From f914e0c0bafc0922ab77a4347462a15b62d2efa7 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Tue, 13 Aug 2019 12:04:30 +0200
Subject: [PATCH] Adapted implementatino for nomad-fairdi.
---
.gitignore | 58 +-----
parser/parser-qbox/setup_paths.py | 6 -
.../parser-qbox => qboxparser}/QboxCommon.py | 1 -
.../QboxInputParser.py | 47 +++--
.../parser-qbox => qboxparser}/QboxParser.py | 173 ++++++++++--------
.../QboxXMLParser.py | 5 +-
qboxparser/__init__.py | 1 +
setup.py | 33 ++++
.../eu/nomad_lab/parsers/QboxParser.scala | 65 -------
.../eu/nomad_lab/parsers/QboxParserSpec.scala | 29 ---
10 files changed, 158 insertions(+), 260 deletions(-)
delete mode 100644 parser/parser-qbox/setup_paths.py
rename {parser/parser-qbox => qboxparser}/QboxCommon.py (97%)
rename {parser/parser-qbox => qboxparser}/QboxInputParser.py (94%)
rename {parser/parser-qbox => qboxparser}/QboxParser.py (87%)
rename {parser/parser-qbox => qboxparser}/QboxXMLParser.py (98%)
create mode 100644 qboxparser/__init__.py
create mode 100644 setup.py
delete mode 100644 src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
delete mode 100644 src/test/scala/eu/nomad_lab/parsers/QboxParserSpec.scala
diff --git a/.gitignore b/.gitignore
index 1df2c2bb..efbcf02a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,55 +1,5 @@
-# use glob syntax.
-syntax: glob
-*.ser
-*.class
-*~
-*.bak
-#*.off
-*.old
+# python
+__pycache__
+.mypy_cache
*.pyc
-*.bk
-*.swp
-*.annotate
-.DS_Store
-
-# logging files
-detailed.log
-
-# eclipse conf file
-.settings
-.classpath
-.project
-.manager
-.scala_dependencies
-
-# idea
-.idea
-*.iml
-
-# building
-target
-build
-null
-tmp*
-temp*
-dist
-test-output
-build.log
-
-# other scm
-.svn
-.CVS
-.hg*
-
-# switch to regexp syntax.
-# syntax: regexp
-# ^\.pc/
-
-#SHITTY output not in target directory
-build.log
-
-#emacs TAGS
-TAGS
-
-lib/
-env/
+*.egg-info/
\ No newline at end of file
diff --git a/parser/parser-qbox/setup_paths.py b/parser/parser-qbox/setup_paths.py
deleted file mode 100644
index e0a0fb00..00000000
--- a/parser/parser-qbox/setup_paths.py
+++ /dev/null
@@ -1,6 +0,0 @@
-import sys, os, os.path
-baseDir = os.path.dirname(os.path.abspath(__file__))
-commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
-
-if not commonDir in sys.path:
- sys.path.insert(0, commonDir)
diff --git a/parser/parser-qbox/QboxCommon.py b/qboxparser/QboxCommon.py
similarity index 97%
rename from parser/parser-qbox/QboxCommon.py
rename to qboxparser/QboxCommon.py
index 80ed478f..5997a07d 100644
--- a/parser/parser-qbox/QboxCommon.py
+++ b/qboxparser/QboxCommon.py
@@ -1,4 +1,3 @@
-import setup_paths
import numpy as np
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion import convert_unit
diff --git a/parser/parser-qbox/QboxInputParser.py b/qboxparser/QboxInputParser.py
similarity index 94%
rename from parser/parser-qbox/QboxInputParser.py
rename to qboxparser/QboxInputParser.py
index 0fb28bc3..d5732763 100644
--- a/parser/parser-qbox/QboxInputParser.py
+++ b/qboxparser/QboxInputParser.py
@@ -1,5 +1,4 @@
from builtins import object
-import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
@@ -16,7 +15,7 @@ import logging, os, re, sys
############################################################
###############[1] transfer PARSER CONTEXT #################
############################################################
-logger = logging.getLogger("nomad.qboxInputParser")
+logger = logging.getLogger("nomad.qboxInputParser")
class QboxInputParserContext(object):
@@ -32,7 +31,7 @@ class QboxInputParserContext(object):
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
-
+
self.singleConfCalcs = []
