Added more parsers to NOMAD

.gitignore

@@ -10,9 +10,7 @@ syntax: glob
 *.bk
 *.swp
 .DS_Store
-
-# logging files
-detailed.log
+*.annotate
 
 # eclipse conf file
 .settings
@@ -52,3 +50,5 @@ TAGS
 
 lib/
 env/
+
+*.egg-info
\ No newline at end of file

gromosparser/__init__.py

+from .GROMOSParser import GromacsParserInterface as GromosParser
\ No newline at end of file

gromosparser/metainfo/__init__.py

+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import gromosparser.metainfo.gromos
+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['gromosparser.metainfo.gromos'].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

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

-# Copyright 2018-2018 Berk Onat
-# 
+# Copyright 2015-2018 Berk Onat
+#
 #   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
-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"))
+from setuptools import setup, find_packages
 
-if not commondir in sys.path:
-    sys.path.insert(0, commondir)
+
+def main():
+    setup(
+        name='gromossparser',
+        version='0.1',
+        description='NOMAD parser implementation for Gromos.',
+        license='APACHE 2.0',
+        package_dir={'': './'},
+        packages=find_packages(),
+        install_requires=[
+            'nomadcore',
+            'nomad'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()

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

-/*
- * Copyright 2018-2018 Berk Onat
- * 
- *   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
-import eu.nomad_lab.DefaultPythonInterpreter
-import org.{ json4s => jn }
-import eu.{ nomad_lab => lab }
-import scala.collection.breakOut
-
-object GromosParser extends SimpleExternalParserGenerator(
-  name = "GromosParser",
-  parserInfo = jn.JObject(
-    ("name" -> jn.JString("GromosParser")) ::
-      ("parserId" -> jn.JString("GromosParser" + lab.GromosVersionInfo.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.GromosVersionInfo.toMap.map {
-            case (key, value) =>
-              (key -> jn.JString(value.toString))
-          }(breakOut): List[(String, jn.JString)])
-      )) :: Nil
-  ),
-  mainFileTypes = Seq("text/.*"),
-  mainFileRe = """^MD\+\+\s*\s*""".r,
-  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/gromos/parser/parser-gromos/GROMOSParser.py",
-    "${mainFilePath}"),
-  resList = Seq(
-    "parser-gromos/GROMOSParser.py",
-    "parser-gromos/GROMOSDictionary.py",
-    "parser-gromos/GROMOSCommon.py",
-    "parser-gromos/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/gromos.nomadmetainfo.json"
-  ) ++ DefaultPythonInterpreter.commonFiles(),
-  dirMap = Map(
-    "parser-gromos" -> "parsers/gromos/parser/parser-gromos",
-    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
-    "python" -> "python-common/common/python/nomadcore"
-  ) ++ DefaultPythonInterpreter.commonDirMapping(),
-  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.gromos)
-)
-

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

-/*
- * Copyright 2018-2018 Berk Onat
- * 
- *   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 GromosParserTests extends Specification {
-  "GromosParserTest_1" >> {
-    "[Peptide in Water with 2792 atoms] test with json-events" >> {
-      ParserRun.parse(GromosParser, "parsers/gromos/test/examples/eq/eq_peptide_1.omd", "json-events") must_== ParseResult.ParseSuccess
-    }
-  }
-  "GromosParserTest_2" >> {
-    "[Peptide in Water with 2792 atoms] test with json" >> {
-      ParserRun.parse(GromosParser, "parsers/gromos/test/examples/eq/eq_peptide_1.omd", "json") must_== ParseResult.ParseSuccess
-    }
-  }
-}