Commit 9a6d0b96 authored by Jungho Shin's avatar Jungho Shin

get configuration for repo from setting.json

parent 6b33e8e8
......@@ -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'])
......
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
......
{'repo_base_path' = '/u/jungho/myscratch/NomadRepositoryParser'}
{"repo_base_path":"/u/jungho/myscratch/NomadRepositoryParser/"}
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