diff --git a/production_tests.sh b/production_tests.sh
index 7cf9db8dbb88e22837a8e0b7fee736c0c7228a25..5c0837658afffab10f5d2e3c1eb564ccad7db6dc 100755
--- a/production_tests.sh
+++ b/production_tests.sh
@@ -11,7 +11,7 @@ curl http://127.0.0.1:8000/contacts/organisations/
curl http://127.0.0.1:8000/contacts/organisations/id/2
curl http://127.0.0.1:8000/contacts/organisations/id/99
curl http://127.0.0.1:8000/contacts/organisations/FZJ
-curl -X POST -H "Content-Type:application/json" -d '{"organisation": {"name": "FZJ2", "longname": "Forschungszentrum Test", "kind": 1, "city": "Jülich", "postcode": "52425", "street_address": "Wilhelm-Johnen-Straße", "country": "Germany", "homepage": "https://www.fz-juelich.de"}}' http://127.0.0.1:8000/contacts/organisations/
+curl -X POST -H "Content-Type:application/json" -d '{"organisation": {"name": "FZJ2", "longname": "Forschungszentrum Test", "kind": "Research", "city": "Jülich", "postcode": "52425", "street_address": "Wilhelm-Johnen-Straße", "country": "Germany", "homepage": "https://www.fz-juelich.de"}}' http://127.0.0.1:8000/contacts/organisations/
curl http://127.0.0.1:8000/contacts/persons/
curl http://127.0.0.1:8000/contacts/persons/id/3
curl http://127.0.0.1:8000/contacts/persons/id/99
@@ -25,12 +25,8 @@ curl http://127.0.0.1:8000/stationmeta_core/China11
curl http://127.0.0.1:8000/stationmeta/China11
# station upload without nested fields
curl -X POST -H "Content-Type:application/json" -d '{"stationmeta": {"codes":["ttt3","ttt4"],"name":"Test_China","coordinates":{"lat":36.256,"lng":17.106,"alt":1534.0},"country":"China","state":"Shandong Sheng","coordinate_validation_status":0,"coordinate_validation_date":"2020-03-11T12:22:18.047974+01:00","type_of_environment":0,"type_of_area":0,"category":"","timezone":"", "coordinate_validator_id": 1, "additional_metadata":"{}"}}' "http://127.0.0.1:8000/stationmeta/"
-# nested upload with enum fields
-curl -X POST -H "Content-Type:application/json" -d '{"stationmeta": {"codes":["ttt3","ttt4"],"name":"Test_China","coordinates":{"lat":36.256,"lng":17.106,"alt":1534.0},"country":"China","state":"Shandong Sheng","coordinate_validation_status":0,"coordinate_validation_date":"2020-03-11T12:22:18.047974+01:00","type_of_environment":0,"type_of_area":0,"category":"","timezone":"", "coordinate_validator_id": 1, "additional_metadata":"{}", roles": [{"role": 0, "person_id": 3, "status": 0},{"role": 1, "person_id": 3, "status": 0}]}}' "http://127.0.0.1:8000/stationmeta/"
-# nested upload including 'global' (not defining all metadata -- getting the rest from default values)
-curl -X POST -H "Content-Type:application/json" -d '{"stationmeta": {"codes":["ttt58"],"name":"Ttt_China58","coordiShandong Sheng","coordinate_validation_status":0,"coordinate_validation_date":"2020-03-11T12:22:18.047974+01:00","type_of_environment":0,"type_of_area":0,"category":"","timezone":"", "coordinate_validator_id": 1, "additional_metadata":"{}", "roles": [{"role": 0, "person_id": 3, "status": 0},{"role": 1, "person_id": 3, "status": 0}], "globalmeta": {"climatic_zone":1}}}' http://127.0.0.1:8000/stationmeta/
-# TBD: (nested) upload with human readable fields
-curl -X POST -H "Content-Type:application/json" -d '{"stationmeta": {"codes":["ttt3","ttt4"],"name":"Test_China","coordinates":{"lat":36.256,"lng":17.106,"alt":1534.0},"country":"China","state":"Shandong Sheng","coordinate_validation_status":0,"coordinate_validation_date":"2020-03-11T12:22:18.047974+01:00","type_of_environment":0,"type_of_area":0,"category":"","timezone":"", "coordinate_validator_id": 1, "additional_metadata":"{}", "roles": [{"role": "PointOfContact", "person": "s.schroeder@fz-juelich.de", "status": "active"},{"role": "Originator", "person": "Stefan.Feigenspan@uba.de", "status": "active"}]}}' "http://127.0.0.1:8000/stationmeta/"
+# (nested) upload including 'global' (not defining all metadata -- getting the rest from default values) with human readable fields
