diff --git a/toardb/contacts/crud.py b/toardb/contacts/crud.py
index 1e3e2cd9d682c0a1ab413086773381d4fdfacf42..16fef48b0ae22ce4b99a00787efbff5cbc48ae56 100644
--- a/toardb/contacts/crud.py
+++ b/toardb/contacts/crud.py
@@ -21,7 +21,7 @@ def get_all_organisations(db: Session, skip : int = 0, limit: int = None):
def get_organisation_by_name(db: Session, name: str):
- return db.query(models.Organisation).filter(models.Organisation.name == name).first()
+ return db.query(models.Organisation).filter(models.Organisation.name == name.upper()).first()
def create_organisation(db: Session, organisation: OrganisationCreate):
diff --git a/toardb/contacts/models.py b/toardb/contacts/models.py
index a3babb0972f40a94f2667c9c8ecd23e2db4421b5..cce5e27bdede16381263359820c64f6bb5f66dd3 100644
--- a/toardb/contacts/models.py
+++ b/toardb/contacts/models.py
@@ -29,11 +29,12 @@ Enumdict=namedtuple("Dict",["value","string","display_str"])
OK_enum = (
Enumdict(1, 'Government', 'government'),
Enumdict(2, 'Research', 'research'),
- Enumdict(3, 'International', 'international'),
- Enumdict(4, 'NonProfit', 'non-profit'),
- Enumdict(5, 'Commercial', 'commercial'),
- Enumdict(6, 'Individual', 'individual'),
- Enumdict(7, 'Other', 'other')
+ Enumdict(3, 'University', 'university'),
+ Enumdict(4, 'International', 'international'),
+ Enumdict(5, 'NonProfit', 'non-profit'),
+ Enumdict(6, 'Commercial', 'commercial'),
+ Enumdict(7, 'Individual', 'individual'),
+ Enumdict(8, 'Other', 'other')
)
CONTACTS_ID_SEQ = Sequence('contacts_id_seq') # define sequence explicitly
diff --git a/toardb/data/crud.py b/toardb/data/crud.py
index 7f7d1b07f3a7a60d8dde83a09c49f06984273ce4..c815174e01fe1a8701e45a7ff2a7545fe906ba9f 100644
--- a/toardb/data/crud.py
+++ b/toardb/data/crud.py
@@ -27,6 +27,7 @@ from io import StringIO
import csv
def get_data(db: Session, timeseries_id: int, format: str):
+ print("now in crud!")
data = db.query(models.Data).filter(models.Data.timeseries_id == timeseries_id).all()
if format == 'json':
return data
@@ -52,8 +53,8 @@ def get_data_by_datetime_and_timeseriesid(db: Session, datetime: dt.datetime, ti
return db.query(models.Data).filter([models.Data.datetime== datetime, models.Data.timeseries_id == timeseries_id]).first()
-def get_all_data(db: Session, skip : int = 0, limit: int = None):
- return db.query(models.Data).offset(skip).limit(limit).all()
+def get_all_data(db: Session, skip : int = 0, limit: int = 100):
+ return db.query(models.Data).limit(limit).all()
def create_data_record(db: Session, engine: Engine,
diff --git a/toardb/data/data.py b/toardb/data/data.py
index cffb54485c49d419461fa9f7e9ce4c1cccf8e6c1..275587b257c20260b8d88d15a7edd4309963a892 100644
--- a/toardb/data/data.py
+++ b/toardb/data/data.py
@@ -18,7 +18,7 @@ router = APIRouter()
#get all data of table data
@router.get('/data/', response_model=List[schemas.Data])
-def get_all_data(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
+def get_all_data(skip: int = 0, limit: int = 100, db: Session = Depends(get_db)):
data = crud.get_all_data(db, skip=skip, limit=limit)
return data
@@ -30,6 +30,15 @@ def get_data(timeseries_id: int, format: str = 'json', db: Session = Depends(get
raise HTTPException(status_code=404, detail="Data not found.")
return db_data
+#get all data of one timeseries
+@router.get('/data/id/{timeseries_id}', response_model=List[schemas.Data])
+def get_data2(timeseries_id: int, format: str = 'json', db: Session = Depends(get_db)):
+ print("in data.py!")
+ db_data = crud.get_data(db, timeseries_id=timeseries_id, format=format)
+ if db_data is None:
+ raise HTTPException(status_code=404, detail="Data not found.")
