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

 # 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__':
 

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

 # 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

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

 # 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

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={'': './'},