From ae97cd460788eaa1ff52b5e55f5fc812c63c42f0 Mon Sep 17 00:00:00 2001 From: speckhard Date: Mon, 25 Feb 2019 15:46:12 +0100 Subject: [PATCH] Ready for Nomad-Faird --- .gitignore | 1 + .../SimpleDL_POLYParser.py | 91 +++++++++----- dlpolyparser/__init__.py | 15 +++ .../dlPolyParser.py | 114 ++++++++++++------ .../libDlPolyParser.py | 0 .../libMomo.py | 0 .../setup_paths.py | 0 setup.py | 33 +++++ .../eu/nomad_lab/parsers/DlPolyParser.scala | 57 --------- .../nomad_lab/parsers/DlPolyParserSpec.scala | 30 ----- 10 files changed, 184 insertions(+), 157 deletions(-) rename {parser/parser-dl_poly => dlpolyparser}/SimpleDL_POLYParser.py (73%) create mode 100644 dlpolyparser/__init__.py rename {parser/parser-dl_poly => dlpolyparser}/dlPolyParser.py (83%) rename {parser/parser-dl_poly => dlpolyparser}/libDlPolyParser.py (100%) rename {parser/parser-dl_poly => dlpolyparser}/libMomo.py (100%) rename {parser/parser-dl_poly => dlpolyparser}/setup_paths.py (100%) create mode 100644 setup.py delete mode 100644 src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala delete mode 100644 src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala diff --git a/.gitignore b/.gitignore index cae25f9..e3efb3a 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,7 @@ syntax: glob *.pyc *.bk *.swp +*.egg-info .DS_Store # eclipse conf file diff --git a/parser/parser-dl_poly/SimpleDL_POLYParser.py b/dlpolyparser/SimpleDL_POLYParser.py similarity index 73% rename from parser/parser-dl_poly/SimpleDL_POLYParser.py rename to dlpolyparser/SimpleDL_POLYParser.py index 019bbfb..a4149ba 100644 --- a/parser/parser-dl_poly/SimpleDL_POLYParser.py +++ b/dlpolyparser/SimpleDL_POLYParser.py @@ -1,11 +1,11 @@ # Copyright 2016-2018 Carl Poelking, 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. @@ -15,7 +15,6 @@ from __future__ import print_function from builtins import range from builtins import object -import setup_paths import numpy as np import math from nomadcore.simple_parser import mainFunction @@ -38,7 +37,7 @@ class DL_POLYParserContext(object): def onClose_section_system(self, backend, gIndex, section): print("") return - def onClose_dl_poly_section_md_molecule_type(self, backend, gIndex, section): + def onClose_x_dl_poly_section_md_molecule_type(self, backend, gIndex, section): print("") return @@ -55,7 +54,7 @@ mainFileDescription = SM(name = 'root', weak = True, startReStr = "", subMatchers = [ - + SM(name = 'newRun', startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**", repeats = False, @@ -67,26 +66,26 @@ mainFileDescription = SM(name = 'root', SM(name = 'progHeader', startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**", subMatchers = [ - SM(r"\s*\*\*\s*\*\* version: (?P[0-9a-zA-Z_.]*) / \s* (?P[\w]*\s*[\w]*)\s*\** O \**"), + SM(r"\s*\*\*\s*\*\* version: (?P[0-9a-zA-Z_.]*) / \s* (?P[\w]*\s*[\w]*)\s*\** O \**"), SM(r"\s*\** when publishing research data obtained using (?P[0-9a-zA-Z_.]*) \**"), - SM(r"\s*\**\s*(?P[0-9a-zA-Z_()]*)\s*\**") + SM(r"\s*\**\s*(?P[0-9a-zA-Z_()]*)\s*\**") ]), SM(name = 'mdParams', startReStr = r"\s*SIMULATION CONTROL PARAMETERS\s*", required = True, sections = ['section_method'], subMatchers = [ - SM(r"\s*simulation temperature \(K\)\s*(?P[-+0-9.eEdD]*)\s*"), - SM(r"\s*equilibration period \(steps\)\s*(?P[0-9]*)\s*"), - SM(r"\s*selected number of timesteps\s*(?P[0-9]*)\s*") + SM(r"\s*simulation temperature \(K\)\s*(?P[-+0-9.eEdD]*)\s*"), + SM(r"\s*equilibration period \(steps\)\s*(?P[0-9]*)\s*"), + SM(r"\s*selected number of timesteps\s*(?P[0-9]*)\s*") ]), - + # Open system # ... open topology # ... ... store # ... ... open molecule type id1 # ... ... open molecule type ... - + SM(name = 'mdSystem', startReStr = r"\s*SYSTEM SPECIFICATION\s*", required = True, @@ -96,18 +95,18 @@ mainFileDescription = SM(name = 'root', startReStr = r"\s*number of molecular