From 07610f448c08a369eaf17bff12ec162e7015129e Mon Sep 17 00:00:00 2001
From: schroeder5 <s.schroeder@fz-juelich.de>
Date: Fri, 29 May 2020 20:05:40 +0200
Subject: [PATCH] created ONE toardb app, also adapted pytests for toardb app
(still very last test will throw an error for teardown; inserted example for
url percent encoding
---
production_tests.sh | 8 ++---
{auth_user => toardb}/__init__.py | 0
{auth_user => toardb/auth_user}/README.md | 0
{contacts => toardb/auth_user}/__init__.py | 0
{auth_user => toardb/auth_user}/auth_user.py | 0
.../auth_user}/fixtures/auth.json | 0
.../auth_user}/fixtures/authtoken.json | 0
{auth_user => toardb/auth_user}/models.py | 0
{auth_user => toardb/auth_user}/schemas.py | 0
{data => toardb/contacts}/__init__.py | 0
{contacts => toardb/contacts}/contacts.py | 23 +++++++------
{contacts => toardb/contacts}/crud.py | 0
.../contacts}/fixtures/organisations.json | 0
.../contacts}/fixtures/persons.json | 0
{contacts => toardb/contacts}/models.py | 0
.../contacts}/models_organisation.py | 0
.../contacts}/models_person.py | 0
{contacts => toardb/contacts}/schemas.py | 0
{contacts => toardb/contacts}/test_base.py | 5 +--
.../contacts}/test_contacts.py | 4 +--
{stationmeta => toardb/data}/__init__.py | 0
{data => toardb/data}/crud.py | 10 +++---
{data => toardb/data}/data.py | 12 +++----
{data => toardb/data}/models.py | 0
{data => toardb/data}/schemas.py | 0
.../stationmeta}/__init__.py | 0
{stationmeta => toardb/stationmeta}/crud.py | 0
.../fixtures/stationmeta_core.json | 0
{stationmeta => toardb/stationmeta}/models.py | 0
.../stationmeta}/models_annotation.py | 2 +-
.../stationmeta}/models_aux.py | 0
.../stationmeta}/models_core.py | 2 +-
.../stationmeta}/models_global.py | 0
.../stationmeta}/models_global_services.py | 0
.../stationmeta}/models_role.py | 2 +-
.../stationmeta}/pydantic_toar_testing.py | 0
.../stationmeta}/schemas.py | 0
.../stationmeta}/stationmeta.py | 12 +++----
.../stationmeta}/test_base.py | 9 ++---
.../stationmeta}/test_stationmeta.py | 12 +++----
{utils => toardb/timeseries}/__init__.py | 0
{timeseries => toardb/timeseries}/crud.py | 1 -
.../timeseries}/fixtures/timeseries.json | 0
{timeseries => toardb/timeseries}/models.py | 0
.../timeseries}/models_annotation.py | 2 +-
.../timeseries}/models_core.py | 4 +--
.../timeseries}/models_programme.py | 0
.../timeseries}/models_role.py | 2 +-
.../timeseries}/pydantic_toar_testing.py | 0
{timeseries => toardb/timeseries}/schemas.py | 0
.../timeseries}/test_base.py | 13 ++++----
.../timeseries}/test_timeseries.py | 22 ++++++-------
.../timeseries}/timeseries.py | 15 +++++----
toardb/toardb.py | 33 +++++++++++++++++++
{variables => toardb/utils}/__init__.py | 0
{utils => toardb/utils}/database.py | 0
toardb/variables/__init__.py | 0
{variables => toardb/variables}/crud.py | 0
.../variables}/fixtures/variables.json | 0
{variables => toardb/variables}/models.py | 0
{variables => toardb/variables}/schemas.py | 0
{variables => toardb/variables}/test_base.py | 5 +--
.../variables}/test_variables.py | 2 +-
{variables => toardb/variables}/variables.py | 16 ++++-----
64 files changed, 125 insertions(+), 91 deletions(-)
rename {auth_user => toardb}/__init__.py (100%)
rename {auth_user => toardb/auth_user}/README.md (100%)
rename {contacts => toardb/auth_user}/__init__.py (100%)
rename {auth_user => toardb/auth_user}/auth_user.py (100%)
rename {auth_user => toardb/auth_user}/fixtures/auth.json (100%)
rename {auth_user => toardb/auth_user}/fixtures/authtoken.json (100%)
rename {auth_user => toardb/auth_user}/models.py (100%)
rename {auth_user => toardb/auth_user}/schemas.py (100%)
rename {data => toardb/contacts}/__init__.py (100%)
rename {contacts => toardb/contacts}/contacts.py (77%)
rename {contacts => toardb/contacts}/crud.py (100%)
rename {contacts => toardb/contacts}/fixtures/organisations.json (100%)
rename {contacts => toardb/contacts}/fixtures/persons.json (100%)
rename {contacts => toardb/contacts}/models.py (100%)
rename {contacts => toardb/contacts}/models_organisation.py (100%)
rename {contacts => toardb/contacts}/models_person.py (100%)
rename {contacts => toardb/contacts}/schemas.py (100%)
rename {contacts => toardb/contacts}/test_base.py (95%)
rename {contacts => toardb/contacts}/test_contacts.py (98%)
rename {stationmeta => toardb/data}/__init__.py (100%)
rename {data => toardb/data}/crud.py (91%)
rename {data => toardb/data}/data.py (82%)
rename {data => toardb/data}/models.py (100%)
rename {data => toardb/data}/schemas.py (100%)
rename {timeseries => toardb/stationmeta}/__init__.py (100%)
rename {stationmeta => toardb/stationmeta}/crud.py (100%)
rename {stationmeta => toardb/stationmeta}/fixtures/stationmeta_core.json (100%)
rename {stationmeta => toardb/stationmeta}/models.py (100%)
rename {stationmeta => toardb/stationmeta}/models_annotation.py (98%)
rename {stationmeta => toardb/stationmeta}/models_aux.py (100%)