@@ -74,20 +73,20 @@ class QboxInputParserContext(object):
def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
functional_list = section["x_qbox_functional_name"]
- if not functional_list: # default is LDA in qbox
+ if not functional_list: # default is LDA in qbox
functional = "LDA"
else :
- functional = functional_list[-1] # use the xc appeared the last time
+ functional = functional_list[-1] # use the xc appeared the last time
+
-
if functional:
functionalMap = {
- "LDA": ["LDA_X", "LDA_C_PZ"],
- "VMN": ["LDA_X", "LDA_C_VWN"],
- "PBE": ["GGA_X_PBE","GGA_C_PBE"],
- "PBE0": ["GGA_X_PBE","GGA_C_PBE"],
- "B3LYP": ["HYB_GGA_XC_B3LYP5"]
- #need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
+ "LDA": ["LDA_X", "LDA_C_PZ"],
+ "VMN": ["LDA_X", "LDA_C_VWN"],
+ "PBE": ["GGA_X_PBE","GGA_C_PBE"],
+ "PBE0": ["GGA_X_PBE","GGA_C_PBE"],
+ "B3LYP": ["HYB_GGA_XC_B3LYP5"]
+ #need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
}
# Push the functional string into the backend
nomadNames = functionalMap.get(functional)
@@ -103,7 +102,7 @@ class QboxInputParserContext(object):
###################################################################
# (3.4) onClose for geometry and force (section_system)
- # todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
+ # todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
###################################################################
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
@@ -148,7 +147,7 @@ class QboxInputParserContext(object):
if unit_cell:
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
-
+
@@ -163,7 +162,7 @@ class QboxInputParserContext(object):
-
+
#############################################################
#################[2] MAIN PARSER STARTS HERE ###############
@@ -178,7 +177,7 @@ def build_QboxInputFileSimpleMatcher():
which allows nice formating of nested SimpleMatchers in python.
Returns:
- SimpleMatcher that parses input file of qbox.
+ SimpleMatcher that parses input file of qbox.
"""
@@ -204,18 +203,18 @@ def build_QboxInputFileSimpleMatcher():
SM(r"\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*"),
SM(r"\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*"),
- #--------set xc---------
+ #--------set xc---------
SM(name = "qboxXC",
startReStr = r"\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*",
sections = ["x_qbox_section_functionals"]
- ),
+ ),
#-------set efield---------
SM (r"\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*",repeats = True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
])
-
-
+
+
@@ -231,7 +230,7 @@ def build_QboxInputFileSimpleMatcher():
subMatchers = [
#=============================================================================
- # read OUPUT file *.r, the method part comes from INPUT file *.i, so we
+ # read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# do not need to parser INPUT file, the OUTPUT file contains all information
#=============================================================================
SM (name = 'NewRun',
@@ -243,11 +242,11 @@ def build_QboxInputFileSimpleMatcher():
fixedStartValues={'program_name': 'qbox', 'program_basis_set_type': 'plane waves'},
sections = ['section_run'],
subMatchers = [
-
+
#-----------input method---------------------
calculationMethodSubMatcher
- ]) # CLOSING SM NewRun
+ ]) # CLOSING SM NewRun
]) # END Root
@@ -259,7 +258,7 @@ def get_cachingLevelForMetaName(metaInfoEnv):
metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
Returns:
- Dictionary with metaname as key and caching level as value.
+ Dictionary with metaname as key and caching level as value.
