Added more parsers to NOMAD

.gitignore

@@ -52,3 +52,5 @@ TAGS
 
 lib/
 env/
+
+*.egg-info/
\ No newline at end of file

asapparser/__init__.py

+from .parser_asap import AsapParser
\ No newline at end of file

asapparser/metainfo/__init__.py

+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import asapparser.metainfo.asap
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['asapparser.metainfo.asap'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package)  # type: ignore

asapparser/metainfo/asap.py

+import numpy as np            # pylint: disable=unused-import
+import typing                 # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+    Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+    name='asap_nomadmetainfo_json',
+    description='None',
+    a_legacy=LegacyDefinition(name='asap.nomadmetainfo.json'))
+
+
+class section_sampling_method(public.section_sampling_method):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_sampling_method'))
+
+    x_asap_langevin_friction = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Friction coeffient used in Langevin dynamics
+        ''',
+        a_legacy=LegacyDefinition(name='x_asap_langevin_friction'))
+
+    x_asap_maxstep = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Maxstep in Angstrom for geometry optimization
+        ''',
+        a_legacy=LegacyDefinition(name='x_asap_maxstep'))
+
+    x_asap_temperature = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temperature used in molecular-dynamics
+        ''',
+        a_legacy=LegacyDefinition(name='x_asap_temperature'))
+
+    x_asap_timestep = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Timestep in molecular dynamics
+        ''',
+        a_legacy=LegacyDefinition(name='x_asap_timestep'))
+
+
+m_package.__init_metainfo__()

parser/parser-asap/parser_asap.py → asapparser/parser_asap.py

 # Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed
-# 
+#
 #   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.
@@ -18,11 +18,9 @@ from contextlib import contextmanager
 import numpy as np
 from ase.io.trajectory import Trajectory
 from ase import units
-import setup_paths
-from constraint_conversion import get_nomad_name
+from .constraint_conversion import get_nomad_name
 from nomadcore.unit_conversion.unit_conversion import convert_unit as cu
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-from nomadcore.parser_backend import JsonParseEventsWriterBackend
+import logging
 
 
 @contextmanager
@@ -39,18 +37,9 @@ def c(value, unit=None):
 
 
 parser_info = {"name": "parser_asap", "version": "1.0"}
-path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
-        'asap.nomadmetainfo.json'
-metaInfoPath = os.path.normpath(
-    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
 
-metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
-                                  dependencyLoader=None,
-                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
-                                  uri=None)
 
-
-def parse(filename):
+def parse(filename, backend):
     t = Trajectory(filename, 'r')
     # some sanity checks
     if hasattr(t.backend, 'calculator'):
@@ -62,7 +51,7 @@ def parse(filename):
     else:
         ds = {}
 
-    p = JsonParseEventsWriterBackend(metaInfoEnv)
+    p = backend
     o = open_section
     p.startedParsingSession(filename, parser_info)
     with o(p, 'section_run'):
@@ -159,7 +148,16 @@ def parse(filename):
 
     p.finishedParsingSession("ParseSuccess", None)
 
-if __name__ == '__main__':
-    import sys
-    filename = sys.argv[1]
-    parse(filename)
+
+class AsapParser():
+    """ A proper class envolop for running this parser from within python. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+            logging.info('asap parser started')
+            logging.getLogger('nomadcore').setLevel(logging.WARNING)
+            backend = self.backend_factory("asap.nomadmetainfo.json")
+            parserInfo = parser_info
+            parse(mainfile, backend)
+            return backend
\ No newline at end of file

parser/parser-asap/setup_paths.py → setup.py

-# Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed
-# 
+# Copyright 2015-2018
+#
 #   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.
 
-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"))
+from setuptools import setup, find_packages
 
-if not commonDir in sys.path:
-    sys.path.insert(0, commonDir)
+
+def main():
+    setup(
+        name='asapparser',
+        version='0.1',
+        description='NOMAD parser implementation for asap.',
+        license='APACHE 2.0',
+        package_dir={'': './'},
+        packages=find_packages(),
+        install_requires=[
+            'nomadcore',
+            'nomad'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()

src/main/scala/eu/nomad_lab/parsers/AsapParser.scala

-/*
- * Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed
- * 
- *   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
-import java.nio.charset.StandardCharsets
-
-object AsapParser extends SimpleExternalParserGenerator(
-  name = "AsapParser",
-  parserInfo = jn.JObject(
-    ("name" -> jn.JString("AsapParser")) ::
-      ("parserId" -> jn.JString("AsapParser" + lab.AsapVersionInfo.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.AsapVersionInfo.toMap.map {
-            case (key, value) =>
-              (key -> jn.JString(value.toString))
-          }(breakOut): List[(String, jn.JString)])
-      )) :: Nil
-  ),
-  mainFileTypes = Seq("application/octet-stream"),
-  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/asap/parser/parser-asap/parser_asap.py",
-    "${mainFilePath}"),
-  mainFileRe = "".r,
-  resList = Seq(
-    "parser-asap/setup_paths.py",
-    "parser-asap/parser_asap.py",
-    "parser-asap/constraint_conversion.py",
-    "nomad_meta_info/public.nomadmetainfo.json",
-    "nomad_meta_info/common.nomadmetainfo.json",
-    "nomad_meta_info/meta_types.nomadmetainfo.json",
-    "nomad_meta_info/asap.nomadmetainfo.json"
-  ) ++ DefaultPythonInterpreter.commonFiles(),
-  dirMap = Map(
-    "parser-asap" -> "parsers/asap/parser/parser-asap",
-    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
-  ) ++ DefaultPythonInterpreter.commonDirMapping(),
-  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.asap)
-) {
-  override def isMainFile(filePath: String, bytePrefix: Array[Byte], stringPrefix: Option[String]): Option[ParserMatch] = {
-    if (bytePrefix.startsWith("AFFormatASE-Trajectory".getBytes(StandardCharsets.US_ASCII)))
-      Some(ParserMatch(mainFileMatchPriority, mainFileMatchWeak))
-    else
-      None
-  }
-}

src/test/scala/eu/nomad_lab/parsers/AsapParserSpec.scala

-/*
- * Copyright 2016-2018 Mikkel Strange, Fawzi Mohamed
- * 
- *   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 AsapParserSpec extends Specification {
-  "AsapParserTest" >> {
-    "test moldyn1 with json-events" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/moldyn1.traj", "json-events") must_== ParseResult.ParseSuccess
-    }
-    "test moldyn1 with json" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/moldyn1.traj", "json") must_== ParseResult.ParseSuccess
-    }
-    "test moldyn2 with json-events" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/moldyn2.traj", "json-events") must_== ParseResult.ParseSuccess
-    }
-    "test moldyn2 with json" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/moldyn2.traj", "json") must_== ParseResult.ParseSuccess
-    }
-    "test geo_opt1 with json-events" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/geo_opt1.traj", "json-events") must_== ParseResult.ParseSuccess
-    }
-    "test geo_opt1 with json" >> {
-      ParserRun.parse(AsapParser, "parsers/asap/test/examples/geo_opt1.traj", "json") must_== ParseResult.ParseSuccess
-    }
-  }
-}