From 4331b49f2cf2aea061ceaaf2159dacaa3700e660 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sabine=20Schr=C3=B6der?= <s.schroeder@fz-juelich.de>
Date: Thu, 13 Aug 2020 17:09:18 +0200
Subject: [PATCH] #4: bug fix done for nested stationmeta (inside timeseries
record); still left to do: clean up of code and adapting pytests
---
toardb/stationmeta/models_role.py | 1 +
toardb/stationmeta/schemas.py | 16 +++++-----------
toardb/timeseries/crud.py | 10 ++++++++++
toardb/timeseries/models_core.py | 2 +-
toardb/timeseries/schemas.py | 20 +++++++-------------
5 files changed, 24 insertions(+), 25 deletions(-)
diff --git a/toardb/stationmeta/models_role.py b/toardb/stationmeta/models_role.py
index ced78b8..7d367e1 100644
--- a/toardb/stationmeta/models_role.py
+++ b/toardb/stationmeta/models_role.py
@@ -57,6 +57,7 @@ class StationmetaRole(Base):
# use the explicit class name here,
# see: https://groups.google.com/forum/#!topic/sqlalchemy/YjGhE4d6K4U
contact_id = Column(ForeignKey(Contact.id, deferrable=True, initially='DEFERRED'), nullable=False, index=True)
+ contact = relationship(Contact)
station = relationship("StationmetaCore",
secondary=stationmeta_core_stationmeta_roles_table,
diff --git a/toardb/stationmeta/schemas.py b/toardb/stationmeta/schemas.py
index d70c842..7bc9314 100644
--- a/toardb/stationmeta/schemas.py
+++ b/toardb/stationmeta/schemas.py
@@ -4,7 +4,7 @@ Pydantic schemas for TOAR database
"""
-from typing import List
+from typing import List, Dict
from pydantic import BaseModel, Field, BaseConfig, Json, validator
from geoalchemy2 import WKTElement
from geoalchemy2.shape import to_shape
@@ -12,7 +12,7 @@ import datetime as dt
from .models import CZ_enum, CV_enum, ST_enum, TA_enum, TC_enum, \
TR_enum, DL_enum
from toardb.generic.models import RC_enum, RS_enum
-from toardb.contacts.models import Contact
+from toardb.contacts.schemas import Contact
# the following class was taken from:
@@ -24,11 +24,6 @@ class Coordinates(BaseModel):
# ======== StationmetaCore =========
-class StationmetaCoreStub(BaseModel):
- id: int = None
- name: str
-
-
class StationmetaCoreBase(BaseModel):
id: int = None
codes: List[str] = Field(..., description="list of station's codes")
@@ -38,15 +33,14 @@ class StationmetaCoreBase(BaseModel):
state: str
coordinate_validation_status: str
coordinate_validation_date: dt.datetime
+ coordinate_validator_id: int
type_of_environment: str
type_of_area: str
timezone: str
additional_metadata: Json
- coordinate_validator_id: int
class Config(BaseConfig):
orm_mode = True
-# arbitrary_types_allowed = True
@validator('coordinate_validation_status')
def check_coordinate_validation_status(cls, v):
@@ -322,8 +316,7 @@ class StationmetaRoleBase(BaseModel):
id: int = None
role: str
status: str
-# contact: Contact
- contact_id: int
+ contact: Contact
@validator('role')
def check_role(cls, v):
@@ -357,6 +350,7 @@ class StationmetaRoleCreate(StationmetaRoleBase):
class StationmetaRole(StationmetaRoleBase):
id: int
+ contact: Contact
class Config:
orm_mode = True
diff --git a/toardb/timeseries/crud.py b/toardb/timeseries/crud.py
index b108b97..04dc438 100644
--- a/toardb/timeseries/crud.py
+++ b/toardb/timeseries/crud.py
@@ -11,6 +11,7 @@ from . import models
from .models import timeseries_timeseries_roles_table, \
timeseries_timeseries_annotations_table, \
DA_enum, SF_enum, AT_enum, DS_enum, MM_enum
+from toardb.stationmeta.schemas import get_coordinates_from_geom
from toardb.generic.models import RS_enum, RC_enum
from .schemas import TimeseriesCreate
from toardb.utils.utils import get_value_from_str, get_str_from_value
@@ -21,6 +22,9 @@ def get_timeseries(db: Session, timeseries_id: int):
# there is a mismatch with additional_metadata
if db_object:
db_object.additional_metadata = str(db_object.additional_metadata).replace("'",'"')
+ # there is also a mismatch with coordinates and additional_metadata from station object
+ db_object.station.coordinates = get_coordinates_from_geom(db_object.station.coordinates)