"""
# manually adjust caching of metadata
cachingLevelForMetaName = {
diff --git a/parser/parser-qbox/QboxParser.py b/qboxparser/QboxParser.py
similarity index 87%
rename from parser/parser-qbox/QboxParser.py
rename to qboxparser/QboxParser.py
index be995ead..fe4edc73 100644
--- a/parser/parser-qbox/QboxParser.py
+++ b/qboxparser/QboxParser.py
@@ -1,14 +1,15 @@
from builtins import object
-import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import AncillaryParser, mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
-from QboxCommon import get_metaInfo
-import QboxXMLParser
+from .QboxCommon import get_metaInfo
+from . import QboxXMLParser
import logging, os, re, sys
+import nomad_meta_info
+
############################################################
# This is the parser for the main file of qbox (for the output file *.r) .
############################################################
@@ -17,7 +18,7 @@ import logging, os, re, sys
############################################################
###############[1] transfer PARSER CONTEXT #################
############################################################
-logger = logging.getLogger("nomad.qboxParser")
+logger = logging.getLogger("nomad.qboxParser")
class QboxParserContext(object):
@@ -33,7 +34,7 @@ class QboxParserContext(object):
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
-
+
self.singleConfCalcs = []
@@ -78,9 +79,9 @@ class QboxParserContext(object):
x_qbox_loading_xml_file_list = section['x_qbox_loading_xml_file']
- xml_file = x_qbox_loading_xml_file_list[-1]
-
- if xml_file is not None:
+ xml_file = x_qbox_loading_xml_file_list[-1]
+
+ if xml_file is not None:
logger.warning("This output showed this calculation need to load xml file, so we need this xml file ('%s') to read geometry information" % os.path.normpath(xml_file) )
fName = os.path.normpath(xml_file)
@@ -94,7 +95,7 @@ class QboxParserContext(object):
try:
with open(fName) as fxml:
xmlParser.parseFile(fxml)
-
+
except IOError:
logger.warning("Could not find xml file in directory '%s'. " % os.path.dirname(os.path.abspath(self.fName)))
@@ -102,20 +103,20 @@ class QboxParserContext(object):
def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
functional_list = section["x_qbox_functional_name"]
- if not functional_list: # default is LDA in qbox
+ if not functional_list: # default is LDA in qbox
functional = "LDA"
else :
- functional = functional_list[-1] # use the xc appeared the last time
+ functional = functional_list[-1] # use the xc appeared the last time
+
-
if functional:
functionalMap = {
- "LDA": ["LDA_X", "LDA_C_PZ"],
- "VMN": ["LDA_X", "LDA_C_VWN"],
- "PBE": ["GGA_X_PBE","GGA_C_PBE"],
- "PBE0": ["GGA_X_PBE","GGA_C_PBE"],
- "B3LYP": ["HYB_GGA_XC_B3LYP5"]
- #need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
+ "LDA": ["LDA_X", "LDA_C_PZ"],
+ "VMN": ["LDA_X", "LDA_C_VWN"],
+ "PBE": ["GGA_X_PBE","GGA_C_PBE"],
+ "PBE0": ["GGA_X_PBE","GGA_C_PBE"],
+ "B3LYP": ["HYB_GGA_XC_B3LYP5"]
+ #need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
}
# Push the functional string into the backend
nomadNames = functionalMap.get(functional)
@@ -132,7 +133,7 @@ class QboxParserContext(object):
# #################################################################
- # # (3.1) onClose for OUTPUT SCF (section_scf_iteration)
+ # # (3.1) onClose for OUTPUT SCF (section_scf_iteration)
# #################################################################
# # Storing the total energy of each SCF iteration in an array
# def onClose_section_scf_iteration(self, backend, gIndex, section):
@@ -140,15 +141,15 @@ class QboxParserContext(object):
