utils¶
BASE_URL_PREFIXES = {'major': f'/v{__api_version__.split('-')[0].split('+')[0].split('.')[0]}', 'minor': f'/v{'.'.join(__api_version__.split('-')[0].split('+')[0].split('.')[:2])}', 'patch': f'/v{'.'.join(__api_version__.split('-')[0].split('+')[0].split('.')[:3])}'}
module-attribute
¶
CONFIG: ServerConfig = ServerConfig()
module-attribute
¶
This singleton loads the config from a hierarchy of sources (see
customise_sources
)
and makes it importable in the server code.
PROVIDER_LIST_URLS = ('https://providers.optimade.org/v1/links', 'https://raw.githubusercontent.com/Materials-Consortia/providers/master/src/links/v1/providers.json')
module-attribute
¶
__all__ = ('BASE_URL_PREFIXES', 'meta_values', 'handle_response_fields', 'get_included_relationships', 'get_base_url', 'get_entries', 'get_single_entry', 'mongo_id_for_database', 'get_providers', 'PROVIDER_LIST_URLS')
module-attribute
¶
__api_version__ = '1.1.0'
module-attribute
¶
BadRequest
¶
Bases: OptimadeHTTPException
400 Bad Request
Source code in optimade/exceptions.py
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|
EntryCollection
¶
Bases: ABC
Backend-agnostic base class for querying collections of
EntryResource
s.
Source code in optimade/server/entry_collections/entry_collections.py
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|
all_fields: set[str]
property
¶
Get the set of all fields handled in this collection, from attribute fields in the schema, provider fields and top-level OPTIMADE fields.
The set of all fields are lazily created and then cached. This means the set is created the first time the property is requested and then cached.
Returns:
Type | Description |
---|---|
set[str]
|
All fields handled in this collection. |
pagination_mechanism = PaginationMechanism('page_offset')
class-attribute
instance-attribute
¶
The default pagination mechansim to use with a given collection, if the user does not provide any pagination query parameters.
__init__(resource_cls, resource_mapper, transformer)
¶
Initialize the collection for the given parameters.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
resource_cls |
EntryResource
|
The |
required |
resource_mapper |
BaseResourceMapper
|
A resource mapper object that handles aliases and format changes between deserialization and response. |
required |
transformer |
Transformer
|
The Lark |
required |
Source code in optimade/server/entry_collections/entry_collections.py
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__len__()
abstractmethod
¶
Returns the total number of entries in the collection.
Source code in optimade/server/entry_collections/entry_collections.py
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count(**kwargs)
abstractmethod
¶
Returns the number of entries matching the query specified by the keyword arguments.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
**kwargs |
Any
|
Query parameters as keyword arguments. |
{}
|
Source code in optimade/server/entry_collections/entry_collections.py
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|
find(params)
¶
Fetches results and indicates if more data is available.
Also gives the total number of data available in the absence of page_limit
.
See EntryListingQueryParams
for more information.
Returns a list of the mapped database reponse.
If no results match the query, then results
is set to None
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params |
Union[EntryListingQueryParams, SingleEntryQueryParams]
|
Entry listing URL query params. |
required |
Returns:
Type | Description |
---|---|
Optional[Union[dict[str, Any], list[dict[str, Any]]]]
|
A tuple of various relevant values: |
Optional[int]
|
( |
Source code in optimade/server/entry_collections/entry_collections.py
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get_attribute_fields()
¶
Get the set of attribute fields
Return only the first-level attribute fields from the schema of the resource class, resolving references along the way if needed.
Note
It is not needed to take care of other special OpenAPI schema keys than allOf
,
since only allOf
will be found in this context.
Other special keys can be found in the Swagger documentation.
Returns:
Type | Description |
---|---|
set[str]
|
Property names. |
Source code in optimade/server/entry_collections/entry_collections.py
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get_next_query_params(params, results)
¶
Provides url query pagination parameters that will be used in the next link.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
results |
Optional[Union[dict[str, Any], list[dict[str, Any]]]]
|
The results produced by find. |
required |
params |
EntryListingQueryParams
|
The parsed request params produced by handle_query_params. |
required |
Returns:
Type | Description |
---|---|
dict[str, list[str]]
|
A dictionary with the necessary query parameters. |
Source code in optimade/server/entry_collections/entry_collections.py
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handle_query_params(params)
¶
Parse and interpret the backend-agnostic query parameter models into a dictionary that can be used by the specific backend.
