diff --git a/normalizer/normalizer-repo-tags/0.GIT_ADD.txt b/normalizer/normalizer-repo-tags/0.GIT_ADD.txt
deleted file mode 100644
index 2285620d4f8f7b0b27a4cceb29887024190d7ce9..0000000000000000000000000000000000000000
--- a/normalizer/normalizer-repo-tags/0.GIT_ADD.txt
+++ /dev/null
@@ -1 +0,0 @@
-model_base.py?
diff --git a/normalizer/normalizer-repo-tags/calculate_repo_tags.py b/normalizer/normalizer-repo-tags/calculate_repo_tags.py
index f1d057df14e2bb87fbb9bee029abdfb27e9550c1..58bca7e1f5a0d71b730bde1b7cc73102037b4c44 100644
--- a/normalizer/normalizer-repo-tags/calculate_repo_tags.py
+++ b/normalizer/normalizer-repo-tags/calculate_repo_tags.py
@@ -1,13 +1,11 @@
import setup_paths
import json
-import os.path, sys
+import os.path, sys, subprocess
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from nomadcore.parse_streamed_dicts import *
import logging
-from nomadrepo.core.api import API
-
base_path = os.path.abspath(os.path.dirname(__file__))
def calculateTags(inputDict, backend, calcUri):
@@ -18,21 +16,21 @@ def calculateTags(inputDict, backend, calcUri):
backend.openContext(calcUri)
repoSect = backend.openSection("section_repository_info")
- work = API()
- for calc, error in work._parse("/nomad/jshin/work/normalizer/scalaOut1.txt", "normalizerRepo"):
- calc, error = work.classify(calc)
+ 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", calc.get_checksum())
- backend.addValue("repository_chemical_formula", calc.info['formula']
- #backend.addValue("repository_parser_id", value)
- backend.addValue("repository_atomic_elements", calc.info['elements'])
- backend.addValue("repository_basis_set_type", calc.info['ansatz'])
- #backend.addValue("repository_code_version", value)
- backend.addValue("repository_crystal_system", calc.info['symmetry'])
- #backend.addValue("repository_program_name", calc.info[''])
- backend.addValue("repository_spacegroup_nr", calc.info['ng'])
- backend.addValue("repository_system_type", calc.info['periodicity'])
- backend.addValue("repository_xc_treatment", calc.info['H_types'])
+ 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'])
+ backend.addValue("repository_basis_set_type", repo_dic['ansatz'])
+ backend.addValue("repository_code_version", repo_dic['prog'].split(repo_dic['prog_name'])[0])
+ backend.addValue("repository_crystal_system", repo_dic['symmetry'])
+ backend.addValue("repository_program_name", repo_dic['prog_name'])
+ backend.addValue("repository_spacegroup_nr", repo_dic['ng'])
+ backend.addValue("repository_system_type", repo_dic['periodicity'])
+ backend.addValue("repository_xc_treatment", repo_dic['H_types'])
if repoSectUri:
backend.closeContext(repoSectUri)
@@ -57,14 +55,14 @@ def main():
calcUri,
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(sys.stdin)
+ #dictReader=ParseStreamedDicts(open("/u/jungho/myscratch/nomad-lab-base/normalizers/repo-tags/test/examples/scalaOut1.txt", 'r'))
while True:
inputDict=dictReader.readNextDict()
if inputDict is None:
break
- calculateTags(inputDict,backend, calcUri)
+ calculateTags(inputDict, backend, calcUri)
backend.finishedParsingSession("ParseSuccess", None)
sys.stdout.flush()
diff --git a/normalizer/normalizer-repo-tags/convert_2to3.sh b/normalizer/normalizer-repo-tags/convert_2to3.sh
deleted file mode 100755
index 3f78ed083b2ce9c7e2c6f6b78e7eabc45f2ed242..0000000000000000000000000000000000000000
--- a/normalizer/normalizer-repo-tags/convert_2to3.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-for python_file in NomadRepositoryParser/python/nomadrepo/core/settings.py NomadRepositoryParser/python/nomadrepo/core/symmetry.py
-do
- 2to3 -w $python_file
-done
diff --git a/normalizer/normalizer-repo-tags/extract_from_repo.py b/normalizer/normalizer-repo-tags/extract_from_repo.py
new file mode 100644
index 0000000000000000000000000000000000000000..dfaf7458a006dff91616bf8badde0b509213de26
--- /dev/null
+++ b/normalizer/normalizer-repo-tags/extract_from_repo.py
@@ -0,0 +1,14 @@
+import setup_paths_repo
+import os.path, sys, json
+from nomadrepo.core.api import API
+
+base_path = os.path.abspath(os.path.dirname(__file__))
+
+inp_str = "".join(sys.argv[1:])
+
+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__)
diff --git a/normalizer/normalizer-repo-tags/extract_from_repo.sh b/normalizer/normalizer-repo-tags/extract_from_repo.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8cb3f33a7101b0abbd5abb15d856d86ebb6503ed
--- /dev/null
+++ b/normalizer/normalizer-repo-tags/extract_from_repo.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+source $1/bin/activate
+python $2/extract_from_repo.py $3
diff --git a/normalizer/normalizer-repo-tags/requirements.txt b/normalizer/normalizer-repo-tags/requirements.txt
deleted file mode 100755
index 477ad42e0c6693f5e0f918fb42e8d8a5d167e082..0000000000000000000000000000000000000000
--- a/normalizer/normalizer-repo-tags/requirements.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-sqlalchemy == 1.0.6
-httplib2
-bcrypt
diff --git a/normalizer/normalizer-repo-tags/setup_paths.py b/normalizer/normalizer-repo-tags/setup_paths.py
index b3214e691ccc511cc774ab7a88e162af90e70edf..820841d681e61dad720c6babb50a9dda4b398c6b 100644
--- a/normalizer/normalizer-repo-tags/setup_paths.py
+++ b/normalizer/normalizer-repo-tags/setup_paths.py
@@ -1,14 +1,10 @@
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/"))
-#repoParserCoreDir = os.path.normpath(os.path.join(baseDir,"NomadRepositoryParser/python/nomadrepo/core/"))
+#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)
-
-#if not repoParserCoreDir in sys.path:
-# sys.path.insert(0, repoParserCoreDir)
+#if not repoParserDir in sys.path:
+# sys.path.insert(0, repoParserDir)
diff --git a/normalizer/normalizer-repo-tags/setup_paths_repo.py b/normalizer/normalizer-repo-tags/setup_paths_repo.py
new file mode 100644
index 0000000000000000000000000000000000000000..392d70cc8d9ea3a679b8493d5b44ac72f897f758
--- /dev/null
+++ b/normalizer/normalizer-repo-tags/setup_paths_repo.py
@@ -0,0 +1,6 @@
+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)