diff --git a/README.md b/README.md index b04c68084b1b5e4d42a2efd6cd30cc48cfe5b419..11d70b638b44ee1a9b1b7a639b415fd61bc82494 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,12 @@ # VIPSCore-Python-Common Lorem Ipsum + +## Unit tests +The tests are located in the `src/vipscore_common/tests` folder, and we're using Python's standard [`unittest` library](https://docs.python.org/3/library/unittest.html) + +To run the unit tests, move to the root folder of the project, and execute: + +``` bash +python3 -m unittest discover -s tests -t src/vipscore_common +``` \ No newline at end of file diff --git a/src/vipscore_common/__init__.py b/src/vipscore_common/__init__.py old mode 100644 new mode 100755 index 71a1d852e88a668f8f745531172305fcdc58e251..9c8fdc2c5615f48bb5ecc4a69976d755320b213d --- a/src/vipscore_common/__init__.py +++ b/src/vipscore_common/__init__.py @@ -1 +1,2 @@ -from .model import * \ No newline at end of file +from .vips_model import * +from .entities import * \ No newline at end of file diff --git a/src/vipscore_common/entities.py b/src/vipscore_common/entities.py old mode 100644 new mode 100755 index 3293f45125c1508f145fa09092968f12f7b99782..d9be988a1c0a190ed6d5eb4b9b49ad139f10c0be --- a/src/vipscore_common/entities.py +++ b/src/vipscore_common/entities.py @@ -23,36 +23,42 @@ along with VIPSCore-Python-Common. If not, see <http://www.nibio.no/licenses/>. # https://www.pedaldrivenprogramming.com/2020/12/fastapi-fundamentals-pydantic/ from datetime import datetime -from shapely import geometry +from shapely.geometry import Point, Polygon from pydantic import BaseModel, validator, constr +from typing import Any, Union class Result(BaseModel): """Represents a set of DSS model result values for a given point in space (Point, Polygon, MultiPolygon) and time (Period or immediate) """ valid_time_start: datetime # TODO make sure it's always timezone aware valid_time_end: datetime # TODO make sure it's always timezone aware - valid_geometry: geometry + valid_geometry: Any warning_status: int all_values: dict def get_keys(self): return set(self.all_values.keys) if self.all_values is not None else set() - @validator(["valid_time_start","valid_time_end"]) + @validator("valid_time_start","valid_time_end") def ensure_timezone(cls, v): if v.tzinfo is None or v.tzinfo.utcoffset(v) is None: raise ValueError("%s must be timezone aware" % v) return v + + @validator("valid_geometry") + def ensure_geometry(cls,v): + if v is not None and not isinstance(v, Point) and not isinstance(v, Polygon): + raise ValueError("%s is not a " % v) class ModelConfiguration(BaseModel): """All the input data for the model.""" - config_parameters: dict model_id: constr(min_length=10, max_length=10) + config_parameters: dict class WeatherObservation(BaseModel): - """Data class for a single weather observatin""" - element_measurement_type_id: str - log_interval_id: int - time_measured: datetime + """Data class for a single weather observation""" + elementMeasurementTypeId: str + logIntervalId: int + timeMeasured: datetime value: float # Log interval categories @@ -66,7 +72,7 @@ class WeatherObservation(BaseModel): LOG_INTERVAL_ID_6H = 7; LOG_INTERVAL_ID_1D = 2; - @validator("time_measured") + @validator("timeMeasured") def ensure_timezone(cls, v): if v.tzinfo is None or v.tzinfo.utcoffset(v) is None: raise ValueError("%s must be timezone aware" % v) diff --git a/src/vipscore_common/reference_model.py b/src/vipscore_common/reference_model.py new file mode 100755 index 0000000000000000000000000000000000000000..54d3c3229df6c6b43f1747693b495153dfe6a652 --- /dev/null +++ b/src/vipscore_common/reference_model.py @@ -0,0 +1,102 @@ +#!/usr/bin/python3 + +LICENSE = """ +Copyright (c) 2023 NIBIO <http://www.nibio.no/>. + +This file is part of VIPSCore-Python-Common. +VIPSCore-Python-Common is free software: you can redistribute it and/or modify +it under the terms of the NIBIO Open Source License as published by +NIBIO, either version 1 of the License, or (at your option) any +later version. + +VIPSCore-Python-Common is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +NIBIO Open Source License for more details. + +You should have received a copy of the NIBIO Open Source License +along with VIPSCore-Python-Common. If not, see <http://www.nibio.no/licenses/>. +""" + +from vips_model import VIPSModel +from entities import Result, ModelConfiguration, WeatherObservation + +class ReferenceModel(VIPSModel): + + MODEL_ID = "REFERENCEM" + COPYRIGHT = "(c) 2023 NIBIO" + + def set_configuration(self, model_configuration: