Added more parsers to NOMAD

.gitignore

@@ -53,3 +53,5 @@ TAGS
 
 lib/
 env/
+
+*.egg-info/
\ No newline at end of file

mopacparser/__init__.py

+from .parser_mopac import MopacParser
\ No newline at end of file

mopacparser/metainfo/__init__.py

+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import mopacparser.metainfo.mopac
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['mopacparser.metainfo.mopac'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package)  # type: ignore

mopacparser/metainfo/mopac.py

+import numpy as np            # pylint: disable=unused-import
+import typing                 # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+    Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+    name='mopac_nomadmetainfo_json',
+    description='None',
+    a_legacy=LegacyDefinition(name='mopac.nomadmetainfo.json'))
+
+
+class section_single_configuration_calculation(public.section_single_configuration_calculation):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+    x_mopac_fhof = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Final heat of formation
+        ''',
+        a_legacy=LegacyDefinition(name='x_mopac_fhof'))
+
+
+class section_method(public.section_method):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+    x_mopac_keyword_line = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Mopac keyword line (it controls the calculation)
+        ''',
+        a_legacy=LegacyDefinition(name='x_mopac_keyword_line'))
+
+    x_mopac_method = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Mopac method, i.e. PM7, AM1, etc..
+        ''',
+        a_legacy=LegacyDefinition(name='x_mopac_method'))
+
+
+m_package.__init_metainfo__()

parser/parser-mopac/parser.py → mopacparser/parser.py

 # Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa
-# 
+#
 #   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.
@@ -92,9 +92,32 @@ parserInfo = {
   "version": "1.0"
 }
 
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/mopac.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
+class MopacParser():
+    """ A proper class envolop for running this parser from within python. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        from unittest.mock import patch
+        logging.info('mopac parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory("mopac.nomadmetainfo.json")
+        context = MopacContext()
+        with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
+            mainFunction(
+                mainFileDescription,
+                None,
+                parserInfo,
+                cachingLevelForMetaName=dict(),
+                superContext=context,
+                superBackend=backend)
+
+        return backend
+
 
 if __name__ == "__main__":
+    metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/mopac.nomadmetainfo.json"))
+    metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
+
     superContext = MopacContext()
     mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext=superContext)

parser/parser-mopac/parser_mopac.py → mopacparser/parser_mopac.py

 # Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa
-# 
+#
 #   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.
@@ -16,11 +16,10 @@ from __future__ import division
 import os
 from contextlib import contextmanager
 import numpy as np
-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 reader import Reader
+from .reader import Reader
+import logging
 
 
 @contextmanager
@@ -36,19 +35,9 @@ def c(value, unit=None):
 
 
 parser_info = {"name": "parser_mopac", "version": "1.0"}
-path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
-        'mopac.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)
-
-
-def parse(filename):
-    p = JsonParseEventsWriterBackend(metaInfoEnv)
+def parse(filename, backend):
+    p = backend
     o = open_section
     r = Reader(filename)
     p.startedParsingSession(filename, parser_info)
@@ -113,6 +102,20 @@ def parse(filename):
 
     p.finishedParsingSession("ParseSuccess", None)
 
+
+class MopacParser():
+    """ A proper class envolop for running this parser from within python. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        logging.info('mopac parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory("mopac.nomadmetainfo.json")
+        parse(mainfile, backend)
+        return backend
+
+
 if __name__ == '__main__':
     import sys
     filename = sys.argv[1]

parser/parser-mopac/setup_paths.py → setup.py

-# Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa
-# 
+# Copyright 2015-2018 Berk Onat
+#
 #   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"))
+from setuptools import setup, find_packages
 
-if not commonDir in sys.path:
-    sys.path.insert(0, commonDir)
+
+def main():
+    setup(
+        name='mopacparser',
+        version='0.1',
+        description='NOMAD parser implementation for Mopac.',
+        license='APACHE 2.0',
+        package_dir={'': './'},
+        packages=find_packages(),
+        install_requires=[
+            'nomadcore',
+            'nomad'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()