move prod night parsing to a func

bin/desi_submit_prod

@@ -12,8 +12,11 @@ def parse_args():  # options=None):
     """
     parser = argparse.ArgumentParser(description="Submit a full production run of the DESI data pipeline for processing.")
 
-    parser.add_argument("--production-yaml", type=str, required=True,
+    parser.add_argument("-p", "--production-yaml", type=str, required=True,
                         help="Relative or absolute pathname to the yaml file summarizing the production.")
+    parser.add_argument("-p", "--queue-threshold", type=int, default=4800,
+                        help="The number of jobs for the current user in the queue at which the"
+                             + " at which the script stops submitting new jobs.")
 
     # Code Flags
     parser.add_argument("--dry-run-level", type=int, default=0,

py/desispec/scripts/submit_prod.py

@@ -22,12 +22,12 @@
 from desispec.workflow.queue import check_queue_count
 
 
-def get_all_nights(first_night, last_night):
+def get_nights_in_date_range(first_night, last_night):
     """
     Returns a full list of all nights that have an exposure table
     exposure
 
-    Inputs:
+    Args:
         first_night, int. First night to include (inclusive).
         last_night, int. Last night to include (inclusive).
 
@@ -52,7 +52,7 @@ def get_all_valid_nights(first_night, last_night):
     Returns a full list of all nights that have at least one valid science
     exposure
 
-    Inputs:
+    Args:
         first_night, int. First night to include (inclusive).
         last_night, int. Last night to include (inclusive).
 
@@ -65,14 +65,80 @@ def get_all_valid_nights(first_night, last_night):
     nights = nights[((nights>=first_night)&(nights<=last_night))]
     return nights
 
+def get_nights_to_process(production_yaml, verbose=False):
+    """
+    Derives the nights to be processed based on a production yaml file and
+    returns a list of int nights.
+
+    Args:
+        production_yaml (str or dict): Production yaml or pathname of the 
+            yaml file that defines the production.
+        verbose (bool): Whether to be verbose in log outputs.
+
+    Returns:
+        nights, list. A list of nights on or after Jan 1 2020 in which data exists at NERSC.
+    """
+    log = get_logger()
+    ## If production_yaml not loaded, load the file
+    if isinstance(production_yaml, str):
+        if not os.path.exists(production_yaml):
+            raise IOError(f"Prod yaml file doesn't exist: {production_yaml} not found.")
+        with open(production_yaml, 'rb') as yamlfile:
+            config = yaml.safe_load(yamlfile)
+    else:
+        config = production_yaml
+
+    all_nights, first_night = None, None
+    if 'NIGHTS' in config and 'LAST_NIGHT' in config:
+        log.error(f"Both NIGHTS and LAST_NIGHT specified. Using NIGHTS "
+                  + f"and ignoring LAST_NIGHT.")
+    if 'NIGHTS' in config:
+        all_nights = np.array(list(config['NIGHTS'])).astype(int)
+        if verbose:
+            log.info(f"Setting all_nights to NIGHTS: {all_nights}")
+            log.info("Setting first_night to earliest night in NIGHTS:"
+                     + f" {np.min(all_nights)}")
+        first_night = np.min(all_nights)
+        if verbose:
+            log.info("Setting last_night to latest night in NIGHTS: "
+                     + f"{np.max(all_nights)}")
+        last_night = np.max(all_nights)
+    elif 'LAST_NIGHT' in config:
+        last_night = int(config['LAST_NIGHT'])
+        if verbose:
+            log.info(f"Setting last_night to LATEST_NIGHT: {last_night}")
+    else:
+        raise ValueError("Either NIGHT or LAST_NIGHT required in yaml "
+                         + f"file {production_yaml}")
+
+    if first_night is None:
+        if 'FIRST_NIGHT' in config:
+            first_night = int(config['FIRST_NIGHT'])
+            if verbose:
+                log.info(f"Setting first_night to FIRST_NIGHT: {first_night}")
+        else:
+            if verbose:
+                log.info("Setting first_night to earliest in a normal prod: 20201214")
+            first_night = 20201214
+
+    if all_nights is None:
+        # all_nights = get_nights_in_date_range(first_night, last_night)
+        if verbose:
+            log.info("Populating all_nights with all of the nights with valid science "
+                     + f"exposures between {first_night} and {last_night} inclusive")
+        all_nights = get_all_valid_nights(first_night, last_night)
+    return sorted(all_nights)
+
 
-def submit_production(production_yaml, dry_run_level=False):
+def submit_production(production_yaml, queue_threshold=4800, dry_run_level=False):
     """
     Interprets a production_yaml file and submits the respective nights for processing
     within the defined production.
 