types\s*[0-9]*\s*", required = True, forwardMatch = True, - sections = ['dl_poly_section_md_topology'], + sections = ['x_dl_poly_section_md_topology'], subMatchers = [ - SM(r"\s*number of molecular types\s*(?P[0-9]*)"), + SM(r"\s*number of molecular types\s*(?P[0-9]*)"), SM(name = 'mdTopologyMolecule', startReStr = r"\s*molecular species type\s*[0-9]*\s*", repeats = True, required = True, forwardMatch = True, - sections = ['dl_poly_section_md_molecule_type'], + sections = ['x_dl_poly_section_md_molecule_type'], subMatchers = [ - SM(r"\s*molecular species type\s*(?P[0-9]*)\s*"), - SM(r"\s*name of species:\s*(?P[\w]* [\w]*)\s*") + SM(r"\s*molecular species type\s*(?P[0-9]*)\s*"), + SM(r"\s*name of species:\s*(?P[\w]* [\w]*)\s*") ]) ]) #SM(r"\s*number of molecular types\s*(?P[0-9]*)\s*"), @@ -118,7 +117,7 @@ mainFileDescription = SM(name = 'root', #sections = ['dl_poly_section_molecule_types'], #subMatchers = [\ #]) - ]) + ]) ]) ]) @@ -182,11 +181,11 @@ mainFileDescription = SM(name = 'root', ]), # CLOSING section_eigenvalues ]), # CLOSING section_eigenvalues_group - + ]), # CLOSING section_single_configuration_calculation - + ]), # CLOSING section_system - + ]), # CLOSING SM newRun @@ -196,22 +195,50 @@ mainFileDescription = SM(name = 'root', # THIS PARSER parserInfo = {'name':'dl_poly-parser', 'version': '0.0'} -# LOAD METADATA -metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json")) -metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None) +# # LOAD METADATA +# metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json")) +# metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None) # CUSTOMIZE CACHING cachingLevelForMetaName = {} +import nomad_meta_info +metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "dl_poly.nomadmetainfo.json")) +metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None) + +class DlPolyParser(): + """ A proper class envolop for running this parser from within python. """ + def __init__(self, backend, **kwargs): + self.backend_factory = backend + + def parse(self, mainfile): + from unittest.mock import patch + logging.info('dl-poly parser started') + logging.getLogger('nomadcore').setLevel(logging.WARNING) + backend = self.backend_factory(metaInfoEnv) + with patch.object(sys, 'argv', ['', '--uri', 'nmd://uri', mainfile]): + mainFunction( + mainFileDescription=mainFileDescription, + metaInfoEnv=metaInfoEnv, + parserInfo = parserInfo, + cachingLevelForMetaName = cachingLevelForMetaName, + superContext=DL_POLYParserContext(), + superBackend=backend, + onClose = {}, + defaultSectionCachingLevel = True) + + return backend + + if __name__ == "__main__": - mainFunction(mainFileDescription, - metaInfoEnv, - parserInfo, - superContext = DL_POLYParserContext(), - cachingLevelForMetaName = cachingLevelForMetaName, + mainFunction(mainFileDescription, + metaInfoEnv, + parserInfo, + superContext = DL_POLYParserContext(), + cachingLevelForMetaName = cachingLevelForMetaName, onClose = {}, defaultSectionCachingLevel = False) - - + + diff --git a/dlpolyparser/__init__.py b/dlpolyparser/__init__.py new file mode 100644 index 0000000..562628c --- /dev/null +++ b/dlpolyparser/__init__.py @@ -0,0 +1,15 @@ +# 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. + +from dlpolyparser.dlPolyParser import DlPolyParserWrapper diff --git a/parser/parser-dl_poly/dlPolyParser.py b/dlpolyparser/dlPolyParser.py similarity index 83% rename from parser/parser-dl_poly/dlPolyParser.py rename to dlpolyparser/dlPolyParser.py index 4c54d69..4b8fa3a 100644 --- a/parser/parser-dl_poly/dlPolyParser.py +++ b/dlpolyparser/dlPolyParser.py @@ -1,11 +1,11 @@ # Copyright 2016-2018 Carl Poelking, 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. @@ -17,30 +17,29 @@ import os import sys import re import json -#import logging -import setup_paths +import logging import numpy