sl-shared-assets 4.0.0__py3-none-any.whl → 5.0.0__py3-none-any.whl

sl_shared_assets/data_classes/surgery_data.py

@@ -65,7 +65,7 @@ class ImplantData:
     """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
+    implant_code: str
     """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
@@ -89,7 +89,7 @@ class InjectionData:
     """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
+    injection_code: str
     """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
@@ -108,22 +108,22 @@ class DrugData:
 
     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
+    lactated_ringers_solution_code: str
     """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
+    ketoprofen_code: str
     """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
+    buprenorphine_code: str
     """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
+    dexamethasone_code: str
     """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."""
 

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