rename {stationmeta => toardb/stationmeta}/models_core.py (99%)
rename {stationmeta => toardb/stationmeta}/models_global.py (100%)
rename {stationmeta => toardb/stationmeta}/models_global_services.py (100%)
rename {stationmeta => toardb/stationmeta}/models_role.py (98%)
rename {stationmeta => toardb/stationmeta}/pydantic_toar_testing.py (100%)
rename {stationmeta => toardb/stationmeta}/schemas.py (100%)
rename {stationmeta => toardb/stationmeta}/stationmeta.py (87%)
rename {stationmeta => toardb/stationmeta}/test_base.py (94%)
rename {stationmeta => toardb/stationmeta}/test_stationmeta.py (96%)
rename {utils => toardb/timeseries}/__init__.py (100%)
rename {timeseries => toardb/timeseries}/crud.py (98%)
rename {timeseries => toardb/timeseries}/fixtures/timeseries.json (100%)
rename {timeseries => toardb/timeseries}/models.py (100%)
rename {timeseries => toardb/timeseries}/models_annotation.py (98%)
rename {timeseries => toardb/timeseries}/models_core.py (98%)
rename {timeseries => toardb/timeseries}/models_programme.py (100%)
rename {timeseries => toardb/timeseries}/models_role.py (98%)
rename {timeseries => toardb/timeseries}/pydantic_toar_testing.py (100%)
rename {timeseries => toardb/timeseries}/schemas.py (100%)
rename {timeseries => toardb/timeseries}/test_base.py (94%)
rename {timeseries => toardb/timeseries}/test_timeseries.py (93%)
rename {timeseries => toardb/timeseries}/timeseries.py (69%)
create mode 100644 toardb/toardb.py
rename {variables => toardb/utils}/__init__.py (100%)
rename {utils => toardb/utils}/database.py (100%)
create mode 100644 toardb/variables/__init__.py
rename {variables => toardb/variables}/crud.py (100%)
rename {variables => toardb/variables}/fixtures/variables.json (100%)
rename {variables => toardb/variables}/models.py (100%)
rename {variables => toardb/variables}/schemas.py (100%)
rename {variables => toardb/variables}/test_base.py (95%)
rename {variables => toardb/variables}/test_variables.py (99%)
rename {variables => toardb/variables}/variables.py (74%)
diff --git a/production_tests.sh b/production_tests.sh
index f3655a6..54493ab 100755
--- a/production_tests.sh
+++ b/production_tests.sh
@@ -1,13 +1,12 @@
#!/bin/bash
+# for running: uvicorn toardb.toardb:app --reload
-# for running: uvicorn variables.variables:app --reload
curl http://127.0.0.1:8000/variables/?limit=3
curl http://127.0.0.1:8000/variables/id/2
curl http://127.0.0.1:8000/variables/id/99
curl http://127.0.0.1:8000/variables/CO
curl -X POST -H "Content-Type:application/json" -d '{"name": "sabinene", "longname": "sabinene", "displayname": "Sabinene", "cf_standardname": "mole_fraction_of_sabinene_in_air", "units": "nmol mol-1", "chemical_formula": "C10H16"}' http://127.0.0.1:8000/variables/
-# for running: uvicorn contacts.contacts:app --reload
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
@@ -16,15 +15,14 @@ curl -X POST -H "Content-Type:application/json" -d '{"organisation": {"name": "F
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
-curl "http://127.0.0.1:8000/contacts/persons/Sabine Schröder"
+curl "http://127.0.0.1:8000/contacts/persons/Ute%20Dauert"
+curl "http://127.0.0.1:8000/contacts/persons/Sabine%20Schr%C3%B6der"
curl -X POST -H "Content-Type:application/json" -d '{"person": {"name": "Martin Schultz", "email": "m.schultz@fz-juelich.de", "phone": "+49-2461-61-96870", "isprivate": true}}' http://127.0.0.1:8000/contacts/persons/
-# for running: uvicorn stationmeta.stationmeta:app --reload
curl http://127.0.0.1:8000/stationmeta_core/
curl http://127.0.0.1:8000/stationmeta_core/China11
curl -X POST -H "Content-Type:application/json" -d '{"stationmeta_core": {"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_core/"
-# for running: uvicorn timeseries.timeseries:app --reload
curl http://127.0.0.1:8000/timeseries/
curl http://127.0.0.1:8000/timeseries/2
curl -X POST -H "Content-Type:application/json" -d '{"timeseries": {"label": "CMA2", "order": 1, "access_rights": 0, "sampling_frequency": 0, "aggregation": 0, "data_start_date": "2003-09-07T15:30:00+02:00", "data_end_date": "2016-12-31T14:30:00+01:00", "measurement_method": "UV absorption", "sampling_height": 7.0, "date_added": "2020-05-15T15:30:00+02:00", "date_modified": "2020-05-16T09:30:00+02:00", "station_id": 2, "variable_id": 7, "additional_metadata":"{}"}}' http://127.0.0.1:8000/timeseries/
diff --git a/auth_user/__init__.py b/toardb/__init__.py
similarity index 100%
rename from auth_user/__init__.py
rename to toardb/__init__.py
diff --git a/auth_user/README.md b/toardb/auth_user/README.md
similarity index 100%
rename from auth_user/README.md
rename to toardb/auth_user/README.md
diff --git a/contacts/__init__.py b/toardb/auth_user/__init__.py
similarity index 100%
rename from contacts/__init__.py
rename to toardb/auth_user/__init__.py
diff --git a/auth_user/auth_user.py b/toardb/auth_user/auth_user.py
similarity index 100%
rename from auth_user/auth_user.py
