get configuration for repo from setting.json

normalizer/normalizer-repo-tags/calculate_repo_tags.py

@@ -7,7 +7,8 @@ from nomadcore.parse_streamed_dicts import *
 import logging
 
 base_path = os.path.abspath(os.path.dirname(__file__))
-## test
+with open(base_path+'/setting.json', 'r') as file_conf: repo_conf = json.load(file_conf)
+repo_base_path = repo_conf['repo_base_path']
 
 def calculateTags(inputDict, backend, calcUri):
     repoSectUri = inputDict.get("section_repository_info.uri")
@@ -16,12 +17,12 @@ 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 = subprocess.Popen([os.path.join(repo_base_path, 'bin/python'), base_path+'/extract_from_repo.py'], stdin = subprocess.PIPE, stdout = subprocess.PIPE)
     inputDict_str = json.dumps(inputDict)+'\n' 
     repo_dic_sub_out = repo_dic_sub.communicate(inputDict_str.encode('utf-8'))[0]
     repo_dic = json.loads(repo_dic_sub_out.decode("utf-8"))
 
-    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'])

normalizer/normalizer-repo-tags/extract_from_repo.py

 import sys, json
-
 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
 
 def extract_metadata(dic_in):
-    session = connect_database(settings, None)()
-    checksum = session.execute("SELECT checksum FROM calculations WHERE calc_id = %d ;" % 4000000).fetchone()[0]
-    session.commit(); session.close()
+    #session = connect_database(settings, None)()
+    #checksum = session.execute("SELECT checksum FROM calculations WHERE calc_id = %d ;" % 4000000).fetchone()[0]
+    #session.commit(); session.close()
 
     work = API()
 
     for calc, error in work._parse(dic_in, "normalizerRepo"):
         calc, error = work.classify(calc)
         calc.info['oadate'] = None
-        calc.info['checksum'] = str(checksum)
+        #calc.info['checksum'] = calc.get_checksum()
         json.dump(calc.info, sys.__stdout__)
         pass
 

normalizer/normalizer-repo-tags/setting.json

-{'repo_base_path' = '/u/jungho/myscratch/NomadRepositoryParser'}
+{"repo_base_path":"/u/jungho/myscratch/NomadRepositoryParser/"}