Commit b3f6f3a8 authored by Daniel Speckhard's avatar Daniel Speckhard
Browse files

Nomad Fair

parent 0c709a6a
......@@ -9,6 +9,7 @@ syntax: glob
*.pyc
*.bk
*.swp
*.egg-info
.DS_Store
# logging files
......
from libatomsparser.libAtomsParser import LibAtomsParserWrapper
# 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.
......@@ -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
......@@ -36,16 +36,36 @@ except:
green = None
parser_info = {
"name": "parser-lib-atoms",
"name": "parser-lib-atoms",
"version": "0.0",
"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
......@@ -53,7 +73,7 @@ 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):
if key2 == None: key2 = key1
......@@ -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
......@@ -142,7 +167,7 @@ def parse(output_file_name):
if frame.has_config_type:
push_value(jbe, frame.config_type, 'x_lib_atoms_config_type')
pass
# FRAME SEQUENCE
with open_section(jbe, 'section_frame_sequence'):
push_value(jbe, len(all_frames), 'number_of_frames_in_sequence')
......@@ -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__':
......
# 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.
......@@ -139,7 +139,7 @@ class LibAtomsParser(object):
x = sp[:-1]
y = sp[-1]
key = ''
for i in range(len(x)-1):
for i in range(len(x)-1):
xi = x[i].replace('(','').replace(')','').lower()
key += '%s_' % xi
key += '%s' % x[-1].replace('(','').replace(')','').lower()
......@@ -148,7 +148,7 @@ class LibAtomsParser(object):
return block_data
def ApplyBlockXyData(self, block_data, key_map):
for key_in in key_map:
key_out = key_map[key_in]
key_out = key_map[key_in]
if key_in not in block_data:
# Missing key in output
self.missing_keys_lh.append(key_in)
......@@ -164,10 +164,10 @@ class LibAtomsParser(object):
# Missing key in transform map
self.ignored_keys.append(key)
return
def ParseOutput(self, output_file):
if self.log:
def ParseOutput(self, output_file):
if self.log:
self.log << self.log.mg << "libAtomsParser::ParseOutput ..." << self.log.endl
if HAVE_ASE:
read_fct = ase.io.read
read_fct_args = { 'index':':' }
......@@ -178,9 +178,9 @@ 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')
return
......@@ -238,7 +238,7 @@ class LibAtomsGapParser(LibAtomsParser):
gp_coord_node_att = XmlGetAttributes(gp_coord_node)
for key in gp_coord_node_att.keys():
self.Set('gpCoordinates.%s' % key, gp_coord_node_att[key].value)
# 'GAP_params/gpSparse/gpCoordinates/theta
key = 'theta'
if key in gp_coord_child_nodes:
......@@ -304,8 +304,8 @@ class LibAtomsTrajectory(LibAtomsParser):
self.ase_configs = None
self.frames = []
self.logtag = 'trj'
def ParseOutput(self, output_file):
if self.log:
def ParseOutput(self, output_file):
if self.log:
self.log << self.log.mg << "libAtomsParser::ParseOutput ..." << self.log.endl
if HAVE_ASE:
read_fct = ase.io.read
......@@ -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
......@@ -383,7 +383,7 @@ class FileStream(object):
break
return ln
def SkipToMatch(self, expr):
while True:
while True:
ln = self.ifs.readline()
m = re.search(expr, ln)
if m:
......@@ -412,12 +412,12 @@ class FileStream(object):
# Block not started yet
pass
if self.all_read(): break
return block_stream
def GetBlockSequence(self,
expr_start,
expr_new,
expr_end,
remove_eol=True,
return block_stream
def GetBlockSequence(self,
expr_start,
expr_new,
expr_end,
remove_eol=True,
skip_empty=True):
inside = False
outside = False
......@@ -442,7 +442,7 @@ class FileStream(object):
while True:
# Log line position
last_pos = self.ifs.tell()
ln = self.ifs.readline()
ln = self.ifs.readline()
# Figure out where we are
if not inside and expr_start in ln:
#print "Enter", expr_start
......@@ -494,7 +494,7 @@ class FileStream(object):
for i in range(n):
self.ln()
return
class BlockStream(FileStream):
def __init__(self, label=None):
super(BlockStream, self).__init__(None)
......@@ -506,7 +506,7 @@ class BlockStream(FileStream):
self.lns.append(ln)
def readline(self):
if self.all_read():
return ''
return ''
ln = self.lns[self.idx]
self.idx += 1
return ln
......
# 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.
......@@ -112,7 +112,7 @@ def NamespaceFromDict(tree_dict):
#print "NSPACE '%s' value added" % s
add_to_nspace.Add(s, v)
return nspace
class XmlTree(list):
def __init__(self, xmlfile, paths_rel_to=None):
......@@ -134,7 +134,7 @@ class XmlNode(object):
def __init__(self, element, path):
self.path = path
self.node = element
self.tag = element.tag
self.tag = element.tag
self.value = element.text
self.attributes = element.attrib
def As(self, typ):
......@@ -220,14 +220,14 @@ 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
def InterpretAsList(self, expr):
array = [ self.subtype(e) for e in expr ]
return array
def AddArg(self, name, typ=str, nickname=None,
def AddArg(self, name, typ=str, nickname=None,
default=None, destination=None, help=None):
# Sort out <name> (e.g. --time) vs <destination> (e.g., time)
if '--' != name[0:2]:
......@@ -270,7 +270,7 @@ class OptionsInterface(object):
else:
raise NotImplementedError("CLIO does not know how to generate type '%s'"\
% typ)
self.cmd_ln_args.add_argument(nickname, name,
self.cmd_ln_args.add_argument(nickname, name,
dest=dest,
action='store',
nargs=nargs,
......@@ -294,13 +294,13 @@ class OptionsInterface(object):
return
def __getitem__(self, key):
try:
return self.xspace.__dict__[key]
return self.xspace.__dict__[key]
except KeyError:
return self.cmd_ln_opts.__dict__[key]
except KeyError:
raise AttributeError('No such option registered: \'%s\'' % key)
return None
# =============================================================================
# OS SHELL INTERFACE
......@@ -315,7 +315,7 @@ class ShellInterface(object):
'mb' : '\033[34m',
'lb' : '\033[1;34m',
'my' : '\033[1;33m',
'mg' : '\033[92m',
'mg' : '\033[92m',
'mr' : '\033[91m',
'ww' : '\033[0;1m',
'ok' : '\033[92m',
......@@ -330,9 +330,9 @@ class ShellInterface(object):
'ro' : '\r o '}
self.pp = OS_COLOR('pp')
self.lb = OS_COLOR('lb')
self.mb = OS_COLOR('mb')
self.mb = OS_COLOR('mb')
self.mg = OS_COLOR('mg')
self.my = OS_COLOR('my')
self.my = OS_COLOR('my')
self.mr = OS_COLOR('mr')
self.ww = OS_COLOR('ww')
self.ok = OS_COLOR('ok')
......@@ -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
......@@ -465,7 +465,7 @@ class ShellInterface(object):
if self.debug: self << self.my << "exe:" << cmmd << endl
if self.os_exe_get:
output = subprocess.getoutput(cmmd)
self.os_exe_get = False
self.os_exe_get = False
return output
else:
sign = os.system(cmmd)
......@@ -528,7 +528,7 @@ class OS_EXE_DEV(object):
class OS_EXE_CATCH(object):
def __init__(self):
self.catch = True
class OS_EXE_ASSERT(object):
def __init__(self):
self.assert_0 = True
......
# 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()
/*
* 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()
)
/*
* 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
}
}
}
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