as np from nomadcore.local_meta_info import loadJsonFile, InfoKindEl from nomadcore.parser_backend import JsonParseEventsWriterBackend from contextlib import contextmanager -from libDlPolyParser import * +from dlpolyparser.libDlPolyParser import * try: - from libMomo import osio, endl, flush + from dlpolyparser.libMomo import osio, endl, flush osio.ConnectToFile('parser.osio.log') green = osio.mg except: osio = endl = flush = None green = None - -parser_info = { - "name": "parser-dl-poly", - "version": "0.0", - "json": "../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json" -} + +# parser_info = { +# "name": "parser-dl-poly", +# "version": "0.0", +# "json": "../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json" +# } # LOGGING def log(msg, highlight=None, enter=endl): @@ -54,7 +53,7 @@ def log(msg, highlight=None, enter=endl): def open_section(p, name): gid = p.openSection(name) yield gid - p.closeSection(name, gid) + p.closeSection(name, gid) def push(jbe, terminal, key1, fct=lambda x: x.As(), key2=None, conv=None): if key2 == None: key2 = key1 @@ -82,27 +81,64 @@ def push_value(jbe, value, key, conv=None): return value def push_array_values(jbe, value, key, conv=None): - if conv: + if conv: jbe.addArrayValues(key, value*conv) else: jbe.addArrayValues(key, value) return value -def parse(output_file_name): - jbe = JsonParseEventsWriterBackend(meta_info_env) + +# class DlPolyParser(): +# """ A proper class envolop for running this parser from within python. """ +# def __init__(self, backend, **kwargs): +# self.backend_factory = backend + +# from unittest.mock import patch +# logging.info('dl-poly parser started') +# logging.getLogger('nomadcore').setLevel(logging.WARNING) +# backend = self.backend_factory(metaInfoEnv) +# # Rename parser +# def parse(self, mainfile): + + +logger = logging.getLogger("nomad.DLPolyParser") + + +class DlPolyParserWrapper(): + """ 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__)), "dl_poly.nomadmetainfo.json")) + metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None) + from unittest.mock import patch + logging.info('dl-poly parser started') + logging.getLogger('nomadcore').setLevel(logging.WARNING) + backend = self.backend_factory(metaInfoEnv) + # Call the old parser without a class. + parserInfo = {'name': 'dl_poly-parser', 'version': '0.0'} + backend = parse_without_class(mainfile, backend, parserInfo) + return backend + + +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)) # PARSE CONTROLS ... ctrl_file_name = os.path.join(base_dir, 'CONTROL') terminal_ctrls = DlPolyControls(osio) - terminal_ctrls.ParseControls(ctrl_file_name) + terminal_ctrls.ParseControls(ctrl_file_name) # PARSE OUTPUT / TOPOLOGY ... output_file_name = os.path.join(base_dir, 'OUTPUT') terminal = DlPolyParser(osio) - terminal.ParseOutput(output_file_name) + terminal.ParseOutput(output_file_name) # PARSE CONFIG ... cfg_file_name = os.path.join(base_dir, 'CONFIG') @@ -126,7 +162,7 @@ def parse(output_file_name): out = terminal top = terminal.topology cfg = terminal_cfg - trj = terminal_trj + trj = terminal_trj terminals = [ctr, out, top, cfg, trj] # ESTABLISH (ENERGY) UNITS @@ -143,13 +179,13 @@ def parse(output_file_name): ofs.write('[%s] %s = %s\n' % (t.logtag, key, t[key].As(str))) ofs.write('\n') ofs.close() - + # PUSH TO BACKEND with open_section(jbe, 'section_run') as gid_run: push(jbe, out, 'program_name') push(jbe, out, 'program_version') #push(jbe, out, 'program_info', key2='program_version_date') - + # TOPOLOGY SECTION with open_section(jbe, 'section_topology') as gid_top: # Cross-referencing is done on-the-fly (as gid's become available) @@ -157,7 +193,7 @@ def parse(output_file_name): # b) : shape=(number_of_atoms_in_molecule, []) # c) : shape=(number_of_topology_atoms, [, ]) push(jbe, top, 'number_of_topology_molecules', lambda s: