Added jobcard runner

km3buu/ctrl.py

+# Filename: ctrl.py
+"""
+Run and control tools for GiBUU
+
+"""
+
+__author__ = "Johannes Schumann"
+__copyright__ = "Copyright 2020, Johannes Schumann and the KM3NeT collaboration."
+__credits__ = []
+__license__ = "MIT"
+__maintainer__ = "Johannes Schumann"
+__email__ = "jschumann@km3net.de"
+__status__ = "Development"
+
+import os
+from spython.main import Client
+from os.path import join, abspath
+from tempfile import NamedTemporaryFile
+from . import MODULE_PATH, IMAGE_PATH
+from thepipe.logger import get_logger
+
+log = get_logger(__file__)
+
+INPUT_PATH = "/opt/buuinput2019/"
+
+GIBUU_SHELL = """
+#!/bin/bash
+
+if [ -z "$CONTAINER_GIBUU_EXEC+x" ];                                            
+then                                                                            
+    echo "No GIBUU executable provided via CONTAINER_GIBUU_EXEC";               
+    exit 1                                                                      
+fi;
+
+cd {0};
+
+$CONTAINER_GIBUU_EXEC < {1};
+"""
+
+
+def run_jobcard(jobcard, outdir):
+    """
+    method for run 
+
+    Parameters
+    ----------
+    jobcard: km3buu.JobCard
+        The jobcard which should be run
+    outdir: str
+        The path to the directory the output should be written to
+    """
+    tmp_dir = join(MODULE_PATH, 'tmp')
+    os.makedirs(tmp_dir, exist_ok=True)
+    outdir = abspath(outdir)
+    log.info("Create temporary file for jobcard")
+    tmpfile_jobcard = NamedTemporaryFile(suffix='.job', dir=tmp_dir)
+    with open(tmpfile_jobcard.name, 'w') as f:
+        f.write(str(jobcard))
+    log.info("Create temporary file for associated runscript")
+    tmpfile_shell = NamedTemporaryFile(suffix='.sh', dir=tmp_dir)
+    with open(tmpfile_shell.name, 'w') as f:
+        ctnt = GIBUU_SHELL.format(outdir, tmpfile_jobcard.name)
+        f.write(ctnt)
+    output = Client.execute(IMAGE_PATH, ['/bin/sh', tmpfile_shell.name],
+                            bind=[outdir, tmp_dir])
+    log.info("GiBUU exited with return code {0}".format(output["return_code"]))
+    return output["return_code"]