diff --git a/nomad/parsing/__init__.py b/nomad/parsing/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..66f282dbd054f45fb4f2276fc363c73924814cc7
--- /dev/null
+++ b/nomad/parsing/__init__.py
@@ -0,0 +1,86 @@
+# Copyright 2018 Markus Scheidgen
+#
+# 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.
+
+"""
+The *parsing* modules is currenlty an abstraction for the existin NOMAD-coe parsers.
+The parser code is used via :mod:`nomad.dependencies`. This module redefines
+some of the old NOMAD-coe python-common functionality to create a more coherent
+interface to the parsers.
+
+Assumption about parsers
+------------------------
+For now, we make a few assumption about parsers
+- they always work on the same *meta-info* version
+- they have no conflicting python requirments
+- they can be loaded at the same time and can be used within the same python process
+- they are uniquely identified by a GIT URL and publicly accessible
+- their version is uniquly identified by a GIT commit SHA
+
+Each parser is defined via an instance of :class:`Parser`.
+
+.. autoclass:: nomad.parsing.Parser
+ :members:
+
+The parser definitions are available via the following two variables.
+
+.. autodata:: nomad.parsing.parsers
+.. autodata:: nomad.parsing.parser_dict
+
+Parsers in NOMAD-coe use a *backend* to create output.
+
+.. autoclass:: nomad.parsing.AbstractParserBackend
+ :members:
+.. autoclass:: nomad.parsing.LocalBackend
+ :members:
+"""
+
+from nomad.parsing.backend import AbstractParserBackend, LocalBackend, LegacyLocalBackend, JSONStreamWriter, BadContextURI, WrongContextState
+from nomad.parsing.parser import Parser, LegacyParser
+from nomad.dependencies import dependencies_dict as dependencies
+
+parsers = [
+ LegacyParser(
+ python_git=dependencies['parsers/vasp'],
+ parser_class_name='vaspparser.VASPParser',
+ main_file_re=r'^.*\.xml(\.[^\.]*)?$',
+ main_contents_re=(
+ r'^\s*<\?xml version="1\.0" encoding="ISO-8859-1"\?>\s*'
+ r'?\s*<modeling>'
+ r'?\s*<generator>'
+ r'?\s*<i name="program" type="string">\s*vasp\s*</i>'
+ r'?')
+ ),
+ LegacyParser(
+ python_git=dependencies['parsers/exciting'],
+ parser_class_name='parser_exciting.ExcitingParser',
+ main_file_re=r'^.*/INFO\.OUT?',
+ main_contents_re=(
+ r'^\s*=================================================+\s*'
+ r'\s*\|\s*EXCITING\s+\S+\s+started\s*='
+ r'\s*\|\s*version hash id:\s*\S*\s*=')
+ ),
+ LegacyParser(
+ python_git=dependencies['parsers/fhi-aims'],
+ parser_class_name='fhiaimsparser.FHIaimsParser',
+ main_file_re=r'^.*\.out$',
+ main_contents_re=(
+ r'^(.*\n)*'
+ r'?\s*Invoking FHI-aims \.\.\.'
+ r'?\s*Version')
+ )
+]
+""" Instanciation and constructor based config of all parsers. """
+
+parser_dict = {parser.name: parser for parser in parsers}
+""" A dict to access parsers by name. Usually 'parsers/<...>', e.g. 'parsers/vasp'. """
\ No newline at end of file
diff --git a/nomad/parsing.py b/nomad/parsing/backend.py
similarity index 75%
rename from nomad/parsing.py
rename to nomad/parsing/backend.py
index a9791fb03dd0bd2d4fb0d848de48954e39e1615e..e3de73c7f936d2c91b7dfda8c51deb6008c07c56 100644
--- a/nomad/parsing.py
+++ b/nomad/parsing/backend.py
@@ -12,54 +12,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-"""
-The *parsing* modules is currenlty an abstraction for the existin NOMAD-coe parsers.
-The parser code is used via :mod:`nomad.dependencies`. This module redefines
-some of the old NOMAD-coe python-common functionality to create a more coherent
-interface to the parsers.
-
-Assumption about parsers
-------------------------
-For now, we make a few assumption about parsers
-- they always work on the same *meta-info* version
-- they have no conflicting python requirments
-- they can be loaded at the same time and can be used within the same python process
-- they are uniquely identified by a GIT URL and publicly accessible
-- their version is uniquly identified by a GIT commit SHA
-
-Each parser is defined via an instance of :class:`Parser`.
-
-.. autoclass:: nomad.parsing.Parser
- :members:
-
-The parser definitions are available via the following two variables.
-
-.. autodata:: nomad.parsing.parsers
-.. autodata:: nomad.parsing.parser_dict
-
-Parsers in NOMAD-coe use a *backend* to create output.