s.As(int)) - push(jbe, top, 'number_of_topology_atoms', lambda s: s.As(int)) + push(jbe, top, 'number_of_topology_atoms', lambda s: s.As(int)) # Atom types mol_type_atom_type_id_to_atom_type_gid = {} for mol in top.molecules: @@ -170,7 +206,7 @@ def parse(output_file_name): mol_type_atom_type_id_to_atom_type_gid[mol_name][atom_id] = gid_atom push(jbe, atom, 'atom_type_name', lambda s: s.As(), 'atom_name') push(jbe, atom, 'atom_type_mass', lambda s: s.As(float), 'atom_mass', conv=UNITCONV_DLPOLY_TO_SI['mass']) - push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge', conv=UNITCONV_DLPOLY_TO_SI['charge']) + push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge', conv=UNITCONV_DLPOLY_TO_SI['charge']) # Molecule types molecule_type_name_to_type_gid = {} for mol in top.molecules: @@ -181,12 +217,12 @@ def parse(output_file_name): for atom in mol.atoms: atom_id = atom['atom_id'].As(int) atom_gid_list.append(atom_type_id_to_atom_type_gid[atom_id]) - # Add molecule + # Add molecule with open_section(jbe, 'section_molecule_type') as gid_mol: molecule_type_name_to_type_gid[mol['molecule_type_name'].As()] = gid_mol push(jbe, mol, 'molecule_type_name') push(jbe, mol, 'number_of_atoms_in_molecule', lambda s: s.As(int)) - + push_array(jbe, mol, 'atom_in_molecule_name') push_array(jbe, mol, 'atom_in_molecule_charge', conv=UNITCONV_DLPOLY_TO_SI['charge']) push_array_values(jbe, np.asarray(atom_gid_list), 'atom_in_molecule_to_atom_type_ref') @@ -219,7 +255,7 @@ def parse(output_file_name): with open_section(jbe, 'section_sampling_method') as gid_sec_sampling_method: sec_sampling_method_ref = gid_sec_sampling_method # Ensemble - ensemble = push(jbe, out, 'ensemble_type', lambda s: s.As().split()[0].upper()) + ensemble = push(jbe, out, 'ensemble_type', lambda s: s.As().split()[0].upper()) # Method push(jbe, out, 'sampling_method') push(jbe, out, 'x_dl_poly_integrator_type') @@ -230,7 +266,7 @@ def parse(output_file_name): push(jbe, out, 'x_dl_poly_thermostat_target_temperature', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['temperature']) push(jbe, out, 'x_dl_poly_thermostat_tau', lambda s: s.As(float)) pass - if 'P' in ensemble: + if 'P' in ensemble: push(jbe, out, 'x_dl_poly_barostat_target_pressure', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['pressure_katm']) push(jbe, out, 'x_dl_poly_barostat_tau', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['time']) pass @@ -241,19 +277,21 @@ def parse(output_file_name): with open_section(jbe, 'section_method') as gid_sec_method: sec_method_ref = gid_sec_method push_value(jbe, 'force_field', 'calculation_method') - + # TODO Store state variables in frames/system description (temperature, pressure) # TODO Store interactions - + # SYSTEM DESCRIPTION refs_system_description = [] all_frames = [cfg] + trj.frames # <- Initial config + trajectory for frame in all_frames: with open_section(jbe, 'section_system') as gid: - refs_system_description.append(gid) + refs_system_description.append(gid) # Configuration core - atom_labels = np.array([ atom['atom_name'].As() for atom in frame.atoms ]) + atom_labels = np.array( + [ atom['atom_name'].As().replace('+','').replace('-','') for atom in frame.atoms ]) push_array_values(jbe, atom_labels, 'atom_labels') + # push_array_values(jbe, atom_species, 'atom_atom_numbers') push_array_values(jbe, frame.position_matrix, 'atom_positions', conv=UNITCONV_DLPOLY_TO_SI['length']) push_array_values(jbe, frame.box_matrix, 'simulation_cell', conv=UNITCONV_DLPOLY_TO_SI['length']) push_array_values(jbe, frame.pbc_booleans, 'configuration_periodic_dimensions') @@ -263,7 +301,7 @@ def parse(output_file_name): # TODO Wouldn't it be simpler if forces were added here? pass pass - + # SINGLE CONFIGURATIONS refs_single_configuration = [] i_frame = -1 @@ -282,8 +320,8 @@ def parse(output_file_name): push_array_values(jbe, frame.force_matrix, 