diff --git a/cpmdparser/parser.py b/cpmdparser/parser.py
index 27e04d58e49b41deda753fef8a011d98e804e137..715291414305293b6263002359cceb0ad1c8cdef 100644
--- a/cpmdparser/parser.py
+++ b/cpmdparser/parser.py
@@ -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)
+
diff --git a/cpmdparser/scalainterface.py b/cpmdparser/scalainterface.py
deleted file mode 100644
index d15ab1bebd424583c1a1aca7996c774cd9c432eb..0000000000000000000000000000000000000000
--- a/cpmdparser/scalainterface.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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)
diff --git a/cpmdparser/setup_paths.py b/cpmdparser/setup_paths.py
deleted file mode 100644
index 4b51dde6b7033423925fdd677509342eea4da6d0..0000000000000000000000000000000000000000
--- a/cpmdparser/setup_paths.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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)
diff --git a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala b/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala
deleted file mode 100644
index 2779dbe69175c4ddaa4bf3e0dc85132bb275cb38..0000000000000000000000000000000000000000
--- a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * 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()
-)
diff --git a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala
deleted file mode 100644
index 42d6f500884c6d43fab0681efa75f74236a516f1..0000000000000000000000000000000000000000
--- a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * 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
- }
-}