# # get cached values for energy_total_scf_iteration
# ev = section['energy_total_scf_iteration']
# self.scfIterNr = len(ev)
- #
+ #
# #self.energy_total_scf_iteration_list.append(ev)
# #backend.addArrayValues('energy_total_scf_iteration_list', np.asarray(ev))
# #backend.addValue('number_of_scf_iterations', self.scfIterNr)
# #-----???shanghui want to know why can not add them.
-
+
#################################################################
- # (3.2) onClose for OUTPUT eigenvalues (section_eigenvalues)
+ # (3.2) onClose for OUTPUT eigenvalues (section_eigenvalues)
#################################################################
#def onClose_section_eigenvalues(self, backend, gIndex, section):
# """Trigger called when _section_eigenvalues is closed.
@@ -158,22 +159,22 @@ class QboxParserContext(object):
# evs = []
# ev = section['qbox_eigenvalue_eigenvalue']
- # if ev is not None:
+ # if ev is not None:
# occ = section['qbox_eigenvalue_occupation']
- # occs.append(occ)
+ # occs.append(occ)
# evs.append(ev)
# self.eigenvalues_occupation = []
# self.eigenvalues_values = []
- # #self.eigenvalues_kpoints = []
+ # #self.eigenvalues_kpoints = []
# self.eigenvalues_occupation.append(occs)
# self.eigenvalues_values.append(evs)
###################################################################
# (3.4) onClose for geometry and force (section_system)
- # todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
+ # todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
###################################################################
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
@@ -227,7 +228,7 @@ class QboxParserContext(object):
if unit_cell:
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
-
+
@@ -251,10 +252,10 @@ class QboxParserContext(object):
backend.addArrayValues('stress_tensor', np.transpose(np.asarray(x_qbox_stress_tensor)))
-
-
+
+
#############################################################
#################[2] MAIN PARSER STARTS HERE ###############
@@ -269,19 +270,19 @@ def build_QboxMainFileSimpleMatcher():
which allows nice formating of nested SimpleMatchers in python.
Returns:
- SimpleMatcher that parses main file of qbox.
+ SimpleMatcher that parses main file of qbox.
"""
#####################################################################
# (1) submatcher for header
- #note: we add x_qbox_section_functionals here because we want to add
- # a default LDA here even 'set xc' is not shown in *.i file.
+ #note: we add x_qbox_section_functionals here because we want to add
+ # a default LDA here even 'set xc' is not shown in *.i file.
#####################################################################
headerSubMatcher = SM(name = 'ProgramHeader',
startReStr = r"\s*I qbox\s+(?P<program_version>[0-9.]+)",
- sections = ["x_qbox_section_functionals"],
+ # sections = ["x_qbox_section_functionals"],
subMatchers = [
SM(r"\s*<nodename>\s+(?P<x_qbox_nodename>[a-zA-Z0-9.-]+)\s+</nodename>")
])
@@ -308,11 +309,11 @@ def build_QboxMainFileSimpleMatcher():
subMatchers = [
#-----load from xml file-----
- # when using 'load *.xml' in *.i file, qbox will read geometry information from xml file,
- # here we call a QboxXMLParser to read the geometry information out.
+ # when using 'load *.xml' in *.i file, qbox will read geometry information from xml file,
+ # here we call a QboxXMLParser to read the geometry information out.
