Adding meta info for uri/file restrictions with section_restricted_uri

parser/parser-amber/AMBERCommon.py

@@ -13,6 +13,12 @@ import json
 import os
 import re
 
+PARSERNAME = "AMBER"
+PROGRAMNAME = "amber"
+PARSERVERSION = "0.0.3"
+PARSERMETANAME = PARSERNAME.lower()
+PARSERTAG = 'x_' + PARSERMETANAME
+
 PARSER_INFO_DEFAULT = {
         'name':'amber-parser', 
         'version': '0.0.1'
@@ -107,6 +113,7 @@ class AMBERParserBase(object):
     def __init__(self,cachingLevelForMetaName=None, coverageIgnoreList=None,
                  re_program_name=None):
         self.metaStorage = mStore.Container('section_run')
+        self.metaStorageRestrict = mStore.Container('section_restricted_uri')
         exclude_dict = { 
             'section_run' : [
             'section_processor_info', 
@@ -120,6 +127,7 @@ class AMBERParserBase(object):
                 META_INFO_PATH
                 )
         self.metaStorage.build(jsonmetadata, 'section_run', exclude_dict)
+        self.metaStorageRestrict.build(jsonmetadata, 'section_restricted_uri', exclude_dict)
         self.re_program_name = re_program_name
         self.unitDict = get_unitDict('si')
         self.fileDict = get_fileListDict()

parser/parser-amber/AMBERDictionary.py

@@ -906,6 +906,41 @@ def get_updateDictionary(self, defname):
             activeSections=['section_energy_van_der_Waals']
             ),
         }
+
+
+    # Info for section_restricted_uri
+    restrictions = {
+        'number_of_restricted_uri_files' : MetaInfoMap(startpage,
+            value=int(1),
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_files' : MetaInfoMap(startpage,
+            subfunction=self.parameter_file_name,
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_license' : MetaInfoMap(startpage,
+            value='AMBER License',
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_restriction' : MetaInfoMap(startpage,
+            value='any access',
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_reason' : MetaInfoMap(startpage,
+            value='propriety license',
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_issue_athority' : MetaInfoMap(startpage,
+            value='AMBER',
+            autoSections=True,
+            activeSections=['section_restricted_uri']
+            ),
+        }
    
     # ------------------------------------------
     #   Definitions for section_frame_sequence
@@ -1227,6 +1262,8 @@ def get_updateDictionary(self, defname):
         dictionary = topology
     elif defname == 'singleconfcalc':
         dictionary = singleconfcalc
+    elif defname == 'restrictions':
+        dictionary = restrictions
     elif defname == 'frameseq':
         dictionary = frameseq
     elif defname == 'atom_type':

parser/parser-amber/AMBERParser.py

@@ -8,6 +8,7 @@ from nomadcore.caching_backend import CachingLevel
 from nomadcore.simple_parser import mainFunction, ParsingContext
 from nomadcore.simple_parser import SimpleMatcher as SM
 from AMBERDictionary import set_excludeList, set_includeList, get_updateDictionary, getList_MetaStrInDict, getDict_MetaStrInDict
+from nomadcore.smart_parser.SmartParserDictionary import isMetaStrInDict
 from contextlib import contextmanager
 import AMBERCommon as AmberC
 import trajectory_reader as TrajRead
@@ -218,6 +219,20 @@ class AMBERParser(AmberC.AMBERParserBase):
         #else:
         #    return False
 
+    def parameter_file_name(self, itemdict):
+        """ Function to generate data for parameter files list
+        """
+        working_dir_name = os.path.dirname(os.path.abspath(self.fName))
+        parmmeta = isMetaStrInDict("PARM",self.fileDict)
+        filename = []
+        if parmmeta is not None:
+            if self.fileDict[parmmeta].value is not None:
+                filename.append(self.fileDict[parmmeta].value)
+        if filename:
+            return False, filename, itemdict
+        else:
+            return False, None, itemdict
+
     def topology_to_dictionary(self):
         """ This function generates self.topologyDict dictionary
             and converts/stores all the topology information 
@@ -478,7 +493,17 @@ class AMBERParser(AmberC.AMBERParserBase):
         self.metaStorage.updateBackend(backend, 
                 startsection=['section_sampling_method'],
                 autoopenclose=False)
-        #backend.closeSection("section_sampling_method", self.secSamplingGIndex)
+        self.secRestrictGIndex = backend.openSection("section_restricted_uri")
+        section_restrictions_Dict = get_updateDictionary(self, 'restrictions')
+        updateDict = {
+            'startSection' : [['section_restricted_uri']],
+            'dictionary' : section_restrictions_Dict
+            }
+        self.metaStorageRestrict.update(updateDict)
+        self.metaStorageRestrict.updateBackend(backend, 
+                startsection=['section_restricted_uri'],
+                autoopenclose=False)
+        backend.closeSection("section_restricted_uri", self.secRestrictGIndex)
     
     def onOpen_section_topology(self, backend, gIndex, section):
         # keep track of the latest topology description section