Updating cp2k parser to work with ParserInterface class and added...

Updating cp2k parser to work with ParserInterface class and added structlogging. Read more here https://docs.google.com/document/d/1fTjSJIuRtbVWqS4CoXVlrf94MzYDWNqU-jtxkYOVAoQ/edit?usp=sharing .

parser/parser-cp2k/cp2kparser/__init__.py

 # Copyright 2015-2018 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.

parser/parser-cp2k/cp2kparser/parser.py

 # Copyright 2015-2018 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.
 
+""" Main parser file to parse simulation files created using CP2K DFT program.
+
+This file creates the parser class for CP2K simulation files. The class extends
+the Parser Interface class created for NOMAD-fair. This class also uses structlog
+to increase analytics on logged errors during parsing uploading data to NOMAD.
+"""
+
 from builtins import next
 from builtins import range
 import os
 import re
 import logging
 import importlib
+import structlog  # New Logging Mechanism introduced for NOMAD-fair.
 from nomadcore.baseclasses import ParserInterface
 
 # Needs to be imported in order for the importlib calls to work in python 2.7
 import cp2kparser.versions.cp2k262.singlepointparser
 
-logger = logging.getLogger("nomad")
+# logger = logging.getLogger("nomad")  # This redefines the global logger.
 
 
 class CP2KParser(ParserInterface):
@@ -34,8 +42,16 @@ class CP2KParser(ParserInterface):
     After the implementation has been setup, you can parse files with
     parse().
     """
-    def __init__(self, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=False, log_level=logging.ERROR, store=True):
-        super(CP2KParser, self).__init__(metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
+    def __init__(
+        self, metainfo_to_keep=None, backend=None, default_units=None,
+        metainfo_units=None, debug=False, logger=None,
+        log_level=logging.ERROR, store=True
+    ):
+        super(CP2KParser, self).__init__(
+            metainfo_to_keep, backend, default_units, metainfo_units,
+            debug, log_level, store
+        )
+        self.logger = structlog.get_logger()  # New logger keep it in this namespace.
 
     def setup_version(self):
         """Setups the version by looking at the output file and the version
@@ -64,11 +80,11 @@ class CP2KParser(ParserInterface):
 
         if version_id is None:
             msg = "Could not find a version specification from the given main file."
-            logger.exception(msg)
+            self.logger.exception(msg)
             raise RuntimeError(msg)
         if run_type is None:
             msg = "Could not find a version specification from the given main file."
-            logger.exception(msg)
+            self.logger.exception(msg)
             raise RuntimeError(msg)
 
         # Setup the root folder to the fileservice that is used to access files
@@ -132,7 +148,7 @@ class CP2KParser(ParserInterface):
         try:
             parser = parser_map[run_type]
         except KeyError:
-            logger.exception(
+            self.logger.exception(
                 "A parser corresponding to the run_type '{}' could not be found."
                 .format(run_type)
             )
@@ -147,7 +163,7 @@ class CP2KParser(ParserInterface):
         try:
             parser_module = importlib.import_module(base)
         except ImportError:
-            logger.warning(
+            self.logger.warning(
                 "Could not find a parser for version '{}' and run type '{}'. "
                 "Trying to default to the base implementation for CP2K 2.6.2"
                 .format(version_id, run_type)
@@ -156,7 +172,7 @@ class CP2KParser(ParserInterface):
             try:
                 parser_module = importlib.import_module(base)
             except ImportError:
-                logger.exception(
+                self.logger.exception(
                     "Tried to default to the CP2K 2.6.2 implementation but "
                     "could not find the correct modules for run_type '{}'."
                     .format(run_type)
@@ -165,7 +181,7 @@ class CP2KParser(ParserInterface):
         try:
             parser_class = getattr(parser_module, "CP2K{}".format(parser))
         except AttributeError:
-            logger.exception(
+            self.logger.exception(
                 "A parser class '{}' could not be found in the module '[]'."
                 .format(parser_class, parser_module)
             )

