diff --git a/nomad/normalizing/fhiaims.py b/nomad/normalizing/fhiaims.py
index 2aeff7ef591b28e8509862d1bf225a04fd101897..7a058be7ea49266ed511abf3887fdd22a59dedf0 100644
--- a/nomad/normalizing/fhiaims.py
+++ b/nomad/normalizing/fhiaims.py
@@ -236,8 +236,6 @@ class FhiAimsBaseNormalizer(Normalizer):
# # matrix_hits[key]=matrix_hits[key]+CompareToDefaults(val[AtomIndex],to_compare[i])
-# Copen=backend.openContext(context)
-
# closest_base_int=min(matrix_hits_int, key=matrix_hits_int.get)
# if (matrix_hits_basis[min(matrix_hits_basis, key=matrix_hits_basis.get)] ==0):
@@ -254,8 +252,6 @@ class FhiAimsBaseNormalizer(Normalizer):
# backend.addValue("basis_set",'custom-'+closest_base_int)
# # print('custom-'+closest_base_int)
-# backend.closeContext(context)
-
# backend.finishedParsingSession("ParseSuccess", None)
# sys.stdout.flush()
# return
diff --git a/nomad/parsing/__init__.py b/nomad/parsing/__init__.py
index 4cfa35be822e101485dcf5f5016b0151ad5ea18f..c2dc92c7df32961ff09a43905bde78605acb16c6 100644
--- a/nomad/parsing/__init__.py
+++ b/nomad/parsing/__init__.py
@@ -70,6 +70,6 @@ based on nomad@fairdi's metainfo:
:members:
'''
-from nomad.parsing.legacy import AbstractParserBackend, Backend, BackendError, BadContextUri, LegacyParser
+from nomad.parsing.legacy import AbstractParserBackend, Backend, BackendError, LegacyParser
from nomad.parsing.parser import Parser, BrokenParser, MissingParser, MatchingParser
from nomad.parsing.artificial import TemplateParser, GenerateRandomParser, ChaosParser, EmptyParser
diff --git a/nomad/parsing/legacy.py b/nomad/parsing/legacy.py
index 0fdd0cfeab3b1de9cd5d645188f19d45b6a94952..bb12b5929d32394016c2d308d0ac3d967a1fadae 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, cast
+from typing import List, Union, Any, Tuple, Type, cast
from abc import ABCMeta, abstractmethod
import importlib
import os.path
@@ -30,7 +30,7 @@ import sys
from nomad import utils, datamodel, config
from nomad.metainfo import (
- SubSection, Quantity, Section, Reference, MResource, MSection, MSectionBound, Property)
+ SubSection, Quantity, Section, SectionProxy, Reference, MResource, MSection, MSectionBound, Property)
from nomad.metainfo.legacy import (
LegacyMetainfoEnvironment, python_package_mapping, normalize_name)
@@ -41,10 +41,6 @@ class BackendError(Exception):
pass
-class BadContextUri(Exception):
- pass
-
-
class AbstractParserBackend(metaclass=ABCMeta):
'''
This ABS provides the parser backend interface used by the NOMAD-coe parsers.
