Commit a3f52f62 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Remove dependency on old metainfo.

parent 49615307
......@@ -21,7 +21,6 @@ from ase.data import chemical_symbols
import setup_paths
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 tar import Reader
from libxc_names import get_libxc_xc_names
from versions import get_prog_version
......@@ -39,23 +38,6 @@ def c(value, unit=None):
parser_info = {"name": "parser_gpaw", "version": "1.0"}
path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
'gpaw.nomadmetainfo.json'
# metaInfoPath = os.path.normpath(
# os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
# metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
# dependencyLoader=None,
# extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
# uri=None)
import nomad_meta_info
metaInfoPath = os.path.normpath(
os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
"gpaw.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(
filePath = metaInfoPath, dependencyLoader = None,
extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
class LibAtomsParserWrapper():
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
......@@ -63,15 +45,13 @@ class LibAtomsParserWrapper():
self.backend_factory = backend
def parse(self, mainfile):
from unittest.mock import patch
logging.info('lib-atoms parser started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
backend = self.backend_factory("gpaw.nomadmetainfo.json")
backend = parse_without_class(mainfile, backend)
return backend
def parse_without_class(filename, backend):
# p = JsonParseEventsWriterBackend(metaInfoEnv)
p = backend
o = open_section
r = Reader(filename)
......
# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
#
#
# 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.
......@@ -26,10 +26,10 @@ from ase.units import Rydberg
import setup_paths
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 libxc_names import get_libxc_name
from default_parameters import parameters as parms
from nomad.parsing.legacy import Backend
@contextmanager
def open_section(p, name):
......@@ -56,7 +56,7 @@ metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
def parse(filename):
p = JsonParseEventsWriterBackend(metaInfoEnv)
p = Backend(metaInfoEnv)
o = open_section
r = ulmopen(filename) # Reader(filename)
p.startedParsingSession(filename, parser_info)
......
......@@ -21,7 +21,6 @@ from ase.data import chemical_symbols
# import setup_paths
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 gpawparser.tar import Reader
from gpawparser.libxc_names import get_libxc_xc_names
from gpawparser.versions import get_prog_version
......@@ -42,29 +41,19 @@ parser_info = {"name": "parser_gpaw", "version": "1.0"}
path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
'gpaw.nomadmetainfo.json'
import nomad_meta_info
metaInfoPath = os.path.normpath(
os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
"gpaw.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(
filePath = metaInfoPath, dependencyLoader = None,
extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
class GPAWParserWrapper():
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
def __init__(self, backend, **kwargs):
self.backend_factory = backend
def parse(self, mainfile):
from unittest.mock import patch
logging.info('GPAW parser started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
backend = self.backend_factory("gpaw.nomadmetainfo.json")
backend = parse_without_class(mainfile, backend)
return backend
def parse_without_class(filename, backend):
# p = JsonParseEventsWriterBackend(metaInfoEnv)
p = backend
o = open_section
r = Reader(filename)
......
......@@ -26,7 +26,6 @@ from ase.data import atomic_masses
from ase.units import Rydberg
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 gpawparser.libxc_names import get_libxc_name
from gpawparser.default_parameters import parameters as parms
......@@ -47,31 +46,21 @@ parser_info = {"name": "parser2_gpaw", "version": "1.0"}
path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
'gpaw.nomadmetainfo.json'
import nomad_meta_info
metaInfoPath = os.path.normpath(
os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
"gpaw.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(
filePath = metaInfoPath, dependencyLoader = None,
extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
class GPAWParser2Wrapper():
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
def __init__(self, backend, **kwargs):
self.backend_factory = backend
def parse(self, mainfile):
from unittest.mock import patch
logging.info('GPAW parser 2 (note the 2) started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
backend = self.backend_factory("gpaw.nomadmetainfo.json")
backend = parse_without_class(mainfile, backend)
return backend
def parse_without_class(filename, backend):
p = backend
# p = JsonParseEventsWriterBackend(metaInfoEnv)
o = open_section
r = ulmopen(filename) # Reader(filename)
p.startedParsingSession(filename, parser_info)
......
# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
#
# 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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