ModelConfiguration): + if not isinstance(model_configuration, ModelConfiguration): + raise ValueError("%s is not a ModelConfiguration object" % model_configuration) + if model_configuration.model_id != ReferenceModel.MODEL_ID: + raise ValueError("%s is not the correct model ID!" % model_configuration.model_id) + self.sowing_date = model_configuration.config_parameters["sowingDate"] + self.observations = [] + for node in model_configuration.config_parameters["observations"]: + self.observations.append(WeatherObservation(**node)) + + def get_result(self) -> list[Result]: + """Get the results as a list of Result objects (TODO ref)""" + pass + + @property + def model_id(self) -> str: + """10-character ID of the model. Must be unique (at least in the current system)""" + return ReferenceModel.MODEL_ID + + + @property + def license(self) -> str: + """Returns the license for this piece of software""" + return LICENSE + + @property + def copyright(self) -> str: + """Name of person/organization that holds the copyright, and contact information""" + return ReferenceModel.COPYRIGHT + + @property + def sample_config(self) -> dict: + """A sample configuration in JSON format (TODO check relation with Dict)""" + return """ + { + model_id:'REFERENCEM', + config_parameters: { + 'sowingDate': '2022-03-01', + 'observations': [ + {'timeMeasured': '2015-03-01T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '1.41025'}, + {'timeMeasured': '2015-03-02T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '2.87608333333333'}, + {'timeMeasured': '2015-03-03T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '1.00854166666667'}, + {'timeMeasured': '2015-03-04T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '-1.44675'} + ] + } +} + """ + + def get_model_name(self, language = VIPSModel.default_language) -> str: + """Returns the model name in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" + return "Reference Model" + + def get_model_description(self, language = VIPSModel.default_language) -> str: + """Returns the model description in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" + return """ + The model is a reference model for developers, showcasing best practices and functionalities of a model. + It's a simple day degree model for an imagined pest, and when thresholds are passed, the warning status progresses. + """ + + def get_warning_status_interpretation(self, language = VIPSModel.default_language) -> str: + """How to interpret the warning status (red-yellow-green, what does it mean?) in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" + return """ + Gray status (warning status == 0): Warning not applicable + Blue status (warning status == 1): Missing data + Green status (warning status == 2): No risk. Sleep well + Yellow status (warning status == 3): Medium risk. Be on the alert, inspect your field + Red status (warning status == 4): High risk. When the going gets tough, the tough get going + """ + + def get_model_usage(self, language = VIPSModel.default_language) -> str: + """Technical manual for this model, in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" + return "TODO" + + \ No newline at end of file diff --git a/src/vipscore_common/modelconfiguration.py b/src/vipscore_common/tests/__init__.py similarity index 100% rename from src/vipscore_common/modelconfiguration.py rename to src/vipscore_common/tests/__init__.py diff --git a/src/vipscore_common/tests/test_reference_model.py b/src/vipscore_common/tests/test_reference_model.py new file mode 100644 index 0000000000000000000000000000000000000000..9732894028a296ef615c80baf9eff8bbc8115bc5 --- /dev/null +++ b/src/vipscore_common/tests/test_reference_model.py @@ -0,0 +1,83 @@ +import unittest + +import json + +from reference_model import * +from entities import * + +def get_model_configuration(): + with open ("src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json") as f: + weather_observations = json.load(f) + return ModelConfiguration( + model_id=ReferenceModel.MODEL_ID, + config_parameters={ + "sowingDate": "2022-03-01", + "observations": weather_observations + } + ) + +class TestReferenceModel(unittest.TestCase): + def test_set_configuration(self): + """ + Passing a configuration object does not fail + """ + #print(get_model_configuration()) + instance = ReferenceModel() + instance.set_configuration(get_model_configuration()) + + def test_get_model_id(self): + """ + The model returns the correct ID + """ + instance = ReferenceModel() + self.assertEqual(instance.model_id, ReferenceModel.MODEL_ID) + + def