rename to toardb/auth_user/auth_user.py
diff --git a/auth_user/fixtures/auth.json b/toardb/auth_user/fixtures/auth.json
similarity index 100%
rename from auth_user/fixtures/auth.json
rename to toardb/auth_user/fixtures/auth.json
diff --git a/auth_user/fixtures/authtoken.json b/toardb/auth_user/fixtures/authtoken.json
similarity index 100%
rename from auth_user/fixtures/authtoken.json
rename to toardb/auth_user/fixtures/authtoken.json
diff --git a/auth_user/models.py b/toardb/auth_user/models.py
similarity index 100%
rename from auth_user/models.py
rename to toardb/auth_user/models.py
diff --git a/auth_user/schemas.py b/toardb/auth_user/schemas.py
similarity index 100%
rename from auth_user/schemas.py
rename to toardb/auth_user/schemas.py
diff --git a/data/__init__.py b/toardb/contacts/__init__.py
similarity index 100%
rename from data/__init__.py
rename to toardb/contacts/__init__.py
diff --git a/contacts/contacts.py b/toardb/contacts/contacts.py
similarity index 77%
rename from contacts/contacts.py
rename to toardb/contacts/contacts.py
index 8b632bd..9f578a8 100644
--- a/contacts/contacts.py
+++ b/toardb/contacts/contacts.py
@@ -3,12 +3,12 @@ Simple API for contacts management
"""
from typing import List
-from fastapi import FastAPI, Depends, HTTPException, Body
+from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session
from . import crud, schemas
-from utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession
-app = FastAPI()
+router = APIRouter()
# Dependency
def get_db():
@@ -22,20 +22,20 @@ def get_db():
# plain views to post and get contacts
#get all entries of table persons
-@app.get('/contacts/persons/', response_model=List[schemas.Person])
+@router.get('/contacts/persons/', response_model=List[schemas.Person])
def get_all_persons(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
persons = crud.get_all_persons(db, skip=skip, limit=limit)
return persons
#get all metadata of one person
-@app.get('/contacts/persons/id/{person_id}', response_model=schemas.Person)
+@router.get('/contacts/persons/id/{person_id}', response_model=schemas.Person)
def get_person(person_id: int, db: Session = Depends(get_db)):
db_person = crud.get_person(db, person_id=person_id)
if db_person is None:
raise HTTPException(status_code=404, detail="Person not found.")
return db_person
-@app.get('/contacts/persons/{name}', response_model=schemas.Person)
+@router.get('/contacts/persons/{name}', response_model=schemas.Person)
def get_person(name: str, db: Session = Depends(get_db)):
db_person = crud.get_person_by_name(db, name=name)
if db_person is None:
@@ -47,7 +47,7 @@ def get_person(name: str, db: Session = Depends(get_db)):
#
#
-@app.post('/contacts/persons/', response_model=schemas.Person)
+@router.post('/contacts/persons/', response_model=schemas.Person)
def create_person(person: schemas.PersonCreate = Body(..., embed = True), db: Session = Depends(get_db)):
db_person = crud.get_person_by_name(db, name=person.name)
if db_person:
@@ -58,20 +58,20 @@ def create_person(person: schemas.PersonCreate = Body(..., embed = True), db: Se
# plain views to post and get organisations
#get all entries of table organisations
-@app.get('/contacts/organisations/', response_model=List[schemas.Organisation])
+@router.get('/contacts/organisations/', response_model=List[schemas.Organisation])
def get_all_organisations(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
organisations = crud.get_all_organisations(db, skip=skip, limit=limit)
return organisations
#get all metadata of one organisation
-@app.get('/contacts/organisations/id/{organisation_id}', response_model=schemas.Organisation)
+@router.get('/contacts/organisations/id/{organisation_id}', response_model=schemas.Organisation)
def get_organisation(organisation_id: int, db: Session = Depends(get_db)):
db_organisation = crud.get_organisation (db, organisation_id=organisation_id)
if db_organisation is None:
raise HTTPException(status_code=404, detail="Organisation not found.")
return db_organisation
-@app.get('/contacts/organisations/{name}', response_model=schemas.Organisation)
+@router.get('/contacts/organisations/{name}', response_model=schemas.Organisation)
def get_organisation(name: str, db: Session = Depends(get_db)):
db_organisation = crud.get_organisation_by_name(db, name=name)
if db_organisation is None:
@@ -84,9 +84,8 @@ def get_organisation(name: str, db: Session = Depends(get_db)):
#
#
-@app.post('/contacts/organisations/', response_model=schemas.Organisation)
+@router.post('/contacts/organisations/', response_model=schemas.Organisation)
def create_organisation(organisation: schemas.OrganisationCreate = Body(..., embed = True), db: Session = Depends(get_db)):
- print("in contacts.py: ", organisation)
db_organisation = crud.get_organisation_by_name(db, name=organisation.name)
if db_organisation:
raise HTTPException(status_code=400, detail="Organisation already registered.")
