - Kushaan Gupta ([kushaangupta](https://github.com/kushaangupta))
-- Yuantao Deng ([YuantaoDeng](https://github.com/YuantaoDeng))
 - Natalie Yeung
 
 ___

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/docs/source/api.rst

@@ -25,6 +25,14 @@ Command Line Interfaces
    :prog: sl-ascend-tyche
    :nested: full
 
+.. click:: sl_shared_assets.cli:start_jupyter_server
+   :prog: sl-start-jupyter
+   :nested: full
+
+.. click:: sl_shared_assets.cli:resolve_dataset_marker
+   :prog: sl-dataset-marker
+   :nested: full
+
 Tools
 =====
 .. automodule:: sl_shared_assets.tools

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/docs/source/conf.py

@@ -5,7 +5,7 @@ import importlib_metadata
 project = 'sl-shared-assets'
 # noinspection PyShadowingBuiltins
 copyright = '2025, Sun (NeuroAI) lab'
-authors = ['Ivan Kondratyev', 'Kushaan Gupta', 'Yuantao Deng', 'Natalie Yeung']
+authors = ['Ivan Kondratyev', 'Kushaan Gupta', 'Natalie Yeung']
 # Extracts the project version from the .toml file.
 release = importlib_metadata.version("sl-shared-assets")
 

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/docs/source/welcome.rst

@@ -1,10 +1,11 @@
 Welcome to sl-shared-assets API documentation page
 ==================================================
 
-sl-shared-assets is a Python library that stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
+sl-shared-assets is a Python library that provides data acquisition and processing assets shared between Sun (NeuroAI)
+lab libraries.
 
 This library is developed in the `Sun lab <https://neuroai.github.io/sunlab/>`_ at Cornell University. The main purpose
-of this library is to provide the tools adn assets used by multiple other data acquisition and processing libraries in
+of this library is to provide the tools and assets used by multiple other data acquisition and processing libraries in
 the lab to avoid cross-dependency issues.
 
 This website only contains the API documentation for the classes and methods offered by this library. See the project

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/pyproject.toml

@@ -8,21 +8,21 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "2.0.1"
-description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
+version = "3.0.0rc2"
+description = "Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries."
 readme = "README.md"
 license = { file = "LICENSE" }
 requires-python = ">=3.11"
 authors = [
-    {name = "Ivan Kondratyev"},
-    {name = "Kushaan Gupta"},
-    {name = "Natalie Yeung"}
+    { name = "Ivan Kondratyev" },
+    { name = "Kushaan Gupta" },
+    { name = "Natalie Yeung" }
 ]
 maintainers = [
-    {name = "Ivan Kondratyev", email = "ik278@cornell.edu"},
+    { name = "Ivan Kondratyev", email = "ik278@cornell.edu" },
 ]
 
-keywords = ["sunlab", "data", "assets", "acquisition", "processing"]
+keywords = ["sunlab", "data", "assets", "acquisition", "processing", "server"]
 
 classifiers = [
     # Development status
@@ -44,7 +44,7 @@ dependencies = [
     "ataraxis-time==3.0.0",
     "ataraxis-base-utilities==3.0.1",
     "ataraxis-data-structures==3.1.1",
-    "numpy>=2.0.2,<2.3.0",
+    "numpy==2.2.6",
     "appdirs==1.4.4",
     "tqdm==4.67.1",
     "xxhash==3.5.0",
@@ -70,7 +70,7 @@ Documentation = "https://sl-shared-assets-api-docs.netlify.app/"
 # (OSX ARM64, WIN AMD64, LIN AMD64). This specification is used by ataraxis-automation to resolve as many
 # project dependencies with conda over pip as possible.
 condarun = [
-    "numpy>=2.0.2,<2.3.0",
+    "numpy==2.2.6",
     "appdirs==1.4.4",
     "tqdm==4.67.1",
     "paramiko==3.5.1",
@@ -144,6 +144,8 @@ sl-verify-session = "sl_shared_assets.cli:verify_session_integrity"
 sl-project-manifest = "sl_shared_assets.cli:generate_project_manifest_file"
 sl-create-server-credentials = "sl_shared_assets.cli:generate_server_credentials_file"
 sl-ascend-tyche = "sl_shared_assets.cli:ascend_tyche_directory"
+sl-start-jupyter = "sl_shared_assets.cli:start_jupyter_server"
+sl-dataset-marker = "sl_shared_assets.cli:resolve_dataset_marker"
 
