hydamo-validation 1.3.0b1__tar.gz

hydamo_validation-1.3.0b1/LICENSE

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+MIT License
+
+Copyright (c) 2021 HyDAMO ValidatieTool
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hydamo_validation-1.3.0b1/PKG-INFO

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+Metadata-Version: 2.1
+Name: hydamo_validation
+Version: 1.3.0b1
+Summary: Validation module for HyDAMO data
+Author-email: Daniel Tollenaar <daniel@d2hydro.nl>
+License: MIT
+Project-URL: Source, https://github.com/HetWaterschapshuis/HyDAMOValidatieModule
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: geopandas
+Requires-Dist: pandas>=2
+Requires-Dist: pyogrio
+Requires-Dist: rasterio
+Requires-Dist: shapely>=2
+Requires-Dist: rasterstats
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+
+# The HyDAMO Validation Module: hydamo_validation
+
+Validation Module for HyDAMO data.
+
+## Installation
+
+### Python installation
+Make sure you have an Miniconda or Anaconda installation. You can download these here:
+ - https://www.anaconda.com/products/individual
+ - https://docs.conda.io/en/latest/miniconda.html
+
+During installation, tick the box "Add Anaconda to PATH", ignore the red remarks
+
+### Create the `validatietool` environment
+Use the `env/environment.yml` in the repository to create the conda environment: `validatietool`
+
+```
+conda env create -f environment.yml
+```
+
+After installation you can activate your environment in command prompt
+
+```
+conda activate validatietool
+```
+
+### Install hydamo_validation
+Simply install the module in the activated environment:
+
+```
+pip install hydamo_validation
+```
+
+### Develop-install hydamo_validation
+Download or clone the repository. Now simply install the module in the activated environment:
+
+```
+pip install .
+```
+
+## Run an example
+A working example with data can be found in `notebooks/test_wrij.ipynb`. In the activated environment launch jupyter notebook by:
+
+```
+jupyter notebook
+```
+
+Select `test_wrij.ipynb` read and run it.

hydamo_validation-1.3.0b1/README.md

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+# The HyDAMO Validation Module: hydamo_validation
+
+Validation Module for HyDAMO data.
+
+## Installation
+
+### Python installation
+Make sure you have an Miniconda or Anaconda installation. You can download these here:
+ - https://www.anaconda.com/products/individual
+ - https://docs.conda.io/en/latest/miniconda.html
+
+During installation, tick the box "Add Anaconda to PATH", ignore the red remarks
+
+### Create the `validatietool` environment
+Use the `env/environment.yml` in the repository to create the conda environment: `validatietool`
+
+```
+conda env create -f environment.yml
+```
+
+After installation you can activate your environment in command prompt
+
+```
+conda activate validatietool
+```
+
+### Install hydamo_validation
+Simply install the module in the activated environment:
+
+```
+pip install hydamo_validation
+```
+
+### Develop-install hydamo_validation
+Download or clone the repository. Now simply install the module in the activated environment:
+
+```
+pip install .
+```
+
+## Run an example
+A working example with data can be found in `notebooks/test_wrij.ipynb`. In the activated environment launch jupyter notebook by:
+
+```
+jupyter notebook
+```
+
+Select `test_wrij.ipynb` read and run it.

hydamo_validation-1.3.0b1/hydamo_validation/__init__.py

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+__author__ = ["Het Waterschapshuis", "D2HYDRO", "HKV", "HydroConsult"]
+__copyright__ = "Copyright 2021, HyDAMO ValidatieTool"
+__credits__ = ["D2HYDRO", "HKV", "HydroConsult"]
+__version__ = "1.3.0b1"
+
+__license__ = "MIT"
+__maintainer__ = "Daniel Tollenaar"
+__email__ = "daniel@d2hydro.nl"
+
+from .functions import topologic as topologic_functions
+from .functions import logic as logic_functions
+from .functions import general as general_functions
+from .validator import validator

