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Epic 1 changes made to Ijob and commandline #246

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Epic 1 changes made to Ijob and commandline #246

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157 changes: 85 additions & 72 deletions MDANSE/Scripts/mdanse
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Original file line number Diff line number Diff line change
Expand Up @@ -291,90 +291,103 @@ class CommandLineParser(optparse.OptionParser):
@type parser: instance of MDANSEOptionParser
'''

if len(parser.rargs) != 1:
raise CommandLineParserError("Invalid number of arguments for %r option" % opt_str)

jobs = REGISTRY["job"]

name = parser.rargs[0]

# A name for the template is built.
filename = os.path.abspath('template_%s.py' % name.lower())
jobs[name].save(filename)
if len(parser.rargs) != 1:
raise CommandLineParserError("Invalid number of arguments for %r option" % opt_str)

jobs = REGISTRY["job"]

name = parser.rargs[0]

try:
job_instance = jobs[name]
except KeyError:
raise CommandLineParserError("The job %r is not a valid MDANSE job" % name)

# Try to save the template for the job.
try:
jobs[name].save(filename)
# Case where an error occured when writing the template.
except IOError:
raise CommandLineParserError("Could not write the job template as %r" % filename)
# If the job class has no save method, thisis not a valid MDANSE job.
except KeyError:
raise CommandLineParserError("The job %r is not a valid MDANSE job" % name)
# Otherwise, print some information about the saved template.
else:
print("Saved template for job %r as %r" % (name, filename))
try:
# Serialize the job instance to JSON format
json_template = job_instance.to_json()

def save_job_template(self, option, opt_str, value, parser):
'''
Save job templates.

@param option: the option that triggered the callback.
@type option: optparse.Option instance

@param opt_str: the option string seen on the command line.
@type opt_str: str
# Define the filename for the JSON template
filename = os.path.abspath('template_%s.json' % name.lower())

# Write the JSON template to the file
with open(filename, 'w') as json_file:
json_file.write(json_template)

@param value: the argument for the option.
@type value: str
print("Saved template for job %r as %r" % (name, filename))

@param parser: the MDANSE option parser.
@type parser: instance of MDANSEOptionParser
'''
except IOError as e:
raise CommandLineParserError("Could not write the job template as %r: %s" % (filename, str(e)))
except Exception as e:
raise CommandLineParserError("An error occurred while saving the job template: %s" % str(e))

nargs = len(parser.rargs)

from MDANSE.Framework.Jobs.IJob import IJob
def save_job(self, option, opt_str, value, parser):
"""
Save job templates.

if nargs != 2:
print("Two arguments required resp. the name and the shortname of the class to be templated")
return
Args:
option: The option that triggered the callback.
opt_str: The option string seen on the command line.
value: The argument for the option.
parser: The MDANSE option parser.
"""

classname,shortname = parser.rargs
if len(parser.rargs) != 1:
raise CommandLineParserError("Invalid number of arguments for %r option" % opt_str)

try:
IJob.save_template(shortname,classname)
except (IOError,KeyError) as e:
LOGGER(str(e),'error',['console'])
return

if __name__ == "__main__":
jobs = REGISTRY["job"]
name = parser.rargs[0]

from MDANSE.__pkginfo__ import __version__, __date__
# Ensure the job class exists in the registry
if name not in jobs:
raise CommandLineParserError("The job %r is not a valid MDANSE job" % name)

# Creates the option parser.
parser = CommandLineParser(formatter=IndentedHelp(), version = 'MDANSE %s (%s)' % (__version__, __date__))
# Create a dictionary to represent the job
job_dict = {
"job_type": name,
"parameters": jobs[name].get_default_parameters() # Assuming get_default_parameters() returns a dictionary
}

# Creates a first the group of general options.
group = optparse.OptionGroup(parser, "General options")
group.add_option('-d', '--database', action='callback', callback=parser.display_element_info, help='Display chemical informations about a given element.')
group.add_option('-r', '--registry', action='callback', callback=parser.query_classes_registry, help='Display the contents of MDANSE classes registry.')
group.add_option('-t', '--traj', action='callback', callback=parser.display_trajectory_contents, help='Display the chemical contents of a trajectory.')
# Specify the filename for the saved job
filename = f"job_{name}.json"

# Add the goup to the parser.
parser.add_option_group(group)

# Creates a second group of job-specific options.
group = optparse.OptionGroup(parser, "Job managing options")
with open(filename, 'w') as json_file:
json.dump(job_dict, json_file, indent=4)