parser/parser-cp2k/cp2kparser/scalainterface.py

-# Copyright 2015-2018 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 cp2kparser import CP2KParser
-
-
-if __name__ == "__main__":
-
-    # Initialise the parser with the main filename and a JSON backend
-    main_file = sys.argv[1]
-    parser = CP2KParser(backend=JsonParseEventsWriterBackend)
-    parser.parse(main_file)

src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala

-/*
- * Copyright 2015-2018 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 Cp2kParser extends SimpleExternalParserGenerator(
-  name = "Cp2kParser",
-  parserInfo = jn.JObject(
-    ("name" -> jn.JString("Cp2kParser")) ::
-      ("parserId" -> jn.JString("Cp2kParser" + lab.Cp2kVersionInfo.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.Cp2kVersionInfo.toMap.map {
-            case (key, value) =>
-              (key -> jn.JString(value.toString))
-          }(breakOut): List[(String, jn.JString)])
-      )) :: Nil
-  ),
-  mainFileTypes = Seq("text/.*"),
-  mainFileRe = """  \*\*\*\* \*\*\*\* \*\*\*\*\*\*  \*\*  PROGRAM STARTED AT\s(?<cp2kStartedAt>.*)
- \*\*\*\*\* \*\* \*\*\*  \*\*\* \*\*   PROGRAM STARTED ON\s*.*
- \*\*    \*\*\*\*   \*\*\*\*\*\*    PROGRAM STARTED BY .*
- \*\*\*\*\* \*\*    \*\* \*\* \*\*   PROGRAM PROCESS ID .*
-  \*\*\*\* \*\*  \*\*\*\*\*\*\*  \*\*  PROGRAM STARTED IN .*
-(?:\s*\n|                                      \s+.*
-)*
-(?:\s*CP2K\| version string:\s*(?<cp2kVersionString>.*)
-)?(?:\s*CP2K\| source code revision number:\s*(?<cp2kRevision>.*)
-)?""".r,
-  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/cp2k/parser/parser-cp2k/cp2kparser/scalainterface.py",
-    "${mainFilePath}"),
-  cmdCwd = "${mainFilePath}/..",
-  resList = Seq(
-    "parser-cp2k/cp2kparser/__init__.py",
-    "parser-cp2k/cp2kparser/setup_paths.py",
-    "parser-cp2k/cp2kparser/parser.py",
-    "parser-cp2k/cp2kparser/generic/__init__.py",
-    "parser-cp2k/cp2kparser/generic/inputparsing.py",
-    "parser-cp2k/cp2kparser/versions/__init__.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/__init__.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py",
-    "parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle",
-    "parser-cp2k/cp2kparser/scalainterface.py",
-    "nomad_meta_info/public.nomadmetainfo.json",
-    "nomad_meta_info/common.nomadmetainfo.json",
-    "nomad_meta_info/meta_types.nomadmetainfo.json",
-    "nomad_meta_info/cp2k.nomadmetainfo.json",
-    "nomad_meta_info/cp2k.general.nomadmetainfo.json"
-  ) ++ DefaultPythonInterpreter.commonFiles(),
-  dirMap = Map(
-    "parser-cp2k" -> "parsers/cp2k/parser/parser-cp2k",
-    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
-  ) ++ DefaultPythonInterpreter.commonDirMapping()
-)

src/test/scala/eu/nomad_lab/parsers/Cp2kParserSpec.scala

-/*
- * Copyright 2015-2018 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 Cp2kParserSpec extends Specification {
-  "Cp2kParserTest" >> {
-    "test with json-events" >> {
-      ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/energy_force/si_bulk8.out", "json-events") must_== ParseResult.ParseSuccess
-    }
-  }
-
-  "test energy_force with json" >> {
-    ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/energy_force/si_bulk8.out", "json") must_== ParseResult.ParseSuccess
-  }
-  "test geo_opt with json" >> {
-    ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/geo_opt/H2O.out", "json") must_== ParseResult.ParseSuccess
-  }
-  "test md with json" >> {
-    ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/md/H2O-32.out", "json") must_== ParseResult.ParseSuccess
-  }
-}