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nomad-lab
nomad-FAIR
Commits
3a21531a
Commit
3a21531a
authored
Jul 24, 2020
by
Lauri Himanen
Browse files
Merge branch 'v0.8.4' into encyclopedia-api
parents
9d74877c
36e681e3
Pipeline
#79335
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in 30 minutes and 2 seconds
Changes
28
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3a21531a
...
...
@@ -29,3 +29,4 @@ build/
dist/
setup.json
parser.osio.log
gui/src/metainfo.json
.gitlab-ci.yml
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3a21531a
...
...
@@ -62,6 +62,12 @@ gui_linting:
-
cd gui
-
yarn
-
yarn run eslint 'src/**/*.js'
except
:
refs
:
-
tags
variables
:
-
$CI_COMMIT_REF_NAME =~ /^dev-.*$/
-
$CI_COMMIT_MESSAGE =~ /\[skip[ _-]tests?\]/i
tests
:
stage
:
test
...
...
@@ -111,6 +117,12 @@ install_tests:
-
python -c "import nomad.datamodel, nomad.datamodel.metainfo, nomad.client"
-
pip install `echo dist/nomad-lab-*.tar.gz`[parsing]
-
python -m nomad.cli parse tests/data/parsers/vasp/vasp.xml
except
:
refs
:
-
tags
variables
:
-
$CI_COMMIT_REF_NAME =~ /^dev-.*$/
-
$CI_COMMIT_MESSAGE =~ /\[skip[ _-]tests?\]/i
dev_setup_tests
:
stage
:
test
...
...
@@ -119,6 +131,12 @@ dev_setup_tests:
-
pip install --upgrade pip
-
./setup.sh
-
python -m nomad.cli parse tests/data/parsers/vasp/vasp.xml
except
:
refs
:
-
tags
variables
:
-
$CI_COMMIT_REF_NAME =~ /^dev-.*$/
-
$CI_COMMIT_MESSAGE =~ /\[skip[ _-]tests?\]/i
deploy
:
stage
:
deploy
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examples/access_metainfo.py
→
examples/
metainfo/
access_metainfo.py
View file @
3a21531a
File moved
examples/metainfo.ipynb
→
examples/metainfo
/metainfo
.ipynb
View file @
3a21531a
File moved
examples/metainfo/use_metainfo.py
0 → 100644
View file @
3a21531a
import
json
from
nomad.datamodel.metainfo
import
public
# A simple example that demonstrates how to set references
run
=
public
.
section_run
()
scc
=
run
.
m_create
(
public
.
section_single_configuration_calculation
)
system
=
run
.
m_create
(
public
.
section_system
)
scc
.
single_configuration_calculation_to_system_ref
=
system
assert
scc
.
single_configuration_calculation_to_system_ref
==
system
print
(
json
.
dumps
(
run
.
m_to_dict
(),
indent
=
2
))
gui/public/env.js
View file @
3a21531a
...
...
@@ -5,7 +5,7 @@ window.nomadEnv = {
'
appBase
'
:
'
http://localhost:8000/fairdi/nomad/latest
'
,
'
debug
'
:
false
,
'
matomoEnabled
'
:
false
,
'
matomoUrl
'
:
'
https://nomad-lab.eu/
prod
/stat
'
,
'
matomoUrl
'
:
'
https://nomad-lab.eu/
fairdi
/stat
'
,
'
matomoSiteId
'
:
'
2
'
,
'
version
'
:
{
"
label
"
:
"
0.8.4
"
,
...
...
nomad/app/api/metainfo.py
View file @
3a21531a
...
...
@@ -102,21 +102,12 @@ class LegacyMetainfoResource(Resource):
Other required packages might also be returned, e.g. a parser might organize its
definitions in multiple packages.
'''
package
=
metainfo_package_name
if
package
.
endswith
(
'.nomadmetainfo.json'
):
package
=
package
[:
-
19
]
if
package
.
endswith
(
'.json'
):
package
=
package
[:
-
5
]
try
:
python_package_name
,
_
=
python_package_mapping
(
package
)
python_package_name
=
'.'
.
join
(
python_package_name
.
split
(
'.'
)[:
-
1
])
python_module
=
importlib
.
import_module
(
python_package_name
)
metainfo
=
getattr
(
python_module
,
'm_env'
)
metainfo
=
LegacyMetainfoEnvironment
.
from_legacy_package_path
(
metainfo_package_name
)
except
(
ImportError
,
KeyError
,
FileNotFoundError
,
AttributeError
):
abort
(
404
,
message
=
'Metainfo package %s does not exist.'