     Args:
         production_yaml (str): Pathname of the yaml file that defines the production.
+        queue_threshold (int): The number of jobs for the current user in the queue
+            at which the script stops submitting new jobs.
         dry_run_level (int, optional): Default is 0. Should the jobs written to the processing table actually be submitted
             for processing. This is passed directly to desi_proc_night.
 
@@ -103,47 +169,15 @@ def submit_production(production_yaml, dry_run_level=False):
         return 0
 
     ## Load the nights to process
-    all_nights, first_night = None, None
-    if 'NIGHTS' in conf and 'LAST_NIGHT' in conf:
-        log.error(f"Both NIGHTS and LAST_NIGHT specified. Using NIGHTS "
-                  + f"and ignoring LAST_NIGHT.")
-    if 'NIGHTS' in conf:
-        all_nights = np.array(list(conf['NIGHTS'])).astype(int)
-        log.info(f"Setting all_nights to NIGHTS: {all_nights}")
-        log.info("Setting first_night to earliest night in NIGHTS:"
-                 + f" {np.min(all_nights)}")
-        first_night = np.min(all_nights)
-        log.info("Setting last_night to latest night in NIGHTS: "
-                 + f"{np.max(all_nights)}")
-        last_night = np.max(all_nights)
-    elif 'LAST_NIGHT' in conf:
-        last_night = int(conf['LAST_NIGHT'])
-        log.info(f"Setting last_night to LATEST_NIGHT: {last_night}")
-    else:
-        raise ValueError("Either NIGHT or LAST_NIGHT required in yaml "
-                         + f"file {production_yaml}")
-
-    if first_night is None:
-        if 'FIRST_NIGHT' in conf:
-            first_night = int(conf['FIRST_NIGHT'])
-            log.info(f"Setting first_night to FIRST_NIGHT: {first_night}")
-        else:
-            log.info("Setting first_night to earliest in a normal prod: 20201214")
-            first_night = 20201214
-
-    if all_nights is None:
-        # all_nights = get_all_nights(first_night, last_night)
-        log.info("Populating all_nights with all of the nights with valid science "
-                 + f"exposures between {first_night} and {last_night} inclusive")
-        all_nights = get_all_valid_nights(first_night, last_night)
+    all_nights = get_nights_to_process(production_yaml=conf, verbose=True)
 
     ## Load the other parameters for running desi_proc_night
     if 'THRU_NIGHT' in conf:
         thru_night = int(conf['THRU_NIGHT'])
         log.info(f"Setting thru_night to THRU_NIGHT: {thru_night}")
     else:
-        thru_night = last_night
-        log.warning(f"Setting thru_night to last_night: {thru_night}")
+        thru_night = np.max(all_nights)
+        log.warning(f"Setting thru_night to last night: {thru_night}")
 
     ## If not specified, run "cumulative" redshifts, otherwise do
     ## as directed
@@ -207,9 +241,10 @@ def submit_production(production_yaml, dry_run_level=False):
     for night in sorted(all_nights):
         num_in_queue = check_queue_count(user=user, include_scron=False,
                                          dry_run_level=dry_run_level)
-        ## In Jura the largest night had 115 jobs, to be conservative say 200
-        if num_in_queue > 4800:
-            log.info(f"{num_in_queue} jobs in the queue, so stopping the job submissions.")
+        ## In Jura the largest night had 115 jobs, to be conservative say 200 by default
+        if num_in_queue > queue_threshold:
+            log.info(f"{num_in_queue} jobs in the queue > {queue_threshold},"
+                     + " so stopping the job submissions.")
             break
         if os.path.exists(findfile('proctable', night=night, readonly=True)):
             skipped_nights.append(night)

py/desispec/workflow/queue.py

@@ -539,6 +539,11 @@ def get_jobs_in_queue(user=None, include_scron=False, dry_run_level=0):
     for col in queue_info_table.colnames:
         queue_info_table.rename_column(col, col.upper())
 
+    ## If the table is empty, return it immediately, otherwise perform
+    ## sanity check and cuts
+    if len(queue_info_table) == 0:
+        return queue_info_table
+
     if np.any(queue_info_table['USER']!=user):
         msg = f"Warning {np.sum(queue_info_table['USER']!=user)} " \
               + f"jobs returned were not {user=}\n" \