From afdd0937aab2681ca3912cfd9d95c7633fdcd7b9 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Wed, 22 Jul 2020 22:32:19 +0200
Subject: [PATCH] Removed smart parser dep on old metainfo.
---
.../nomadcore/md_data_access/MDDataAccess.py | 7 +++-
.../metainfo_storage/MetaInfoStorage.py | 34 +++----------------
.../smart_parser/SmartParserCommon.py | 14 +++-----
3 files changed, 14 insertions(+), 41 deletions(-)
diff --git a/common/python/nomadcore/md_data_access/MDDataAccess.py b/common/python/nomadcore/md_data_access/MDDataAccess.py
index 60d9ebd..21dc648 100644
--- a/common/python/nomadcore/md_data_access/MDDataAccess.py
+++ b/common/python/nomadcore/md_data_access/MDDataAccess.py
@@ -26,7 +26,12 @@ import MDAnalysis.core.universe as mda_u
import MDAnalysis.coordinates as mda_c
import panedr
import parmed as pmd
-import pymolfile as pym
+# this might not be available on all development systems, we still want to pass the import
+# eventhough not all code will work
+try:
+ import pymolfile as pym
+except:
+ pass
from nomadcore.md_data_access import GromosTopoObjects as gto
from nomadcore.md_data_access.GromosTopoObjects import get_zipType, get_fileExtensions
import io
diff --git a/common/python/nomadcore/metainfo_storage/MetaInfoStorage.py b/common/python/nomadcore/metainfo_storage/MetaInfoStorage.py
index 5d0a6fe..13ae298 100644
--- a/common/python/nomadcore/metainfo_storage/MetaInfoStorage.py
+++ b/common/python/nomadcore/metainfo_storage/MetaInfoStorage.py
@@ -7,16 +7,6 @@ import re
import ast
from collections import namedtuple
-import metainfo
-
-COMMON_META_INFO_PATH = os.path.normpath(os.path.join(
- os.path.dirname(os.path.abspath(metainfo.__file__)),
- "common.nomadmetainfo.json"))
-
-PUBLIC_META_INFO_PATH = os.path.normpath(os.path.join(
- os.path.dirname(os.path.abspath(metainfo.__file__)),
- "public.nomadmetainfo.json"))
-
NOTEXCEPT = re.compile(r'[a-cf-zA-CF-Z!\?,{}\[\]]')
def is_number(val):
@@ -756,25 +746,8 @@ class JsonMetaInfo(object):
Loads data and extracts values of items
with specified superNames
"""
- def __init__(self, *args):
- self.jsonList = None
- for filepath in args:
- try:
- with open(filepath, encoding="utf-8") as f:
- jsonDict = json.load(f)
- except:
- logging.exception("Error while loading file %s" % filepath)
- raise
- typeStr = jsonDict.get("type","nomad_meta_info_1_0")
- typeRe = re.compile(r"nomad_meta_info_(?P<major>[0-9]+)_(?P<minor>[0-9]+)$")
- m = typeRe.match(typeStr)
- if not m:
- raise Exception("unexpected type '%s', expected nomad_meta_info_1_0" % typeStr)
- newJsonList = jsonDict.get("metaInfos",[])
- if self.jsonList:
- self.jsonList = self.jsonList + newJsonList
- else:
- self.jsonList = newJsonList
+ def __init__(self, metainfo_env):
+ self.jsonList = metainfo_env.to_legacy_dict(metainfo_env.packages)['metaInfos']
def attributes(self, sectionname):
attributes = {}
@@ -889,7 +862,8 @@ if __name__ == "__main__":
'section_repository_info'
]}
- jsonmetadata = JsonMetaInfo(COMMON_META_INFO_PATH, PUBLIC_META_INFO_PATH)
+ from nomad.datamodel.metainfo import m_env
+ jsonmetadata = JsonMetaInfo(m_env)
updateDict = {
'startSection' : [['section_topology']],
diff --git a/common/python/nomadcore/smart_parser/SmartParserCommon.py b/common/python/nomadcore/smart_parser/SmartParserCommon.py
index 401b9ae..f662bfa 100644
--- a/common/python/nomadcore/smart_parser/SmartParserCommon.py
+++ b/common/python/nomadcore/smart_parser/SmartParserCommon.py
@@ -3,7 +3,6 @@ from nomadcore.unit_conversion.unit_conversion import convert_unit
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.metainfo_storage.MetaInfoStorage import COMMON_META_INFO_PATH, PUBLIC_META_INFO_PATH
from nomadcore.metainfo_storage import MetaInfoStorage as mStore
from nomadcore.metainfo_storage.MetaInfoStorage import strcleaner, strisinstance, literal_eval
from nomadcore.smart_parser.SmartParserDictionary import getDict_MetaStrInDict, getList_MetaStrInDict, get_unitDict
@@ -14,6 +13,8 @@ import os
import re
import io
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+
@contextmanager
def open_section(parser, name):
gid = parser.openSection(name)
@@ -45,10 +46,7 @@ def conv_float(n, default=None):
return None
def get_metaInfo(self):
- metaInfoEnv, warnings = loadJsonFile(filePath=self.META_INFO_PATH,
- dependencyLoader=None,
- extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
- uri=None)
+ metaInfoEnv = LegacyMetainfoEnvironment.from_legacy_package_path(self.META_INFO_PATH)
metaInfoEnv = set_section_metaInfoEnv(self.PARSERTAG, metaInfoEnv, self.sectionDict)
metaInfoEnv = setDict_metaInfoEnv(metaInfoEnv, self.metaDicts)
return metaInfoEnv
@@ -170,11 +168,7 @@ class ParserBase(object):
]}
self.META_INFO_PATH = metainfopath
PARSER_INFO_DEFAULT = parserinfodef
- jsonmetadata = mStore.JsonMetaInfo(
- COMMON_META_INFO_PATH,
- PUBLIC_META_INFO_PATH,
- self.META_INFO_PATH
- )
+ jsonmetadata = mStore.JsonMetaInfo(LegacyMetainfoEnvironment.from_legacy_package_path(metainfopath))
self.metaStorage.build(jsonmetadata, 'section_run', exclude_dict)
self.metaStorageRestrict.build(jsonmetadata, 'section_restricted_uri', exclude_dict)
self.re_program_name = re_program_name
--
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