test_get_license(self): + """ + The model returns its license + """ + instance = ReferenceModel() + self.assertIsNotNone(instance.license) + + def test_get_copyright(self): + """ + The model returns its copyright notice + """ + instance = ReferenceModel() + self.assertEqual(instance.copyright, ReferenceModel.COPYRIGHT) + + def test_get_sample_config(self): + """ + The model returns its sample configuration + """ + instance = ReferenceModel() + self.assertIsNotNone(instance.sample_config) + + def test_get_model_name(self): + """ + The model returns its name in the default language + """ + instance = ReferenceModel() + self.assertEqual(instance.get_model_name(), "Reference Model") + + def test_get_model_description(self): + """ + The model returns a description + """ + instance = ReferenceModel() + self.assertIsNotNone(instance.get_model_description()) + + def test_get_warning_status_interpretation(self): + """ + The model returns a warning status interpretation + """ + instance = ReferenceModel() + self.assertIsNotNone(instance.get_warning_status_interpretation()) + + def test_get_model_usage(self): + """ + The model returns a description of usage + """ + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git 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b/src/vipscore_common/vips_model.py @@ -21,8 +21,8 @@ along with VIPSCore-Python-Common. If not, see <http://www.nibio.no/licenses/>. # All models in VIPSCore-Python must extend this abstract class # @author Tor-Einar Skog <tor-einar.skog@nibio.no> -from abc import ABC, abstractmethod -from vipscore_common.entities import Result +from abc import ABC, abstractmethod, abstractproperty +from entities import Result, ModelConfiguration class VIPSModel(ABC): @@ -32,7 +32,7 @@ class VIPSModel(ABC): # Set the configuration object (with all its possible parameters) # Must be done before you call get_result @abstractmethod - def set_configuration(self, model_configuration): + def set_configuration(self, model_configuration: ModelConfiguration): """ Set the configuration object (with all its possible parameters) Must be done before you call get_result @@ -44,62 +44,50 @@ class VIPSModel(ABC): """Get the results as a list of Result objects (TODO ref)""" pass + @property @abstractmethod - def get_model_id(self) -> str: + def model_id(self) -> str: """10-character ID of the model. Must be unique (at least in the current system)""" pass + @property @abstractmethod - def get_model_name(self) -> str: - """Returns the model name in the default language""" - pass - - @abstractmethod - def get_model_name(self, language: str) -> str: - """Returns the model name in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" + def sample_config(self) -> dict: + """A sample configuration in JSON format (TODO check relation with Dict)""" pass + @property @abstractmethod - def get_license(self) -> str: + def license(self) -> str: """Returns the license for this piece of software""" pass + @property @abstractmethod - def get_copyright(self) -> str: + def copyright(self) -> str: """Name of person/organization that holds the copyright, and contact information""" pass + @abstractmethod - def get_model_description(self) -> str: - """Description of model (In default_language). Should include interpretation of the red-yellow-green warning system""" + def get_model_name(self, language: str) -> str: + """Returns the model name in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" pass + @abstractmethod def get_model_description(self, language: str) -> str: """Returns the model description in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" pass - @abstractmethod - def get_warning_status_interpretation(self) -> str: - """How to interpret the warning status (red-yellow-green, what does it mean?) in the default language""" - pass - @abstractmethod def get_warning_status_interpretation(self, language: str) -> str: """How to interpret the warning status (red-yellow-green, what does it mean?) in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" pass - @abstractmethod - def get_model_usage(self) -> str: - """Technical manual for this model, in the default language""" - pass - @abstractmethod def get_model_usage(self, language: str) -> str: """Technical manual for this model, in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)""" pass - @abstractmethod - def get_sample_config(self) -> dict: - """A sample configuration in JSON format (TODO check relation with Dict)""" - pass \ No newline at end of file + \ No newline at end of file