Nomad Fair

.gitignore

@@ -9,6 +9,7 @@ syntax: glob
 *.pyc
 *.bk
 *.swp
+*.egg-info
 .DS_Store
 
 # logging files

libatomsparser/__init__.py

+from libatomsparser.libAtomsParser import LibAtomsParserWrapper

parser/parser-lib-atoms/libAtomsParser.py → libatomsparser/libAtomsParser.py

@@ -17,15 +17,15 @@ import os
 import sys
 import re
 import json
-#import logging
-import setup_paths
+import logging
+# import setup_paths
 import numpy as np
 
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.parser_backend import JsonParseEventsWriterBackend
 from contextlib import contextmanager
 
-from libLibAtomsParser import *
+from libatomsparser.libLibAtomsParser import *
 
 try:
     from libMomo import osio, endl, flush
@@ -41,11 +41,31 @@ parser_info = {
     "json": "../../../../nomad-meta-info/meta_info/nomad_meta_info/lib_atoms.nomadmetainfo.json"
 }
 
+
+class LibAtomsParserWrapper():
+    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        import nomad_meta_info
+        metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "lib_atoms.nomadmetainfo.json"))
+        metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+        from unittest.mock import patch
+        logging.info('lib-atoms parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory(metaInfoEnv)
+        # Call the old parser without a class.
+        parserInfo = {'name': 'lib_atoms-parser', 'version': '0.0'}
+        backend = parse_without_class(mainfile, backend, parserInfo)
+        return backend
+
+
 # LOGGING
 def log(msg, highlight=None, enter=endl):
-    if osio:
-        if highlight==None: hightlight = osio.ww
-        osio << highlight << msg << enter
+    # if osio:
+    #     if highlight==None: hightlight = osio.ww
+    #     osio << highlight << msg << enter
     return
 
 # CONTEXT GUARD
@@ -75,18 +95,23 @@ def push_array_values(jbe, value, key):
     jbe.addArrayValues(key, value)
     return value
 
-def parse(output_file_name):
-    jbe = JsonParseEventsWriterBackend(meta_info_env)
+def parse_without_class(output_file_name, backend, parser_info):
+    """ Parse method to parse mainfile and write output to backend."""
+    jbe = backend
     jbe.startedParsingSession(output_file_name, parser_info)
-
     base_dir = os.path.dirname(os.path.abspath(output_file_name))
+
+    # jbe = JsonParseEventsWriterBackend(meta_info_env)
+    # jbe.startedParsingSession(output_file_name, parser_info)
+
+    # base_dir = os.path.dirname(os.path.abspath(output_file_name))
     terminal_gap = LibAtomsGapParser(osio)
     terminal_gap.ParseOutput(output_file_name, base_dir)
     terminal_trj = terminal_gap.trj
 
 
-    osio << "Start parsing ..." << osio.endl
-    osio << "Base directory = '%s'" % base_dir << osio.endl
+    # osio << "Start parsing ..." << osio.endl
+    # osio << "Base directory = '%s'" % base_dir << osio.endl
 
     gap = terminal_gap
     trj = terminal_trj
@@ -167,7 +192,7 @@ def parse(output_file_name):
                     push_array_values(jbe, gap['gpCoordinates.%s' % key].As(), 'x_lib_atoms_gpCoordinates_%s' % key.replace('.', '_'))
 
     jbe.finishedParsingSession("ParseSuccess", None)
-    return
+    return jbe
 
 if __name__ == '__main__':
 

parser/parser-lib-atoms/libLibAtomsParser.py → libatomsparser/libLibAtomsParser.py

@@ -178,8 +178,8 @@ class LibAtomsParser(object):
 
