Adapted to new version of optimade-python-tools.

optimade-python-tools @ da841920

-Subproject commit b9619d6b34a8f8e66120fb02f5fd3dbc16d26517
+Subproject commit da84192020f08e8d1c847a83ffbfd20d532ae75d

nomad/app/optimade/api.py

@@ -60,7 +60,7 @@ def base_request_args():
 api = Api(
     blueprint,
     version='1.0', title='NOMAD\'s OPTiMaDe API implementation',
-    description='NOMAD\'s OPTiMaDe API implementation, version 0.10.0.',
+    description='NOMAD\'s OPTiMaDe API implementation, version 0.10.1.',
     validate=True)
 ''' Provides the flask restplust api instance for the optimade api'''
 

nomad/app/optimade/endpoints.py

@@ -187,10 +187,10 @@ class Info(Resource):
             'type': 'info',
             'id': '/',
             'attributes': {
-                'api_version': '0.10.0',
+                'api_version': '0.10.1',
                 'available_api_versions': [{
-                    'url': url(),
-                    'version': '0.10.0'
+                    'url': url(version=None),
+                    'version': '0.10.1'
                 }],
                 'formats': ['json'],
                 'entry_types_by_format': {

nomad/app/optimade/filterparser.py

@@ -25,7 +25,7 @@ class FilterException(Exception):
 
 
 _quantities: Dict[str, Quantity] = None
-_parser = LarkParser(version=(0, 10, 0))
+_parser = LarkParser(version=(0, 10, 1))
 _transformer = None
 
 

nomad/app/optimade/index.py

@@ -37,10 +37,10 @@ class Info(Resource):
             'type': 'info',
             'id': '/',
             'attributes': {
-                'api_version': '0.10.0',
+                'api_version': '0.10.1',
                 'available_api_versions': [{
-                    'url': url(prefix='index'),
-                    'version': '0.10.0'
+                    'url': url(version=None, prefix='index'),
+                    'version': '0.10.1'
                 }],
                 'formats': ['json'],
                 'entry_types_by_format': {
@@ -75,7 +75,7 @@ class Links(Resource):
                     "name": config.meta.name,
                     "description": config.meta.description,
                     "base_url": {
-                        "href": url(),
+                        "href": url(version=None),
                     },
                     "homepage": config.meta.homepage
                 }

nomad/app/optimade/models.py

@@ -112,15 +112,15 @@ class Meta():
 
     def __init__(self, query: str, returned: int, available: int = None, last_id: str = None):
         self.query = dict(representation=query)
-        self.api_version = '0.10.0'
+        self.api_version = '0.10.1'
         self.time_stamp = datetime.datetime.now()
         self.data_returned = returned
         self.more_data_available = available > returned if available is not None else False
         self.provider = dict(
-            name='NOMAD',
-            description='The NOvel MAterials Discovery project and database.',
+            name=config.meta.name,
+            description=config.meta.name,
             prefix='nomad',
-            homepage='https//nomad-coe.eu',
+            homepage=config.meta.homepage,
             index_base_url=base_url
         )
 
@@ -129,8 +129,8 @@ class Meta():
         self.implementation = dict(
             name='nomad@fairdi',
             version=config.meta.version,
-            source_url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR',
-            maintainer=dict(email='markus.scheidgen@physik.hu-berlin.de'))
+            source_url=config.meta.source_url,
+            maintainer=dict(email=config.meta.maintainer_email))
 
 
 class ToplevelLinks:
@@ -174,7 +174,7 @@ def Links(endpoint: str, available: int, page_number: int, page_limit: int, **kw
     rest.update(**{key: value for key, value in kwargs.items() if value is not None})
 
     result = dict(
-        base_url=url(),
+        base_url=url(version=None),
         first=url(endpoint, page_number=1, **rest),
         last=url(endpoint, page_number=last_page, **rest))
 
