executing python2 directly

normalizer/normalizer-repo-tags/calculate_repo_tags.py

@@ -15,12 +15,11 @@ def calculateTags(inputDict, backend, calcUri):
     else:
         backend.openContext(calcUri)
         repoSect = backend.openSection("section_repository_info")
+    repo_dic_sub = subprocess.Popen(['/u/jungho/myscratch/NomadRepositoryParser/bin/python', 'extract_from_repo.py'], stdin = subprocess.PIPE, stdout = subprocess.PIPE)
+    repo_dic_sub_out = repo_dic_sub.communicate(json.dumps(inputDict)+'\n')[0]
+    repo_dic = json.loads(repo_dic_sub_out)
 
-    repo_dic_sub = subprocess.Popen([os.path.join(base_path, 'extract_from_repo.sh'), '/scratch/u/jungho/NomadRepositoryParser/', base_path, '/nomad/jshin/work/normalizer/scalaOut1.txt'], stdout = subprocess.PIPE)
-
-    repo_dic = json.load(repo_dic_sub.stdout)
-
-    backend.addValue("repository_checksum", repo_dic['checksum'])
+    #backend.addValue("repository_checksum", repo_dic['checksum'])
     backend.addValue("repository_chemical_formula", repo_dic['formula'])
     backend.addValue("repository_parser_id", repo_dic['prog_name'] + ' v1.0')
     backend.addValue("repository_atomic_elements", repo_dic['elements'])
@@ -56,7 +55,7 @@ def main():
         parserInfo = {'name':'RepoTagsNormalizer', 'version': '1.0'})
 
     dictReader=ParseStreamedDicts(sys.stdin)
-    #dictReader=ParseStreamedDicts(open("/u/jungho/myscratch/nomad-lab-base/normalizers/repo-tags/test/examples/scalaOut1.txt", 'r'))
+    #dictReader=ParseStreamedDicts(open("/u/jungho/myscratch/nomad-lab-base/normalizers/repo-tags/test/examples/scalaOut2.txt", 'r'))
 
     while True:
         inputDict=dictReader.readNextDict()

normalizer/normalizer-repo-tags/extract_from_repo.py

-import setup_paths_repo
-import os.path, sys, json
+#import setup_paths, setup_paths_repo
+import sys, json
+import sqlalchemy
+base_path= sys.exec_prefix + '/python'
+sys.path.insert(0, base_path)
+from nomadrepo.core.settings import connect_database, settings
 from nomadrepo.core.api import API
+inputStr = sys.stdin.readline()
 
-base_path = os.path.abspath(os.path.dirname(__file__))
+def extract_metadata(dic):
+    work = API()
 
-inp_str = "".join(sys.argv[1:])
+    for calc, error in work._parse(dic, "normalizerRepo"):
+        calc, error = work.classify(calc)
+        calc.info['oadate'] = None
+        #calc.info['checksum'] = calc.get_checksum()
+        json.dump(calc.info, sys.__stdout__)
+        pass
 
-work = API()
-for calc, error in work._parse(inp_str, "normalizerRepo"):
-    calc, error = work.classify(calc)
-    calc.info['oadate'] = None
-    calc.info['checksum'] = calc.get_checksum()
-    json.dump(calc.info, sys.__stdout__)
+def main():
+    inputDict = json.loads(inputStr)
+    extract_metadata(inputDict)
+
+if __name__ == "__main__":
+    main()

normalizer/normalizer-repo-tags/extract_from_repo.sh

-#!/bin/bash
-
-source $1/bin/activate
-python $2/extract_from_repo.py $3

normalizer/normalizer-repo-tags/normalizer/manifest.json

-{"enabled": 1}

normalizer/normalizer-repo-tags/normalizer/normalizer.py

-from ase import Atoms
-from nomadrepo.parsers import Output
-from numpy import array
-
-class normalizerRepo(Output):
-
-    def __init__(self, filename, **kwargs):
-        Output.__init__(self, filename)
-
-        # fill out i.e. backend.addValue unsing input Dict
-        #  "repository_checksum",
-        #  "repository_chemical_formula",
-        #  "repository_parser_id",
-        #  "repository_atomic_elements",
-        #  "repository_basis_set_type",
-        #  "repository_code_version",
-        #  "repository_crystal_system",
-        #  "repository_program_name",
-        #  "repository_spacegroup_nr",
-        #  "repository_system_type",
-        #  "repository_xc_treatment"
-        # add more?
-
-        filename_f = open(filename, 'r')
-        import json
-        inputDict = json.load(filename_f)[0]
-        filename_f.close()
- 
-        atom_symbols = inputDict['section_system.last']['atom_labels']['flatData']
- 
-        ## Change these ##
-        simulation_cell = [50.0, 50.0, 50.0]
-        configuration_periodic_dimensions = [False, False, False]
-        ####
-
-        atom_positions_flat = inputDict['section_system.last']['atom_positions']['flatData']
-        atom_positions_shape = inputDict['section_system.last']['atom_positions']['shape']
-
-        atom_positions_list = []
-        for atom_i in range(0, atom_positions_shape[0]):
-            atom_i_start = atom_i*atom_positions_shape[1]
-            atom_positions_list.append(atom_positions_flat[atom_i_start:atom_i_start+atom_positions_shape[1]])
-        atom_positions = array(atom_positions_list)
-
-        self.structures.append(Atoms(symbols   = atom_symbols,
-                                     cell      = simulation_cell,
-                                     positions = atom_positions,
-                                     pbc       = configuration_periodic_dimensions))
-
-        self.info['energy'] = inputDict['energy_total.last']
-        self.info['prog'] = inputDict['program_name'][0] + ' ' + inputDict['program_version'][0]
-        ## Need the path of mainly parsed file.
-
-        from nomadrepo.parsers.LAB.LAB import ParsingContext
-        from nomadrepo.parsers.LAB.LAB import save_xcFunctional
-        context = ParsingContext()
-        self.electrons['type'] = context.toDict_bs_type()[inputDict['program_name'][0]]
-        save_xcFunctional(self, inputDict['XC_functional_name'])
-
-        #  "repository_xc_treatment"
-
-    @staticmethod
-    def fingerprints(test_string, file=None):
-        # fake method
-        return False

normalizer/normalizer-repo-tags/setting.json

+{'repo_base_path' = '/u/jungho/myscratch/NomadRepositoryParser'}

normalizer/normalizer-repo-tags/setup_paths.py

 import sys, os, os.path
 baseDir = os.path.dirname(os.path.abspath(__file__))
 commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
-#repoParserDir = os.path.normpath(os.path.join(baseDir,"/u/jungho/myscratch/NomadRepositoryParser/python/"))
 
 if not commonDir in sys.path:
     sys.path.insert(0, commonDir)
-
-#if not repoParserDir in sys.path:
-#    sys.path.insert(0, repoParserDir)

normalizer/normalizer-repo-tags/setup_paths_repo.py

-import sys, os, os.path
-baseDir = os.path.dirname(os.path.abspath(__file__))
-repoParserDir = os.path.normpath(os.path.join(baseDir,"/u/jungho/myscratch/NomadRepositoryParser/python/"))
-
-if not repoParserDir in sys.path:
-    sys.path.insert(0, repoParserDir)

src/test/scala/eu/nomad_lab/normalizers/FhiAimsBasisNormalizer.scala

+package eu.nomad_lab.normalizers
+
+import eu.nomad_lab.{ parsers, DefaultPythonInterpreter }
+import org.scalacheck.Properties
+import org.specs2.mutable.Specification
+import org.{ json4s => jn }
+
+object FhiAimsBasisNormalizerSpec extends Specification {
+
+}