sl-shared-assets 4.0.1__py3-none-any.whl → 5.0.1__py3-none-any.whl

sl_shared_assets/server/__init__.py

@@ -1,8 +1,28 @@
-"""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."""
+"""This package provides the classes and methods used by all Sun lab libraries to work with the data stored on remote
+compute servers, such as the BioHPC server. It provides tools for submitting and monitoring jobs, running complex
+processing pipelines and interactively working with the data via a Jupyter lab server."""
 
 from .job import Job, JupyterJob
 from .server import Server, ServerCredentials, generate_server_credentials
+from .pipeline import (
+    ProcessingStatus,
+    TrackerFileNames,
+    ProcessingTracker,
+    ProcessingPipeline,
+    ProcessingPipelines,
+    generate_manager_id,
+)
 
-__all__ = ["Server", "ServerCredentials", "generate_server_credentials", "Job", "JupyterJob"]
+__all__ = [
+    "Job",
+    "JupyterJob",
+    "ProcessingPipeline",
+    "ProcessingPipelines",
+    "ProcessingStatus",
+    "ProcessingTracker",
+    "Server",
+    "ServerCredentials",
+    "TrackerFileNames",
+    "generate_manager_id",
+    "generate_server_credentials",
+]

sl_shared_assets/server/job.py

@@ -7,7 +7,6 @@ Since version 3.0.0, this module also provides the specialized JupyterJob class
 notebook servers.
 """
 
-# noinspection PyProtectedMember
 import re
 from pathlib import Path
 import datetime
@@ -49,7 +48,7 @@ class _JupyterConnectionInfo:
 
 
 class Job:
-    """Aggregates the data of a single SLURM-managed job to be executed on the Sun lab BioHPC cluster.
+    """Aggregates the data of a single SLURM-managed job to be executed on the Sun lab's remote compute server.
 
     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
@@ -222,7 +221,7 @@ class JupyterJob(Job):
         connection_info: Stores the JupyterConnectionInfo instance after the Jupyter server is instantiated.
         host: Stores the hostname of the remote server.
         user: Stores the username used to connect with the remote server.
-        connection_info_file: The absolute path to the file that stores connection information, relative to the remote
+        connection_info_file: The absolute path to the file that stores connection information relative to the remote
             server root.
         _command: Stores the shell command for launching the Jupyter server.
     """
@@ -273,12 +272,12 @@ class JupyterJob(Job):
         """Builds the command to launch the Jupyter notebook server on the remote Sun lab server."""
 
         # Gets the hostname of the compute node and caches it in the connection data file. Also caches the port name.
-        self.add_command('echo "COMPUTE_NODE: $(hostname)" > {}'.format(self.connection_info_file))
-        self.add_command('echo "PORT: {}" >> {}'.format(self.port, self.connection_info_file))
+        self.add_command(f'echo "COMPUTE_NODE: $(hostname)" > {self.connection_info_file}')
+        self.add_command(f'echo "PORT: {self.port}" >> {self.connection_info_file}')
 
         # Generates a random access token for security and caches it in the connection data file.
         self.add_command("TOKEN=$(openssl rand -hex 24)")
-        self.add_command('echo "TOKEN: $TOKEN" >> {}'.format(self.connection_info_file))
+        self.add_command(f'echo "TOKEN: $TOKEN" >> {self.connection_info_file}')
 
         # Builds Jupyter startup command.
         jupyter_cmd = [
@@ -312,7 +311,7 @@ class JupyterJob(Job):
                 information to be parsed.
         """
 
-        with open(info_file, "r") as f:
+        with info_file.open() as f:
             content = f.read()
 
         # Extracts information using regex