From 10f066f30370d8b7826d7cc404da360e3b3d92f2 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Fri, 20 Mar 2020 10:28:33 +0100
Subject: [PATCH] Remove dependency on old metainfo.
---
atkparser/parser_atk.py | 24 ++++--------------------
atkparser/setup_paths.py | 20 --------------------
2 files changed, 4 insertions(+), 40 deletions(-)
delete mode 100644 atkparser/setup_paths.py
diff --git a/atkparser/parser_atk.py b/atkparser/parser_atk.py
index 58c8f84..cec4af0 100644
--- a/atkparser/parser_atk.py
+++ b/atkparser/parser_atk.py
@@ -13,7 +13,6 @@
# limitations under the License.
from __future__ import division
-import os
from contextlib import contextmanager
import numpy as np
import logging
@@ -22,8 +21,6 @@ from ase.data import chemical_symbols
from atkparser.atkio import Reader
from ase.data import atomic_masses
from nomadcore.unit_conversion.unit_conversion import convert_unit as cu
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-from nomadcore.parser_backend import JsonParseEventsWriterBackend
from atkparser.libxc_names import get_libxc_xc_names
@@ -40,15 +37,7 @@ def c(value, unit=None):
parser_info = {"name": "parser_atk", "version": "1.0"}
-path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
- 'atk.nomadmetainfo.json'
-import nomad_meta_info
-metaInfoPath = os.path.normpath(
- os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
- "atk.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(
- filePath = metaInfoPath, dependencyLoader = None,
- extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
class ATKParserWrapper():
""" A proper class envolop for running this parser using nomad-FAIRDI infra. """
@@ -58,12 +47,13 @@ class ATKParserWrapper():
def parse(self, mainfile):
logging.info('ATK parser started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
- backend = self.backend_factory(metaInfoEnv)
+ backend = self.backend_factory('atk.nomadmetainfo.json')
parse_without_class(mainfile, backend)
return backend
+
def parse_without_class(filename, backend):
- p = backend # JsonParseEventsWriterBackend(metaInfoEnv)
+ p = backend
o = open_section
r = Reader(filename)
@@ -191,9 +181,3 @@ def parse_without_class(filename, backend):
p.addValue('program_name', 'ATK')
p.addValue('program_version', r.atk_version)
return p
-
-
-if __name__ == '__main__':
- import sys
- filename = sys.argv[1]
- parse(filename)
diff --git a/atkparser/setup_paths.py b/atkparser/setup_paths.py
deleted file mode 100644
index 52c258f..0000000
--- a/atkparser/setup_paths.py
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import sys, os, os.path
-baseDir = os.path.dirname(os.path.abspath(__file__))
-commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
-
-if not commonDir in sys.path:
- sys.path.insert(0, commonDir)
--
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