SM(name = "qboxXMLfile",
startReStr = r"\s*LoadCmd",
- forwardMatch = True, #use this or not like qboxXC
+ forwardMatch = True, #use this or not like qboxXC
sections = ["x_qbox_section_xml_file"],
subMatchers = [
SM(r"\s*LoadCmd:\s*loading from\s+(?P<x_qbox_loading_xml_file>[A-Za-z0-9./-_]+)"),
@@ -327,17 +328,17 @@ def build_QboxMainFileSimpleMatcher():
SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*</cmd>"),
SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*</cmd>"),
- #--------set xc---------
+ #--------set xc---------
SM(name = "qboxXC",
startReStr = r"\s*\[qbox\]\s+<cmd>\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*</cmd>",
sections = ["x_qbox_section_functionals"]
- ),
+ ),
#-------set efield---------
SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats = True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
])
-
+
####################################################################
# (3.1) submatcher for OUPUT SCF, this Dmol parser, we need to change to qbox later
####################################################################
@@ -348,18 +349,18 @@ def build_QboxMainFileSimpleMatcher():
# SM(r"\s*Ef\s+(?P<energy_total_scf_iteration__hartree>[-+0-9.eEdD]+)\s+(?P<dmol3_binding_energy_scf_iteration__hartree>[-+0-9.eEdD]+)\s+(?P<dmol3_convergence_scf_iteration>[-+0-9.eEdD]+)\s+(?P<dmol3_time_scf_iteration>[0-9.eEdD]+)\s+(?P<dmol3_number_scf_iteration>[0-9]+)\s*",
# sections = ['section_scf_iteration'],
# repeats = True)
-#
-# ])
-
+#
+# ])
+
####################################################################
# (3.2) submatcher for OUPUT eigenvalues, this Dmol parser, we need to change to qbox later
- ####################################################################
-# eigenvalueSubMatcher = SM(name = 'Eigenvalues',
-# startReStr = r"\s*state\s+eigenvalue\s+occupation\s*",
-# sections = ['section_eigenvalues'],
-# subMatchers = [
+ ####################################################################
+# eigenvalueSubMatcher = SM(name = 'Eigenvalues',
+# startReStr = r"\s*state\s+eigenvalue\s+occupation\s*",
+# sections = ['section_eigenvalues'],
+# subMatchers = [
# SM(r"\s*[0-9]+\s+[+-]\s+[0-9]+\s+[A-Za-z]+\s+[-+0-9.eEdD]+\s+(?P<dmol3_eigenvalue_e igenvalue__eV>[-+0-9.eEdD]+)\s+(?P<dmol3_eigenvalue_occupation>[0-9.eEdD]+)", repeats = True)
-# ])
+# ])
#
####################################################################
@@ -368,9 +369,9 @@ def build_QboxMainFileSimpleMatcher():
totalenergySubMatcher = SM(name = 'Totalenergy',
startReStr = r"\s*<ekin>",
subMatchers = [
- SM(r"\s*<etotal>\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)\s+</etotal>",repeats = True )
- ])
-
+ SM(r"\s*<etotal>\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)\s+</etotal>",repeats = True )
+ ])
+
#####################################################################
# (3.4) submatcher for OUTPUT relaxation_geometry(section_system)
@@ -439,7 +440,7 @@ def build_QboxMainFileSimpleMatcher():
subMatchers = [
#=============================================================================
- # read OUPUT file *.r, the method part comes from INPUT file *.i, so we
+ # read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# do not need to parser INPUT file, the OUTPUT file contains all information
#=============================================================================
SM (name = 'NewRun',
@@ -451,15 +452,15 @@ def build_QboxMainFileSimpleMatcher():
fixedStartValues={'program_name': 'qbox', 'program_basis_set_type': 'plane waves'},
sections = ['section_run'],
subMatchers = [
- #-----------(1)output: header---------------------
+ #-----------(1)output: header---------------------
headerSubMatcher,
-
+
#-----------(2)output: method---------------------
calculationMethodSubMatcher,
#-----------(2.2) efield----------------------
# efieldSubMatcher,
- #-----------(3)output: single configuration-------
+ #-----------(3)output: single configuration-------
SM(name = "single configuration matcher",
startReStr = r"\s*<iteration count*",
#endReStr = r"\s*</iteration>",
@@ -479,13 +480,13 @@ def build_QboxMainFileSimpleMatcher():
]
),
- #-----------(4)output: properties-------
+ #-----------(4)output: properties-------
#-----------(4.1) MLWF----------------------
MLWFSubMatcher,
#-----------(4.3) dipole----------------------
dipoleSubMatcher
- ]) # CLOSING SM NewRun
+ ]) # CLOSING SM NewRun
]) # END Root
@@ -497,7 +498,7 @@ def get_cachingLevelForMetaName(metaInfoEnv):
metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
Returns:
- Dictionary with metaname as key and caching level as value.