hydamo_validation-1.3.0b1/hydamo_validation/datamodel.py

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+"""HyDAMO datamodel for ValidatieTool."""
+
+import json
+import logging
+import re
+import warnings
+from pathlib import Path
+from typing import Any, Literal
+
+import fiona
+import geopandas as gpd
+from geopandas import GeoSeries
+import numpy as np
+from shapely.geometry import LineString, MultiLineString, MultiPolygon, Point, Polygon
+
+from hydamo_validation import geometry
+from hydamo_validation.styles import add_styles_to_geopackage
+
+warnings.filterwarnings("ignore", category=UserWarning)
+warnings.filterwarnings("ignore", category=RuntimeWarning)
+warnings.filterwarnings("ignore", category=FutureWarning)
+
+FIELD_TYPES_MAP_REV = fiona.schema.FIELD_TYPES_MAP_REV
+FIELD_TYPES_MAP = fiona.schema.FIELD_TYPES_MAP
+MODEL_CRS = "epsg:28992"
+SCHEMAS_DIR = Path(__file__).parent.joinpath("schemas", "hydamo")
+
+GEOTYPE_MAPPING = {
+    "LineString": LineString,
+    "MultiLineString": MultiLineString,
+    "Point": Point,
+    "PointZ": Point,
+    "Polygon": Polygon,
+    "MultiPolygon": MultiPolygon,
+}
+
+DTYPE_MAPPING = {
+    "string": "str",
+    "integer": "int64",
+    "date-time": "datetime",
+    "number": "float",
+}
+
+default_properties: dict[str, Any] = {
+    "id": None,
+    "dtype": "str",
+    "required": False,
+    "unique": False,
+}
+
+
+def map_definition(definition: dict[str, Any]) -> list[dict[str, Any]]:
+    """
+
+
+    Parameters
+    ----------
+    definition : dict[str, Any]
+        HyDAMO definition as specified in the HyDAMO JSON specification.
+
+    Returns
+    -------
+    list[dict[str, Any]]
+        Validation schema for the HyDAMO class.
+
+    """
+
+    # start with an empty list to populate
+    result = []
+
+    for k, v in definition.items():
+        # convert geometry if shape
+        if k == "shape":
+            properties: dict[str, Any] = {"id": "geometry"}
+            dtype = v["type"]
+            if not isinstance(dtype, list):
+                dtype = [dtype]
+            properties["dtype"] = dtype
+            properties["required"] = True
+            result.append(properties)
+
+        # set properties if not shape
+        else:
+            properties = default_properties.copy()
+            properties["id"] = k
+            if "type" in v.keys():
+                properties["dtype"] = DTYPE_MAPPING[v["type"]]
+                if "format" in v.keys():
+                    properties["dtype"] = DTYPE_MAPPING[v["format"]]
+
+            # set required
+            if "minItems" in v.keys():
+                if v["minItems"] == 1:
+                    properties["required"] = True
+
+            # set unique
+            if "uniqueItems" in v.keys():
+                properties["unique"] = v["uniqueItems"]
+
+            # set domain
+            if "enum" in v.keys():
+                properties["domain"] = [{"value": i} for i in v["enum"]]
+            result.append(properties)
+    return result
+
+
+class ExtendedGeoDataFrame(gpd.GeoDataFrame):  # type: ignore
+    """A GeoPandas GeoDataFrame with extended properties and methods."""
+
+    # ignores subclassing Any: https://github.com/geopandas/geopandas/discussions/2750
+
+    _metadata = [
+        "required_columns",
+        "geotype",
+        "layer_name",
+    ] + gpd.GeoDataFrame._metadata
+
+    def __init__(
+        self,
+        validation_schema: list[dict[str, Any]],
+        geotype: (
+            list[
+                Literal[
+                    "LineString",
+                    "MultiLineString",
+                    "Point",
+                    "PointZ",
+                    "Polygon",
+                    "MultiPolygon",
+                ]
+            ]
+            | None
+        ),
+        layer_name: str = "",
+        required_columns: list[str] = [],
+        logger=logging,
+        *args,
+        **kwargs,
+    ):
+        # Check type
+        required_columns = [i.lower() for i in required_columns]
+
+        # Add required columns to column list
+        kwargs["columns"] = required_columns
+        kwargs["geometry"] = GeoSeries()
+
+        super().__init__(*args, **kwargs)
+
+        self.validation_schema = validation_schema
+        self.required_columns = required_columns
+        self.layer_name = layer_name
+        self.geotype = geotype
+
+        if "geometry" not in self.required_columns:
+            self.required_columns += ["geometry"]
+        self.crs = MODEL_CRS
+
+    def _check_columns(self, gdf):
+        """Check presence of columns in GeoDataFrame"""
+        present_columns = gdf.columns.tolist()
+        for column in self.required_columns:
+            if column not in present_columns:
+                raise KeyError(
+                    'Column "{}" not found. Got {}, Expected at least {}'.format(
