reorg models

.travis.yml

@@ -4,6 +4,8 @@ language: python
 python:
   - "3.6"
 script:
-   - pip install -e .[schema-validation]
+   - pip install -e .
+   - pip install -r requirements.txt
+   - pip install -r requirements-optional.txt
    - pytest
    - openapi-spec-validator openapi.json

optimade/server/collections.py

@@ -9,7 +9,9 @@
 from optimade.filterparser import Parser
 from optimade.filtertransformers.mongo import MongoTransformer
 
-from .models import NonnegativeInt, Resource, StructureMapper
+from .models.util import NonnegativeInt
+from .models.jsonapi import Resource
+from .models.structures import StructureMapper
 from .deps import EntryListingQueryParams
 
 

optimade/server/deps.py

@@ -2,9 +2,9 @@
 from pathlib import Path
 
 from fastapi import Query
-from pydantic import EmailStr, Schema, BaseModel
+from pydantic import EmailStr
 
-from .models import NonnegativeInt
+from .models.util import NonnegativeInt
 
 config = ConfigParser()
 config.read(Path(__file__).resolve().parent.joinpath('config.ini'))

optimade/server/main.py

@@ -8,10 +8,9 @@
 
 from .deps import EntryListingQueryParams
 from .collections import MongoCollection
-from .models import (
-    Link, Links, StructureResource, OptimadeResponseMeta, OptimadeResponseMetaQuery,
-    OptimadeStructureResponse,
-)
+from .models.jsonapi import Link, Links
+from .models.structures import StructureResource
+from. models.toplevel import OptimadeResponseMeta, OptimadeResponseMetaQuery, OptimadeStructureResponse
 
 config = ConfigParser()
 config.read(Path(__file__).resolve().parent.joinpath('config.ini'))

optimade/server/models/baseinfo.py

@@ -0,0 +1,17 @@
+from typing import Dict, List
+
+from pydantic import BaseModel, UrlStr
+
+
+class BaseInfoAttributes(BaseModel):
+    api_version: str
+    available_api_versions: Dict[str, UrlStr]
+    formats: List[str] = ["json"]
+    entry_types_by_format: Dict[str, List[str]]
+    available_endpoints: List[str] = ["structure", "all", "info"]
+
+
+class BaseInfoResource(BaseModel):
+    id: str = "/"
+    type: str = "info"
+    attributes: BaseInfoAttributes

optimade/server/models/entries.py

@@ -0,0 +1,34 @@
+from datetime import datetime
+from typing import Optional, Dict, List
+
+from pydantic import BaseModel
+
+from .jsonapi import Resource
+
+
+class EntryResourceAttributes(BaseModel):
+    local_id: str
+    last_modified: datetime
+    immutable_id: Optional[str]
+
+
+class EntryResource(Resource):
+    attributes: EntryResourceAttributes
+
+
+class EntryPropertyInfo(BaseModel):
+    description: str
+    unit: Optional[str]
+
+
+class EntryInfoAttributes(BaseModel):
+    description: str
+    properties: Dict[str, EntryPropertyInfo]
+    formats: List[str] = ["json"]
+    output_fields_by_format: Dict[str, List[str]]
+
+
+class EntryInfoResource(BaseModel):
+    id: str
+    type: str = "info"
+    attributes: EntryInfoAttributes

optimade/server/models/jsonapi.py

@@ -0,0 +1,20 @@
+"""
+This module should reproduce https://jsonapi.org/schema
+"""
+from typing import Optional
+
+from pydantic import BaseModel, UrlStr
+
+
+class Link(BaseModel):
+    href: UrlStr
+    meta: Optional[dict]
+
+
+class Links(BaseModel):
+    next: Optional[Link]
+
+
+class Resource(BaseModel):
+    id: str
+    type: str

optimade/server/models/structures.py

@@ -0,0 +1,59 @@
+from optimade.server.models.entries import EntryResourceAttributes, EntryResource
+
+
+class StructureResourceAttributes(EntryResourceAttributes):
+    elements: str = None
+    nelements: int = None
+    chemical_formula: str = None
+    formula_prototype: str = None
+
+
+class StructureResource(EntryResource):
+    type = "structure"
+    attributes: StructureResourceAttributes
+
+
+class StructureMapper:
+    aliases = (
+        ("id", "task_id"),
+        ("local_id", "task_id"),
+        ("last_modified", "last_updated"),
+        ("formula_prototype", "formula_anonymous"),
+        ("chemical_formula", "pretty_formula"),
+    )
+
+    list_fields = (
+        "elements",
+    )
+
+    @classmethod
+    def alias_for(cls, field):
+        return dict(cls.aliases).get(field, field)
+
+    @classmethod
+    def map_back(cls, doc):
+        if "_id" in doc:
+            del doc["_id"]
+        print(doc)
+        mapping = ((real, alias) for alias, real in cls.aliases)
+        newdoc = {}
+        reals = {real for alias, real in cls.aliases}
+        for k in doc:
+            if k not in reals:
+                newdoc[k] = doc[k]
+        for real, alias in mapping:
+            if real in doc:
+                newdoc[alias] = doc[real]
+        for k in newdoc:
+            if k in cls.list_fields:
+                newdoc[k] = ",".join(sorted(newdoc[k]))
+
+        print(newdoc)
+        if "attributes" in newdoc:
+            raise Exception("Will overwrite doc field!")
+        newdoc["attributes"] = newdoc.copy()
+        newdoc["attributes"].pop("id")
+        for k in list(newdoc.keys()):
+            if k not in ("id", "attributes"):
+                del newdoc[k]
+        return newdoc

optimade/server/models/toplevel.py

@@ -0,0 +1,47 @@
+from datetime import datetime
+from typing import Union, List
+
+from pydantic import BaseModel, validator, UrlStr, Schema
+
+from optimade.server.models.jsonapi import Links, Resource
+from optimade.server.models.structures import StructureResource
+from optimade.server.models.util import NonnegativeInt
+
+
+class OptimadeResponseMetaQuery(BaseModel):
+    representation: str
+
+    @validator('representation')
+    def representation_must_be_valid_url_with_base(cls, v):
+        UrlStr(f'https://baseurl.net{v}')
+        return v
+
+
+class OptimadeResponseMeta(BaseModel):
+    """
+    A JSON API meta member that contains JSON API meta objects of non-standard meta-information.
+
+    In addition to the required fields, it MAY contain
+
+    - `data_available`: an integer containing the total number of data objects available in the database.
+    - `last_id`: a string containing the last ID returned.
+    - `response_message`: response string from the server.
+
+    Other OPTIONAL additional information global to the query that is not specified in this document, MUST start with
+    a database-provider-specific prefix
+    """
+    query: OptimadeResponseMetaQuery
+    api_version: str = Schema(..., description="a string containing the version of the API implementation.")
+    time_stamp: datetime
+    data_returned: NonnegativeInt
+    more_data_available: bool
+
+
+class OptimadeResponse(BaseModel):
+    links: Links
+    meta: OptimadeResponseMeta
+    data: Union[Resource, List[Resource]]
+
+
+class OptimadeStructureResponse(OptimadeResponse):
+    data: Union[StructureResource, List[StructureResource]]

optimade/server/models/util.py

@@ -0,0 +1,5 @@
+from pydantic import ConstrainedInt
+
+
+class NonnegativeInt(ConstrainedInt):
+    ge = 0