+ Dictionary with metaname as key and caching level as value.
"""
# manually adjust caching of metadata
cachingLevelForMetaName = {
@@ -513,29 +514,45 @@ def get_cachingLevelForMetaName(metaInfoEnv):
return cachingLevelForMetaName
+# get main file description
+QboxMainFileSimpleMatcher = build_QboxMainFileSimpleMatcher()
+# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "qbox.nomadmetainfo.json"))
+metaInfoEnv = get_metaInfo(metaInfoPath)
+# set parser info
+parserInfo = {'name':'qbox-parser', 'version': '1.0'}
+# get caching level for metadata
+cachingLevelForMetaName = get_cachingLevelForMetaName(metaInfoEnv)
-def main():
- """Main function.
- Set up everything for the parsing of the qbox main file and run the parsing.
- """
- # get main file description
- QboxMainFileSimpleMatcher = build_QboxMainFileSimpleMatcher()
- # loading metadata from nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json
- metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json"))
- metaInfoEnv = get_metaInfo(metaInfoPath)
- # set parser info
- parserInfo = {'name':'qbox-parser', 'version': '1.0'}
- # get caching level for metadata
- cachingLevelForMetaName = get_cachingLevelForMetaName(metaInfoEnv)
- # start parsing
- mainFunction(mainFileDescription = QboxMainFileSimpleMatcher,
- metaInfoEnv = metaInfoEnv,
- parserInfo = parserInfo,
- cachingLevelForMetaName = cachingLevelForMetaName,
- superContext = QboxParserContext())
+class QboxParser():
+ """ A proper class envolop for running this parser from within python. """
+ def __init__(self, backend, **kwargs):
+ self.backend_factory = backend
+
+ def parse(self, mainfile):
+ from unittest.mock import patch
+ logging.debug('qbox parser started')
+ logging.getLogger('nomadcore').setLevel(logging.WARNING)
+ backend = self.backend_factory(metaInfoEnv)
+ with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
+ mainFunction(
+ mainFileDescription=QboxMainFileSimpleMatcher,
+ metaInfoEnv=metaInfoEnv,
+ parserInfo=parserInfo,
+ cachingLevelForMetaName=cachingLevelForMetaName,
+ superContext=QboxParserContext(),
+ superBackend=backend)
+
+ return backend
+
if __name__ == "__main__":
- main()
+ mainFunction(
+ mainFileDescription = QboxMainFileSimpleMatcher,
+ metaInfoEnv = metaInfoEnv,
+ parserInfo = parserInfo,
+ cachingLevelForMetaName = cachingLevelForMetaName,
+ superContext = QboxParserContext())
diff --git a/parser/parser-qbox/QboxXMLParser.py b/qboxparser/QboxXMLParser.py
similarity index 98%
rename from parser/parser-qbox/QboxXMLParser.py
rename to qboxparser/QboxXMLParser.py
index 570f4051..1a4b923d 100644
--- a/parser/parser-qbox/QboxXMLParser.py
+++ b/qboxparser/QboxXMLParser.py
@@ -1,18 +1,17 @@
from builtins import object
-import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
-from QboxCommon import get_metaInfo
+from .QboxCommon import get_metaInfo
import logging, os, re, sys
#################################################################################
# This is the parser for the *.xml file of qbox to read the geometry information.
-# Only needed when 'load *.xml' is used in the *.r file.
+# Only needed when 'load *.xml' is used in the *.r file.