Note
Currently this method returns the pymongo interpretation of the parameters, which will need modification for modified for other backends.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params |
Union[EntryListingQueryParams, SingleEntryQueryParams]
|
The initialized query parameter model from the server. |
required |
Raises:
Type | Description |
---|---|
Forbidden
|
If too large of a page limit is provided. |
BadRequest
|
If an invalid request is made, e.g., with incorrect fields or response format. |
Returns:
Type | Description |
---|---|
dict[str, Any]
|
A dictionary representation of the query parameters. |
Source code in optimade/server/entry_collections/entry_collections.py
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|
insert(data)
abstractmethod
¶
Add the given entries to the underlying database.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data |
list[EntryResource]
|
The entry resource objects to add to the database. |
required |
Source code in optimade/server/entry_collections/entry_collections.py
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|
parse_sort_params(sort_params)
¶
Handles any sort parameters passed to the collection, resolving aliases and dealing with any invalid fields.
Raises:
Type | Description |
---|---|
BadRequest
|
if an invalid sort is requested. |
Returns:
Type | Description |
---|---|
Iterable[tuple[str, int]]
|
A list of tuples containing the aliased field name and |
Iterable[tuple[str, int]]
|
sort direction encoded as 1 (ascending) or -1 (descending). |
Source code in optimade/server/entry_collections/entry_collections.py
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EntryListingQueryParams
¶
Bases: BaseQueryParams
Common query params for all Entry listing endpoints.
Attributes:
Name | Type | Description |
---|---|---|
filter |
str
|
A filter string, in the format described in section API Filtering Format Specification of the specification. |
response_format |
str
|
The output format requested (see section Response Format). Defaults to the format string 'json', which specifies the standard output format described in this specification. Example: |
email_address |
EmailStr
|
An email address of the user making the request. The email SHOULD be that of a person and not an automatic system. Example: |
response_fields |
str
|
A comma-delimited set of fields to be provided in the output. If provided, these fields MUST be returned along with the REQUIRED fields. Other OPTIONAL fields MUST NOT be returned when this parameter is present. Example: |
sort |
str
|
If supporting sortable queries, an implementation MUST use the An implementation MAY support multiple sort fields for a single query. If it does, it again MUST conform to the JSON API 1.0 specification. If an implementation supports sorting for an entry listing endpoint, then the |
page_limit |
int
|
Sets a numerical limit on the number of entries returned.
See JSON API 1.0.
The API implementation MUST return no more than the number specified.
It MAY return fewer. The database MAY have a maximum limit and not accept larger numbers
(in which case an error code -- Example: |
page_offset |
int
|
RECOMMENDED for use with offset-based pagination: using Example: Skip 50 structures and fetch up to 100: |
page_number |
int
|
RECOMMENDED for use with page-based pagination: using Example: Fetch page 2 of up to 50 structures per page: |
page_cursor |
int
|
RECOMMENDED for use with cursor-based pagination: using |
page_above |
str
|
RECOMMENDED for use with value-based pagination: using Example: Fetch up to 100 structures above sort-field value 4000 (in this example, server chooses to fetch results sorted by
increasing |
page_below |
str
|
RECOMMENDED for use with value-based pagination: using |
include |
str
|
A server MAY implement the JSON API concept of returning compound documents
by utilizing the All related resource objects MUST be returned as part of an array value for the top-level The value of The default value for Note: A query with the parameter |
api_hint |
str
|
If the client provides the parameter, the value SHOULD have the format |
Source code in optimade/server/query_params.py
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|
check_params(query_params)
¶
This method checks whether all the query parameters that are specified
in the URL string are implemented in the relevant *QueryParams
class.
This method handles four cases:
- If a query parameter is passed that is not defined in the relevant
*QueryParams
class, and it is not prefixed with a known provider prefix, then aBadRequest
is raised. - If a query parameter is passed that is not defined in the relevant
*QueryParams
class, that is prefixed with a known provider prefix, then the parameter is silently ignored - If a query parameter is passed that is not defined in the relevant
*QueryParams
class, that is prefixed with an unknown provider prefix, then aUnknownProviderQueryParameter
warning is emitted. - If a query parameter is passed that is on the
unsupported_params
list for the inherited class, then aQueryParamNotUsed
warning is emitted.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
query_params |
Iterable[str]
|
An iterable of the request's string query parameters. |
required |
Raises:
Type | Description |
---|---|
`BadRequest`
|
if the query parameter was not found in the relevant class, or if it does not have a valid prefix. |
Source code in optimade/server/query_params.py
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|
EntryResource
¶
Bases: Resource
The base model for an entry resource.
Source code in optimade/models/entries.py
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InternalServerError
¶
Bases: OptimadeHTTPException
500 Internal Server Error
Source code in optimade/exceptions.py
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JSONAPIResponse
¶
Bases: JSONResponse
This class simply patches fastapi.responses.JSONResponse
to use the
JSON:API 'application/vnd.api+json' MIME type.
Source code in optimade/server/routers/utils.py
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|
ResponseMeta
¶
Bases: Meta
A JSON API meta member that contains JSON API meta objects of non-standard meta-information.
OPTIONAL additional information global to the query that is not specified in this document, MUST start with a database-provider-specific prefix.
Source code in optimade/models/optimade_json.py
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SingleEntryQueryParams
¶
Bases: BaseQueryParams
Common query params for single entry endpoints.