 # Specifies files that should not be included in the source-code distribution but are also not part of gitignore.
 [tool.hatch.build.targets.sdist]

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/src/sl_shared_assets/__init__.py

@@ -2,13 +2,17 @@
 
 See https://github.com/Sun-Lab-NBB/sl-shared-assets for more details.
 API documentation: https://sl-shared-assets-api-docs.netlify.app/
-Authors: Ivan Kondratyev (Inkaros), Kushaan Gupta, Yuantao Deng, Natalie Yeung
+Authors: Ivan Kondratyev (Inkaros), Kushaan Gupta, Natalie Yeung
 """
 
 from ataraxis_base_utilities import console
 
-from .tools import transfer_directory, verify_session_checksum, generate_project_manifest, calculate_directory_checksum
-from .server import Job, Server, ServerCredentials
+from .tools import (
+    resolve_p53_marker,
+    transfer_directory,
+    calculate_directory_checksum,
+)
+from .server import Job, Server, JupyterJob, ServerCredentials
 from .data_classes import (
     RawData,
     DrugData,
@@ -48,6 +52,7 @@ __all__ = [
     "Server",
     "ServerCredentials",
     "Job",
+    "JupyterJob",
     # Data classes package
     "DrugData",
     "ImplantData",
@@ -77,8 +82,7 @@ __all__ = [
     "get_system_configuration_data",
     "set_system_configuration_file",
     # Tools package
+    "resolve_p53_marker",
     "transfer_directory",
-    "generate_project_manifest",
-    "verify_session_checksum",
     "calculate_directory_checksum",
 ]

{sl_shared_assets-2.0.1 → sl_shared_assets-3.0.0rc2}/src/sl_shared_assets/__init__.pyi

@@ -1,12 +1,12 @@
 from .tools import (
+    resolve_p53_marker as resolve_p53_marker,
     transfer_directory as transfer_directory,
-    verify_session_checksum as verify_session_checksum,
-    generate_project_manifest as generate_project_manifest,
     calculate_directory_checksum as calculate_directory_checksum,
 )
 from .server import (
     Job as Job,
     Server as Server,
+    JupyterJob as JupyterJob,
     ServerCredentials as ServerCredentials,
 )
 from .data_classes import (
@@ -43,6 +43,7 @@ __all__ = [
     "Server",
     "ServerCredentials",
     "Job",
+    "JupyterJob",
     "DrugData",
     "ImplantData",
     "SessionData",
@@ -70,8 +71,7 @@ __all__ = [
     "MesoscopeAdditionalFirmware",
     "get_system_configuration_data",
     "set_system_configuration_file",
+    "resolve_p53_marker",
     "transfer_directory",
-    "generate_project_manifest",
-    "verify_session_checksum",
     "calculate_directory_checksum",
 ]

