From 20e1e357d4f9f0b4121c6de7f7902617a1d28073 Mon Sep 17 00:00:00 2001
From: Alvin Noe Ladines <ladinesalvinnoe@gmail.com>
Date: Tue, 3 Sep 2024 14:03:44 +0200
Subject: [PATCH] Fix file parser handling

---
 atomisticparsers/dftbplus/parser.py | 3 +++
 atomisticparsers/gromacs/parser.py  | 3 ++-
 atomisticparsers/h5md/parser.py     | 3 ++-
 atomisticparsers/lammps/parser.py   | 8 ++++----
 atomisticparsers/namd/parser.py     | 2 ++
 atomisticparsers/tinker/parser.py   | 2 ++
 6 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/atomisticparsers/dftbplus/parser.py b/atomisticparsers/dftbplus/parser.py
index 5566267..6f02484 100644
--- a/atomisticparsers/dftbplus/parser.py
+++ b/atomisticparsers/dftbplus/parser.py
@@ -194,6 +194,7 @@ def parse(self, key=None):
         self._results = dict()
 
         geometry = self.mainfile_obj.read()
+        self.mainfile_obj.close()
         if geometry is None:
             return
 
@@ -281,6 +282,8 @@ def parse(self, key=None):
             line = self.hsd.readline()
 
         self.gen_parser.mainfile = self.mainfile
+        # TODO why is this necessary when you assign mainfile?
+        # private variables should not be set
         self.gen_parser._mainfile_obj = io.StringIO(
             self._results.get('data', {}).get('Geometry', {}).get('_block', '')
         )
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
index 9a86404..6fa84a7 100644
--- a/atomisticparsers/gromacs/parser.py
+++ b/atomisticparsers/gromacs/parser.py
@@ -31,7 +31,6 @@
     logging.warning('Required module MDAnalysis not found.')
     MDAnalysis = False
 from ase.symbols import symbols2numbers
-from nomad.datamodel import EntryArchive
 from nomad.units import ureg
 from nomad.parsing.file_parser import TextParser, Quantity, FileParser
 from runschema.run import Run, Program, TimeRun
@@ -1578,3 +1577,5 @@ def write_to_archive(self):
         self.parse_workflow()
 
         self.traj_parser.clean()
+        self.traj_parser.close()
+        self.energy_parser.close()
diff --git a/atomisticparsers/h5md/parser.py b/atomisticparsers/h5md/parser.py
index 5aff159..860e5de 100644
--- a/atomisticparsers/h5md/parser.py
+++ b/atomisticparsers/h5md/parser.py
@@ -24,7 +24,6 @@
 from typing import List, Dict, Union, Any
 from h5py import Group
 
-from nomad.datamodel import EntryArchive
 from nomad.metainfo.util import MEnum
 from nomad.parsing.file_parser import FileParser
 from runschema.run import Run, Program, MSection
@@ -898,3 +897,5 @@ def write_to_archive(self) -> None:
         self.parse_calculation()
 
         self.parse_workflow()
+
+        self._data_parser.close()
diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py
index 555a763..a200800 100644
--- a/atomisticparsers/lammps/parser.py
+++ b/atomisticparsers/lammps/parser.py
@@ -18,7 +18,6 @@
 #
 import numpy as np
 import os
-import logging
 from ase import data as asedata
 import re
 
@@ -33,7 +32,6 @@
     Method,
     Model,
     AtomParameters,
-    Interaction,
 )
 from runschema.system import AtomsGroup
 from simulationworkflowschema import (
@@ -1556,8 +1554,6 @@ def parse_method(self):
         #         if quantity_def and quantity_def.shape:
         #             # TODO reshape properly
         #             interaction[key] = [val]
-        # print("---------", self._mdanalysistraj_parser.mainfile)
-        # print(interactions)
         self.parse_interactions(interactions, sec_model)
 
         # Force Calculation Parameters
@@ -1751,3 +1747,7 @@ def write_to_archive(self):
         self.parse_thermodynamic_data()
 
         self.parse_workflow()
+
+        self._mdanalysistraj_parser.close()
+        for parser in parsers:
+            parser.close()
diff --git a/atomisticparsers/namd/parser.py b/atomisticparsers/namd/parser.py
index e00f123..955264f 100644
--- a/atomisticparsers/namd/parser.py
+++ b/atomisticparsers/namd/parser.py
@@ -308,3 +308,5 @@ def get_system_data(index):
 
         # workflow
         self.archive.workflow2 = MolecularDynamics()
+
+        self.traj_parser.close()
diff --git a/atomisticparsers/tinker/parser.py b/atomisticparsers/tinker/parser.py
index 5fbc71e..6e6baf1 100644
--- a/atomisticparsers/tinker/parser.py
+++ b/atomisticparsers/tinker/parser.py
@@ -681,3 +681,5 @@ def get_reference_filename(program):
             self.parse_method()
 
             self.parse_workflow(program, run)
+
+            self.traj_parser.close()