diff --git a/contacts/crud.py b/toardb/contacts/crud.py
similarity index 100%
rename from contacts/crud.py
rename to toardb/contacts/crud.py
diff --git a/contacts/fixtures/organisations.json b/toardb/contacts/fixtures/organisations.json
similarity index 100%
rename from contacts/fixtures/organisations.json
rename to toardb/contacts/fixtures/organisations.json
diff --git a/contacts/fixtures/persons.json b/toardb/contacts/fixtures/persons.json
similarity index 100%
rename from contacts/fixtures/persons.json
rename to toardb/contacts/fixtures/persons.json
diff --git a/contacts/models.py b/toardb/contacts/models.py
similarity index 100%
rename from contacts/models.py
rename to toardb/contacts/models.py
diff --git a/contacts/models_organisation.py b/toardb/contacts/models_organisation.py
similarity index 100%
rename from contacts/models_organisation.py
rename to toardb/contacts/models_organisation.py
diff --git a/contacts/models_person.py b/toardb/contacts/models_person.py
similarity index 100%
rename from contacts/models_person.py
rename to toardb/contacts/models_person.py
diff --git a/contacts/schemas.py b/toardb/contacts/schemas.py
similarity index 100%
rename from contacts/schemas.py
rename to toardb/contacts/schemas.py
diff --git a/contacts/test_base.py b/toardb/contacts/test_base.py
similarity index 95%
rename from contacts/test_base.py
rename to toardb/contacts/test_base.py
index 377af35..70113f7 100644
--- a/contacts/test_base.py
+++ b/toardb/contacts/test_base.py
@@ -7,9 +7,10 @@ from sqlalchemy.engine import Engine as Database
from sqlalchemy.orm import Session
from sqlalchemy_utils import database_exists, create_database, drop_database
-from utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL
from .models import Base
-from .contacts import app, get_db
+from toardb.toardb import app
+from toardb.contacts.contacts import get_db
url = str(DATABASE_URL+ "_test")
_db_conn = create_engine(url)
diff --git a/contacts/test_contacts.py b/toardb/contacts/test_contacts.py
similarity index 98%
rename from contacts/test_contacts.py
rename to toardb/contacts/test_contacts.py
index 840b584..162883b 100644
--- a/contacts/test_contacts.py
+++ b/toardb/contacts/test_contacts.py
@@ -29,7 +29,7 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE organisations_id_seq RESTART WITH 1")
fake_conn.commit()
- infilename = "contacts/fixtures/persons.json"
+ infilename = "toardb/contacts/fixtures/persons.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -37,7 +37,7 @@ class TestApps:
db.add(new_person)
db.commit()
db.refresh(new_person)
- infilename = "contacts/fixtures/organisations.json"
+ infilename = "toardb/contacts/fixtures/organisations.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
diff --git a/stationmeta/__init__.py b/toardb/data/__init__.py
similarity index 100%
rename from stationmeta/__init__.py
rename to toardb/data/__init__.py
diff --git a/data/crud.py b/toardb/data/crud.py
similarity index 91%
rename from data/crud.py
rename to toardb/data/crud.py
index b4e4954..8158dcd 100644
--- a/data/crud.py
+++ b/toardb/data/crud.py
@@ -10,14 +10,14 @@ from sqlalchemy.engine import Engine
from fastapi import File, UploadFile
from fastapi.responses import JSONResponse
from . import models, schemas
-from variables import models as variables_models
-from stationmeta import models as stationmeta_models
-from stationmeta.crud import get_stationmeta_core
-from timeseries.crud import get_timeseries_by_unique_constraints
+from toardb.variables import models as variables_models
+from toardb.stationmeta import models as stationmeta_models
+from toardb.stationmeta.crud import get_stationmeta_core
+from toardb.timeseries.crud import get_timeseries_by_unique_constraints
import datetime as dt
import pandas as pd
from io import StringIO
-from utils.database import engine
+from toardb.utils.database import engine
def get_data(db: Session, timeseries_id: int):
return db.query(models.Data).filter(models.Data.timeseries_id == timeseries_id).all()
diff --git a/data/data.py b/toardb/data/data.py
similarity index 82%
rename from data/data.py
rename to toardb/data/data.py
index 4f972fd..c042383 100644
--- a/data/data.py
+++ b/toardb/data/data.py
@@ -3,13 +3,13 @@ Simple test API for data management
"""
from typing import List
-from fastapi import FastAPI, Depends, HTTPException, \
+from fastapi import APIRouter, Depends, HTTPException, \
File, UploadFile
from sqlalchemy.orm import Session
from . import crud, schemas
-from utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession
-app = FastAPI()
+router = APIRouter()
# Dependency
def get_db():
@@ -24,13 +24,13 @@ def get_db():
# plain views to post and get data
#get all data of table data
-@app.get('/data/', response_model=List[schemas.Data])
+@router.get('/data/', response_model=List[schemas.Data])
def get_all_data(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
data = crud.get_all_data(db, skip=skip, limit=limit)
return data
#get all data of one timeseries
-@app.get('/data/{timeseries_id}', response_model=List[schemas.Data])
+@router.get('/data/{timeseries_id}', response_model=List[schemas.Data])
def get_data(timeseries_id: int, db: Session = Depends(get_db)):
db_data = crud.get_data(db, timeseries_id=timeseries_id)
if db_data is None:
@@ -42,7 +42,7 @@ def get_data(timeseries_id: int, db: Session = Depends(get_db)):
# - get all data of one special timestamp and timeseries
# - ...
-@app.post('/data/', response_model=schemas.DataCreate)
+@router.post('/data/', response_model=schemas.DataCreate)
async def create_data(file: UploadFile = File(...), db: Session = Depends(get_db)):
