Refactor job handling to improve scratch directory management and enhance test paths

Author: calvinp0

autotst/job/job.py

@@ -149,25 +149,32 @@ def write_input(self, conformer, ase_calculator):
         """
 
         ase_calculator.write_input(conformer.ase_molecule)
-        try:
-            os.makedirs(ase_calculator.scratch)
-        except OSError:
-            pass
+        scratch = getattr(ase_calculator, "scratch", None) or ase_calculator.parameters.get("scratch")
+        if not scratch:
+            raise AttributeError("ASE Gaussian calculator has no scratch location (no .scratch and no parameters['scratch']).")
+        os.makedirs(scratch, exist_ok=True)
 
-        shutil.move(
-            ase_calculator.label + ".com",
-            os.path.join(
-                ase_calculator.scratch,
-                ase_calculator.label + ".com"
-            ))
+        base = ase_calculator.label
+        com_src = f"{base}.com"
+        if not os.path.exists(com_src):
+            raise FileNotFoundError(f"Expected ASE to write {com_src} in CWD={os.getcwd()}")
 
         shutil.move(
-            ase_calculator.label + ".ase",
+            com_src,
             os.path.join(
-                ase_calculator.scratch,
-                ase_calculator.label + ".ase"
+                scratch,
+                com_src
             ))
 
+        ase_src = f"{base}.ase"
+        if os.path.exists(ase_src):
+            shutil.move(
+                ase_src,
+                os.path.join(
+                    scratch,
+                    ase_src
+                ))
+
     def check_complete(self, label):
         """
         A method to determine if a job is still running
@@ -271,7 +278,10 @@ def submit_conformer(self, conformer, restart=False):
         self.calculator.conformer = conformer
         ase_calculator = self.calculator.get_conformer_calc()
         label = conformer.smiles + f"_{conformer.index}"
-        file_path = os.path.join(ase_calculator.scratch, label)
+        scratch = getattr(ase_calculator, "scratch", None) or ase_calculator.parameters.get("scratch")
+        if not scratch:
+            raise AttributeError("ASE Gaussian calculator has no scratch location (no .scratch and no parameters['scratch']).")
+        file_path = os.path.join(scratch, label)
         # for testing
         os.environ["FILE_PATH"] = file_path
 
@@ -604,7 +614,9 @@ def submit_transitionstate(self, transitionstate, opt_type, restart=False):
         self.write_input(transitionstate, ase_calculator)
 
         label = ase_calculator.label
-        scratch = ase_calculator.scratch
+        scratch = getattr(ase_calculator, "scratch", None) or ase_calculator.parameters.get("scratch")
+        if not scratch:
+            raise AttributeError("ASE Gaussian calculator has no scratch location (no .scratch and no parameters['scratch']).")
         file_path = os.path.join(scratch, label)
         # for testing
         os.environ["FILE_PATH"] = file_path
@@ -853,7 +865,10 @@ def submit_rotor(self, conformer, torsion_index, restart=False):
         self.calculator.conformer = conformer
         ase_calculator = self.calculator.get_rotor_calc(torsion_index)
         label = ase_calculator.label
-        file_path = os.path.join(ase_calculator.scratch, ase_calculator.label)
+        scratch = getattr(ase_calculator, "scratch", None) or ase_calculator.parameters.get("scratch")
+        if not scratch:
+            raise AttributeError("ASE Gaussian calculator has no scratch location (no .scratch and no parameters['scratch']).")
+        file_path = os.path.join(scratch, ase_calculator.label)
 
         os.environ["FILE_PATH"] = file_path
 

autotst/job/job_test.py

@@ -35,17 +35,18 @@
 from autotst.data.base import TransitionStates
 from autotst.job.job import Job
 from autotst.calculator.gaussian import Gaussian
+from autotst.utils.paths import test_bin_dir, test_data_dir, test_dir
 import multiprocessing
 import subprocess
 import time
 
 class JobTest(unittest.TestCase):
 
     def setUp(self):
-        os.environ["PATH"] = os.path.expandvars("$AUTOTST/test/bin:") + os.environ["PATH"]
+        os.environ["PATH"] = f"{test_bin_dir()}:{os.environ['PATH']}"
         os.environ["TEST_STATUS"] = "None"
         self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
-        self.calculator = Gaussian(directory=os.path.expandvars("$AUTOTST/test"))
+        self.calculator = Gaussian(directory=str(test_dir()))
         self.job = Job(
             reaction=self.reaction,
             calculator=self.calculator,
@@ -77,9 +78,9 @@ def test_setup2(self):
 
     def test_read_log(self):
 
-        path = os.path.expandvars("$AUTOTST/test/bin/log-files/CC_0.log")
+        path = test_data_dir() / "CC_0.log"
 
-        atoms = self.job.read_log(path)
+        atoms = self.job.read_log(str(path))
 
         self.assertEqual(len(atoms), 8)
 
@@ -132,11 +133,8 @@ def test_calculate_species(self):
         for species in self.reaction.reactants + self.reaction.products:
             self.job.calculate_species(species)
             for smiles in species.conformers.keys():
-                self.assertTrue(os.path.exists(os.path.join(
-                    os.path.expandvars("$AUTOTST/test/species/"),
-                    smiles,
-                    smiles + ".log"
-                )))
+                log_path = test_dir() / "species" / smiles / f"{smiles}.log"
+                self.assertTrue(log_path.exists())
 
     def test_submit_transitionstate(self):
         ts = self.reaction.ts["forward"][0]
@@ -173,4 +171,3 @@ def test_calculate_reaction(self):
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
 
-