+ return db_data
+
#some more gets to be tested:
# - get all data of one special timestamp
# - get all data of one special timestamp and timeseries
diff --git a/toardb/stationmeta/crud.py b/toardb/stationmeta/crud.py
index f1a153fd06b21f5d931af988b8e2e236c70dbf4f..e4147238e14d71635cedbb8e733045c40cf81e3e 100644
--- a/toardb/stationmeta/crud.py
+++ b/toardb/stationmeta/crud.py
@@ -43,6 +43,16 @@ def get_stationmeta(db: Session, station_code: str):
return db_object
+def get_stationmeta_by_id(db: Session, station_id: int):
+ db_object = db.query(models.StationmetaCore).filter(models.StationmetaCore.id == station_id).first()
+ # there is a mismatch with coordinates and additional_metadata
+ if db_object:
+ if isinstance(db_object.coordinates, (WKBElement, WKTElement)):
+ db_object.coordinates = get_coordinates_from_geom(db_object.coordinates)
+ db_object.additional_metadata = str(db_object.additional_metadata).replace("'",'"')
+ return db_object
+
+
def get_all_stationmeta_core(db: Session, skip : int = 0, limit: int = None):
db_objects = db.query(models.StationmetaCore).offset(skip).limit(limit).all()
for db_object in db_objects:
diff --git a/toardb/stationmeta/stationmeta.py b/toardb/stationmeta/stationmeta.py
index ec7f50df79341c096967c2eb52b67d06a947564b..cdf5ccce21722747152f906758aa307ad66cddf6 100644
--- a/toardb/stationmeta/stationmeta.py
+++ b/toardb/stationmeta/stationmeta.py
@@ -31,7 +31,7 @@ def get_all_stationmeta(skip: int = 0, limit: int = None, db: Session = Depends(
def get_stationmeta_core(station_code: str, db: Session = Depends(get_db)):
db_stationmeta_core = crud.get_stationmeta_core(db, station_code=station_code)
if db_stationmeta_core is None:
- raise HTTPException(status_code=404, detail="Data not found.")
+ raise HTTPException(status_code=404, detail=f"Metadata for station '{station_code}' not found.")
return db_stationmeta_core
# the same as above, but nested view
@@ -40,7 +40,15 @@ def get_stationmeta_core(station_code: str, db: Session = Depends(get_db)):
def get_stationmeta(station_code: str, db: Session = Depends(get_db)):
db_stationmeta = crud.get_stationmeta(db, station_code=station_code)
if db_stationmeta is None:
- raise HTTPException(status_code=404, detail="Data not found.")
+ raise HTTPException(status_code=404, detail=f"Metadata for station '{station_code}' not found.")
+ return db_stationmeta
+
+#get all core metadata of one station (given its ID)
+@router.get('/stationmeta/id/{station_id}', response_model=schemas.Stationmeta)
+def get_stationmeta_by_id(station_id: int, db: Session = Depends(get_db)):
+ db_stationmeta = crud.get_stationmeta_by_id(db, station_id=station_id)
+ if db_stationmeta is None:
+ raise HTTPException(status_code=404, detail=f"Metadata for station with ID '{station_id}' not found.")
return db_stationmeta
@router.get('/stationmeta_changelog/{station_id}', response_model=List[schemas.StationmetaChangelog])
diff --git a/toardb/timeseries/models_core.py b/toardb/timeseries/models_core.py
index 691f2c42848d5aa1d257b5b66231bf8f64557757..ea095e3c079ae18b0b0e85ed90a2c9a6600603c9 100644
--- a/toardb/timeseries/models_core.py
+++ b/toardb/timeseries/models_core.py
@@ -101,7 +101,6 @@ class Timeseries(Base):
data_end_date = Column(DateTime(True), nullable=False)
measurement_method = Column(ForeignKey('mm_vocabulary.enum_val'), nullable=False, server_default=text("1"))
sampling_height = Column(Float(53), nullable=False)
- additional_metadata = Column(JSONB(astext_type=Text()), nullable=True)
date_added = Column(DateTime(True), nullable=False, server_default=text("now()"))
date_modified = Column(DateTime(True), nullable=False, server_default=text("now()"))
# do not use string declaration here (not working for pytest)
@@ -118,6 +117,8 @@ class Timeseries(Base):