+curl -X POST -H "Content-Type:application/json" -d '{"stationmeta": {"codes":["ttt71"],"name":"Ttt_China71","coordinates":{"lat":36.256,"lng":17.106,"alt":1534.0},"country":"China","state":"Shandong Sheng","coordinate_validation_status":0,"coordinate_validation_date":"2020-03-11T12:22:18.047974+01:00","type_of_environment":0,"type_of_area":0,"category":"","timezone":"", "coordinate_validator_id": 1, "additional_metadata":"{}", "roles": [{"role": 0, "person_id": 3, "status": 0},{"role": 1, "person_id": 3, "status": 0}], "globalmeta": {"climatic_zone": "WarmTemperateMoist"}}}' http://127.0.0.1:8000/stationmeta/
curl http://127.0.0.1:8000/timeseries/
curl http://127.0.0.1:8000/timeseries/2
diff --git a/toardb/contacts/crud.py b/toardb/contacts/crud.py
index 5ce94f69ff62d5826d6e1baba64219bf280568ea..6fbbda776a722ada56a0082ac01799d4e20a0d4b 100644
--- a/toardb/contacts/crud.py
+++ b/toardb/contacts/crud.py
@@ -7,7 +7,9 @@ Create, Read, Update, Delete functionality
from sqlalchemy.orm import Session
from fastapi.responses import JSONResponse
from . import models
+from .models import OK_enum
from .schemas import PersonCreate, OrganisationCreate
+from toardb.utils.utils import get_value_from_str
def get_organisation(db: Session, organisation_id: int):
@@ -23,6 +25,7 @@ def get_organisation_by_name(db: Session, name: str):
def create_organisation(db: Session, organisation: OrganisationCreate):
db_organisation = models.Organisation(**organisation.dict())
+ db_organisation.kind = get_value_from_str(db,OK_enum,db_organisation.kind)
db.add(db_organisation)
result = db.commit()
db.refresh(db_organisation)
diff --git a/toardb/contacts/models.py b/toardb/contacts/models.py
index f863c1a218f89603eeec066d5b186a58b16ce35c..b112305a2c44d765e43c54c5e6af1aaf56a23ff9 100644
--- a/toardb/contacts/models.py
+++ b/toardb/contacts/models.py
@@ -4,3 +4,16 @@ from toardb.base import Base
from .models_person import Person
from .models_organisation import Organisation
+from sqlalchemy import Table, Column, Integer, String
+from sqlalchemy.ext.declarative import declarative_base
+
+# controlled vocabulary
+
+# Kind of Organizations
+OK_enum = Table("ok_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+ )
+
diff --git a/toardb/contacts/schemas.py b/toardb/contacts/schemas.py
index 39a50249d95c3646da7dda998d29dfc59d4eaedd..91ab7dc1e682202f66e0bda0f7d21ad8353a28c3 100644
--- a/toardb/contacts/schemas.py
+++ b/toardb/contacts/schemas.py
@@ -11,7 +11,7 @@ class OrganisationBase(BaseModel):
id: int = None
name: str
longname: str
- kind: int
+ kind: str
city: str
postcode: str
street_address: str
diff --git a/toardb/generic/__init__.py b/toardb/generic/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/toardb/generic/models.py b/toardb/generic/models.py
new file mode 100644
index 0000000000000000000000000000000000000000..51101e039345efe4e67b835ad2fdfb708c488869
--- /dev/null
+++ b/toardb/generic/models.py
@@ -0,0 +1,23 @@
+from sqlalchemy import Table, Column, Integer, String
+from sqlalchemy.ext.declarative import declarative_base
+
+from toardb.base import Base
+
+# controlled vocabulary
+
+# Role Status
+RS_enum = Table("rs_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+ )
+
+# Role Codes
+RC_enum = Table("rc_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+ )
+
diff --git a/toardb/stationmeta/crud.py b/toardb/stationmeta/crud.py
index 6afe64c32ba2da3b478edf2ee2b53d700a48fbdc..122939bbbf994ef0179d4bcda69a72e9ecf9ea94 100644
--- a/toardb/stationmeta/crud.py
+++ b/toardb/stationmeta/crud.py
@@ -13,9 +13,12 @@ from fastapi import File, UploadFile
from fastapi.responses import JSONResponse
from fastapi.encoders import jsonable_encoder
from . import models
-from .models import stationmeta_core_stationmeta_roles_table, stationmeta_core_stationmeta_annotations_table
+from .models import stationmeta_core_stationmeta_roles_table, stationmeta_core_stationmeta_annotations_table, \
+ CZ_enum
+from toardb.generic.models import RS_enum, RC_enum