sl_shared_assets-3.0.0rc2/src/sl_shared_assets/cli.py

@@ -0,0 +1,459 @@
+"""This module stores the Command-Line Interfaces (CLIs) exposes by the library as part of the installation process."""
+
+from pathlib import Path
+
+import click
+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
+
+
+@click.command()
+@click.option(
+    "-sp",
+    "--session_path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the session directory whose raw data needs to be verified for potential corruption.",
+)
+@click.option(
+    "-c",
+    "--create_processed_directories",
+    is_flag=True,
+    show_default=True,
+    default=False,
+    help=(
+        "Determines whether to create the processed data hierarchy. This flag should be disabled for most runtimes. "
+        "Primarily, it is used by lab acquisition system code to generate processed data directories on the remote "
+        "compute servers as part of the data preprocessing pipeline."
+    ),
+)
+@click.option(
+    "-pdr",
+    "--processed_data_root",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=False,
+    help=(
+        "The absolute path to the directory where processed data from all projects is stored on the machine that runs "
+        "this command. This argument is used when calling the CLI on the BioHPC server, which uses different data "
+        "volumes for raw and processed data. Note, the input path must point to the root directory, as it will be "
+        "automatically modified to include the project name, the animal id, and the session ID. This argument is only "
+        "used if 'create_processed_directories' flag is True."
+    ),
+)
+def verify_session_integrity(
+    session_path: Path, create_processed_directories: bool, processed_data_root: Path | None
+) -> None:
+    """Checks the integrity of the target session's raw data (contents of the raw_data directory).
+
+    This command assumes that the data has been checksummed during acquisition and contains an ax_checksum.txt file
+    that stores the data checksum generated before transferring the data to long-term storage destination. This function
+    always verified the integrity of the 'raw_data' directory. It does not work with 'processed_data' or any other
+    directories. If the session data was corrupted, the command removes the 'telomere.bin' file, marking the session as
+    'incomplete' and automatically excluding it from all further automated processing runtimes. if the session data
+    is intact, generates a 'verified.bin' marker file inside the session's raw_data folder.
+
+    The command is also used by Sun lab data acquisition systems to generate the processed data hierarchy for each
+    processed session. This use case is fully automated and should not be triggered manually by the user.
+    """
+    session = Path(session_path)
+    session_data = SessionData.load(session_path=session)
+
+    # Runs the verification process
+    verify_session_checksum(
+        session, create_processed_data_directory=create_processed_directories, processed_data_root=processed_data_root
+    )
+
+    # Checks the outcome of the verification process
+    tracker = ProcessingTracker(file_path=session_data.raw_data.integrity_verification_tracker_path)
+    if tracker.is_complete:
+        # noinspection PyTypeChecker
+        console.echo(message=f"Session {session.stem} raw data integrity: Verified.", level=LogLevel.SUCCESS)
+    else:
+        # noinspection PyTypeChecker
+        console.echo(message=f"Session {session.stem} raw data integrity: Compromised!", level=LogLevel.ERROR)
+
+
+@click.command()
+@click.option(
+    "-pp",
+    "--project_path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the project directory where raw session data is stored.",
+)
+@click.option(
+    "-od",
+    "--output_directory",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the directory where to store the generated project manifest file.",
+)
+@click.option(
+    "-ppp",
+    "--project_processed_path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=False,
+    help=(
+        "The absolute path to the project directory where processed session data is stored, if different from the "
+        "directory used to store raw session data. Typically, this extra argument is only used when processing data "
+        "stored on remote compute server(s)."
+    ),
+)
+def generate_project_manifest_file(
+    project_path: Path, output_directory: Path, project_processed_path: Path | None
+) -> None:
+    """Generates the manifest .feather file that provides information about the data-processing state of all available
+    project sessions.
+
+    The manifest file is typically used when batch-processing session data on the remote compute server. It contains the
+    comprehensive snapshot of the available project's data in a table-compatible format that can also be transferred
+    between machines (as it is cached in a file).
+    """
+    generate_project_manifest(
+        raw_project_directory=Path(project_path),
+        output_directory=Path(output_directory),
+        processed_project_directory=Path(project_processed_path) if project_processed_path else None,
+    )
+    # noinspection PyTypeChecker
+    console.echo(message=f"Project {Path(project_path).stem} data manifest file: generated.", level=LogLevel.SUCCESS)
+
+
+@click.command()
+@click.option(
+    "-od",
+    "--output_directory",
+    type=click.Path(exists=False, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the directory where to store the generated server credentials file.",
+)
+@click.option(
+    "-h",
+    "--host",
+    type=str,
+    required=True,
+    show_default=True,
+    default="cbsuwsun.biohpc.cornell.edu",
+    help="The host name or IP address of the server to connect to.",
+)
+@click.option(
+    "-u",
+    "--username",
+    type=str,
+    required=True,
+    help="The username to use for server authentication.",