programme = relationship('TimeseriesProgramme')
changelog = relationship('TimeseriesChangelog')
+ additional_metadata = Column(JSONB(astext_type=Text()), nullable=True)
+
# da_vocabulary = relationship('DaVocabulary')
# at_vocabulary = relationship('AtVocabulary')
# mm_vocabulary = relationship('MmVocabulary')
diff --git a/toardb/timeseries/schemas.py b/toardb/timeseries/schemas.py
index 8cae379d4b01e8815a03b52b6a80a1e0b985834c..649495adef6acd34baa491999cfe99a14c856d7d 100644
--- a/toardb/timeseries/schemas.py
+++ b/toardb/timeseries/schemas.py
@@ -21,7 +21,7 @@ from toardb.stationmeta.schemas import StationmetaCoreBase
# ======== Timeseries =========
-class TimeseriesCoreBaseStub(BaseModel):
+class TimeseriesCoreBase(BaseModel):
id: int = None
label: str = Field(..., description="a short string to distinguish this timeseries from others with the same combination of station and variable")
order: int = Field(..., description="indicates position of this timeseries in a list when several timeseries share the same station and variable combination")
@@ -62,12 +62,6 @@ class TimeseriesCoreBaseStub(BaseModel):
return tuple(filter(lambda x: x.value == int(v), MM_enum))[0].string
-class TimeseriesCoreBase(TimeseriesCoreBaseStub):
- station_id: int
- variable_id: int
- programme_id: int = None
-
-
class TimeseriesCoreCreate(TimeseriesCoreBase):
pass
@@ -236,10 +230,26 @@ class TimeseriesChangelog(TimeseriesChangelogBase):
# ======== for nested view/upload =========
-class TimeseriesBase(TimeseriesCoreBaseStub):
+class TimeseriesBase(TimeseriesCoreBase):
+ label: str
+ order: int
+ access_rights: str
+ sampling_frequency: str
+ aggregation: str
+ source: str
+ data_start_date: dt.datetime
+ data_end_date: dt.datetime
+ measurement_method: str
+ sampling_height: float
+ date_added: dt.datetime
+ date_modified: dt.datetime
+ station: StationmetaCoreBase
+ variable: Variable
+ programme: TimeseriesProgramme
+ additional_metadata: Json
roles: List[TimeseriesRole] = None
annotations: List[TimeseriesAnnotation] = None
- variable: Variable
+ changelog: List[TimeseriesChangelog] = None
# station: StationmetaCoreCreate
# station: StationmetaCore
# station: StationmetaCreate
@@ -247,9 +257,6 @@ class TimeseriesBase(TimeseriesCoreBaseStub):
# station: Stationmeta
# Try, which one of the above is wanted for station
# The next one works:
- station: StationmetaCoreBase
- programme: TimeseriesProgramme
- changelog: List[TimeseriesChangelog] = None
class Config:
orm_mode = True
@@ -268,7 +275,6 @@ class TimeseriesPatch(BaseModel):
sampling_height: float = None
date_added: dt.datetime = None
date_modified: dt.datetime = None
- additional_metadata: Json = None
# roles: List[TimeseriesRole] = None
# annotations: List[TimeseriesAnnotation] = None
# variable: Variable = None
@@ -277,6 +283,7 @@ class TimeseriesPatch(BaseModel):
station_id: int = None
variable_id: int = None
programme_id: int = None
+ additional_metadata: Json = None
class Config:
orm_mode = True
diff --git a/toardb/timeseries/timeseries.py b/toardb/timeseries/timeseries.py
index d8d569a920f7e43c58a083e46a020d0631570ffd..83a7b9180c7b1bef34680c1065b7da7c15a01f4e 100644
--- a/toardb/timeseries/timeseries.py
+++ b/toardb/timeseries/timeseries.py
@@ -28,6 +28,14 @@ def get_timeseries(timeseries_id: int, db: Session = Depends(get_db)):
raise HTTPException(status_code=404, detail="Timeseries not found.")
return db_timeseries
+#get all metadata of one timeseries (known its ID)
+@router.get('/timeseries/id/{timeseries_id}', response_model=schemas.Timeseries)
+def get_timeseries2(timeseries_id: int, db: Session = Depends(get_db)):
+ db_timeseries = crud.get_timeseries(db, timeseries_id=timeseries_id)
+ if db_timeseries is None:
+ raise HTTPException(status_code=404, detail="Timeseries not found.")