+                        column,
+                        ", ".join(present_columns),
+                        ", ".join(self.required_columns),
+                    )
+                )
+
+    def _check_geotype(self):
+        """Check geometry type"""
+        if self.geotype:
+            if not all(
+                any(isinstance(geo, GEOTYPE_MAPPING[i]) for i in self.geotype)
+                for geo in self.geometry
+            ):
+                raise TypeError(
+                    'Geometry-type "{}" required in layer "{}". The input feature-file has geometry type(s) {}.'.format(
+                        re.findall("([A-Z].*)'", repr(self.geotype))[0],
+                        self.layer_name,
+                        self.geometry.type.unique().tolist(),
+                    )
+                )
+
+    def _get_schema(self):
+        """Return fiona schema dict from validation_schema."""
+        properties = {
+            i["id"]: i["dtype"] for i in self.validation_schema if i["id"] != "geometry"
+        }
+        # properties = {k: (v if v != "datetime" else "str") for k, v in properties}
+        geometry = next(
+            (i["dtype"] for i in self.validation_schema if i["id"] == "geometry"),
+            None,
+        )
+        return {"properties": properties, "geometry": geometry}
+
+    def set_data(
+        self,
+        gdf,
+        layer="",
+        index_col=None,
+        check_columns=True,
+        check_geotype=True,
+        extra_attributes={},
+    ):
+        """
+
+
+        Parameters
+        ----------
+        gdf : GeoDataFrame
+            GeoDataFrame with a HyDAMO object-layer
+        index_col : str, optional
+            Column to be used as index. The default is None.
+        check_columns : bool, optional
+            Check if all required columns are present in the GeoDataFrame.
+            The default is True.
+        check_geotype : bool, optional
+            Check if the geometry is of the required type. The default is True.
+
+        Returns
+        -------
+        None.
+
+        """
+
+        if not self.empty:
+            self.delete_all()
+
+        # reproject to crs if necessary
+        if (gdf.crs is not None) and ("geometry" in self.required_columns):
+            if f"epsg:{gdf.crs.to_epsg()}" == MODEL_CRS:
+                gdf.set_crs(MODEL_CRS, inplace=True, allow_override=True)
+            else:
+                gdf.to_crs(MODEL_CRS, inplace=True)
+
+        # Check columns
+        gdf.columns = [i.lower() for i in gdf.columns]
+        if check_columns:
+            self._check_columns(gdf)
+
+        # Copy content
+        for col, values in gdf.items():
+            self[col] = values.to_numpy()
+
+        if index_col is None:
+            self.index = gdf.index
+            self.index.name = gdf.index.name
+
+        else:
+            self.index = gdf[index_col]
+            self.index.name = index_col
+
+        # Check geometry types
+        if check_geotype:
+            self._check_geotype()
+
+        # Set extra attribute-values
+        for k, v in extra_attributes.items():
+            if k not in self.columns:
+                self[k] = v
+
+    def delete_all(self):
+        """Empty the dataframe"""
+        if not self.empty:
+            self.iloc[:, 0] = np.nan
+            self.dropna(inplace=True)
+
+    def snap_to_branch(self, branches, snap_method, maxdist=5):
+        """
+
+
+        Parameters
+        ----------
+        branches : GeoDataFrame
+            GeoDataFrame with branches
+        snap_method : str
+            Options for snapping
+        maxdist : float, optional
+            The maximal distance for snapping. The default is 5.
+
+        Returns
+        -------
+        None.
+
+        """
+
+        """Snap the geometries to the branch."""
+        geometry.find_nearest_branch(
+            branches=branches, geometries=self, method=snap_method, maxdist=maxdist
+        )
+
+
+class HyDAMO:
+    """Definition of the HyDAMO datamodel."""
+
+    def __init__(
+        self,
+        version: str = "2.2",
+        schemas_path: Path = SCHEMAS_DIR,
+        ignored_layers: list[str] = [
+            "afvoeraanvoergebied",
+            "imwa_geoobject",
+            "leggerwatersysteem",
+            "leggerwaterveiligheid",
+            "waterbeheergebied",
+        ],
+    ):
+        self.version = version
+        self.schema_json = schemas_path.joinpath(f"HyDAMO_{version}.json")
+        self.layers: list[str] = []
+        self.ignored_layers = ignored_layers
+
+        self.init_datamodel()
+
+    @property
+    def data_layers(self):
+        return [layer for layer in self.layers if not getattr(self, layer).empty]
+
+    def init_datamodel(self) -> None:
+        """Initialize DataModel from self.schemas_path."""
