From d98e25e0bcae6b83fbc442cfeaaa2a4fe94d0053 Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Tue, 10 Apr 2018 16:16:35 +0100
Subject: [PATCH] Adding restricted_uri info
---
parser/parser-gromos/GROMOSDictionary.py | 45 ++++++++++++++++++++
parser/parser-gromos/GROMOSParser.py | 52 +++++++++++++++++++++++-
2 files changed, 96 insertions(+), 1 deletion(-)
diff --git a/parser/parser-gromos/GROMOSDictionary.py b/parser/parser-gromos/GROMOSDictionary.py
index 569710e..66e1c2d 100644
--- a/parser/parser-gromos/GROMOSDictionary.py
+++ b/parser/parser-gromos/GROMOSDictionary.py
@@ -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':
diff --git a/parser/parser-gromos/GROMOSParser.py b/parser/parser-gromos/GROMOSParser.py
index f3ab44e..62d5ffc 100644
--- a/parser/parser-gromos/GROMOSParser.py
+++ b/parser/parser-gromos/GROMOSParser.py
@@ -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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