-
-.. autoclass:: nomad.parsing.AbstractParserBackend
- :members:
-.. autoclass:: nomad.parsing.LocalBackend
- :members:
-"""
-
-from typing import TextIO, Tuple, List, Any, Callable, IO
+from typing import TextIO, Tuple, List, Any, Callable
from abc import ABCMeta, abstractmethod
from io import StringIO
-import sys
import json
import re
-import importlib
-import inspect
-from unittest.mock import patch
import io
from nomadcore.local_backend import LocalBackend as LegacyLocalBackend
from nomadcore.local_backend import Section, Results
-from nomad.dependencies import dependencies_dict as dependencies, PythonGit
from nomad.utils import get_logger
logger = get_logger(__name__)
@@ -572,130 +534,3 @@ class LocalBackend(LegacyParserBackend):
out = StringIO()
self.write_json(JSONStreamWriter(out), filter=filter)
return out.getvalue()
-
-
-class Parser(metaclass=ABCMeta):
- """
- Instances specify a parser. It allows to find *main files* from given uploaded
- and extracted files. Further, allows to run the parser on those 'main files'.
-
- Arguments:
- python_git: The :class:`PythonGit` that describes the parser code.
- parser_class_name: Full qualified name of the main parser class. We assume it have one
- parameter for the backend.
- main_file_re: A regexp that matches main file paths that this parser can handle.
- main_contents_re: A regexp that matches main file headers that this parser can parse.
- """
- @abstractmethod
- def is_mainfile(self, filename: str, open: Callable[[str], IO[Any]]) -> bool:
- """ Checks if a file is a mainfile via the parsers ``main_contents_re``. """
- pass
-
- @abstractmethod
- def run(self, mainfile: str) -> LocalBackend:
- """
- Runs the parser on the given mainfile. It uses :class:`LocalBackend` as
- a backend. The meta-info access is handled by the underlying NOMAD-coe parser.
-
- Args:
- mainfile: A path to a mainfile that this parser can parse.
-
- Returns:
- The used :class:`LocalBackend` with status information and result data.
- """
-
-
-class LegacyParser(Parser):
- """
- A parser implementation for legacy NOMAD-coe parsers. Uses a
- :class:`nomad.dependencies.PythonGit` to specify the old parser repository.
- """
- def __init__(
- self, python_git: PythonGit, parser_class_name: str, main_file_re: str,
- main_contents_re: str) -> None:
-
- self.name = python_git.name
- self.python_git = python_git
- self.parser_class_name = parser_class_name
- self._main_file_re = re.compile(main_file_re)
- self._main_contents_re = re.compile(main_contents_re)
-
- def is_mainfile(self, filename: str, open: Callable[[str], IO[Any]]) -> bool:
- if self._main_file_re.match(filename):
- file = None
- try:
- file = open(filename)
- contents = file.read(500)
- return self._main_contents_re.match(contents) is not None
- finally:
- if file:
- file.close()
-
- return False
-
- def run(self, mainfile: str) -> LocalBackend:
- def create_backend(meta_info):
- return LocalBackend(meta_info, debug=False)
-
- module_name = self.parser_class_name.split('.')[:-1]
- parser_class = self.parser_class_name.split('.')[1]
- module = importlib.import_module('.'.join(module_name))
- Parser = getattr(module, parser_class)
-
- init_signature = inspect.getargspec(Parser.__init__)
- kwargs = dict(
- backend=create_backend,
- mainfile=mainfile, main_file=mainfile,
- debug=True)
- kwargs = {key: value for key, value in kwargs.items() if key in init_signature.args}
- parser = Parser(**kwargs)
-
- with patch.object(sys, 'argv', []):
- backend = parser.parse(mainfile)
-
- # TODO we need a homogeneous interface to parsers, but we dont have it right now
- # thats a hack to distringuish between ParserInterface parser and simple_parser
- if backend is None or not hasattr(backend, 'status'):
- backend = parser.parser_context.super_backend
-
- return backend
-
- def __repr__(self):
- return self.python_git.__repr__()
-
-
-parsers = [
- LegacyParser(
- python_git=dependencies['parsers/vasp'],
- parser_class_name='vaspparser.VASPParser',
- main_file_re=r'^.*\.xml(\.[^\.]*)?$',
- main_contents_re=(
- r'^\s*<\?xml version="1\.0" encoding="ISO-8859-1"\?>\s*'
- r'?\s*<modeling>'
- r'?\s*<generator>'
- r'?\s*<i name="program" type="string">\s*vasp\s*</i>'
- r'?')
