Conform with GAPs-style Status class

sup3r/utilities/cli.py

@@ -8,20 +8,39 @@
 import os
 import json
 
-from reV.pipeline.status import Status
+from gaps import Status
+from gaps.config import load_config
 
 from rex.utilities.execution import SubprocessManager
 from rex.utilities.hpc import SLURM
 from rex.utilities.loggers import init_mult
 
 from sup3r.version import __version__
-from sup3r.pipeline.config import BaseConfig
 from sup3r.utilities import ModuleName
 
 
 logger = logging.getLogger(__name__)
 
 
+class SlurmManager(SLURM):
+ """GAPs-compliant SLURM manager"""
+
+ def check_status_using_job_id(self, job_id):
+ """Check the status of a job using the HPC queue and job ID.
+
+ Parameters
+ ----------
+ job_id : int
+ Job integer ID number.
+
+ Returns
+ -------
+ status : str | None
+ Queue job status string or `None` if not found.
+ """
+ return self.check_status(job_id=job_id)
+
+
 class BaseCLI:
  """Base CLI class used to create CLI for modules in ModuleName"""
 
@@ -89,7 +108,7 @@ def from_config_preflight(cls, module_name, ctx, config_file, verbose):
  ctx.obj['VERBOSE'] = verbose
  status_dir = os.path.dirname(os.path.abspath(config_file))
  ctx.obj['OUT_DIR'] = status_dir
- config = BaseConfig(config_file)
+ config = load_config(config_file)
  config['status_dir'] = status_dir
  log_file = config.get('log_file', None)
  log_pattern = config.get('log_pattern', None)
@@ -167,20 +186,21 @@ def kickoff_slurm_job(cls, module_name, ctx, cmd, alloc='sup3r',
  out_dir = ctx.obj['OUT_DIR']
  slurm_manager = ctx.obj.get('SLURM_MANAGER', None)
  if slurm_manager is None:
- slurm_manager = SLURM()
+ slurm_manager = SlurmManager()
  ctx.obj['SLURM_MANAGER'] = slurm_manager
 
  status = Status.retrieve_job_status(out_dir,
- module=module_name,
+ command=module_name,
  job_name=name,
- hardware='slurm',
  subprocess_manager=slurm_manager)
 
  msg = f'sup3r {module_name} CLI failed to submit jobs!'
  if status == 'successful':
  msg = (f'Job "{name}" is successful in status json found in '
  f'"{out_dir}", not re-running.')
- elif 'fail' not in str(status).lower() and status is not None:
+ elif ('fail' not in str(status).lower()
+ and status != 'not submitted'
+ and status is not None):
  msg = (f'Job "{name}" was found with status "{status}", not '
  'resubmitting')
  else:
@@ -193,15 +213,16 @@ def kickoff_slurm_job(cls, module_name, ctx, cmd, alloc='sup3r',
  feature=feature,
  name=name,
  stdout_path=stdout_path)[0]
+
  if out:
  msg = (f'Kicked off sup3r {module_name} job "{name}" '
  f'(SLURM jobid #{out}).')
 
  # add job to sup3r status file.
- Status.add_job(out_dir, module=module_name,
- job_name=name, replace=True,
- job_attrs={'job_id': out, 'hardware': 'slurm'})
-
+ Status.mark_job_as_submitted(out_dir, command=module_name,
+  job_name=name, replace=True,
+  job_attrs={'job_id': out,
+ 'hardware': 'slurm'})
  click.echo(msg)
  logger.info(msg)
 
@@ -225,20 +246,22 @@ def kickoff_local_job(cls, module_name, ctx, cmd):
  out_dir = ctx.obj['OUT_DIR']
  subprocess_manager = SubprocessManager
  status = Status.retrieve_job_status(out_dir,
- module=module_name,
+ command=module_name,
  job_name=name)
  msg = f'sup3r {module_name} CLI failed to submit jobs!'
  if status == 'successful':
  msg = (f'Job "{name}" is successful in status json found in '
  f'"{out_dir}", not re-running.')
- elif 'fail' not in str(status).lower() and status is not None:
+ elif ('fail' not in str(status).lower()
+ and status != 'not submitted'
+ and status is not None):
  msg = (f'Job "{name}" was found with status "{status}", not '
  'resubmitting')
  else:
  logger.info(f'Running sup3r {module_name} locally with job '
  f'name "{name}".')
- Status.add_job(out_dir, module=module_name, job_name=name,
- replace=True)
+ Status.mark_job_as_submitted(out_dir, command=module_name,
+  job_name=name, replace=True)
  subprocess_manager.submit(cmd)
  msg = (f'Completed sup3r {module_name} job "{name}".')
 
@@ -269,7 +292,7 @@ def add_status_cmd(cls, config, module_name, cmd):
  status_dir = config.get('status_dir', None)
  if job_name is not None and status_dir is not None:
  status_file_arg_str = f'"{status_dir}", '
- status_file_arg_str += f'module="{module_name}", '
+ status_file_arg_str += f'command="{module_name}", '
  status_file_arg_str += f'job_name="{job_name}", '
  status_file_arg_str += 'attrs=job_attrs'
 
@@ -279,6 +302,6 @@ def add_status_cmd(cls, config, module_name, cmd):
  .replace("true", "True")))
  cmd += 'job_attrs.update({"job_status": "successful"});\n'
  cmd += 'job_attrs.update({"time": t_elap});\n'
- cmd += f"Status.make_job_file({status_file_arg_str})"
+ cmd += f"Status.make_single_job_file({status_file_arg_str})"
 
  return cmd