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Commit ffbca208 authored by Daniel Speckhard's avatar Daniel Speckhard
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removed scala references. removed nomad-fairdi logging.

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cpmdparser/parser.py
+ 10
− 21
View file @ ffbca208
......@@ -19,6 +19,7 @@ import re
import logging
import importlib
from nomadcore.baseclasses import ParserInterface
logger = logging.getLogger("nomad")
class CPMDRunType(object):
......@@ -35,21 +36,8 @@ class CPMDParser(ParserInterface):
After the implementation has been setup, you can parse the files with
parse().
"""
def __init__(
self, metainfo_to_keep=None, backend=None, default_units=None,
metainfo_units=None, debug=True, logger=None,
log_level=logging.ERROR, store=True
):
super(CPMDParser, self).__init__(
metainfo_to_keep, backend, default_units, metainfo_units,
debug, log_level, store
)
if logger is not None:
self.logger = logger
self.logger.debug('received logger')
else:
self.logger = logging.getLogger(__name__)
def __init__(self, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True):
super(CPMDParser, self).__init__(metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
def setup_version(self):
"""Setups the version by looking at the output file and the version
......@@ -58,7 +46,7 @@ class CPMDParser(ParserInterface):
# Search for the CPMD version specification and the run type for the
# calculation. The correct and optimized parser is initialized based on
# this information.
regex_version = re.compile(r"\s+VERSION ([\d\.]+)")
regex_version = re.compile("\s+VERSION ([\d\.]+)")
regex_single_point = re.compile(r" SINGLE POINT DENSITY OPTIMIZATION")
regex_geo_opt = re.compile(r" OPTIMIZATION OF IONIC POSITIONS")
regex_md = re.compile(r"( CAR-PARRINELLO MOLECULAR DYNAMICS)|( BORN-OPPENHEIMER MOLECULAR DYNAMICS)")
......@@ -106,12 +94,12 @@ class CPMDParser(ParserInterface):
if version_id is None:
msg = "Could not find a version specification from the given main file."
self.logger.exception(msg)
logger.exception(msg)
raise RuntimeError(msg)
if run_type is None:
msg = "Could not find a run type specification from the given main file at: {}".format(self.parser_context.main_file)
self.logger.exception(msg)
logger.exception(msg)
raise RuntimeError(msg)
# Setup the root folder to the fileservice that is used to access files
......@@ -139,16 +127,17 @@ class CPMDParser(ParserInterface):
try:
parser_module = importlib.import_module(base)
except ImportError:
self.logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for CPMD 4.1".format(version_id))
logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for CPMD 4.1".format(version_id))
base = "cpmdparser.versions.cpmd41.{}".format(run_type.module_name)
try:
parser_module = importlib.import_module(base)
except ImportError:
self.logger.exception("Tried to default to the CPMD 4.1 implementation but could not find the correct module.")
logger.exception("Tried to default to the CPMD 4.1 implementation but could not find the correct module.")
raise
try:
parser_class = getattr(parser_module, "{}".format(run_type.class_name))
except AttributeError:
self.logger.exception("A parser class '{}' could not be found in the module '[]'.".format(run_type.class_name, parser_module))
logger.exception("A parser class '{}' could not be found in the module '[]'.".format(run_type.class_name, parser_module))
raise
self.main_parser = parser_class(self.parser_context)
cpmdparser/scalainterface.py deleted 100644 → 0
+ 0
− 31
View file @ 66f2f270
# Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
#
# 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.
"""
This is the access point to the parser for the scala layer in the
nomad project.
"""
from __future__ import absolute_import
import sys
import setup_paths
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from cpmdparser import CPMDParser
if __name__ == "__main__":
# Initialise the parser with the main filename and a JSON backend
main_file = sys.argv[1]
parser = CPMDParser(backend=JsonParseEventsWriterBackend)
parser.parse(main_file)
cpmdparser/setup_paths.py deleted 100644 → 0
+ 0
− 31
View file @ 66f2f270
# Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
#
# 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.
"""
Setups the python-common library in the PYTHONPATH system variable.
