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nomad-lab
normalizer-repo-tags
Commits
fd783d7f
Commit
fd783d7f
authored
Sep 13, 2017
by
Jungho Shin
Browse files
enhance interface to the Repository codebase
parent
2b0999a9
Changes
8
Hide whitespace changes
Inline
Side-by-side
normalizer/normalizer-repo-tags/0.GIT_ADD.txt
deleted
100644 → 0
View file @
2b0999a9
model_base.py?
normalizer/normalizer-repo-tags/calculate_repo_tags.py
View file @
fd783d7f
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
()
...
...
normalizer/normalizer-repo-tags/convert_2to3.sh
deleted
100755 → 0
View file @
2b0999a9
#!/bin/bash
for
python_file
in
NomadRepositoryParser/python/nomadrepo/core/settings.py NomadRepositoryParser/python/nomadrepo/core/symmetry.py
do
2to3
-w
$python_file
done
normalizer/normalizer-repo-tags/extract_from_repo.py
0 → 100644
View file @
fd783d7f
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__
)
normalizer/normalizer-repo-tags/extract_from_repo.sh
0 → 100755
View file @
fd783d7f
#!/bin/bash
source
$1
/bin/activate
python
$2
/extract_from_repo.py
$3
normalizer/normalizer-repo-tags/requirements.txt
deleted
100755 → 0
View file @
2b0999a9
sqlalchemy == 1.0.6
httplib2
bcrypt
normalizer/normalizer-repo-tags/setup_paths.py
View file @
fd783d7f
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)
normalizer/normalizer-repo-tags/setup_paths_repo.py
0 → 100644
View file @
fd783d7f
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
)
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