Clean up

solosis/cli.py

@@ -3,7 +3,7 @@
 import click
 
 from solosis.commands.alignment import cellranger_arc, cellranger_count, starsolo
-from solosis.commands.farm import farm
+from solosis.commands.farm import single_job
 from solosis.commands.filesystem import disk_usage, file_count
 from solosis.commands.irods import iget_cellranger, iget_fastqs
 from solosis.commands.ncl_bsu import migrate
@@ -91,7 +91,7 @@ def sc_rna():
 
 # farm
 farm_cmds.add_command(farm.single_cmd)
-farm_cmds.add_command(farm.run_ipynb)
+#farm_cmds.add_command(farm.run_ipynb)
 
 if __name__ == "__main__":
     cli()

solosis/commands/farm/run_notebook.py

@@ -0,0 +1,37 @@
+import os
+import subprocess
+import click
+from .. import helpers
+from solosis.utils import echo_lsf_submission_message, echo_message, log_command, bash_submit
+
+# Script directory in the solosis package
+script_dir = os.path.dirname(os.path.abspath(__file__))  
+codebase = os.path.join(script_dir, "..", "..", "codebase")
+
+
+
+@click.command("run_ipynb")
+@helpers.farm
+@click.option(
+    "-n", "--notebook", required=True, type=str, help="Path to the notebook to run"
+)
+@click.option(
+    "-j",
+    "--job_name",
+    required=False,
+    type=str,
+    help="Name of the job"
+)  
+
+def run_ipynb(notebook, job_name, **kwargs):
+    """
+    Run a jupyter notebook on the farm.
+    """
+    job_runner = os.path.join(codebase, "single_job.sh")
+    # To do: Install jupyter in base solosis conda env
+    command_to_exec = f"source ~/.bashrc && conda activate /software/cellgen/team298/shared/envs/hl-conda/hl_minimal_v1.0.0 && jupyter nbconvert --to notebook --execute {notebook}"
+    bash_submit(
+        job_runner, command_to_exec=command_to_exec, job_name="notebook", **kwargs
+    )
+
+

solosis/commands/farm/farm.py → solosis/commands/farm/single_job.py

@@ -6,7 +6,7 @@
 
 # Script directory in the solosis package
 script_dir = os.path.dirname(os.path.abspath(__file__))  
-
+codebase = os.path.join(script_dir, "..", "..", "..", "bin")
 
 ## Functions supporting farm submission
 def bash_submit(job_runner: str, **kwargs) -> None:
@@ -33,7 +33,7 @@ def _single_command_bsub(command_to_exec, job_name, queue, time, cores, mem, **k
     Run a single command on the farm.
     """
     job_runner = os.path.abspath(
-        os.path.join(script_dir, "../../../bin/farm/single_job.sh")
+        os.path.join(codebase, "/farm/single_job.sh")
         )
     if len(command_to_exec) == 0:
         echo_message("No command to execute", type="error")
@@ -68,38 +68,13 @@ def single_cmd(ctx, command_to_exec, job_name, **kwargs):
     mem = kwargs.get("mem")
     log_command(ctx)
     if job_name == "default":
-        job_name = f"{ctx.command_path}_{ctx.obj['execution_id']}"
+        job_name = f"{ctx.obj['execution_id']}"
     else:
         job_name = f"{job_name}_{ctx.obj['execution_id']}"
-    echo_lsf_submission_message(f"Job name :{job_name} submitted to queue: {queue}")
+    echo_message(f"Job name :{job_name} submitted to queue: {queue}")
     _single_command_bsub(command_to_exec, job_name=job_name, **kwargs)
 
 
-@click.command("run_ipynb")
-@helpers.farm
-@click.option(
-    "-n", "--notebook", required=True, type=str, help="Path to the notebook to run"
-)
-@click.option(
-    "-j",
-    "--job_name",
-    required=False,
-    type=str,
-    help="Name of the job",
-)  # random val to be implemented (from import random)
-
-
-def run_ipynb(notebook, job_name, **kwargs):
-    """
-    Run a jupyter notebook on the farm.
-    """
-    job_runner = os.path.join(codebase, "single_job.sh")
-    # To do: Install jupyter in base solosis conda env
-    command_to_exec = f"source ~/.bashrc && conda activate /software/cellgen/team298/shared/envs/hl-conda/hl_minimal_v1.0.0 && jupyter nbconvert --to notebook --execute {notebook}"
-    bash_submit(
-        job_runner, command_to_exec=command_to_exec, job_name="notebook", **kwargs
-    )
-
 
 if __name__ == "__main__":
     cmd = os.path.join(codebase, "test.sh")

solosis/utils.py

@@ -2,7 +2,7 @@
 import os
 import re
 from datetime import datetime
-
+import subprocess
 import click
 
 
@@ -104,3 +104,25 @@ def echo_lsf_submission_message(job_stdout):
 
     echo_message("Use `bjobs` to monitor job completion.", "info")
     echo_message("View job logs at $HOME/logs.", "info")
+
+
+## Functions supporting farm submission
+def bash_submit(job_runner: str, **kwargs) -> None:
+    """
+    Runs a command. Command can be a bash command (du -hs ) or a script (test.sh)
+    While running exports all kwargs as environment variables
+    This can be reused to run any bash script in all the subcommands
+    If the command needs to be submitted to farm use single_command or array_command
+    """
+    # env variables are set to
+    for k, v in kwargs.items():
+        kwargs[str(k)] = str(v)
+    # Capture result
+    result = subprocess.run(
+        [job_runner], capture_output=True, text=True, env={**os.environ, **kwargs}
+    )
+
+    click.echo(result.stdout)
+    click.echo(result.stderr)
+
+