+ db_object.station.additional_metadata = str(db_object.station.additional_metadata).replace("'",'"')
return db_object
@@ -29,6 +33,9 @@ def get_all_timeseries(db: Session, skip : int = 0, limit: int = None):
for db_object in db_objects:
# there is a mismatch with additional_metadata
db_object.additional_metadata = str(db_object.additional_metadata).replace("'",'"')
+ # there is also a mismatch with coordinates and additional_metadata from station object
+ db_object.station.coordinates = get_coordinates_from_geom(db_object.station.coordinates)
+ db_object.station.additional_metadata = str(db_object.station.additional_metadata).replace("'",'"')
return db_objects
@@ -40,6 +47,9 @@ def get_timeseries_by_unique_constraints(db: Session, station_id: int, variable_
# there is a mismatch with additional_metadata
if db_object:
db_object.additional_metadata = str(db_object.additional_metadata).replace("'",'"')
+ # there is also a mismatch with coordinates and additional_metadata from station object
+ db_object.station.coordinates = get_coordinates_from_geom(db_object.station.coordinates)
+ db_object.station.additional_metadata = str(db_object.station.additional_metadata).replace("'",'"')
return db_object
diff --git a/toardb/timeseries/models_core.py b/toardb/timeseries/models_core.py
index ecd51e4..8a8b3d5 100644
--- a/toardb/timeseries/models_core.py
+++ b/toardb/timeseries/models_core.py
@@ -113,7 +113,7 @@ class Timeseries(Base):
# for the nested view
# problems with station and coordinates in nested views!!!
- station = relationship('StationmetaCore_WithoutCoords')
+ station = relationship('StationmetaCore')
variable = relationship('Variable')
programme = relationship('TimeseriesProgramme')
diff --git a/toardb/timeseries/schemas.py b/toardb/timeseries/schemas.py
index e2c4154..eb6fe0f 100644
--- a/toardb/timeseries/schemas.py
+++ b/toardb/timeseries/schemas.py
@@ -9,16 +9,15 @@ from typing import List, Any
from pydantic import BaseModel, Json, validator, Field
import datetime as dt
from toardb.generic.models import RS_enum, RC_enum
-from toardb.contacts.models import Contact
+from toardb.contacts.schemas import Contact
from .models import DA_enum, SF_enum, AT_enum, DS_enum, MM_enum
from toardb.variables.schemas import Variable
#from toardb.stationmeta.schemas import StationmetaCoreCreate
-#from toardb.stationmeta.schemas import StationmetaCoreBase
+from toardb.stationmeta.schemas import StationmetaCoreBase
#from toardb.stationmeta.schemas import StationmetaCore
#from toardb.stationmeta.schemas import StationmetaCreate
#from toardb.stationmeta.schemas import StationmetaBase
#from toardb.stationmeta.schemas import Stationmeta
-from toardb.stationmeta.schemas import StationmetaCoreStub
# ======== Timeseries =========
@@ -120,9 +119,7 @@ class TimeseriesRoleBase(BaseModel):
id: int = None
role: str
status: str
- contact_id: int # works
-# contact: Contact # does not work!
-# contact: Any # also works (but contact_id has to be extracted!)
+ contact: Contact
@validator('role')
def check_role(cls, v):
@@ -153,6 +150,7 @@ class TimeseriesRoleCreate(TimeseriesRoleBase):
class TimeseriesRole(TimeseriesRoleBase):
id: int
+ contact: Contact
class Config:
orm_mode = True
@@ -206,17 +204,13 @@ class TimeseriesBase(TimeseriesCoreBaseStub):
annotations: List[TimeseriesAnnotation] = None
variable: Variable
# station: StationmetaCoreCreate
-# station: StationmetaCoreBase
# station: StationmetaCore
# station: StationmetaCreate
# station: StationmetaBase
# station: Stationmeta
-# station: StationmetaCoreStub
-# None of the above is working for station
-# ==> therefore now go with Any!
-# (which means not showing human readable controlled vocabulary!)
-# ==> still to be investigated!
- station: Any
+# Try, which one of the above is wanted for station
+# The next one works:
+ station: StationmetaCoreBase
programme: TimeseriesProgramme
class Config:
--
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