diff --git a/dependencies/parsers/crystal b/dependencies/parsers/crystal
index 24a12012effc70d296ec45dcc0bd5fbeb0a0b2ff..a58cfed379d240e5241bb69689441d42a5fb5e0f 160000
--- a/dependencies/parsers/crystal
+++ b/dependencies/parsers/crystal
@@ -1 +1 @@
-Subproject commit 24a12012effc70d296ec45dcc0bd5fbeb0a0b2ff
+Subproject commit a58cfed379d240e5241bb69689441d42a5fb5e0f
diff --git a/dependencies/parsers/fhi-aims b/dependencies/parsers/fhi-aims
index ad90ca934bb42fad1c95cfe8c1c6aac8317514c8..89e18d81a5a6fa658c1c0008f0078cb58dd2cbd2 160000
--- a/dependencies/parsers/fhi-aims
+++ b/dependencies/parsers/fhi-aims
@@ -1 +1 @@
-Subproject commit ad90ca934bb42fad1c95cfe8c1c6aac8317514c8
+Subproject commit 89e18d81a5a6fa658c1c0008f0078cb58dd2cbd2
diff --git a/dependencies/parsers/gaussian b/dependencies/parsers/gaussian
index ab61bf9c4300d5c3bc91a444d646e486f68cfa40..2e2a4cc93fe2f2f91b8ce44f1da983f315cf1453 160000
--- a/dependencies/parsers/gaussian
+++ b/dependencies/parsers/gaussian
@@ -1 +1 @@
-Subproject commit ab61bf9c4300d5c3bc91a444d646e486f68cfa40
+Subproject commit 2e2a4cc93fe2f2f91b8ce44f1da983f315cf1453
diff --git a/dependencies/parsers/gpaw b/dependencies/parsers/gpaw
index a3f52f6249c59899f7373ac1e9f88d4b7531490c..56354bd376ac8d97a0476be1c6dc396cd1e2c3c2 160000
--- a/dependencies/parsers/gpaw
+++ b/dependencies/parsers/gpaw
@@ -1 +1 @@
-Subproject commit a3f52f6249c59899f7373ac1e9f88d4b7531490c
+Subproject commit 56354bd376ac8d97a0476be1c6dc396cd1e2c3c2
diff --git a/dependencies/parsers/octopus b/dependencies/parsers/octopus
index cf7a94db5e606d1da5c65d16dac05b405bcf12ae..b2eaed00f3b74363c875826cb39ee4d24d27cd8d 160000
--- a/dependencies/parsers/octopus
+++ b/dependencies/parsers/octopus
@@ -1 +1 @@
-Subproject commit cf7a94db5e606d1da5c65d16dac05b405bcf12ae
+Subproject commit b2eaed00f3b74363c875826cb39ee4d24d27cd8d
diff --git a/dependencies/parsers/orca b/dependencies/parsers/orca
index 18e24ef0a192c13f83098330a2a7575fe1608c57..cfc88f526cee932fa25fdc1fc6236383f843d025 160000
--- a/dependencies/parsers/orca
+++ b/dependencies/parsers/orca
@@ -1 +1 @@
-Subproject commit 18e24ef0a192c13f83098330a2a7575fe1608c57
+Subproject commit cfc88f526cee932fa25fdc1fc6236383f843d025
diff --git a/dependencies/parsers/quantum-espresso b/dependencies/parsers/quantum-espresso
index 7c7a5c991123a3687c4f3bb659286aea54c3a45d..bc0e599c58252f791c3cb809b3c8cfbf652d3b73 160000
--- a/dependencies/parsers/quantum-espresso
+++ b/dependencies/parsers/quantum-espresso
@@ -1 +1 @@
-Subproject commit 7c7a5c991123a3687c4f3bb659286aea54c3a45d
+Subproject commit bc0e599c58252f791c3cb809b3c8cfbf652d3b73
diff --git a/dependencies/parsers/vasp b/dependencies/parsers/vasp
index edc78862afa35250d43cf7c4748f961f8fe57543..660338bb96b347b9118ea9942d8f76d6cfb1aa0e 160000
--- a/dependencies/parsers/vasp
+++ b/dependencies/parsers/vasp
@@ -1 +1 @@
-Subproject commit edc78862afa35250d43cf7c4748f961f8fe57543
+Subproject commit 660338bb96b347b9118ea9942d8f76d6cfb1aa0e
diff --git a/dependencies/parsers/wien2k b/dependencies/parsers/wien2k
index 2ef508e9fe2523af787581c4309a616b0da75365..16f7a7f6909dbe16908d1be2e1fa03d3bddd17b5 160000
--- a/dependencies/parsers/wien2k
+++ b/dependencies/parsers/wien2k
@@ -1 +1 @@
-Subproject commit 2ef508e9fe2523af787581c4309a616b0da75365
+Subproject commit 16f7a7f6909dbe16908d1be2e1fa03d3bddd17b5
