diff --git a/dependencies/parsers/aptfim b/dependencies/parsers/aptfim
index d394f7ae375cd2355127abc67e07b1592f18d4f4..ed482b9956088163db9370dd5eee9b184c47870a 160000
--- a/dependencies/parsers/aptfim
+++ b/dependencies/parsers/aptfim
@@ -1 +1 @@
-Subproject commit d394f7ae375cd2355127abc67e07b1592f18d4f4
+Subproject commit ed482b9956088163db9370dd5eee9b184c47870a
diff --git a/dependencies/parsers/eels b/dependencies/parsers/eels
index 6f0e7ec897284382d8ef30b0ee0372f010ce468f..136ab4f5c17e340009a14df8dbb72dc101acb1b1 160000
--- a/dependencies/parsers/eels
+++ b/dependencies/parsers/eels
@@ -1 +1 @@
-Subproject commit 6f0e7ec897284382d8ef30b0ee0372f010ce468f
+Subproject commit 136ab4f5c17e340009a14df8dbb72dc101acb1b1
diff --git a/dependencies/parsers/mpes b/dependencies/parsers/mpes
index aa701e8f2780419e7911972c8e2a16d188008902..d4083cdadd4b34b9d99cbeed579c56c09aa7606b 160000
--- a/dependencies/parsers/mpes
+++ b/dependencies/parsers/mpes
@@ -1 +1 @@
-Subproject commit aa701e8f2780419e7911972c8e2a16d188008902
+Subproject commit d4083cdadd4b34b9d99cbeed579c56c09aa7606b
diff --git a/dependencies/parsers/vasp b/dependencies/parsers/vasp
index 2c8b7763eae8a27e7c1ca3a8ce86533978f42f73..8c2e56b0d9d17b777b5fa6a61c8e2877444ab603 160000
--- a/dependencies/parsers/vasp
+++ b/dependencies/parsers/vasp
@@ -1 +1 @@
-Subproject commit 2c8b7763eae8a27e7c1ca3a8ce86533978f42f73
+Subproject commit 8c2e56b0d9d17b777b5fa6a61c8e2877444ab603
diff --git a/nomad/cli/parse.py b/nomad/cli/parse.py
index 32f8b5ab80f8e5e34ceec99577fb0ce3f2af496e..c998837e6e92d4072045aa647ff33215ca52121c 100644
--- a/nomad/cli/parse.py
+++ b/nomad/cli/parse.py
@@ -43,17 +43,6 @@ def parse(
parser_backend = parser.run(mainfile_path, logger=logger)
- from nomad.metainfo import MSection
- from nomad.parsing.legacy import Backend
-
- if isinstance(parser_backend, MSection):
- backend = Backend(parser._metainfo_env, parser.domain)
- root_section = parser_backend.m_def.name
- section_def = getattr(datamodel.EntryArchive, root_section)
- backend.entry_archive.m_add_sub_section(section_def, parser_backend)
- backend.resource.add(parser_backend)
- parser_backend = backend
-
if not parser_backend.status[0] == 'ParseSuccess':
logger.error('parsing was not successful', status=parser_backend.status)
@@ -74,7 +63,7 @@ def normalize(
if normalizer_instance.__class__.__name__ == normalizer)
assert normalizer is not None, 'there is no normalizer %s' % str(normalizer)
- normalizer_instance = typing.cast(typing.Callable, normalizer)(parser_backend)
+ normalizer_instance = typing.cast(typing.Callable, normalizer)(parser_backend.entry_archive)
logger = logger.bind(normalizer=normalizer_instance.__class__.__name__)
logger.info('identified normalizer')
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index b155f4e5bdab47dad3d1428f4d09d9075c3e4641..fb57f6c2e01da88456ff315954a6e22e244990c4 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -18,12 +18,18 @@ import re
import importlib
from nomad.metainfo import Environment
+from nomad.datamodel import EntryArchive
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'.
+
+ TODO: There are currently two "run" functions. :func:`run` and :func:`parse`.
+ Because we are in the middle of transitioning out of the backend dependence we currently
+ have both, where 'run' creates a backend and 'parse' simply gets an archive that the
+ parser is supposed to populate. Eventually, we will only have the 'parse' function.
'''
name = "parsers/parser"
@@ -64,6 +70,19 @@ class Parser(metaclass=ABCMeta):
The used :class:`Backend` with status information and result data.