###################################################################################
logger = logging.getLogger("nomad.QboxXMLParser")
diff --git a/qboxparser/__init__.py b/qboxparser/__init__.py
new file mode 100644
index 00000000..f1c8d3f8
--- /dev/null
+++ b/qboxparser/__init__.py
@@ -0,0 +1 @@
+from qboxparser.QboxParser import QboxParser
\ No newline at end of file
diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000..f4eac5a7
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,33 @@
+# Copyright 2016-2018 Fawzi Mohamed, Lauri Himanen, Danio Brambila, Ankit Kariryaa, Henning Glawe
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from setuptools import setup, find_packages
+
+
+def main():
+ setup(
+ name='qboxparser',
+ version='0.1',
+ description='NOMAD parser implementation for qbox.',
+ author='Fawzi Mohamed, Honghui Shang',
+ license='APACHE 2.0',
+ packages=find_packages(),
+ install_requires=[
+ 'nomadcore'
+ ],
+ )
+
+
+if __name__ == '__main__':
+ main()
diff --git a/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala b/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
deleted file mode 100644
index b934dd05..00000000
--- a/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- Copyright 2016-2017 The NOMAD Developers Group
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
- */
-package eu.nomad_lab.parsers
-
-import eu.{ nomad_lab => lab }
-import eu.nomad_lab.DefaultPythonInterpreter
-import org.{ json4s => jn }
-import scala.collection.breakOut
-
-object QboxParser extends SimpleExternalParserGenerator(
- name = "QboxParser",
- parserInfo = jn.JObject(
- ("name" -> jn.JString("QboxParser")) ::
- ("parserId" -> jn.JString("QboxParser" + lab.QboxVersionInfo.version)) ::
- ("versionInfo" -> jn.JObject(
- ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
- case (k, v) => k -> jn.JString(v.toString)
- }(breakOut): List[(String, jn.JString)])) ::
- (lab.QboxVersionInfo.toMap.map {
- case (key, value) =>
- (key -> jn.JString(value.toString))
- }(breakOut): List[(String, jn.JString)])
- )) :: Nil
- ),
- mainFileTypes = Seq("application/xml"),
- mainFileRe = """<\?xml version="1.0" encoding="UTF-8"\?>\s*
-\s*<fpmd:simulation xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">\s*
-\s*
-\s*=+\s*
-\s*I\s*qbox\s*(?<version>[-_.0-9A-Za-z]+).*I
-(?:\s*I.+I
-)*\s*I\s+http://qboxcode.org\s*I
-(?:\s*I.+I
-)*\s*=+\s*
-""".r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/qbox/parser/parser-qbox/QboxParser.py",
- "--uri", "${mainFileUri}", "${mainFilePath}"),
- resList = Seq(
- "parser-qbox/QboxParser.py",
- "parser-qbox/QboxCommon.py",
- "parser-qbox/QboxXMLParser.py",
- "parser-qbox/setup_paths.py",
- "nomad_meta_info/public.nomadmetainfo.json",
- "nomad_meta_info/common.nomadmetainfo.json",
- "nomad_meta_info/meta_types.nomadmetainfo.json",
- "nomad_meta_info/qbox.nomadmetainfo.json"
- ) ++ DefaultPythonInterpreter.commonFiles(),
- dirMap = Map(
- "parser-qbox" -> "parsers/qbox/parser/parser-qbox",
- "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
- ) ++ DefaultPythonInterpreter.commonDirMapping()
-)
diff --git a/src/test/scala/eu/nomad_lab/parsers/QboxParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/QboxParserSpec.scala
deleted file mode 100644
index 200e53e9..00000000
--- a/src/test/scala/eu/nomad_lab/parsers/QboxParserSpec.scala
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- Copyright 2016-2017 The NOMAD Developers Group
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
- */
-package eu.nomad_lab.parsers
-
-import org.specs2.mutable.Specification
-
-object QboxParserSpec extends Specification {
- "QboxParserTest" >> {
- "test with json-events" >> {
- ParserRun.parse(QboxParser, "parsers/qbox/test/examples/01_h2ogs.r", "json-events") must_== ParseResult.ParseSuccess
- }
- "test with json" >> {
- ParserRun.parse(QboxParser, "parsers/qbox/test/examples/01_h2ogs.r", "json") must_== ParseResult.ParseSuccess
- }
- }
-}
--
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