%
package
)
abort
(
404
,
message
=
'Metainfo package %s does not exist.'
%
metainfo_
package
_name
)
if
isinstance
(
metainfo
,
LegacyMetainfoEnvironment
):
return
metainfo
.
to_legacy_dict
(
metainfo
.
packages
)
else
:
abort
(
404
,
message
=
'Metainfo package %s is not a legacy package.'
%
package
)
abort
(
404
,
message
=
'Metainfo package %s is not a legacy package.'
%
metainfo_
package
_name
)
nomad/app/optimade/models.py
View file @
3a21531a
...
...
@@ -123,7 +123,7 @@ class Meta():
self
.
more_data_available
=
available
>
returned
if
available
is
not
None
else
False
self
.
provider
=
dict
(
name
=
config
.
meta
.
name
,
description
=
config
.
meta
.
name
,
description
=
config
.
meta
.
description
,
prefix
=
'nomad'
,
homepage
=
config
.
meta
.
homepage
,
index_base_url
=
url
(
version
=
None
,
prefix
=
'index'
)
...
...
@@ -200,10 +200,10 @@ json_api_data_object_model = api.model('DataObject', {
description
=
'The id of the object.'
),
'attributes'
:
fields
.
Raw
(
description
=
'A dictionary, containing key-value pairs representing the entries properties'
)
description
=
'A dictionary, containing key-value pairs representing the entries properties'
)
,
# TODO
# further optional fields: links, meta, relationships
'relationships'
:
fields
.
Raw
(
description
=
'In accordance with section Relationships, all entry types MAY use relationships to describe relations to other entries.'
)
})
...
...
nomad/cli/dev.py
View file @
3a21531a
...
...
@@ -43,6 +43,22 @@ def qa(skip_tests: bool, exitfirst: bool):
sys
.
exit
(
ret_code
)
@
dev
.
command
(
help
=
'Generates a JSON with all metainfo.'
)
def
metainfo
():
import
json
from
nomad.metainfo
import
Package
from
nomad.parsing.parsers
import
parsers
# Ensure all metainfo is loaded
for
parser
in
parsers
:
_
=
parser
.
metainfo_env
data
=
{
key
:
value
.
m_to_dict
()
for
key
,
value
in
Package
.
registry
.
items
()}
print
(
json
.
dumps
(
data
,
indent
=
2
))
@
dev
.
command
(
help
=
'Generates source-code for the new metainfo from .json files of the old.'
)
@
click
.
argument
(
'path'
,
nargs
=-
1
)
def
legacy_metainfo
(
path
):
...
...
nomad/config.py
View file @
3a21531a
...
...
@@ -169,10 +169,14 @@ def api_url(ssl: bool = True):
services
.
api_base_path
.
strip
(
'/'
))
def
gui_url
():
def
gui_url
(
page
:
str
=
None
):
base
=
api_url
(
True
)[:
-
3
]
if
base
.
endswith
(
'/'
):
base
=
base
[:
-
1
]
if
page
is
not
None
:
return
'%s/gui/%s'
%
(
base
,
page
)
return
'%s/gui'
%
base
...
...
@@ -269,7 +273,7 @@ meta = NomadConfig(
service
=
'unknown nomad service'
,
name
=
'novel materials discovery (NOMAD)'
,
description
=
'A FAIR data sharing platform for materials science data'
,
homepage
=
'https://
https://
nomad-lab.eu'
,
homepage
=
'https://nomad-lab.eu'
,
source_url
=
'https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR'
,
maintainer_email
=
'markus.scheidgen@physik.hu-berlin.de'
)
...
...
@@ -397,7 +401,8 @@ def load_config(config_file: str = os.environ.get('NOMAD_CONFIG', 'nomad.yaml'))
else
:
logger
.
error
(
'config key %s does not exist'
%
key
)
adapt
(
globals
(),
config_data
)
if
config_data
is
not
None
:
adapt
(
globals
(),
config_data
)
# load env and override yaml and defaults
kwargs
=
{
...
...
nomad/metainfo/__init__.py
View file @
3a21531a
...
...
@@ -293,4 +293,5 @@ from .metainfo import (
SectionAnnotation
,
SectionProxy
,
derived
,
constraint
)
constraint
,
units
)
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