@@ -296,29 +296,16 @@ class StructureObject:
         self.attributes = attrs
 
 
-class ReferenceObject:
-    def __init__(self, calc: EntryMetadata):
-        attrs = dict(
-            immutable_id=calc.calc_id,
-            last_modified=calc.last_processing if calc.last_processing is not None else calc.upload_time,
-            authors=calc.authors)
+# class ReferenceObject:
+#     def __init__(self, calc: EntryMetadata):
+#         attrs = dict(
+#             immutable_id=calc.calc_id,
+#             last_modified=calc.last_processing if calc.last_processing is not None else calc.upload_time,
+#             authors=calc.authors)
 
-        self.type = 'calculation'
-        self.id = calc.calc_id
-        self.attributes = attrs
-
-
-class LinkObject:
-    def __init__(self, calc: EntryMetadata, page_number: int, **kwargs):
-        attrs = dict(
-            name='Calculation %s' % calc.calc_id,
-            description='Calculation entry in NOMAD database.',
-            base_url=url('structures', page_number=page_number, **kwargs),
-            homepage=url()
-        )
-        self.type = 'child'
-        self.id = calc.calc_id
-        self.attributes = attrs
+#         self.type = 'calculation'
+#         self.id = calc.calc_id
+#         self.attributes = attrs
 
 
 class Property:

nomad/config.py

@@ -269,7 +269,9 @@ meta = NomadConfig(
     service='unknown nomad service',
     name='novel materials discovery (NOMAD)',
     description='A FAIR data sharing platform for materials science data',
-    homepage='https://nomad-coe.eu'
+    homepage='https://repository.nomad-coe.eu/v0.8',
+    source_url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR',
+    maintainer_email='markus.scheidgen@physik.hu-berlin.de'
 )
 
 auxfile_cutoff = 100

tests/app/test_optimade.py

@@ -41,7 +41,7 @@ def test_index(index_api):
     rv = index_api.get('/links')
     assert rv.status_code == 200
     data = json.loads(rv.data)
-    assert data['data'][0]['attributes']['base_url']['href'].endswith('optimade/v0')
+    assert data['data'][0]['attributes']['base_url']['href'].endswith('optimade')
 
 
 def test_get_entry(published: Upload):
@@ -128,17 +128,19 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
     ('chemical_formula_descriptive CONTAINS "C" AND NOT chemical_formula_descriptive STARTS WITH "O"', 1),
     ('NOT chemical_formula_anonymous STARTS WITH "A"', 0),
     ('chemical_formula_anonymous CONTAINS "AB2" AND chemical_formula_anonymous ENDS WITH "C"', 1),
-    ('nsites >=3 AND LENGTH elements = 2', 2),
-    ('LENGTH elements = 2', 3),
-    ('LENGTH elements = 3', 1),
-    ('LENGTH dimension_types = 0', 3),
-    ('LENGTH dimension_types = 1', 1),
-    ('nelements = 2 AND LENGTH dimension_types = 1', 1),
-    ('nelements = 3 AND LENGTH dimension_types = 1', 0),
-    ('nelements = 3 OR LENGTH dimension_types = 1', 2),
-    ('nelements > 1 OR LENGTH dimension_types = 1 AND nelements = 2', 4),
-    ('(nelements > 1 OR LENGTH dimension_types = 1) AND nelements = 2', 3),
-    ('NOT LENGTH dimension_types = 1', 3),
+    ('nsites >=3 AND elements LENGTH = 2', 2),
+    ('elements LENGTH = 2', 3),
+    ('elements LENGTH 2', 3),
+    ('elements LENGTH = 3', 1),
+    ('dimension_types LENGTH = 0', 3),
+    ('dimension_types LENGTH = 1', 1),
+    ('nelements = 2 AND dimension_types LENGTH = 1', 1),
+    ('nelements = 3 AND dimension_types LENGTH = 1', 0),
+    ('nelements = 3 OR dimension_types LENGTH = 1', 2),
+    ('nelements > 1 OR dimension_types LENGTH = 1 AND nelements = 2', 4),
+    ('(nelements > 1 OR dimension_types LENGTH = 1) AND nelements = 2', 3),
+    ('NOT dimension_types LENGTH 1', 3),
+    ('nelements LENGTH = 1', -1),
     ('LENGTH nelements = 1', -1),
     ('chemical_formula_anonymous starts with "A"', -1),
     ('elements HAS ONY "H", "O"', -1)