Removed smart parser dep on old metainfo.

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

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']],

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