from .schemas import get_coordinates_from_geom, get_geom_from_coordinates, StationmetaCreate, Coordinates
from pydantic import ValidationError
+from toardb.utils.utils import get_value_from_str
def get_stationmeta_core(db: Session, station_code: str):
@@ -96,9 +99,10 @@ def create_stationmeta(db: Session, stationmeta: StationmetaCreate):
stationmeta_core_id = db_stationmeta.id
# store roles and update association table
if roles_data:
- print("====roles_data============", roles_data)
for r in roles_data:
db_role = models.StationmetaRole(**r)
+ db_role.role = get_value_from_str(db,RC_enum,db_role.role)
+ db_role.status = get_value_from_str(db,RS_enum,db_role.status)
# check whether role is already present in database
db_object = get_unique_stationmeta_role(db, db_role.role, db_role.person_id, db_role.status)
if db_object:
@@ -152,6 +156,8 @@ def create_stationmeta(db: Session, stationmeta: StationmetaCreate):
# store globalmeta
if globalmeta_data:
db_global = models.StationmetaGlobal(**globalmeta_data)
+ if db_global.climatic_zone:
+ db_global.climatic_zone = get_value_from_str(db,CZ_enum,db_global.climatic_zone)
db_global.station_id = stationmeta_core_id
db.add(db_global)
db.commit()
diff --git a/toardb/stationmeta/models.py b/toardb/stationmeta/models.py
index 7a674c37920dab8e18df1c4b3600be4336e5315c..8110560521db69836878d930833dd7a6b793f25c 100644
--- a/toardb/stationmeta/models.py
+++ b/toardb/stationmeta/models.py
@@ -27,3 +27,51 @@ CV_enum = Table("cv_vocabulary",
Column("enum_display_str", String)
)
+# Station Types
+ST_enum = Table("st_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
+# Station Types of Area
+TA_enum = Table("ta_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
+# Station TOAR Categories
+TC_enum = Table("tc_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
+# Station HTAP Regions (TIER1)
+TR_enum = Table("tr_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
+# Station Dominant Landcover Types
+DL_enum = Table("dl_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
+# Result Types
+RT_enum = Table("rt_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+)
+
diff --git a/toardb/stationmeta/schemas.py b/toardb/stationmeta/schemas.py
index 0d65a3a392e5902921dcb5f99fda616368f6e823..6faad6e63e1436ecabb33e86a69e7b5cfef65d22 100644
--- a/toardb/stationmeta/schemas.py
+++ b/toardb/stationmeta/schemas.py
@@ -151,7 +151,7 @@ class StationmetaGlobalBase(BaseModel):
id: int = None
population_density_year2010: float
max_population_density_25km_year2010: float
- climatic_zone: int
+ climatic_zone: str
nightlight_1km_year2013: float
nightlight_5km_year2013: float
max_nightlight_25km_year2013: float
@@ -183,7 +183,7 @@ class StationmetaGlobalBaseNested(BaseModel):
id: int = None
population_density_year2010: float = None
max_population_density_25km_year2010: float = None
- climatic_zone: int = None
+ climatic_zone: str = None
nightlight_1km_year2013: float = None
nightlight_5km_year2013: float = None
max_nightlight_25km_year2013: float = None
diff --git a/toardb/timeseries/crud.py b/toardb/timeseries/crud.py
index d8fd17e7ec3467339a9d20038f434a083d60851f..1d8324d777702c5a9d8ec27ac4ff5f3dc2a6ba8c 100644
--- a/toardb/timeseries/crud.py
+++ b/toardb/timeseries/crud.py
@@ -8,9 +8,11 @@ from sqlalchemy import insert
from sqlalchemy.orm import Session
from fastapi.responses import JSONResponse
from . import models
-from .models import RS_enum, RC_enum, timeseries_timeseries_roles_table, \
+from .models import timeseries_timeseries_roles_table, \
timeseries_timeseries_annotations_table, timeseries_timeseries_programmes_table
+from toardb.generic.models import RS_enum, RC_enum
from .schemas import TimeseriesCreate
+from toardb.utils.utils import get_value_from_str
def get_timeseries(db: Session, timeseries_id: int):
@@ -73,17 +75,7 @@ def get_unique_timeseries_annotation(db: Session, text: str, contributor_id: int
return db_object
-def __get_status_enum(db: Session):
