Commit d98e25e0 authored by Berk Onat's avatar Berk Onat

Adding restricted_uri info

parent 610e52ae
Pipeline #27132 failed with stage
in 11 minutes and 1 second
......@@ -795,6 +795,49 @@ 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,
activeInfo=True,
activeSections=['section_restricted_uri']
),
'restricted_uri_files' : MetaInfoMap(startpage,
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri'],
subfunction={
'function' : self.parameter_file_name,
'supportDict' : self.fileDict,
},
),
'restricted_uri_license' : MetaInfoMap(startpage,
value='GROMOS License',
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri']
),
'restricted_uri_restriction' : MetaInfoMap(startpage,
value='any access',
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri']
),
'restricted_uri_reason' : MetaInfoMap(startpage,
value='propriety license',
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri']
),
'restricted_uri_issue_authority' : MetaInfoMap(startpage,
value='GROMOS',
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri']
),
}
# ------------------------------------------
# Definitions for section_frame_sequence
......@@ -1427,6 +1470,8 @@ def get_updateDictionary(self, defname):
dictionary = topology
elif defname == 'singleconfcalc':
dictionary = singleconfcalc
elif defname == 'restrictions':
dictionary = restrictions
elif defname == 'frameseq':
dictionary = frameseq
elif defname == 'frameseqend':
......
......@@ -269,8 +269,23 @@ class GROMOSParser(SmartParser.ParserBase):
#self.initialize_values()
self.secRunOpen = False
self.metaStorage.reset({'startSection' : [['section_run']]})
self.metaStorageRestrict.reset({'startSection' : [['section_restricted_uri']]})
self.reset_values()
def parameter_file_name(self, filedict, itemdict):
""" Function to generate data for parameter files list
"""
working_dir_name = os.path.dirname(os.path.normpath(os.path.abspath(self.fName)))
parmmeta = isMetaStrInDict("structure",self.fileDict)
filename = []
if parmmeta is not None:
if self.fileDict[parmmeta].value is not None:
fname = self.fileDict[parmmeta].value
filename.append(fname.replace(working_dir_name, '.'+os.path.sep))
if filename:
return False, filename, itemdict
else:
return False, None, itemdict
def gromos_input_output_files(self, backend, gIndex, section):
"""Called with onClose_x_gromos_section_control_parameters to setup
topology and trajectory inputs/outputs
......@@ -381,7 +396,7 @@ class GROMOSParser(SmartParser.ParserBase):
trajDone = True
self.newTraj = True
#if atLeastOneFileExist:
if atLeastOneFileExist:
# updateDict = {
# 'startSection' : [[PARSERTAG+'_section_input_output_files']],
# 'dictionary' : self.fileDict
......@@ -390,6 +405,17 @@ class GROMOSParser(SmartParser.ParserBase):
# self.metaStorage.updateBackend(backend.superBackend,
# startsection=[PARSERTAG+'_section_input_output_files'],
# autoopenclose=False)
self.secRestrictGIndex = backend.superBackend.openSection("section_restricted_uri")
restrictionsDict = get_updateDictionary(self, 'restrictions')
updateDict = {
'startSection' : [['section_restricted_uri']],
'dictionary' : restrictionsDict
}
self.metaStorageRestrict.update(updateDict)
self.metaStorageRestrict.updateBackend(backend.superBackend,
startsection=['section_restricted_uri'],
autoopenclose=False)
backend.superBackend.closeSection("section_restricted_uri", self.secRestrictGIndex)
if self.newTopo:
if topoDone and atLeastOneFileExist:
......@@ -554,6 +580,30 @@ class GROMOSParser(SmartParser.ParserBase):
#self.stepcontrolDict.update({"follow" : followsteps})
self.onOpen_section_sampling_method(backend, None, None)
self.onClose_section_sampling_method(backend, None, None)
if self.topology:
if self.newTopo:
section_file_Dict = {}
section_file_Dict.update(self.fileDict)
updateDict = {
'startSection' : [[PARSERTAG+'_section_control_parameters']],
'dictionary' : section_file_Dict
}
self.metaStorage.update(updateDict)
self.metaStorage.updateBackend(backend.superBackend,
startsection=[PARSERTAG+'_section_control_parameters'],
autoopenclose=False)
self.secRestrictGIndex = backend.superBackend.openSection("section_restricted_uri")
restrictionsDict = get_updateDictionary(self, 'restrictions')
updateDict = {
'startSection' : [['section_restricted_uri']],
'dictionary' : restrictionsDict
}
self.metaStorageRestrict.update(updateDict)
self.metaStorageRestrict.updateBackend(backend.superBackend,
startsection=['section_restricted_uri'],
autoopenclose=False)
backend.superBackend.closeSection("section_restricted_uri", self.secRestrictGIndex)
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
......
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