diff --git a/dependencies/python_common b/dependencies/python_common
index fd3199aed68b5c3f09a515e687d075755f415f06..75a663a7e1ba8ff13c49bcdc62bca8bdb2f2d108 160000
--- a/dependencies/python_common
+++ b/dependencies/python_common
@@ -1 +1 @@
-Subproject commit fd3199aed68b5c3f09a515e687d075755f415f06
+Subproject commit 75a663a7e1ba8ff13c49bcdc62bca8bdb2f2d108
diff --git a/nomad/parsing/__init__.py b/nomad/parsing/__init__.py
index f92d76016c39f34de5f7d6a2c989ca46a702185b..1da3a95fcd15cf2a6c2b3a4a10fc7c22e52d9b29 100644
--- a/nomad/parsing/__init__.py
+++ b/nomad/parsing/__init__.py
@@ -173,7 +173,7 @@ parsers = [
),
LegacyParser(
name='parsers/vasp', code_name='VASP',
- parser_class_name='vaspparser.VASPRunParserInterface',
+ parser_class_name='vaspparser.VASPRunParser',
mainfile_mime_re=r'(application/.*)|(text/.*)',
mainfile_contents_re=(
r'^\s*<\?xml version="1\.0" encoding="ISO-8859-1"\?>\s*'
diff --git a/nomad/parsing/legacy.py b/nomad/parsing/legacy.py
index 50efa6c905f2e6364fcd5a8df88354ed82862913..06b2b16e776a843ec6f91620bb52d7bd07b28681 100644
--- a/nomad/parsing/legacy.py
+++ b/nomad/parsing/legacy.py
@@ -18,7 +18,7 @@ new nomad@fairdi infrastructure. This covers aspects like the new metainfo, a un
wrapper for parsers, parser logging, and a parser backend.
'''
-from typing import Dict, List, Union, Any, Tuple, Type
+from typing import Dict, List, Union, Any, Tuple, Type, cast
from abc import ABCMeta, abstractmethod
import importlib
import os.path
@@ -28,8 +28,6 @@ import logging
import glob
import sys
-from nomadcore.local_meta_info import InfoKindEnv
-
from nomad import utils, datamodel, config
from nomad.metainfo import (
SubSection, Quantity, Section, Reference, MResource, MSection, MSectionBound, Property)
@@ -227,21 +225,21 @@ class Backend(AbstractParserBackend):
warnings and errors.
'''
- def __init__(self, metainfo: Union[str, InfoKindEnv], domain: str = None, logger=None):
+ def __init__(self, metainfo: Union[str, LegacyMetainfoEnvironment], domain: str = None, logger=None):
+ assert metainfo is not None
if logger is None:
logger = utils.get_logger(__name__)
self.logger = logger
self.domain = domain if domain is not None else 'dft' # TODO
- if isinstance(metainfo, InfoKindEnv):
- print('#################') # TODO remove
- metainfo = metainfo.name
+ if isinstance(metainfo, str):
+ python_package_name, _ = python_package_mapping(metainfo)
+ python_package_name = '.'.join(python_package_name.split('.')[:-1])
+ python_module = importlib.import_module(python_package_name)
+ metainfo = getattr(python_module, 'm_env')
- python_package_name, _ = python_package_mapping(metainfo)
- python_package_name = '.'.join(python_package_name.split('.')[:-1])
- python_module = importlib.import_module(python_package_name)
- self.env: LegacyMetainfoEnvironment = getattr(python_module, 'm_env')
+ self.env: LegacyMetainfoEnvironment = cast(LegacyMetainfoEnvironment, metainfo)
self.__legacy_env = None
self.resource = MResource()
@@ -540,27 +538,33 @@ class LegacyParser(MatchingParser):
self.parser_class_name = parser_class_name
self.backend_factory = backend_factory
+ module_name = self.parser_class_name.split('.')[:-1]
+ parser_class = self.parser_class_name.split('.')[-1]
+ module = importlib.import_module('.'.join(module_name))
+ self.parser_class = getattr(module, parser_class)
+
def run(self, mainfile: str, logger=None) -> Backend:
# TODO we need a homogeneous interface to parsers, but we dont have it right now.
# There are some hacks to distinguish between ParserInterface parser and simple_parser
# using hasattr, kwargs, etc.
+
+ if issubclass(self.parser_class, CoEParser):
+ # TODO reuse parser
+ parser = self.parser_class()
+ return parser.run(mainfile, logger)
+
def create_backend(meta_info):
if self.backend_factory is not None:
return self.backend_factory(meta_info, logger=logger)
return Backend(meta_info, logger=logger, domain=self.domain)
- 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__)
+ init_signature = inspect.getargspec(self.parser_class.__init__)
kwargs = dict(backend=create_backend, log_level=logging.DEBUG, debug=True)
kwargs = {key: value for key, value in kwargs.items() if key in init_signature.args}
with utils.legacy_logger(logger):
- self.parser = Parser(**kwargs)
+ self.parser = self.parser_class(**kwargs)
with patch.object(sys, 'argv', []):
backend = self.parser.parse(mainfile)
@@ -572,6 +576,86 @@ class LegacyParser(MatchingParser):
return backend
+class CoEParser(metaclass=ABCMeta):
+
+ @abstractmethod
+ def run(self, mainfile, logger) -> Backend:
+ pass
+
+
+class CoEInterfaceParser(CoEParser):
+
+ def __init__(self, interface_class):
+ super().__init__()
+ self.interface_class = interface_class
+ self.__interface = None
+
+ def run(self, mainfile, logger):
+ if self.__interface is None:
+ self.__interface = self.interface_class()
+
+ self.__interface.setup_logger(logger)
+ self.__interface.parse(mainfile)
+ return self.__interface.parser_context.super_backend
+
+
+class CoESimpleMatcherParser(CoEParser):
+
+ def __init__(self):
+ super().__init__()
+ self.parser_description = self.create_parser_description()
+ self.simple_matcher = self.create_simple_matcher()
+
+ self._metainfo_env = self.metainfo_env()
+ self.__legacy_metainfo_env = None
+
+ self.caching_levels = self.create_caching_levels()
+
+ @abstractmethod
+ def metainfo_env(self) -> LegacyMetainfoEnvironment:
+ pass
+
+ @property
+ def metaInfoEnv(self) -> LegacyMetainfoEnvironment:
+ if self.__legacy_metainfo_env is None:
+ self.__legacy_metainfo_env = self._metainfo_env.legacy_info_env()
+ return self.__legacy_metainfo_env
+
+ def create_caching_levels(self) -> dict:
+ return dict()
+
+ @abstractmethod
+ def create_simple_matcher(self):
+ pass
+
+ @abstractmethod
+ def create_parser_description(self) -> dict:
+ raise NotImplementedError()
+
+ @abstractmethod
+ def create_super_context(self):
+ pass
+
+ def simple_parser(self, mainfile, logger) -> Backend:
+ from nomadcore.simple_parser import mainFunction
+ backend = Backend(self._metainfo_env, logger=logger)
+ from unittest.mock import patch
+ with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
+ mainFunction(
+ mainFileDescription=self.simple_matcher,
+ metaInfoEnv=self.metaInfoEnv,
+ parserInfo=self.parser_description,
+ cachingLevelForMetaName=self.caching_levels,
+ superContext=self.create_super_context(),
+ superBackend=backend)
+
+ return backend
+
+ def run(self, mainfile, logger) -> Backend:
+ with utils.legacy_logger(logger):
+ return self.simple_parser(mainfile, logger)
+
+
class VaspOutcarParser(LegacyParser):
'''
LegacyParser that only matches mailfiles, if there is no .xml in the
diff --git a/tests/test_normalizing.py b/tests/test_normalizing.py
index 0c14eb61e1f371883150a3fe43deb6a0d7c263c3..cf3d52fae737032120cadc4ea73244d3ac6f3b93 100644
--- a/tests/test_normalizing.py
+++ b/tests/test_normalizing.py
@@ -362,7 +362,6 @@ def test_vasp_incar_system():
# backend_value = backend.get_value('x_vasp_atom_kind_refs') # OK
backend_value = backend.get_value('x_vasp_incar_SYSTEM') # OK
- print("backend_value: ", backend_value)
assert expected_value == backend_value
diff --git a/tests/test_parsing.py b/tests/test_parsing.py
index adce1e2da6ca8702f66bdd33df4caf9bcf283e25..96ad805a80f9ae7ebc0a570111d68f1b57c87aea 100644
--- a/tests/test_parsing.py
+++ b/tests/test_parsing.py
@@ -391,3 +391,32 @@ def test_match(raw_files, with_latin_1_file, no_warn):
assert len(matched_mainfiles) == correct_num_output_files, ', '.join([
'%s: %s' % (parser.name, mainfile)
for mainfile, parser in matched_mainfiles.items()])
+
+
+def parser_in_dir(dir):
+ for root, _, files in os.walk(dir):
+ for file_name in files:
+ file_path = os.path.join(root, file_name)
+
+ if 'test' not in file_path:
+ continue
+
+ parser = match_parser(file_path)
+ if parser is not None:
+
+ try:
+ parser.run(file_path)
+ except Exception as e:
+ print(file_path, parser, 'FAILURE', e)
+ else:
+ print(file_path, parser, 'SUCCESS')
+
+
+if __name__ == '__main__':
+ import sys
+ import os
+
+ assert len(sys.argv) == 2 and os.path.isdir(sys.argv[1]), \
+ 'One argument with an directory path is required.'
+
+ parser_in_dir(sys.argv[1])