Attributes:
Name | Type | Description |
---|---|---|
response_format |
str
|
The output format requested (see section Response Format). Defaults to the format string 'json', which specifies the standard output format described in this specification. Example: |
email_address |
EmailStr
|
An email address of the user making the request. The email SHOULD be that of a person and not an automatic system. Example: |
response_fields |
str
|
A comma-delimited set of fields to be provided in the output. If provided, these fields MUST be returned along with the REQUIRED fields. Other OPTIONAL fields MUST NOT be returned when this parameter is present. Example: |
include |
str
|
A server MAY implement the JSON API concept of returning compound documents
by utilizing the All related resource objects MUST be returned as part of an array value for the top-level The value of The default value for Note: A query with the parameter |
api_hint |
str
|
If the client provides the parameter, the value SHOULD have the format |
Source code in optimade/server/query_params.py
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|
check_params(query_params)
¶
This method checks whether all the query parameters that are specified
in the URL string are implemented in the relevant *QueryParams
class.
This method handles four cases:
- If a query parameter is passed that is not defined in the relevant
*QueryParams
class, and it is not prefixed with a known provider prefix, then aBadRequest
is raised. - If a query parameter is passed that is not defined in the relevant
*QueryParams
class, that is prefixed with a known provider prefix, then the parameter is silently ignored - If a query parameter is passed that is not defined in the relevant
*QueryParams
class, that is prefixed with an unknown provider prefix, then aUnknownProviderQueryParameter
warning is emitted. - If a query parameter is passed that is on the
unsupported_params
list for the inherited class, then aQueryParamNotUsed
warning is emitted.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
query_params |
Iterable[str]
|
An iterable of the request's string query parameters. |
required |
Raises:
Type | Description |
---|---|
`BadRequest`
|
if the query parameter was not found in the relevant class, or if it does not have a valid prefix. |
Source code in optimade/server/query_params.py
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|
ToplevelLinks
¶
Bases: BaseModel
A set of Links objects, possibly including pagination
Source code in optimade/models/jsonapi.py
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|
check_additional_keys_are_links()
¶
The ToplevelLinks
class allows any additional keys, as long as
they are also Links or Urls themselves.
Source code in optimade/models/jsonapi.py
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|
get_base_url(parsed_url_request)
¶
Get base URL for current server
Take the base URL from the config file, if it exists, otherwise use the request.
Source code in optimade/server/routers/utils.py
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|
get_entries(collection, request, params)
¶
Generalized /{entry} endpoint getter
Source code in optimade/server/routers/utils.py
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get_included_relationships(results, ENTRY_COLLECTIONS, include_param)
¶
Filters the included relationships and makes the appropriate compound request to include them in the response.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
results |
Union[EntryResource, list[EntryResource], dict, list[dict]]
|
list of returned documents. |
required |
ENTRY_COLLECTIONS |
dict[str, EntryCollection]
|
dictionary containing collections to query, with key based on endpoint type. |
required |
include_param |
list[str]
|
list of queried related resources that should be included in
|
required |
Returns:
Type | Description |
---|---|
list[Union[EntryResource, dict[str, Any]]]
|
Dictionary with the same keys as ENTRY_COLLECTIONS, each containing the list of resource objects for that entry type. |
Source code in optimade/server/routers/utils.py
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|
get_providers(add_mongo_id=False)
¶
Retrieve Materials-Consortia providers (from https://providers.optimade.org/v1/links).
Fallback order if providers.optimade.org is not available:
- Try Materials-Consortia/providers on GitHub.
- Try submodule
providers
' list of providers. - Log warning that providers list from Materials-Consortia is not included in the
/links
-endpoint.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
add_mongo_id |
bool
|
Whether to populate the |
False
|
Returns:
Type | Description |
---|---|
list
|
List of raw JSON-decoded providers including MongoDB object IDs. |
Source code in optimade/utils.py
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|
get_single_entry(collection, entry_id, request, params)
¶
Source code in optimade/server/routers/utils.py
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handle_response_fields(results, exclude_fields, include_fields)
¶
Handle query parameter response_fields
.
It is assumed that all fields are under attributes
.
This is due to all other top-level fields are REQUIRED in the response.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
exclude_fields |
set[str]
|
Fields under |
required |
include_fields |
set[str]
|
Fields under |
required |
Returns:
Type | Description |
---|---|
list[dict[str, Any]]
|
List of resulting resources as dictionaries after pruning according to |
list[dict[str, Any]]
|
the |
Source code in optimade/server/routers/utils.py
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|
meta_values(url, data_returned, data_available, more_data_available, schema=None, **kwargs)
¶
Helper to initialize the meta values
Source code in optimade/server/routers/utils.py
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|
mongo_id_for_database(database_id, database_type)
¶
Produce a MongoDB ObjectId for a database
Source code in optimade/utils.py
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|