"""
import sys
import os
import os.path
baseDir = os.path.dirname(os.path.abspath(__file__))
commonDir = os.path.normpath(os.path.join(baseDir, "../../../../../python-common/common/python"))
parserDir = os.path.normpath(os.path.join(baseDir, "../../parser-cpmd"))
# Using sys.path.insert(1, ...) instead of sys.path.insert(0, ...) based on
# this discusssion:
# http://stackoverflow.com/questions/10095037/why-use-sys-path-appendpath-instead-of-sys-path-insert1-path
if commonDir not in sys.path:
sys.path.insert(1, commonDir)
sys.path.insert(1, parserDir)
src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala deleted 100644 → 0
+ 0
− 77
View file @ 66f2f270
/*
* Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
*
* 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 CpmdParser extends SimpleExternalParserGenerator(
name = "CpmdParser",
parserInfo = jn.JObject(
("name" -> jn.JString("CpmdParser")) ::
("parserId" -> jn.JString("CpmdParser" + lab.CpmdVersionInfo.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.CpmdVersionInfo.toMap.map {
case (key, value) =>
(key -> jn.JString(value.toString))
}(breakOut): List[(String, jn.JString)])
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """\s* \*\*\*\*\*\* \*\*\*\*\*\* \*\*\*\* \*\*\*\* \*\*\*\*\*\*\s*
\s* \*\*\*\*\*\*\* \*\*\*\*\*\*\* \*\*\*\*\*\*\*\*\*\* \*\*\*\*\*\*\*\s*
\s* \*\*\* \*\* \*\*\* \*\* \*\*\*\* \*\* \*\* \*\*\*\s*
\s* \*\* \*\* \*\*\* \*\* \*\* \*\* \*\* \*\*\s*
\s* \*\* \*\*\*\*\*\*\* \*\* \*\* \*\* \*\*\s*
\s* \*\*\* \*\*\*\*\*\* \*\* \*\* \*\* \*\*\*\s*
\s* \*\*\*\*\*\*\* \*\* \*\* \*\* \*\*\*\*\*\*\*\s*
\s* \*\*\*\*\*\* \*\* \*\* \*\* \*\*\*\*\*\*\s*
""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/cpmd/parser/parser-cpmd/cpmdparser/scalainterface.py",
"${mainFilePath}"),
cmdCwd = "${mainFilePath}/..",
resList = Seq(
"parser-cpmd/cpmdparser/__init__.py",
"parser-cpmd/cpmdparser/setup_paths.py",
"parser-cpmd/cpmdparser/parser.py",
"parser-cpmd/cpmdparser/scalainterface.py",
"parser-cpmd/cpmdparser/versions/__init__.py",
"parser-cpmd/cpmdparser/versions/cpmd41/__init__.py",
"parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py",
"parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py",
"parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py",
"parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py",
"parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py",
"parser-cpmd/cpmdparser/versions/cpmd41/input_data/cpmd_input_tree.pickle",
"parser-cpmd/cpmdparser/generic/__init__.py",
"parser-cpmd/cpmdparser/generic/inputparsing.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/cpmd.general.nomadmetainfo.json",
"nomad_meta_info/cpmd.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-cpmd" -> "parsers/cpmd/parser/parser-cpmd",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
) ++ DefaultPythonInterpreter.commonDirMapping()
)
src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala deleted 100644 → 0
+ 0
− 37
View file @ 66f2f270
/*
* Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
*
* 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 CpmdParserSpec extends Specification {
"CpmdParserTest" >> {
"test with json-events" >> {
ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/single_point/output.out", "json-events") must_== ParseResult.ParseSuccess
}
}
"test energy_force with json" >> {
ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/single_point/output.out", "json") must_== ParseResult.ParseSuccess
}
"test geo_opt with json" >> {
ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/geo_opt/output.out", "json") must_== ParseResult.ParseSuccess
}
"test md with json" >> {
ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/md/output.out", "json") must_== ParseResult.ParseSuccess
}
}
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