'''
+ def parse(self, mainfile: str, archive: EntryArchive, logger=None) -> None:
+ '''
+ Runs the parser on the given mainfile and populates the result in the given
+ archive root_section. It allows to be run repeatedly for different mainfiles.
+
+ Args:
+ mainfile: A path to a mainfile that this parser can parse.
+ archive: An instance of the section :class:`EntryArchive`. It might contain
+ a ``section_metadata`` with information about the entry.
+ logger: A optional logger
+ '''
+ pass
+
class BrokenParser(Parser):
'''
@@ -156,28 +175,22 @@ class MatchingParser(Parser):
class FairdiParser(MatchingParser):
- def __init__(self, parser_class_name: str, *args, **kwargs):
- super().__init__(*args, **kwargs)
- self.parser_class_name = parser_class_name
-
- module_name = self.parser_class_name.split('.')[:-1]
- parser_class_name = self.parser_class_name.split('.')[-1]
- self.__parser_impl = module_name, parser_class_name
- self.__parser_class = None
-
- @property
- def parser_class(self):
- if self.__parser_class is None:
- module_name, parser_class_name = self.__parser_impl
- module = importlib.import_module('.'.join(module_name))
- self.__parser_class = getattr(module, parser_class_name)
-
- return self.__parser_class
-
def run(self, mainfile: str, logger=None):
- parser = self.parser_class() # pylint: disable=not-callable
- root_section = parser.parse(mainfile, logger)
- return root_section
+ from .legacy import Backend
+ python_module = importlib.import_module(self.__module__ + '.metainfo')
+ metainfo = getattr(python_module, 'm_env')
+ backend = Backend(metainfo, domain=self.domain, logger=logger)
+ self.parse(mainfile, backend.entry_archive, logger=logger)
+ return backend
+
+ def parse(self, mainfile: str, archive: EntryArchive, logger=None):
+ raise NotImplementedError()
+
+ @classmethod
+ def main(cls, mainfile):
+ archive = EntryArchive()
+ cls().parse(mainfile, archive) # pylint: disable=no-value-for-parameter
+ return archive
class MissingParser(MatchingParser):
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 33492bbb35d2744daeec9aad168b89729ca4fe39..63fd024af153b38d7003b515c4ee9f4a5deea4ac 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -46,7 +46,6 @@ from nomad.archive import query_archive
from nomad.datamodel.encyclopedia import (
EncyclopediaMetadata,
)
-from nomad.metainfo import MSection
import phonopyparser.metainfo
@@ -386,14 +385,6 @@ class Calc(Proc):
self._parser_backend = parser.run(
self.upload_files.raw_file_object(self.mainfile).os_path, logger=logger)
- if isinstance(self._parser_backend, MSection):
- backend = Backend(parser._metainfo_env, parser.domain)
- root_section = self._parser_backend.m_def.name
- section_def = getattr(datamodel.EntryArchive, root_section)
- backend.entry_archive.m_add_sub_section(section_def, self._parser_backend)
- backend.resource.add(self._parser_backend)
- self._parser_backend = backend
-
except Exception as e:
self.fail('parser failed with exception', exc_info=e, error=str(e), **context)
return
diff --git a/tests/test_parsing.py b/tests/test_parsing.py
index b5985b8f59a87f21bce331a38f683fd7abadebf3..a33e98927edc47d13d7b25810571b1b5e3ffc478 100644
--- a/tests/test_parsing.py
+++ b/tests/test_parsing.py
@@ -23,7 +23,6 @@ from nomad import utils, files, datamodel
from nomad.parsing import BrokenParser, Backend
from nomad.parsing.parsers import parser_dict, match_parser
from nomad.app import dump_json
-from nomad.metainfo import MSection
parser_examples = [
('parsers/random', 'test/data/parsers/random_0'),
@@ -259,13 +258,7 @@ def assert_parser_dir_unchanged(previous_wd, current_wd):
def run_parser(parser_name, mainfile):
parser = parser_dict[parser_name]
result = parser.run(mainfile, logger=utils.get_logger(__name__))
- if isinstance(result, MSection):
- backend = Backend(parser._metainfo_env, parser.domain)
- root_section = result.m_def.name
- section_def = getattr(datamodel.EntryArchive, root_section)
- backend.entry_archive.m_add_sub_section(section_def, result)
- backend.resource.add(result)
- result = backend
+
result.domain = parser.domain
return add_calculation_info(result, parser_name=parser_name)