# Add the goup to the parser.
parser.add_option_group(group)
print(f"Saved template for job {name} as {filename}")


if __name__ == "__main__":
from MDANSE.__pkginfo__ import __version__, __date__

group.add_option('--jc', action='callback', callback=parser.check_job, help='Check the status of a given job.')
group.add_option('--jl', action='callback', callback=parser.display_jobs_list, help='Display the jobs list.')
group.add_option('--jr', action='callback', callback=parser.run_job, help='Run MDANSE job(s).')
group.add_option('--js', action='callback', callback=parser.save_job, help='Save a job script with default patameters.', metavar = "MDANSE_SCRIPT")
group.add_option('--jt', action='callback', callback=parser.save_job_template, help='Save a job template.', metavar = "MDANSE_SCRIPT")

# The command line is parsed.
options, _ = parser.parse_args()
# Create the option parser.
parser = CommandLineParser(formatter=IndentedHelp(), version='MDANSE %s (%s)' % (__version__, __date__))

# Create a group for general options.
general_options = optparse.OptionGroup(parser, "General options")
general_options.add_option('-d', '--database', action='callback', callback=parser.display_element_info,
help='Display chemical information about a given element.')
general_options.add_option('-r', '--registry', action='callback', callback=parser.query_classes_registry,
help='Display the contents of MDANSE classes registry.')
general_options.add_option('-t', '--traj', action='callback', callback=parser.display_trajectory_contents,
help='Display the chemical contents of a trajectory.')

# Add the general option group to the parser.
parser.add_option_group(general_options)

# Create a group for job-specific options.
job_options = optparse.OptionGroup(parser, "Job managing options")
job_options.add_option('--jc', action='callback', callback=parser.check_job, help='Check the status of a given job.')
job_options.add_option('--jl', action='callback', callback=parser.display_jobs_list, help='Display the jobs list.')
job_options.add_option('--jr', action='callback', callback=parser.run_job, help='Run MDANSE job(s).')
job_options.add_option('--js', action='callback', callback=parser.save_job,
help='Save a job script with default parameters.', metavar="MDANSE_SCRIPT")
job_options.add_option('--jt', action='callback', callback=parser.save_job_template, help='Save a job template.',
metavar="MDANSE_SCRIPT")

# Add the job-specific option group to the parser.
parser.add_option_group(job_options)

# The command line is parsed.
options, _ = parser.parse_args()
71 changes: 31 additions & 40 deletions MDANSE/Src/Framework/Jobs/IJob.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
#
# **************************************************************************

import json
import abc
import glob
import os
Expand Down Expand Up @@ -156,47 +157,37 @@ def save(cls, jobFile, parameters=None):
#. jobFile (str): The name of the output job file.\n
#. parameters (dict): optional. If not None, the parameters with which the job file will be built.
"""

job_data = {
"job_type": cls._type,
"parameters": parameters if parameters else cls.get_default_parameters()
}

with open(jobFile, 'w') as json_file:
json.dump(job_data, json_file, indent=4)

f = open(jobFile, "w")

# The first line contains the call to the python executable. This is necessary for the file to
# be autostartable.
f.write("#!%s\n\n" % sys.executable)

# Writes the input file header.
f.write("########################################################\n")
f.write("# This is an automatically generated MDANSE run script #\n")
f.write("########################################################\n\n")

# Write the import.
f.write("from MDANSE import REGISTRY\n\n")

f.write("################################################################\n")
f.write("# Job parameters #\n")
f.write("################################################################\n\n")

# Writes the line that will initialize the |parameters| dictionary.
f.write("parameters = {}\n")

if parameters is None:
parameters = cls.get_default_parameters()

for k, v in sorted(parameters.items()):
f.write("parameters[%r] = %r\n" % (k, v))

f.write("\n")
f.write("################################################################\n")
f.write("# Setup and run the analysis #\n")
f.write("################################################################\n")
f.write("\n")

f.write('if __name__ == "__main__":\n')
f.write(" %s = REGISTRY[%r][%r]()\n" % (cls._type, "job", cls._type))
f.write(" %s.run(parameters,status=True)" % (cls._type))

f.close()

os.chmod(jobFile, stat.S_IRWXU)
@classmethod
def from_json(cls, filename):
"""
Load a job object from a JSON file.

Args:
filename (str): The name of the JSON file to load.

Returns:
IJob: An instance of the job class.
"""
with open(filename, 'r') as json_file:
job_data = json.load(json_file)

job_type = job_data["job_type"]
parameters = job_data["parameters"]

# Create an instance of the job class and set its parameters
job = cls()
job.set_parameters(parameters)

return job

def combine(self):
if self._status is not None:
Expand Down
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