Add region info to jh endpoint

This makes better region information available, for example ISO country codes,
and allows the user to filter based on them.

This addresses #43

Example:

    http://127.0.0.1:8000/v1/jh/daily-reports/?country_code_iso2=GB

      {
        "id": 100477,
        "country_region": "United Kingdom",
        "province_state": "Channel Islands",
        "fips": null,
        "admin2": null,
        "last_update": "2020-04-04T23:34:00",
        "confirmed": 262,
        "deaths": 5,
        "recovered": 13,
        "region_info": {
          "uid": 8261,
          "scope": "Province_State",
          "country_code_iso2": "GB",
          "country_code_iso3": "GBR",
          "country_region": "United Kingdom",
          "province_state": "Channel Islands",
          "fips": null,
          "admin2": null
        }
      }

This example includes province/state level reports as well as country/region level. The scope parameter
can be used to filter these out:

    http://127.0.0.1:8000/v1/jh/daily-reports/?country_code_iso2=GB&scope=Country_Region

      {
        "id": 100709,
        "country_region": "United Kingdom",
        "province_state": null,
        "fips": null,
        "admin2": null,
        "last_update": "2020-04-04T23:34:00",
        "confirmed": 41903,
        "deaths": 4313,
        "recovered": 135,
        "region_info": {
          "uid": 826,
          "scope": "Country_Region",
          "country_code_iso2": "GB",
          "country_code_iso3": "GBR",
          "country_region": "United Kingdom",
          "province_state": null,
          "fips": null,
          "admin2": null
        }
      },

The country_region, province_state, fips, admin2 fields duplicate the top level one, but I think we should
include them for backwards compatability. Then if we create a V2 of the API we can drop the top level ones.

The ones in region info are the cleaned versions - they ensure that the same region will always be presented
the same way. The top level ones come from the reports themselves and are inconsistent from day to day.

README.md

@@ -24,28 +24,51 @@ The next step will be to add more data sources.
 ```
 In [1]: import requests
 
-In [2]: response = requests.get('https://api.covid19data.cloud/v1/jh/daily-reports?last_update_from=2020-04-01&last_update_to=2020-04-03&country=Italy')
+In [2]: response = requests.get('https://api.covid19data.cloud/v1/jh/daily-reports?last_update_from=2020-04-01&last_update_to=2020-04-03&country_code_iso2=IT&scope=Country_Region')
 
 In [3]: response.json()
 Out[3]:
-[{'id': 35343,
+[{'id': 92789,
   'country_region': 'Italy',
   'province_state': None,
   'fips': None,
   'admin2': None,
   'last_update': '2020-04-01T21:58:34',
   'confirmed': 110574,
   'deaths': 13155,
-  'recovered': 16847},
- {'id': 37895,
+  'recovered': 16847,
+  'region_info': {
+    'uid': 380,
+    'scope': 'Country_Region',
+    'country_code_iso2': 'IT',
+    'country_code_iso3': 'ITA',
+    'country_region': 'Italy',
+    'province_state': None,
+    'fips': None,
+    'admin2': None
+  }
+},
+{
+  'id': 95346,
   'country_region': 'Italy',
   'province_state': None,
   'fips': None,
   'admin2': None,
-  'last_update': '2020-04-02T23:25:14',
+  'last_update': '2020-04-02T23:25:00',
   'confirmed': 115242,
   'deaths': 13915,
-  'recovered': 18278}]
+  'recovered': 18278,
+  'region_info': {
+    'uid': 380,
+    'scope': 'Country_Region',
+    'country_code_iso2': 'IT',
+    'country_code_iso3': 'ITA',
+    'country_region': 'Italy',
+    'province_state': None,
+    'fips': None,
+    'admin2': None
+  }
+}]
 ```
 