- return db.query(RS_enum).all()
-
-
-def __get_role_enum(db: Session):
- return db.query(RC_enum).all()
-
-
def create_timeseries(db: Session, timeseries: TimeseriesCreate):
- enum_RS = __get_status_enum(db)
- enum_RC = __get_role_enum(db)
timeseries_dict = timeseries.dict()
roles_data = timeseries_dict.pop('roles', None)
annotations_data = timeseries_dict.pop('annotations', None)
@@ -98,6 +90,8 @@ def create_timeseries(db: Session, timeseries: TimeseriesCreate):
if roles_data:
for r in roles_data:
db_role = models.TimeseriesRole(**r)
+ db_role.role = get_value_from_str(db,RC_enum,db_role.role)
+ db_role.status = get_value_from_str(db,RS_enum,db_role.status)
# check whether role is already present in database
db_object = get_unique_timeseries_role(db, db_role.role, db_role.person_id, db_role.status)
if db_object:
diff --git a/toardb/timeseries/models.py b/toardb/timeseries/models.py
index 4314698276028f5c6703ebfb1b9fed037f5d1cbe..2e9bf7ed3196c2ba88428b66ed429d4a5da32529 100644
--- a/toardb/timeseries/models.py
+++ b/toardb/timeseries/models.py
@@ -4,17 +4,37 @@ from .models_annotation import TimeseriesAnnotation, timeseries_timeseries_annot
from .models_programme import TimeseriesProgramme, timeseries_timeseries_programmes_table
from toardb.base import Base
-from sqlalchemy import Table, String, Column, ForeignKey, Integer
+from sqlalchemy import Table, Column, Integer, String
+from sqlalchemy.ext.declarative import declarative_base
# controlled vocabulary
-RS_enum = Table("rs_vocabulary",
+
+# Data Access Rights
+DA_enum = Table("da_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+ )
+
+# Sampling Frequencies
+SF_enum = Table("sf_vocabulary",
+ Base.metadata,
+ Column("enum_val", Integer, primary_key=True),
+ Column("enum_str", String),
+ Column("enum_display_str", String)
+ )
+
+# Aggregation Types
+AT_enum = Table("at_vocabulary",
Base.metadata,
Column("enum_val", Integer, primary_key=True),
Column("enum_str", String),
Column("enum_display_str", String)
)
-RC_enum = Table("rc_vocabulary",
+# Data Sources
+DS_enum = Table("ds_vocabulary",
Base.metadata,
Column("enum_val", Integer, primary_key=True),
Column("enum_str", String),
diff --git a/toardb/timeseries/schemas.py b/toardb/timeseries/schemas.py
index 0a21ebea5caa4d211732992ecffb8d476ddb4cb4..75fd67149a469813080c164a415acc97756697ab 100644
--- a/toardb/timeseries/schemas.py
+++ b/toardb/timeseries/schemas.py
@@ -43,8 +43,8 @@ class TimeseriesCore(TimeseriesCoreBase):
class TimeseriesRoleBase(BaseModel):
id: int = None
- role: int
- status: int
+ role: str
+ status: str
person_id: int
class TimeseriesRoleCreate(TimeseriesRoleBase):
diff --git a/toardb/utils/utils.py b/toardb/utils/utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..b933c05c73f21b1a3aff47bfbf11a14cb70b9dc8
--- /dev/null
+++ b/toardb/utils/utils.py
@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+"""
+Helper functions for TOAR database
+
+"""
+from sqlalchemy import Table
+from sqlalchemy.orm import Session
+from collections import namedtuple
+
+# get the controlled vocabulary from table
+def __get_enum_dict(db: Session, table: Table):
+ Enumdict=namedtuple("Dict",["value","string","display_str"])
+ enum_dict = []
+ for entry in db.query(table).all():
+ enum_dict.append(Enumdict(*entry))
+ return enum_dict
+
+# function to return code for given value
+def get_str_from_value(db: Session, table: Table, value: int) -> str:
+ enum_error = "Invalid " + table.name
+ enum_dict = __get_enum_dict(db, table)
+ enum_entry = tuple(filter(lambda x: x.value == value, enum_dict))
+ return enum_entry[0].string
+
+ raise ValueError(enum_error)
+
+# function to return value for given code
+def get_value_from_str(db: Session, table: Table, string: str) -> int:
+ enum_error = "Invalid " + table.name
+ enum_dict = __get_enum_dict(db, table)
+ enum_entry = tuple(filter(lambda x: x.string == string, enum_dict))
+ return enum_entry[0].value
+
+ raise ValueError(enum_error)