fixes polcal 47 (#619)

Co-authored-by: bennahugo <[email protected]>
Co-authored-by: Sphesihle Makhathini <[email protected]>

stimela/cargo/cab/casa47_polcal/src/run.py

@@ -2,17 +2,21 @@
 import sys
 import logging
 import Crasa.Crasa as crasa
-
-sys.path.append("/scratch/stimela")
-
-utils = __import__('utils')
+from casacore.tables import table
+import numpy
+import glob
+import yaml
+import shutil
 
 CONFIG = os.environ["CONFIG"]
 INPUT = os.environ["INPUT"]
 OUTPUT = os.environ["OUTPUT"]
 MSDIR = os.environ["MSDIR"]
 
-cab = utils.readJson(CONFIG)
+with open(CONFIG, "r") as _std:
+    cab = yaml.safe_load(_std)
+
+junk = cab["junk"]
 
 args = {}
 for param in cab['parameters']:
@@ -25,4 +29,37 @@
     args[name] = value
 
 task = crasa.CasaTask(cab["binary"], **args)
-task.run()
+try:
+    task.run()
+finally:
+    for item in junk:
+        for dest in [OUTPUT, MSDIR]: # these are the only writable volumes in the container
+            items = glob.glob("{dest}/{item}".format(**locals()))
+            for f in items:
+                if os.path.isfile(f):
+                    os.remove(f)
+                elif os.path.isdir(f):
+                    shutil.rmtree(f)
+                # Leave other types
+
+gtab = args["caltable"]
+if not os.path.exists(gtab):
+    raise RuntimeError("The gaintable was not created. Please refer to CASA {0:s} logfile for further details".format(cab["binary"]))
+
+tab = table(gtab)
+field_ids = numpy.unique(tab.getcol("FIELD_ID"))
+tab.close()
+
+tab = table(gtab+"::FIELD")
+field_names = tab.getcol("NAME")
+tab.close()
+
+field_in = args["field"].split(",")
+
+try:
+    ids = map(int, field_in)
+except ValueError:
+    ids = map(lambda a: field_names.index(a), field_in)
+
+if not set(ids).intersection(field_ids):
+    raise RuntimeError("None of the fields has solutions after the calibration. Please refer to CASA the {} logfile for further details".format(cab["binary"]))