+)
+@click.option(
+    "-p",
+    "--password",
+    type=str,
+    required=True,
+    help="The password to use for server authentication.",
+)
+@click.option(
+    "-sr",
+    "--storage_root",
+    type=str,
+    required=True,
+    show_default=True,
+    default="/local/storage",
+    help=(
+        "The absolute path to to the root storage (slow) server directory. Typically, this is the path to the "
+        "top-level (root) directory of the HDD RAID volume."
+    ),
+)
+@click.option(
+    "-wr",
+    "--working_root",
+    type=str,
+    required=True,
+    show_default=True,
+    default="/local/workdir",
+    help=(
+        "The absolute path to the root working (fast) server directory. Typically, this is the path to the top-level "
+        "(root) directory of the NVME RAID volume. If the server uses the same volume for both storage and working "
+        "directories, enter the same path under both 'storage_root' and 'working_root'."
+    ),
+)
+@click.option(
+    "-sdn",
+    "--shared_directory_name",
+    type=str,
+    required=True,
+    show_default=True,
+    default="sun_data",
+    help=(
+        "The name of the shared directory used to store all Sun lab project data on the storage and working server "
+        "volumes."
+    ),
+)
+def generate_server_credentials_file(
+    output_directory: Path,
+    host: str,
+    username: str,
+    password: str,
+    storage_root: str,
+    working_root: str,
+    shared_directory_name: str,
+) -> None:
+    """Generates a new server_credentials.yaml file under the specified directory, using input information.
+
+    This command is used to set up access to compute servers and clusters on new machines (PCs). The data stored inside
+    the server_credentials.yaml file generated by this command is used by the Server and Job classes used in many Sun
+    lab data processing libraries.
+    """
+
+    # If necessary, generates the output directory hierarchy before creating the credentials' file.
+    ensure_directory_exists(output_directory)
+
+    # Generates the credentials' file
+    generate_server_credentials(
+        output_directory=Path(output_directory),
+        username=username,
+        password=password,
+        host=host,
+        storage_root=storage_root,
+        working_root=working_root,
+        shared_directory_name=shared_directory_name,
+    )
+    message = (
+        f"Server access credentials file: generated. If necessary, remember to edit the data acquisition system "
+        f"configuration file to include the path to the credentials file generated via this CLI."
+    )
+    # noinspection PyTypeChecker
+    console.echo(message=message, level=LogLevel.SUCCESS)
+    message = f"File location: {output_directory}"
+    # noinspection PyTypeChecker
+    console.echo(message=message, level=LogLevel.SUCCESS)
+
+
+@click.command()
+@click.option(
+    "-id",
+    "--input_directory",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the directory that stores original Tyche animal folders.",
+)
+def ascend_tyche_directory(input_directory: Path) -> None:
+    """Restructures old Tyche project data to use the modern Sun lab data structure and uploads them to the processing
+    server.
+
+    This command is used to convert ('ascend') the old Tyche project data to the modern Sun lab structure. After
+    ascension, the data can be processed and analyzed using all modern Sun lab (sl-) tools and libraries. Note, this
+    process expects the input data to be preprocessed using an old Sun lab mesoscope data preprocessing pipeline. It
+    will not work for any other project or data. Also, this command will only work on a machine (PC) that belongs to a
+    valid Sun lab data acquisition system, such as VRPC of the Mesoscope-VR system.
+    """
+    ascend_tyche_data(root_directory=Path(input_directory))
+
+
+@click.command()
+@click.option(
+    "-cp",
+    "--credentials_path",
+    type=click.Path(exists=True, file_okay=True, dir_okay=False, path_type=Path),
+    required=True,
+    help=(
+        "The absolute path to the server_credentials.yaml file that stores access credentials for the target Sun lab "
+        "server. If necessary, use the 'sl-create-server-credentials' command to generate the file."
+    ),
+)
+@click.option(
+    "-n",
+    "--name",
+    type=str,
+    required=True,
+    show_default=True,
+    default="jupyter_server",
+    help=(
+        "The descriptive name to be given to the remote Jupyter server job. Primarily, this is used to identify the "
+        "job inside the log files."
+    ),
+)
+@click.option(
+    "-e",
+    "--environment",
+    type=str,
+    required=True,
+    help=(
+        "The name of the conda environment to use for running the Jupyter server. At a minimum, the target environment "
+        "must contain the 'jupyterlab' and the 'notebook' Python packages. Note, the user whose credentials are used "
+        "to connect to the server must have a configured conda / mamba shell that exposes the target environment for "
+        "the job to run as expected."
+    ),
+)
+@click.option(
+    "-d",
+    "--directory",
+    type=click.Path(exists=False, file_okay=True, dir_okay=True, path_type=Path),
+    required=False,
+    help=(
+        "The absolute path to the server directory to use as the root directory for the jupyter session. If not "
+        "provided, this is automatically resolved to user's working directory. Note, during runtime, Jupyter will only "
+        "have access to files stored in or under that root directory."
+    ),
+)
+@click.option(
+    "-c",
+    "--cores",
+    type=int,
+    required=True,
+    show_default=True,
+    default=2,
+    help=(
+        "The number of CPU cores to allocate to the Jupyter server. Note, during the interactive Jupyter runtime, it "
+        "is be impossible to use more than this number of CPU cores."