# # the next three lines are automatically done by database management,
# # but we do want helpful error messages!
diff --git a/data/models.py b/toardb/data/models.py
similarity index 100%
rename from data/models.py
rename to toardb/data/models.py
diff --git a/data/schemas.py b/toardb/data/schemas.py
similarity index 100%
rename from data/schemas.py
rename to toardb/data/schemas.py
diff --git a/timeseries/__init__.py b/toardb/stationmeta/__init__.py
similarity index 100%
rename from timeseries/__init__.py
rename to toardb/stationmeta/__init__.py
diff --git a/stationmeta/crud.py b/toardb/stationmeta/crud.py
similarity index 100%
rename from stationmeta/crud.py
rename to toardb/stationmeta/crud.py
diff --git a/stationmeta/fixtures/stationmeta_core.json b/toardb/stationmeta/fixtures/stationmeta_core.json
similarity index 100%
rename from stationmeta/fixtures/stationmeta_core.json
rename to toardb/stationmeta/fixtures/stationmeta_core.json
diff --git a/stationmeta/models.py b/toardb/stationmeta/models.py
similarity index 100%
rename from stationmeta/models.py
rename to toardb/stationmeta/models.py
diff --git a/stationmeta/models_annotation.py b/toardb/stationmeta/models_annotation.py
similarity index 98%
rename from stationmeta/models_annotation.py
rename to toardb/stationmeta/models_annotation.py
index 7c78215..40cb5fc 100644
--- a/stationmeta/models_annotation.py
+++ b/toardb/stationmeta/models_annotation.py
@@ -7,7 +7,7 @@ from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, Strin
Text, Boolean, CheckConstraint
#from sqlalchemy.orm import relationship
from sqlalchemy.ext.declarative import declarative_base
-from auth_user.models import AuthUser
+from toardb.auth_user.models import AuthUser
from .models_core import StationmetaCore
Base = declarative_base()
diff --git a/stationmeta/models_aux.py b/toardb/stationmeta/models_aux.py
similarity index 100%
rename from stationmeta/models_aux.py
rename to toardb/stationmeta/models_aux.py
diff --git a/stationmeta/models_core.py b/toardb/stationmeta/models_core.py
similarity index 99%
rename from stationmeta/models_core.py
rename to toardb/stationmeta/models_core.py
index c8059d3..e275996 100644
--- a/stationmeta/models_core.py
+++ b/toardb/stationmeta/models_core.py
@@ -10,7 +10,7 @@ from sqlalchemy.orm import relationship
from sqlalchemy.dialects.postgresql import JSONB, ARRAY
from sqlalchemy.ext.declarative import declarative_base
from shapely import wkt
-from auth_user.models import AuthUser
+from toardb.auth_user.models import AuthUser
Base = declarative_base()
metadata = Base.metadata
diff --git a/stationmeta/models_global.py b/toardb/stationmeta/models_global.py
similarity index 100%
rename from stationmeta/models_global.py
rename to toardb/stationmeta/models_global.py
diff --git a/stationmeta/models_global_services.py b/toardb/stationmeta/models_global_services.py
similarity index 100%
rename from stationmeta/models_global_services.py
rename to toardb/stationmeta/models_global_services.py
diff --git a/stationmeta/models_role.py b/toardb/stationmeta/models_role.py
similarity index 98%
rename from stationmeta/models_role.py
rename to toardb/stationmeta/models_role.py
index d872d24..f7dc21e 100644
--- a/stationmeta/models_role.py
+++ b/toardb/stationmeta/models_role.py
@@ -7,7 +7,7 @@ from sqlalchemy import Column, ForeignKey, Integer, text, \
CheckConstraint, UniqueConstraint
#from sqlalchemy.orm import relationship
from sqlalchemy.ext.declarative import declarative_base
-from contacts.models import Person
+from toardb.contacts.models import Person
from .models_core import StationmetaCore
Base = declarative_base()
diff --git a/stationmeta/pydantic_toar_testing.py b/toardb/stationmeta/pydantic_toar_testing.py
similarity index 100%
rename from stationmeta/pydantic_toar_testing.py
rename to toardb/stationmeta/pydantic_toar_testing.py
diff --git a/stationmeta/schemas.py b/toardb/stationmeta/schemas.py
similarity index 100%
rename from stationmeta/schemas.py
rename to toardb/stationmeta/schemas.py
diff --git a/stationmeta/stationmeta.py b/toardb/stationmeta/stationmeta.py
similarity index 87%
rename from stationmeta/stationmeta.py
rename to toardb/stationmeta/stationmeta.py
index a5ed0e6..6367f09 100644
--- a/stationmeta/stationmeta.py
+++ b/toardb/stationmeta/stationmeta.py
@@ -3,13 +3,13 @@ Simple test API for stationmeta management
"""
from typing import List
-from fastapi import FastAPI, Depends, HTTPException, Body
+from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session, sessionmaker
from . import crud, schemas
from sqlalchemy import create_engine
-from utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL
-app = FastAPI()
+router = APIRouter()
# Dependency
#def get_db():
@@ -38,13 +38,13 @@ async def get_db():
# plain views to post and get stationmeta
#get all entries of table stationmeta
-@app.get('/stationmeta_core/', response_model=List[schemas.StationmetaCore])
+@router.get('/stationmeta_core/', response_model=List[schemas.StationmetaCore])
def get_all_stationmeta_core(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
stationmeta_core = crud.get_all_stationmeta_core(db, skip=skip, limit=limit)
return stationmeta_core
#get all core metadata of one station
-@app.get('/stationmeta_core/{station_code}', response_model=schemas.StationmetaCore)
+@router.get('/stationmeta_core/{station_code}', response_model=schemas.StationmetaCore)
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:
@@ -56,7 +56,7 @@ def get_stationmeta_core(station_code: str, db: Session = Depends(get_db)):
# - get stationmeta_aux
# - ...
-@app.post('/stationmeta_core/', response_model=schemas.StationmetaCore)
+@router.post('/stationmeta_core/', response_model=schemas.StationmetaCore)
#curl -X POST -H "Content-Type:application/json" -d '{"stationmeta_core": {"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_core/"
