Merge branch 'v0.8.4' into encyclopedia-api

.gitignore

@@ -29,3 +29,4 @@ build/
 dist/
 setup.json
 parser.osio.log
+gui/src/metainfo.json

.gitlab-ci.yml

@@ -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

amber @ e7077c9a

-Subproject commit 56e9412d0d322fd88240fe2af41716a0016831c7
+Subproject commit e7077c9a824e01b45b0e4989858ecd35f59f4cc7

charmm @ cc6c9545

-Subproject commit 7decbdcf25ef48b019bde17c472f54d65a124c9a
+Subproject commit cc6c9545300cf6ea3347357fedffc6798415a299

dftbplus @ 1211d4b7

-Subproject commit 0a3e003535d12b987f5774fc631cb142b6d245c6
+Subproject commit 1211d4b79907d9a987422193b3f97efd69962a3c

dl-poly @ fa54fe56

-Subproject commit 059d4c7f1a452383d67f0ecf0c9bc267580083dc
+Subproject commit fa54fe567a1250af3009ecc9692d14c64a399f29

gromacs @ 2310b63f

-Subproject commit f7f156204c16b54e4df998a8a275bcf4a5aaf901
+Subproject commit 2310b63ff3904ddd6f912c32789568787c6ab250

gromos @ b7d913f0

-Subproject commit 8d896ede93e794d0fdb905e42281ef7c871bc05d
+Subproject commit b7d913f0d8f82a9bb564e346bb60f66008ac791b

namd @ a741cfe6

-Subproject commit 97b653e3fe695775f53a96249a0bb9ad694ef742
+Subproject commit a741cfe607e9dfd1f2d65aeddbcc4bc5a15bbc13

tinker @ 7f5fc6a3

-Subproject commit 85cc99b320454f8c8a68bdf376e128c156cf2ac2
+Subproject commit 7f5fc6a358dc7e40e716cc5205fa04e8cf9c6d6c

python_common @ afdd0937

-Subproject commit cf843eda3e4650bc240eb0d1a1ab5b0cea6dda96
+Subproject commit afdd0937aab2681ca3912cfd9d95c7633fdcd7b9

examples/metainfo/use_metainfo.py

+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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -293,4 +293,5 @@ from .metainfo import (
     SectionAnnotation,
     SectionProxy,
     derived,
-    constraint)
+    constraint,
+    units)