- ),
- LegacyParser(
- python_git=dependencies['parsers/exciting'],
- parser_class_name='parser_exciting.ExcitingParser',
- main_file_re=r'^.*/INFO\.OUT?',
- main_contents_re=(
- r'^\s*=================================================+\s*'
- r'\s*\|\s*EXCITING\s+\S+\s+started\s*='
- r'\s*\|\s*version hash id:\s*\S*\s*=')
- ),
- LegacyParser(
- python_git=dependencies['parsers/fhi-aims'],
- parser_class_name='fhiaimsparser.FHIaimsParser',
- main_file_re=r'^.*\.out$',
- main_contents_re=(
- r'^(.*\n)*'
- r'?\s*Invoking FHI-aims \.\.\.'
- r'?\s*Version')
- )
-]
-""" Instanciation and constructor based config of all parsers. """
-
-parser_dict = {parser.name: parser for parser in parsers}
-""" A dict to access parsers by name. Usually 'parsers/<...>', e.g. 'parsers/vasp'. """
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..a2eed68978ee8c18e5a0ff38bbbdfbd66897fb05
--- /dev/null
+++ b/nomad/parsing/parser.py
@@ -0,0 +1,114 @@
+# Copyright 2018 Markus Scheidgen
+#
+# 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.
+
+from typing import Any, Callable, IO
+from abc import ABCMeta, abstractmethod
+import sys
+import re
+import importlib
+import inspect
+from unittest.mock import patch
+
+from nomad.parsing.backend import LocalBackend
+from nomad.dependencies import PythonGit
+
+
+class Parser(metaclass=ABCMeta):
+ """
+ Instances specify a parser. It allows to find *main files* from given uploaded
+ and extracted files. Further, allows to run the parser on those 'main files'.
+
+ Arguments:
+ python_git: The :class:`PythonGit` that describes the parser code.
+ parser_class_name: Full qualified name of the main parser class. We assume it have one
+ parameter for the backend.
+ main_file_re: A regexp that matches main file paths that this parser can handle.
+ main_contents_re: A regexp that matches main file headers that this parser can parse.
+ """
+ @abstractmethod
+ def is_mainfile(self, filename: str, open: Callable[[str], IO[Any]]) -> bool:
+ """ Checks if a file is a mainfile via the parsers ``main_contents_re``. """
+ pass
+
+ @abstractmethod
+ def run(self, mainfile: str) -> LocalBackend:
+ """
+ Runs the parser on the given mainfile. It uses :class:`LocalBackend` as
+ a backend. The meta-info access is handled by the underlying NOMAD-coe parser.
+
+ Args:
+ mainfile: A path to a mainfile that this parser can parse.
+
+ Returns:
+ The used :class:`LocalBackend` with status information and result data.
+ """
+
+
+class LegacyParser(Parser):
+ """
+ A parser implementation for legacy NOMAD-coe parsers. Uses a
+ :class:`nomad.dependencies.PythonGit` to specify the old parser repository.
+ """
+ def __init__(
+ self, python_git: PythonGit, parser_class_name: str, main_file_re: str,
+ main_contents_re: str) -> None:
+
+ self.name = python_git.name
+ self.python_git = python_git
+ self.parser_class_name = parser_class_name
+ self._main_file_re = re.compile(main_file_re)
+ self._main_contents_re = re.compile(main_contents_re)
+
+ def is_mainfile(self, filename: str, open: Callable[[str], IO[Any]]) -> bool:
+ if self._main_file_re.match(filename):
+ file = None
+ try:
+ file = open(filename)
+ contents = file.read(500)
+ return self._main_contents_re.match(contents) is not None
+ finally:
+ if file:
+ file.close()
+
+ return False
+
+ def run(self, mainfile: str) -> LocalBackend:
+ def create_backend(meta_info):
+ return LocalBackend(meta_info, debug=False)
+
+ module_name = self.parser_class_name.split('.')[:-1]
+ parser_class = self.parser_class_name.split('.')[1]
+ module = importlib.import_module('.'.join(module_name))
+ Parser = getattr(module, parser_class)
+
+ init_signature = inspect.getargspec(Parser.__init__)
+ kwargs = dict(
+ backend=create_backend,
+ mainfile=mainfile, main_file=mainfile,
+ debug=True)
+ kwargs = {key: value for key, value in kwargs.items() if key in init_signature.args}
+ parser = Parser(**kwargs)
+
+ with patch.object(sys, 'argv', []):
+ backend = parser.parse(mainfile)
+
+ # TODO we need a homogeneous interface to parsers, but we dont have it right now
+ # thats a hack to distringuish between ParserInterface parser and simple_parser
+ if backend is None or not hasattr(backend, 'status'):
+ backend = parser.parser_context.super_backend
+
+ return backend
+
+ def __repr__(self):
+ return self.python_git.__repr__()