# The following command was not working as long as the upload via Body was defined.
# See bug report: https://github.com/tiangolo/fastapi/issues/300
diff --git a/stationmeta/test_base.py b/toardb/stationmeta/test_base.py
similarity index 94%
rename from stationmeta/test_base.py
rename to toardb/stationmeta/test_base.py
index 2871a87..bd411c7 100644
--- a/stationmeta/test_base.py
+++ b/toardb/stationmeta/test_base.py
@@ -7,11 +7,12 @@ from sqlalchemy.engine import Engine as Database
from sqlalchemy.orm import Session
from sqlalchemy_utils import database_exists, create_database, drop_database
-from utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL
from .models import Base
-from auth_user.models import Base as AuthUserBase
-from contacts.models import Base as ContactBase
-from .stationmeta import app, get_db
+from toardb.auth_user.models import Base as AuthUserBase
+from toardb.contacts.models import Base as ContactBase
+from toardb.toardb import app
+from toardb.stationmeta.stationmeta import get_db
url = str(DATABASE_URL+ "_test")
_db_conn = create_engine(url)
diff --git a/stationmeta/test_stationmeta.py b/toardb/stationmeta/test_stationmeta.py
similarity index 96%
rename from stationmeta/test_stationmeta.py
rename to toardb/stationmeta/test_stationmeta.py
index 64bec38..b7b9a18 100644
--- a/stationmeta/test_stationmeta.py
+++ b/toardb/stationmeta/test_stationmeta.py
@@ -1,8 +1,8 @@
import pytest
import json
from .models import StationmetaCore
-from auth_user.models import AuthUser
-from contacts.models import Person, Organisation
+from toardb.auth_user.models import AuthUser
+from toardb.contacts.models import Person, Organisation
from .schemas import get_geom_from_coordinates, Coordinates
# Required imports 'create_test_database'
from .test_base import (
@@ -50,7 +50,7 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE organisations_id_seq RESTART WITH 1")
fake_conn.commit()
- infilename = "auth_user/fixtures/auth.json"
+ infilename = "toardb/auth_user/fixtures/auth.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -58,7 +58,7 @@ class TestApps:
db.add(new_auth_user)
db.commit()
db.refresh(new_auth_user)
- infilename = "contacts/fixtures/persons.json"
+ infilename = "toardb/contacts/fixtures/persons.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -66,7 +66,7 @@ class TestApps:
db.add(new_person)
db.commit()
db.refresh(new_person)
- infilename = "contacts/fixtures/organisations.json"
+ infilename = "toardb/contacts/fixtures/organisations.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -74,7 +74,7 @@ class TestApps:
db.add(new_organisation)
db.commit()
db.refresh(new_organisation)
- infilename = "stationmeta/fixtures/stationmeta_core.json"
+ infilename = "toardb/stationmeta/fixtures/stationmeta_core.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
diff --git a/utils/__init__.py b/toardb/timeseries/__init__.py
similarity index 100%
rename from utils/__init__.py
rename to toardb/timeseries/__init__.py
diff --git a/timeseries/crud.py b/toardb/timeseries/crud.py
similarity index 98%
rename from timeseries/crud.py
rename to toardb/timeseries/crud.py
index 9b2eaa7..7abde34 100644
--- a/timeseries/crud.py
+++ b/toardb/timeseries/crud.py
@@ -43,7 +43,6 @@ def create_timeseries(db: Session, timeseries: TimeseriesCreate):
# in upload command, we have now: "additional_metadata": "{}"
# but return from this method gives: "additional_metadata": {}
# ==> there is a mismatch between model(JSONB) and schema(JSON)
- print("in crud: ",db_timeseries)
db_timeseries.additional_metadata = str(db_timeseries.additional_metadata)
db.add(db_timeseries)
result = db.commit()
diff --git a/timeseries/fixtures/timeseries.json b/toardb/timeseries/fixtures/timeseries.json
similarity index 100%
rename from timeseries/fixtures/timeseries.json
rename to toardb/timeseries/fixtures/timeseries.json
diff --git a/timeseries/models.py b/toardb/timeseries/models.py
similarity index 100%
rename from timeseries/models.py
rename to toardb/timeseries/models.py
diff --git a/timeseries/models_annotation.py b/toardb/timeseries/models_annotation.py
similarity index 98%
rename from timeseries/models_annotation.py
rename to toardb/timeseries/models_annotation.py
index 2e61ab7..058c9e6 100644
--- a/timeseries/models_annotation.py
+++ b/toardb/timeseries/models_annotation.py
@@ -7,7 +7,7 @@ from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, Strin
Text, Boolean, CheckConstraint
#from sqlalchemy.orm import relationship
from sqlalchemy.ext.declarative import declarative_base
-from auth_user.models import AuthUser
+from toardb.auth_user.models import AuthUser
from .models_core import Timeseries
Base = declarative_base()
diff --git a/timeseries/models_core.py b/toardb/timeseries/models_core.py
similarity index 98%
rename from timeseries/models_core.py
rename to toardb/timeseries/models_core.py
index 1298ad7..f713009 100644
--- a/timeseries/models_core.py
+++ b/toardb/timeseries/models_core.py
@@ -4,8 +4,8 @@ from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, Strin
#from sqlalchemy.orm import relationship
from sqlalchemy.dialects.postgresql import JSONB
from sqlalchemy.ext.declarative import declarative_base
-from stationmeta.models import StationmetaCore
-from variables.models import Variable
+from toardb.stationmeta.models import StationmetaCore
+from toardb.variables.models import Variable
Base = declarative_base()
metadata = Base.metadata
diff --git a/timeseries/models_programme.py b/toardb/timeseries/models_programme.py
similarity index 100%
rename from timeseries/models_programme.py
rename to toardb/timeseries/models_programme.py
diff --git a/timeseries/models_role.py b/toardb/timeseries/models_role.py
similarity index 98%
rename from timeseries/models_role.py
rename to toardb/timeseries/models_role.py
index 9e3191e..65c2327 100644
--- a/timeseries/models_role.py
+++ b/toardb/timeseries/models_role.py
@@ -7,7 +7,7 @@ from sqlalchemy import Column, ForeignKey, Integer, text, \
CheckConstraint, UniqueConstraint
#from sqlalchemy.orm import relationship
from sqlalchemy.ext.declarative import declarative_base
-from contacts.models import Person
+from toardb.contacts.models import Person