@@ -71,16 +67,6 @@ class AbstractParserBackend(metaclass=ABCMeta):
''' Called when the parsing finishes. '''
pass
- @abstractmethod
- def openContext(self, contextUri: str):
- ''' Open existing archive data to introduce new data into an existing section. '''
- pass
-
- @abstractmethod
- def closeContext(self, contextUri: str):
- ''' Close priorly opened existing archive data again. '''
- pass
-
@abstractmethod
def openSection(self, metaName, parent_index=-1):
''' Opens a new section and returns its new unique gIndex. '''
@@ -229,7 +215,6 @@ class Backend(AbstractParserBackend):
self.entry_archive = datamodel.EntryArchive()
self.resource.add(self.entry_archive)
- self.__open_sections: Dict[Tuple[Section, int], MSection] = {}
self.strict = False # TODO
self.reset_status()
@@ -238,15 +223,31 @@ class Backend(AbstractParserBackend):
# self._known_attributes = ['results']
# self.fileOut = io.StringIO()
+ def __open_section(self, section_def: Union[Section, SectionProxy], index: int = -1) -> MSection:
+ ''' Returns the last opened section with the given parent index. '''
+ sections = self.resource.all(section_def.section_cls)
+
+ if sections is None:
+ raise KeyError(
+ 'section %s with given parent index %s does not exist' % (section_def.name, index))
+
+ if index == -1:
+ return sections[-1]
+
+ for section in reversed(sections):
+ if section.m_parent_index == index:
+ return section
+
+ raise KeyError(
+ 'section %s with given parent index %s does not exist (B)' % (section_def.name, index))
+
def __getitem__(self, key):
property_def = self.resolve_definition(key, Property)
section_def = property_def.m_parent
if section_def.extends_base_section:
section_def = section_def.base_sections[0]
- section = self.__open_sections.get((section_def, -1), None)
- if not section:
- section = self.open_sections[(section_def, -1)]
+ section = self.__open_section(section_def)
if isinstance(property_def, Quantity):
return section.m_get(property_def)
@@ -262,69 +263,6 @@ class Backend(AbstractParserBackend):
return self.env.resolve_definition(
normalize_name(name), section_cls, Backend.filter_legacy_defs)
- def resolve_context(self, context_uri: str):
- path = context_uri.strip('/').split('/')
- path.reverse()
- current = None
- while len(path) > 0:
- section = path.pop()
- if len(path) == 0:
- raise BadContextUri(context_uri)
- index = int(path.pop())
- if current is None:
- section_def = self.resolve_definition(section, Section)
- if section_def is None:
- raise BadContextUri(context_uri)
- i = 0
- for content in self.entry_archive.m_contents():
- if content.m_follows(section_def):
- if i == index:
- current = content
- break
-
- i += 1
-
- else:
- sub_section_def = self.resolve_definition(section, SubSection)
- if sub_section_def is None:
- raise BadContextUri(context_uri)
- current = current.m_get_sub_section(sub_section_def, index)
-
- if current is None:
- raise BadContextUri(context_uri)
-
- return current
-
- def openContext(self, context_uri: str):
- ''' Open existing archive data to introduce new data into an existing section. '''
- section = self.resolve_context(context_uri)
- self.__open(section)
-
- def closeContext(self, context_uri: str):
- ''' Close priorly opened existing archive data again. '''
- section = self.resolve_context(context_uri)
- self.__close(section)
-
- @property
- def open_sections(self):
- for section in self.entry_archive.m_all_contents():
- self.__open(section)
- return self.__open_sections
-
- def __open(self, section):
- if section.m_parent_index != -1:
- self.__open_sections[(section.m_def, section.m_parent_index)] = section
-
- # here -1 meaning the last opened section
- self.__open_sections[(section.m_def, -1)] = section
-
- def __close(self, section):
- # TODO
- pass
- # if section.m_parent_index != -1 and self.__open_sections.get((section.m_def, -1)) == section:
- # del(self.__open_sections[(section.m_def, -1)])
- # del(self.__open_sections[(section.m_def, section.m_parent_index)])
-
def openSection(self, name, parent_index: int = -1, return_section=False):
'''
It will assume that there is a sub-section def with the given name.