+ return db_timeseries
+
#get all metadata of one timeseries (known its unique label)
@router.get('/timeseries/unique/', response_model=schemas.Timeseries)
def get_timeseries(station_id: int, variable_id: int, resource_provider: str , label: str='', db: Session = Depends(get_db)):
diff --git a/toardb/toardb.py b/toardb/toardb.py
index 92f6893abf3a89a185b3bcb9ce23782d55fe4815..4b5840e840b96c44ab514687ec08acef16d1fa9e 100644
--- a/toardb/toardb.py
+++ b/toardb/toardb.py
@@ -4,6 +4,7 @@ Simple test API for variable management
from typing import List
from fastapi import FastAPI, Depends, HTTPException, APIRouter
+from fastapi.responses import JSONResponse
from sqlalchemy.orm import Session
from toardb.utils.database import ToarDbSession, engine
@@ -33,6 +34,8 @@ async def info():
"Measurement Methods": settings.MM_vocab,
"Climatic Zones": settings.CZ_vocab,
"Coordinate Validity": settings.CV_vocab,
+ "Countries": settings.CN_vocab,
+ "Timezones": settings.TZ_vocab,
"Station Types": settings.ST_vocab,
"Station Type of Area": settings.TA_vocab,
"Station TOAR Categories": settings.TC_vocab,
@@ -47,27 +50,34 @@ async def info():
@app.get("/controlled_vocabulary/{name}")
async def info(name: str):
controlled_vocabulary = {
- "Role Codes": settings.RC_vocab,
- "Role Status": settings.RS_vocab,
- "Kind of Annotations": settings.AK_vocab,
- "Kind of Organizations": settings.OK_vocab,
- "Data Access Rights": settings.DA_vocab,
- "Sampling Frequencies": settings.SF_vocab,
- "Aggregation Types": settings.AT_vocab,
- "Data Sources": settings.DS_vocab,
- "Measurement Methods": settings.MM_vocab,
- "Climatic Zones": settings.CZ_vocab,
- "Coordinate Validity": settings.CV_vocab,
- "Station Types": settings.ST_vocab,
- "Station Type of Area": settings.TA_vocab,
- "Station TOAR Categories": settings.TC_vocab,
- "Station HTAP Regions": settings.TR_vocab,
- "Station Dominant Landcover Types": settings.DL_vocab,
- "Result Types": settings.RT_vocab,
- "Data Flags": settings.DF_vocab,
- "Type of Change": settings.CL_vocab,
+ "role codes": settings.RC_vocab,
+ "role status": settings.RS_vocab,
+ "kind of ANnotations": settings.AK_vocab,
+ "kind of organizations": settings.OK_vocab,
+ "data access rights": settings.DA_vocab,
+ "sampling frequencies": settings.SF_vocab,
+ "aggregation types": settings.AT_vocab,
+ "data sources": settings.DS_vocab,
+ "measurement methods": settings.MM_vocab,
+ "climatic zones": settings.CZ_vocab,
+ "coordinate validity": settings.CV_vocab,
+ "countries": settings.CN_vocab,
+ "timezones": settings.TZ_vocab,
+ "station types": settings.ST_vocab,
+ "station type of Area": settings.TA_vocab,
+ "station tOAR Categories": settings.TC_vocab,
+ "station hTAP Regions": settings.TR_vocab,
+ "station dominant Landcover Types": settings.DL_vocab,
+ "result types": settings.RT_vocab,
+ "data flags": settings.DF_vocab,
+ "type of change": settings.CL_vocab,
}
- return controlled_vocabulary[name]
+ if name.lower() in controlled_vocabulary.keys():
+ return controlled_vocabulary[name.lower()]
+ else:
+ status_code=200
+ message = f"No controlled vocabulary found for '{name}'"
+ return JSONResponse(status_code=status_code, content=message)
db_stats= {
"users": 358,
@@ -130,6 +140,8 @@ async def startup_event():
MM_vocabulary = __get_enum_dict(fake_cur, "mm_vocabulary")
CZ_vocabulary = __get_enum_dict(fake_cur, "cz_vocabulary")
CV_vocabulary = __get_enum_dict(fake_cur, "cv_vocabulary")
+ CN_vocabulary = __get_enum_dict(fake_cur, "cn_vocabulary")
+ TZ_vocabulary = __get_enum_dict(fake_cur, "tz_vocabulary")
ST_vocabulary = __get_enum_dict(fake_cur, "st_vocabulary")
TA_vocabulary = __get_enum_dict(fake_cur, "ta_vocabulary")
TC_vocabulary = __get_enum_dict(fake_cur, "tc_vocabulary")
@@ -154,6 +166,8 @@ DS_vocabulary = __get_enum_dict(fake_cur, "ds_vocabulary")
MM_vocabulary = __get_enum_dict(fake_cur, "mm_vocabulary")
CZ_vocabulary = __get_enum_dict(fake_cur, "cz_vocabulary")
CV_vocabulary = __get_enum_dict(fake_cur, "cv_vocabulary")
+CN_vocabulary = __get_enum_dict(fake_cur, "cn_vocabulary")
+TZ_vocabulary = __get_enum_dict(fake_cur, "tz_vocabulary")
ST_vocabulary = __get_enum_dict(fake_cur, "st_vocabulary")
TA_vocabulary = __get_enum_dict(fake_cur, "ta_vocabulary")
TC_vocabulary = __get_enum_dict(fake_cur, "tc_vocabulary")
@@ -177,6 +191,8 @@ class Settings(BaseSettings):
MM_vocab = MM_vocabulary
CZ_vocab = CZ_vocabulary
CV_vocab = CV_vocabulary
+ CN_vocab = CN_vocabulary
+ TZ_vocab = TZ_vocabulary
ST_vocab = ST_vocabulary
TA_vocab = TA_vocabulary
TC_vocab = TC_vocabulary