from .models_core import Timeseries
Base = declarative_base()
diff --git a/timeseries/pydantic_toar_testing.py b/toardb/timeseries/pydantic_toar_testing.py
similarity index 100%
rename from timeseries/pydantic_toar_testing.py
rename to toardb/timeseries/pydantic_toar_testing.py
diff --git a/timeseries/schemas.py b/toardb/timeseries/schemas.py
similarity index 100%
rename from timeseries/schemas.py
rename to toardb/timeseries/schemas.py
diff --git a/timeseries/test_base.py b/toardb/timeseries/test_base.py
similarity index 94%
rename from timeseries/test_base.py
rename to toardb/timeseries/test_base.py
index 8a76e31..259b2b3 100644
--- a/timeseries/test_base.py
+++ b/toardb/timeseries/test_base.py
@@ -7,13 +7,14 @@ from sqlalchemy.engine import Engine as Database
from sqlalchemy.orm import Session
from sqlalchemy_utils import database_exists, create_database, drop_database
-from utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL
from .models import Base
-from variables.models import Base as VariableBase
-from stationmeta.models import Base as StationmetaBase
-from auth_user.models import Base as AuthUserBase
-from contacts.models import Base as ContactBase
-from .timeseries import app, get_db
+from toardb.variables.models import Base as VariableBase
+from toardb.stationmeta.models import Base as StationmetaBase
+from toardb.auth_user.models import Base as AuthUserBase
+from toardb.contacts.models import Base as ContactBase
+from toardb.toardb import app
+from toardb.timeseries.timeseries import get_db
url = str(DATABASE_URL+ "_test")
_db_conn = create_engine(url)
diff --git a/timeseries/test_timeseries.py b/toardb/timeseries/test_timeseries.py
similarity index 93%
rename from timeseries/test_timeseries.py
rename to toardb/timeseries/test_timeseries.py
index f15df0a..0c1dd03 100644
--- a/timeseries/test_timeseries.py
+++ b/toardb/timeseries/test_timeseries.py
@@ -1,11 +1,11 @@
import pytest
import json
from .models import Timeseries
-from stationmeta.models import StationmetaCore
-from stationmeta.schemas import get_geom_from_coordinates, Coordinates
-from variables.models import Variable
-from contacts.models import Person, Organisation
-from auth_user.models import AuthUser
+from toardb.stationmeta.models import StationmetaCore
+from toardb.stationmeta.schemas import get_geom_from_coordinates, Coordinates
+from toardb.variables.models import Variable
+from toardb.contacts.models import Person, Organisation
+from toardb.auth_user.models import AuthUser
# Required imports 'create_test_database'
from .test_base import (
client,
@@ -60,7 +60,7 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE timeseries_id_seq RESTART WITH 1")
fake_conn.commit()
- infilename = "auth_user/fixtures/auth.json"
+ infilename = "toardb/auth_user/fixtures/auth.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -68,7 +68,7 @@ class TestApps:
db.add(new_auth_user)
db.commit()
db.refresh(new_auth_user)
- infilename = "contacts/fixtures/persons.json"
+ infilename = "toardb/contacts/fixtures/persons.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -76,7 +76,7 @@ class TestApps:
db.add(new_person)
db.commit()
db.refresh(new_person)
- infilename = "contacts/fixtures/organisations.json"
+ infilename = "toardb/contacts/fixtures/organisations.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -84,7 +84,7 @@ class TestApps:
db.add(new_organisation)
db.commit()
db.refresh(new_organisation)
- infilename = "variables/fixtures/variables.json"
+ infilename = "toardb/variables/fixtures/variables.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -92,7 +92,7 @@ class TestApps:
db.add(new_variable)
db.commit()
db.refresh(new_variable)
- infilename = "stationmeta/fixtures/stationmeta_core.json"
+ infilename = "toardb/stationmeta/fixtures/stationmeta_core.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
@@ -108,7 +108,7 @@ class TestApps:
db.add(new_stationmeta_core)
db.commit()
db.refresh(new_stationmeta_core)
- infilename = "timeseries/fixtures/timeseries.json"
+ infilename = "toardb/timeseries/fixtures/timeseries.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
diff --git a/timeseries/timeseries.py b/toardb/timeseries/timeseries.py
similarity index 69%
rename from timeseries/timeseries.py
rename to toardb/timeseries/timeseries.py
index 9ce91d9..8c0fa82 100644
--- a/timeseries/timeseries.py
+++ b/toardb/timeseries/timeseries.py
@@ -3,12 +3,12 @@ Simple test API for timeseries management
"""
from typing import List
-from fastapi import FastAPI, Depends, HTTPException, Body
+from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session
from . import crud, schemas
-from utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession
-app = FastAPI()
+router = APIRouter()
# Dependency
def get_db():
@@ -23,13 +23,13 @@ def get_db():
# plain views to post and get timeseries
#get all entries of table timeseries
-@app.get('/timeseries/', response_model=List[schemas.Timeseries])
+@router.get('/timeseries/', response_model=List[schemas.Timeseries])
def get_all_timeseries(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
timeseries = crud.get_all_timeseries(db, skip=skip, limit=limit)
return timeseries
#get all metadata of one timeseries
-@app.get('/timeseries/{timeseries_id}', response_model=schemas.Timeseries)
+@router.get('/timeseries/{timeseries_id}', response_model=schemas.Timeseries)
def get_timeseries(timeseries_id: int, db: Session = Depends(get_db)):
db_timeseries = crud.get_timeseries(db, timeseries_id=timeseries_id)
if db_timeseries is None:
@@ -42,9 +42,10 @@ def get_timeseries(timeseries_id: int, db: Session = Depends(get_db)):
#
# still to be tested:
-@app.post('/timeseries/', response_model=schemas.Timeseries)
+@router.post('/timeseries/', response_model=schemas.Timeseries)
def create_timeseries(timeseries: schemas.TimeseriesCreate = Body(..., embed = True), db: Session = Depends(get_db)):
- db_timeseries = crud.get_timeseries(db, timeseries_id=timeseries.id)
+ db_timeseries = crud.get_timeseries_by_unique_constraints(db, station_id=timeseries.station_id,
+ variable_id=timeseries.variable_id, label=timeseries.label)
if db_timeseries:
raise HTTPException(status_code=400, detail="Timeseries already registered.")