 Further API documentation is available at https://api.covid19data.cloud/docs

covidapi/api/views.py

@@ -1,13 +1,15 @@
 import pkg_resources
 from fastapi import Depends
 from fastapi import APIRouter
+from fastapi import Query
 from starlette.responses import HTMLResponse
 from typing import List
 from datetime import date
 
 from ..services.crud import JHCRUD
 from ..services.session import get_db, Session
 from ..schemas.schemas import JHDailyReport
+from ..schemas.enums import Scope
 
 router = APIRouter()
 
@@ -29,13 +31,25 @@ def get_daily_reports(
     last_update_to: date = None,
     country: str = None,
     province: str = None,
+    country_code_iso2: str = Query(None, min_length=2, max_length=2),
+    country_code_iso3: str = Query(None, min_length=2, max_length=3),
+    scope: Scope = None
 ):
+    if country_code_iso2:
+        country_code_iso2 = country_code_iso2.upper()
+
+    if country_code_iso3:
+        country_code_iso3 = country_code_iso3.upper()
+
     daily_reports = JHCRUD().get_daily_reports(
         db, skip=skip, limit=limit,
         last_update_from=last_update_from,
         last_update_to=last_update_to,
         country=country,
         province=province,
+        country_code_iso2=country_code_iso2,
+        country_code_iso3=country_code_iso3,
+        scope=scope
     )
 
     return daily_reports

covidapi/schemas/enums.py

@@ -1,6 +1,6 @@
 from enum import Enum
 
 class Scope(Enum):
-    COUNTRY_REGION = 1
-    PROVINCE_STATE = 2
-    ADMIN2 = 3
+    COUNTRY_REGION = 'Country_Region'
+    PROVINCE_STATE = 'Province_State'
+    ADMIN2 = 'Admin2'

covidapi/schemas/schemas.py

@@ -1,6 +1,21 @@
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
 from datetime import datetime
 from typing import Optional
+from .enums import Scope
+
+class JHRegionInfo(BaseModel):
+    jh_id: int = Field(None, alias='uid')
+    scope: Scope
+    country_code_iso2: str
+    country_code_iso3: str
+    country_region: str
+    province_state: Optional[str]
+    fips: Optional[str]
+    admin2: Optional[str]
+
+    class Config:
+        orm_mode = True
+        allow_population_by_field_name = True
 
 
 class JHDailyReport(BaseModel):
@@ -13,6 +28,7 @@ class JHDailyReport(BaseModel):
     confirmed: int
     deaths: int
     recovered: int
+    region_info: JHRegionInfo
 
     class Config:
         orm_mode = True

covidapi/services/crud.py

@@ -1,8 +1,9 @@
-from sqlalchemy.orm import Session
+from sqlalchemy.orm import Session, joinedload
 from datetime import date
 
 from ..db import models
 from ..schemas import schemas
+from ..schemas.enums import Scope
 
 
 class JHCRUD:
@@ -19,8 +20,13 @@ def get_daily_reports(
         last_update_to: date = None,
         country: str = None,
         province: str = None,
+        country_code_iso2: str = None,
+        country_code_iso3: str = None,
+        scope: Scope = None
     ):
-        query = db.query(models.JHDailyReport)
+        query = db.query(models.JHDailyReport).join(
+            models.JHRegionInfo
+        )
 
         if last_update_from:
             query = query.filter(models.JHDailyReport.last_update >= last_update_from)
@@ -30,6 +36,12 @@ def get_daily_reports(
             query = query.filter(models.JHDailyReport.country_region == country)
         if province:
             query = query.filter(models.JHDailyReport.province_state == province)
+        if country_code_iso2:
+            query = query.filter(models.JHRegionInfo.country_code_iso2 == country_code_iso2)
+        if country_code_iso3:
+            query = query.filter(models.JHRegionInfo.country_code_iso2 == country_code_iso3)
+        if scope:
+            query = query.filter(models.JHRegionInfo.scope == scope)
 
         query = query.offset(skip).limit(limit)
         return query.all()