@@ -349,11 +287,9 @@ class Backend(AbstractParserBackend):
if parent_section_def.extends_base_section:
parent_section_def = parent_section_def.base_sections[0]
- parent = self.__open_sections[(parent_section_def, parent_index)]
+ parent = self.__open_section(parent_section_def, parent_index)
section = parent.m_create(section_def.section_cls, sub_section_def)
- self.__open(section)
-
if return_section:
return section
return section.m_parent_index
@@ -366,18 +302,12 @@ class Backend(AbstractParserBackend):
if section_def.extends_base_section:
section_def = section_def.base_sections[0]
- section = self.__open_sections.get((section_def, g_index), None)
- if not section:
- section = self.open_sections[(section_def, g_index)]
+ section = self.__open_section(section_def, g_index)
return section, quantity_def
def closeSection(self, name, g_index):
- # TODO
- if self.strict:
- section_def = self.resolve_definition(name, Section)
- section = self.__open_sections[(section_def, g_index)]
- self.__close(section)
+ pass
def openNonOverlappingSection(self, metaName):
return self.openSection(metaName)
@@ -404,14 +334,11 @@ class Backend(AbstractParserBackend):
section, quantity_def = self.get_open_section_for_quantity(name, g_index)
if isinstance(quantity_def.type, Reference):
# quantity is a reference
- possible_targets = self.resource.all(quantity_def.type.target_section_def.section_cls)
- referenced_target = None
- for target in possible_targets:
- if target.m_parent_index == value:
- referenced_target = target
-
- if referenced_target is None:
- raise BackendError('There is not section for the given reference index')
+ try:
+ referenced_target = self.__open_section(
+ quantity_def.type.target_section_def, value)
+ except KeyError as e:
+ raise BackendError(str(e))
value = referenced_target
@@ -444,15 +371,12 @@ class Backend(AbstractParserBackend):
section, quantity_def = self.get_open_section_for_quantity(name, gIndex)
if isinstance(quantity_def.type, Reference):
# quantity is a reference
- possible_targets = self.resource.all(quantity_def.type.target_section_def.section_cls)
resolved_values = []
for value in values:
- referenced_target = None
- for target in possible_targets:
- if target.m_parent_index == value:
- referenced_target = target
-
- if referenced_target is None:
+ # quantity is a reference
+ try:
+ referenced_target = self.__open_section(quantity_def.type.target_section_def, value)
+ except KeyError:
raise BackendError('There is not section for the given reference index')
resolved_values.append(referenced_target)
diff --git a/tests/test_parsing.py b/tests/test_parsing.py
index 4378f0c0e763063ab3fa39103f5465393d269057..b5985b8f59a87f21bce331a38f683fd7abadebf3 100644
--- a/tests/test_parsing.py
+++ b/tests/test_parsing.py
@@ -20,7 +20,7 @@ import os
from shutil import copyfile
from nomad import utils, files, datamodel
-from nomad.parsing import BrokenParser, BadContextUri, Backend
+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
@@ -225,62 +225,6 @@ class TestBackend(object):
assert len(run['section_single_configuration_calculation'][0].section_dos) == 1
assert len(run['section_single_configuration_calculation'][1].section_dos) == 0
- def test_context(self, backend: Backend, no_warn):
- backend.openSection('section_run')
- backend.openSection('section_method')
- backend.closeSection('section_method', -1)
- backend.closeSection('section_run', -1)
-
- backend.openSection('section_run')
- backend.closeSection('section_run', -1)
-
- backend.openContext('/section_run/0')
- backend.addValue('program_name', 't1')
- backend.closeContext('/section_run/0')
-
- backend.openContext('/section_run/1')
- backend.addValue('program_name', 't2')
- backend.closeContext('/section_run/1')
-
- backend.openContext('/section_run/0/section_method/0')
- backend.closeContext('/section_run/0/section_method/0')
-
- from nomad.datamodel.metainfo.public import section_run
- runs = backend.resource.all(section_run)
- assert runs[0]['program_name'] == 't1'
- assert runs[1]['program_name'] == 't2'
-
- def test_multi_context(self, backend: Backend, no_warn):
- backend.openSection('section_run')
- backend.closeSection('section_run', -1)
-
- backend.openContext('/section_run/0')
- backend.openSection('section_method')
- backend.closeSection('section_method', -1)
- backend.closeContext('/section_run/0')
-
- backend.openContext('/section_run/0')
- backend.openSection('section_method')
- backend.closeSection('section_method', -1)
- backend.closeContext('/section_run/0')
-
- from nomad.datamodel.metainfo.public import section_run
- runs = backend.resource.all(section_run)
- assert len(runs[0].section_method) == 2
-
- def test_bad_context(self, backend: Backend, no_warn):
- try:
- backend.openContext('section_run/0')
- assert False
- except BadContextUri:
- pass
-
- try:
- backend.openContext('dsfds')
- assert False
- except BadContextUri:
- pass
-
def create_reference(data, pretty):
if (pretty):