         # PARSE CONFIGURATIONS
         self.ase_configs = read_fct(output_file, **read_fct_args)
-        for config in ase_configs:
-            print(config)
+        # for config in ase_configs:
+        #     print(config)
 
         self.Set('program_name', 'libAtoms')
         self.Set('program_version', 'n/a')
@@ -340,7 +340,7 @@ class LibAtomsFrame(LibAtomsParser):
         self.config_type = None
     def LoadAseConfig(self, ase_config):
         self.ase_config = ase_config
-        print("INFO", self.ase_config.info)
+        # print("INFO", self.ase_config.info)
         key = 'energy'
         if key in self.ase_config.info:
             self.has_energy = True

parser/parser-lib-atoms/libMomo.py → libatomsparser/libMomo.py

@@ -220,7 +220,7 @@ class OptionsInterface(object):
 		except KeyError:
 			raise ValueError('CLIO does not know how to convert %s into a boolean.' % expr)
 	def InterpretAsNumpyArray(self, expr):
-		print("Interpret", expr)
+		# print("Interpret", expr)
 		array = [ float(e) for e in expr ]
 		array = np.array(array)
 		return array
@@ -374,7 +374,7 @@ class ShellInterface(object):
 			mssg = self.color_dict[c] + mssg + self.color_dict['endcolor']
 		if h:
 			mssg = self.os_generate_header(mssg, t)
-		print(mssg)
+		# print(mssg)
 	# LOGFILE ADAPTOR =========================================================
 	def ConnectToFile(self, logfile):
 		self.logfile = logfile
@@ -419,7 +419,7 @@ class ShellInterface(object):
 			mssg = OS_COLOR_DICT[c] + mssg + OS_COLOR_DICT['endcolor']
 		if h:
 			mssg = os_generate_header(mssg, t)
-		print(mssg)
+		# print(mssg)
 		return
 	def os_print_config(self, c=None, j=None, h=False, t="=", tl=' '):
 		self.sel_color = c

setup.py

+# Copyright 2015-2019 NOMAD
+#
+#   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.
+
+from setuptools import setup, find_packages
+
+
+def main():
+    setup(
+        name='libatomsparser',
+        version='0.1',
+        description='NOMAD parser implementation for Lib-Atoms.',
+        license='APACHE 2.0',
+        package_dir={'': './'},
+        packages=find_packages(),
+        install_requires=[
+            'nomadcore'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()

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

-/*
- * Copyright 2016-2018 Fawzi Mohamed, Carl Poelking, Daria Tomecka
- * 
- *   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 LibAtomsParser extends SimpleExternalParserGenerator(
-  name = "LibAtomsParser",
-  parserInfo = jn.JObject(
-    ("name" -> jn.JString("LibAtomsParser")) ::
-      ("parserId" -> jn.JString("LibAtomsParser" + lab.LibAtomsVersionInfo.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.LibAtomsVersionInfo.toMap.map {
-            case (key, value) =>
-              (key -> jn.JString(value.toString))
-          }(breakOut): List[(String, jn.JString)])
-      )) :: Nil
-  ),
-  mainFileTypes = Seq("application/xml"),
-  mainFileRe = """\s*<GAP_params\s""".r,
-  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/lib-atoms/parser/parser-lib-atoms/libAtomsParser.py",
-    "${mainFilePath}"),
-  resList = Seq(
-    "parser-lib-atoms/libAtomsParser.py",
-    "parser-lib-atoms/libLibAtomsParser.py",
-    "parser-lib-atoms/libMomo.py",
-    "parser-lib-atoms/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/lib_atoms.nomadmetainfo.json"
-  ) ++ DefaultPythonInterpreter.commonFiles(),
-  dirMap = Map(
-    "parser-lib-atoms" -> "parsers/lib-atoms/parser/parser-lib-atoms",
-    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
-  ) ++ DefaultPythonInterpreter.commonDirMapping()
-)

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

-/*
- * Copyright 2016-2018 Fawzi Mohamed, Carl Poelking, Daria Tomecka
- * 
- *   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 LibAtomsParserSpec extends Specification {
-  "LibAtomsParserTest" >> {
-    "test with json-events" >> {
-      ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-gap-test/gp.xml", "json-events") must_== ParseResult.ParseSuccess
-    }
-    "test with json" >> {
-      ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-gap-test/gp.xml", "json") must_== ParseResult.ParseSuccess
-    }
-  }
-}