Commit a3c66ab1 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Renamed and moved stuff, added initial support for the scala call.

parent 7e159a94
import cp2kparser.utils.logconfig
from cp2kparser.parsing.parser import CP2KParser
import parsercp2k.utils.logconfig
from parsercp2k.parser import CP2KParser
import re
import logging
from cp2kparser.utils.baseclasses import Parser
from cp2kparser.parsing.implementations import *
import parsercp2k.setup_paths
from parsercp2k.utils.baseclasses import Parser
from parsercp2k.parsing.implementations import *
logger = logging.getLogger(__name__)
......@@ -75,7 +76,5 @@ class CP2KParser(Parser):
# This is what gets run when the scala layer calls for this parser
if __name__ == "__main__":
cp2kparser = CP2KParser()
import sys
import os
import cStringIO
from cp2kparser.implementation.cp2kparserversioner import CP2KParserVersioner
from cp2kparser.generics.testing import get_parser
from parsercp2k.implementation.cp2kparserversioner import CP2KParserVersioner
from parsercp2k.generics.testing import get_parser
......@@ -249,8 +249,9 @@ class CP2KOutputParser262(object):
def onClose_cp2k_section_atom_position(self, backend, gIndex, section):
"""Get the initial atomic positions from cp2kparser.
positions, unit = self.cp2kparser.get_initial_atom_positions_and_unit()
backend.addArrayValues("atom_position", positions)
# positions, unit = self.cp2kparser.get_initial_atom_positions_and_unit()
# backend.addArrayValues("atom_position", positions)
def onClose_cp2k_section_md_coordinate_atom(self, backend, gIndex, section):
"""Given the string with the coordinate components for one atom, make it
import sys
import os
baseDir = os.path.dirname(os.path.abspath(__file__))
commonDir = os.path.normpath(os.path.join(baseDir, "../../../../python-common/common/python"))
if os.path.exists(commonDir):
if not commonDir in sys.path:
sys.path.insert(0, commonDir)
import os
import sys
import json
import logging
import StringIO
import argparse
from abc import ABCMeta, abstractmethod
from parsercp2k.parsing.outputparsing import *
from nomadcore.simple_parser import SimpleParserBuilder, defaultParseFile, extractOnCloseTriggers
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from nomadcore.caching_backend import CachingLevel, ActiveBackend
from nomadcore.parse_streamed_dicts import ParseStreamedDicts
from nomadcore.simple_parser import mainFunction
logger = logging.getLogger(__name__)
class Parser(object):
"""A base class for nomad parsers.
self.implementation: an object that actually does the parsing and is
setup by this class based on the given contents.
......@@ -45,6 +44,7 @@ class Parser(object):
contents = [contents]
# Figure out all the files from the contents
if contents:
files = set()
for content in contents:
if os.path.isdir(content):
......@@ -95,40 +95,41 @@ class Parser(object):
if not self.implementation:
logger.error("No parser implementation has been setup.")
# Write the starting bracket
# Write the ending bracket
def scala_main_function(self):
"""This function gets called when the scala calls for a parser.
# Parse the command line options
parser = argparse.ArgumentParser()
parser.add_argument('--specialize', help='Provide specialization information as the first JSON dictionary on stdin.')
parser.add_argument('--stream', type=str, nargs='+', help='Expects the files to parse via JSON dictionary on stdin.')
parser.add_argument('mainFilePath', type=str, nargs='+', help='Path to the main file.')
args = parser.parse_args()
# Get the outputparser class
outputparser = globals()["CP2KOutputParser{}".format("262")](None, None)
# Setup the metainfos
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/{}".format(self.get_metainfo_filename())))
metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
# Setup the JSON backend
backend = JsonParseEventsWriterBackend(metaInfoEnv, sys.stdout)
# Parser info
parserInfo = {'name': 'cp2k-parser', 'version': '1.0'}
# Setup the contents
contents = [args.mainFilePath]
# contents.extend(auxiliary_files)
# Adjust caching of metadata
cachingLevelForMetaName = outputparser.cachingLevelForMetaName
# Setup the specilalization info
dictReader = ParseStreamedDicts(sys.stdin)
if args.specialize:
specializationInfo = dictReader.readNextDict()
if specializationInfo is None or specializationInfo.get("type", "") != "nomad_parser_specialization_1_0":
raise Exception("expected a nomad_parser_specialization_1_0 as first dictionary, got " + json.dumps(specializationInfo))
metainfo_to_keep = specializationInfo.get("metaInfoToKeep")
# Supercontext is where the objet where the callback functions for
# section closing are found
superContext = outputparser
# Parse
self.initialize(contents, metainfo_to_keep, backend)
# Main file description is the SimpleParser tree
mainFileDescription = outputparser.outputstructure
# Use the main function from nomadcore
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext=superContext, cachingLevelForMetaName=cachingLevelForMetaName, onClose={})
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