'atom_forces', conv=UNITCONV_DLPOLY_TO_SI['mass']*UNITCONV_DLPOLY_TO_SI['length']/UNITCONV_DLPOLY_TO_SI['time']**2) # Method reference push_value(jbe, sec_method_ref, 'single_configuration_to_calculation_method_ref') - pass - + pass + # FRAME-SEQUENCE SECTION with open_section(jbe, 'section_frame_sequence'): push_value(jbe, len(all_frames), 'number_of_frames_in_sequence') @@ -296,7 +334,7 @@ def parse(output_file_name): pass jbe.finishedParsingSession("ParseSuccess", None) - return + return jbe if __name__ == '__main__': @@ -316,5 +354,5 @@ if __name__ == '__main__': output_file_name = sys.argv[1] parse(output_file_name) - + diff --git a/parser/parser-dl_poly/libDlPolyParser.py b/dlpolyparser/libDlPolyParser.py similarity index 100% rename from parser/parser-dl_poly/libDlPolyParser.py rename to dlpolyparser/libDlPolyParser.py diff --git a/parser/parser-dl_poly/libMomo.py b/dlpolyparser/libMomo.py similarity index 100% rename from parser/parser-dl_poly/libMomo.py rename to dlpolyparser/libMomo.py diff --git a/parser/parser-dl_poly/setup_paths.py b/dlpolyparser/setup_paths.py similarity index 100% rename from parser/parser-dl_poly/setup_paths.py rename to dlpolyparser/setup_paths.py diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..be54ef3 --- /dev/null +++ b/setup.py @@ -0,0 +1,33 @@ +# Copyright 2015-2018 Lorenzo Pardini +# +# 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='dlpolyparser', + version='0.1', + description='NOMAD parser implementation for DL-Poly.', + license='APACHE 2.0', + package_dir={'': './'}, + packages=find_packages(), + install_requires=[ + 'nomadcore' + ], + ) + + +if __name__ == '__main__': + main() diff --git a/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala b/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala deleted file mode 100644 index a052383..0000000 --- a/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala +++ /dev/null @@ -1,57 +0,0 @@ -/* - * Copyright 2016-2018 Carl Poelking, 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 DlPolyParser extends SimpleExternalParserGenerator( - name = "DlPolyParser", - parserInfo = jn.JObject( - ("name" -> jn.JString("DlPolyParser")) :: - ("parserId" -> jn.JString("DlPolyParser" + lab.DlPolyVersionInfo.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.DlPolyVersionInfo.toMap.map { - case (key, value) => - (key -> jn.JString(value.toString)) - }(breakOut): List[(String, jn.JString)]) - )) :: Nil - ), - mainFileTypes = Seq("text/.*"), - mainFileRe = """ DL_POLY """.r, - cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/dl_poly/parser/parser-dl_poly/dlPolyParser.py", - "${mainFilePath}"), - resList = Seq( - "parser-dl_poly/dlPolyParser.py", - "parser-dl_poly/libDlPolyParser.py", - "parser-dl_poly/libMomo.py", - "parser-dl_poly/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/dl_poly.nomadmetainfo.json" - ) ++ DefaultPythonInterpreter.commonFiles(), - dirMap = Map( - "parser-dl_poly" -> "parsers/dl_poly/parser/parser-dl_poly", - "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info" - ) ++ DefaultPythonInterpreter.commonDirMapping() -) diff --git a/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala deleted file mode 100644 index 6759e57..0000000 --- a/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala +++ /dev/null @@ -1,30 +0,0 @@ -/* - * Copyright 2016-2018 Carl Poelking, 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 DlPolyParserSpec extends Specification { - "DlPolyParserTest" >> { - "test with json-events" >> { - ParserRun.parse(DlPolyParser, "parsers/dl-poly/test/examples/dl-poly-test1/OUTPUT", "json-events") must_== ParseResult.ParseSuccess - } - "test with json" >> { - ParserRun.parse(DlPolyParser, "parsers/dl-poly/test/examples/dl-poly-test1/OUTPUT", "json") must_== ParseResult.ParseSuccess - } - } -} -- GitLab