return crud.create_timeseries(db=db, timeseries=timeseries)
diff --git a/toardb/toardb.py b/toardb/toardb.py
new file mode 100644
index 0000000..95d30c7
--- /dev/null
+++ b/toardb/toardb.py
@@ -0,0 +1,33 @@
+"""
+Simple test API for variable management
+"""
+
+from typing import List
+from fastapi import FastAPI, Depends, HTTPException, APIRouter
+from sqlalchemy.orm import Session
+
+from toardb.utils.database import ToarDbSession
+
+from toardb.variables import variables
+from toardb.contacts import contacts
+from toardb.stationmeta import stationmeta
+from toardb.timeseries import timeseries
+from toardb.data import data
+
+
+app = FastAPI()
+
+# Dependency
+def get_db():
+ try:
+ db = ToarDbSession()
+ yield db
+ finally:
+ db.close()
+
+app.include_router(variables.router)
+app.include_router(contacts.router)
+app.include_router(stationmeta.router)
+app.include_router(timeseries.router)
+app.include_router(data.router)
+
diff --git a/variables/__init__.py b/toardb/utils/__init__.py
similarity index 100%
rename from variables/__init__.py
rename to toardb/utils/__init__.py
diff --git a/utils/database.py b/toardb/utils/database.py
similarity index 100%
rename from utils/database.py
rename to toardb/utils/database.py
diff --git a/toardb/variables/__init__.py b/toardb/variables/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/variables/crud.py b/toardb/variables/crud.py
similarity index 100%
rename from variables/crud.py
rename to toardb/variables/crud.py
diff --git a/variables/fixtures/variables.json b/toardb/variables/fixtures/variables.json
similarity index 100%
rename from variables/fixtures/variables.json
rename to toardb/variables/fixtures/variables.json
diff --git a/variables/models.py b/toardb/variables/models.py
similarity index 100%
rename from variables/models.py
rename to toardb/variables/models.py
diff --git a/variables/schemas.py b/toardb/variables/schemas.py
similarity index 100%
rename from variables/schemas.py
rename to toardb/variables/schemas.py
diff --git a/variables/test_base.py b/toardb/variables/test_base.py
similarity index 95%
rename from variables/test_base.py
rename to toardb/variables/test_base.py
index 71ac0fd..a8b05f1 100644
--- a/variables/test_base.py
+++ b/toardb/variables/test_base.py
@@ -7,9 +7,10 @@ from sqlalchemy.engine import Engine as Database
from sqlalchemy.orm import Session
from sqlalchemy_utils import database_exists, create_database, drop_database
-from utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL
from .models import Base
-from .variables import app, get_db
+from toardb.toardb import app
+from toardb.variables.variables import get_db
url = str(DATABASE_URL+ "_test")
_db_conn = create_engine(url)
diff --git a/variables/test_variables.py b/toardb/variables/test_variables.py
similarity index 99%
rename from variables/test_variables.py
rename to toardb/variables/test_variables.py
index 1a7027a..c58b2d0 100644
--- a/variables/test_variables.py
+++ b/toardb/variables/test_variables.py
@@ -27,7 +27,7 @@ class TestApps:
fake_cur = fake_conn.cursor()
fake_cur.execute("ALTER SEQUENCE variables_id_seq RESTART WITH 1")
fake_conn.commit()
- infilename = "variables/fixtures/variables.json"
+ infilename = "toardb/variables/fixtures/variables.json"
with open(infilename) as f:
metajson=json.load(f)
for entry in metajson:
diff --git a/variables/variables.py b/toardb/variables/variables.py
similarity index 74%
rename from variables/variables.py
rename to toardb/variables/variables.py
index 6067934..dbc633c 100644
--- a/variables/variables.py
+++ b/toardb/variables/variables.py
@@ -3,12 +3,12 @@ Simple test API for variable management
"""
from typing import List
-from fastapi import FastAPI, Depends, HTTPException
+from fastapi import APIRouter, Depends, HTTPException
from sqlalchemy.orm import Session
-from variables import crud, schemas
-from utils.database import ToarDbSession
+from toardb.variables import crud, schemas
+from toardb.utils.database import ToarDbSession
-app = FastAPI()
+router= APIRouter()
# Dependency
def get_db():
@@ -20,26 +20,26 @@ def get_db():
# plain views to post and get variables
-@app.post('/variables/', response_model=schemas.Variable)
+@router.post('/variables/', response_model=schemas.Variable)
def create_variable(variable: schemas.VariableCreate, db: Session = Depends(get_db)):
db_variable = crud.get_variable_by_name(db, name=variable.name)
if db_variable:
raise HTTPException(status_code=400, detail="Variable already registered.")
return crud.create_variable(db=db, variable=variable)
-@app.get('/variables/', response_model=List[schemas.Variable])
+@router.get('/variables/', response_model=List[schemas.Variable])
def get_variables(skip: int = 0, limit: int = None, db: Session = Depends(get_db)):
variables = crud.get_variables(db, skip=skip, limit=limit)
return variables
-@app.get('/variables/{name}', response_model=schemas.Variable)
+@router.get('/variables/{name}', response_model=schemas.Variable)
def get_variable(name: str, db: Session = Depends(get_db)):
db_variable = crud.get_variable_by_name(db, name=name)
if db_variable is None:
raise HTTPException(status_code=404, detail="Variable not found.")
return db_variable
-@app.get('/variables/id/{variable_id}', response_model=schemas.Variable)
+@router.get('/variables/id/{variable_id}', response_model=schemas.Variable)
def get_variable(variable_id: int, db: Session = Depends(get_db)):
db_variable = crud.get_variable(db, variable_id=variable_id)
if db_variable is None:
--
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