+    ),
+)
+@click.option(
+    "-m",
+    "--memory",
+    type=int,
+    required=True,
+    show_default=True,
+    default=32,
+    help=(
+        "The RAM, in Gigabytes, to allocate to the Jupyter server. Note, during the interactive Jupyter runtime, it "
+        "is be impossible to use more than this amount of RAM."
+    ),
+)
+@click.option(
+    "-t",
+    "--time",
+    type=int,
+    required=True,
+    show_default=True,
+    default=240,
+    help=(
+        "The maximum runtime duration for this Jupyter server instance, in minutes. If the server job is still running "
+        "at the end of this time limit, the job will be forcibly terminated by SLURM. Note, to prevent hogging the "
+        "server, make sure this parameter is always set to the smallest feasible period of time you intend to interact "
+        "with the server."
+    ),
+)
+@click.option(
+    "-p",
+    "--port",
+    type=int,
+    required=True,
+    show_default=True,
+    default=0,
+    help=(
+        "The port to use for the Jupyter server communication on the remote server. Valid port values are from 8888 "
+        "to 9999. Most runtimes should leave this set to the default value (0), which will randomly select one of the "
+        "valid ports. Using random selection minimizes the chances of colliding with other interactive jupyter "
+        "sessions."
+    ),
+)
+def start_jupyter_server(
+    credentials_path: Path, name: str, environment: str, directory: Path, cores: int, memory: int, time: int, port: int
+) -> None:
+    """Starts an interactive Jupyter session on the remote Sun lab server.
+
+    This command should be used to run Jupyter lab and notebooks sessions on the remote Sun lab server. Since all lab
+    data is stored on the server, this allows running light interactive analysis sessions on the same node as the data,
+    while leveraging considerable compute resources of the server.
+
+    Calling this command initializes a SLURM session that runs the interactive Jupyter server. Since this server
+    directly competes for resources with all other headless jobs running on the server, it is imperative that each
+    jupyter runtime uses only the minimum amount of resources and run-time as necessary. Do not use this command to run
+    heavy data processing pipelines! Instead, consult with library documentation and use the headless Job class.
+    """
+    # Initializes server connection
+    server = Server(credentials_path)
+    job: JupyterJob | None = None
+    try:
+        # If the caller did not provide an explicit notebook directory, defaults to user's working directory
+        if directory is None:
+            directory = (server.user_working_root,)
+
+        # Launches the specified Jupyter server
+        job = server.launch_jupyter_server(
+            job_name=name,
+            conda_environment=environment,
+            notebook_directory=directory,
+            cpus_to_use=cores,
+            ram_gb=memory,
+            port=port,
+            time_limit=time,
+        )
+
+        # Displays the server connection details to the user via terminal
+        job.print_connection_info()
+
+        # Blocks in-place until the user shuts down the server. This allows terminating the jupyter job early if the
+        # user is done working with the server
+        input("Enter anything to shut down the server: ")
+
+    # Ensures that the server created as part of this CLI is always terminated when the CLI terminates
+    finally:
+        # Terminates the server job
+        if job is not None:
+            server.abort_job(job)
+
+        # Closes server connection if it is still open
+        server.close()
+
+
+@click.command()
+@click.option(
+    "-sp",
+    "--session_path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    help="The absolute path to the session directory for which to resolve the dataset integration readiness marker.",
+)
+@click.option(
+    "-c",
+    "--create_processed_directories",
+    is_flag=True,
+    show_default=True,
+    default=False,
+    help="Determines whether to create the processed data hierarchy. This flag should be disabled for most runtimes.",
+)
+@click.option(
+    "-ppp",
+    "--project_processed_path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=False,
+    help=(
+        "The absolute path to the project directory where processed session data is stored, if different from the "
+        "directory used to store raw session data. Typically, this extra argument is only used when processing data "
+        "stored on remote compute server(s)."
+    ),
+)
+@click.option(
+    "-r",
+    "--remove",
+    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."
+    ),
+)
+def resolve_dataset_marker(
+    session_path: Path, create_processed_directories: bool, project_processed_path: Path | None, remove: bool
+) -> None:
+    """Depending on configuration, either creates or removes the p53.bin marker from the target session.
+
+    The p53.bin marker determines whether the session is ready for dataset integration. When the marker exists,
+    processing pipelines are not allowed to work with the session data, ensuring that all processed data remains
+    unchanged. If the marker does not exist, dataset integration pipelines are not allowed to work with the session
+    data, enabling processing pipelines to safely modify the data at any time.
+
+    This command is automatically called at the end of each processing runtime to automatically transfer processed
+    sessions to the dataset integration step by creating the p53.bin marker. In contrast, removing the marker can only
+    be done manually.
+    """
+    resolve_p53_marker(
+        session_path=session_path,
+        create_processed_data_directory=create_processed_directories,
+        processed_data_root=project_processed_path,
+        remove=remove,
+    )