+        self.validation_schemas: dict[str, Any] = {}
+
+        # read schema as dict
+        with open(self.schema_json) as src:
+            schema = json.load(src)
+            hydamo_layers = [
+                Path(i["$ref"]).name for i in schema["properties"]["HyDAMO"]["anyOf"]
+            ]
+            self.layers = [i for i in hydamo_layers if i not in self.ignored_layers]
+
+        for hydamo_layer in self.layers:
+            definition = schema["definitions"][hydamo_layer]["properties"]
+            layer_schema = map_definition(definition)
+            self.validation_schemas[hydamo_layer] = layer_schema
+
+            # add layer to data_model
+            geotype = next(
+                (i["dtype"] for i in layer_schema if i["id"] == "geometry"), None
+            )
+
+            required_columns = [
+                i["id"]
+                for i in [i for i in layer_schema if "required" in i.keys()]
+                if i["required"]
+            ]
+
+            setattr(
+                self,
+                hydamo_layer,
+                ExtendedGeoDataFrame(
+                    validation_schema=layer_schema,
+                    layer_name=hydamo_layer,
+                    geotype=geotype,
+                    required_columns=required_columns,
+                ),
+            )
+
+    def get(self, layer: str, global_id: str):
+        """
+        Get a DataFrame row (feature) providing a layer an global_id.
+
+        Parameters
+        ----------
+        layer : str
+            DESCRIPTION.
+        global_id : str
+            DESCRIPTION.
+
+        Returns
+        -------
+        TYPE
+            DESCRIPTION.
+
+        """
+        return getattr(self, layer).set_index("globalid").loc[global_id]
+
+    def set_data(
+        self,
+        gdf,
+        layer,
+        index_col=None,
+        check_columns=True,
+        check_geotype=True,
+        extra_attributes={},
+    ):
+        """
+
+
+        Parameters
+        ----------
+        gdf : GeoDataFrame
+            GeoDataFrame with a HyDAMO object-layer
+        layer : TYPE
+            HyDAMO layer to be set
+        index_col : str, optional
+            Column to be used as index. The default is None.
+        check_columns : bool, optional
+            Check if all required columns are present in the GeoDataFrame.
+            The default is True.
+        check_geotype : bool, optional
+            Check if the geometry is of the required type. The default is True.
+
+        Returns
+        -------
+        None.
+
+        """
+
+        getattr(self, layer).set_data(
+            gdf,
+            index_col=index_col,
+            check_columns=check_columns,
+            check_geotype=check_geotype,
+            extra_attributes={},
+        )
+
+    def to_geopackage(self, file_path, use_schema=True):
+        """
+
+        Parameters
+        ----------
+        file_path : path-string
+            Path-string where the file should be written to
+        use_schema : bool, optional
+            Use the schema to specify column-properties The default is True.
+
+        Returns
+        -------
+        None.
+
+        """
+        file_path = Path(file_path)
+        for layer in self.layers:
+            gdf = getattr(self, layer).copy()
+            if not gdf.empty:
+                if use_schema:
+                    # match fiona layer schema keys with gdf.columns
+                    schema = getattr(self, layer)._get_schema()
+                    schema_cols = list(schema["properties"].keys()) + ["geometry"]
+                    drop_cols = [i for i in gdf.columns if i not in schema_cols]
+                    gdf.drop(columns=drop_cols, inplace=True)
+
+                    schema["properties"] = {
+                        k: v
+                        for k, v in schema["properties"].items()
+                        if k in gdf.columns
+                    }
+
+                    # write gdf to geopackage, including schema
+                    if gdf.index.name in gdf.columns:
+                        gdf.reset_index(drop=True, inplace=True)
+                    gdf.to_file(
+                        file_path,
+                        layer=layer,
+                        driver="GPKG",
+                        engine="pyogrio",
+                    )
+                else:
+                    # write gdf to geopackage as is
+                    if gdf.index.name in gdf.columns:
+                        gdf = gdf.reset_index(drop=True).copy()
+                    gdf.to_file(file_path, layer=layer, driver="GPKG", engine="pyogrio")
+        if file_path.is_file():
+            add_styles_to_geopackage(file_path)
+
+    @classmethod
+    def from_geopackage(
+        cls, file_path, version="2.2", check_columns=True, check_geotype=True
+    ):
+        """
+        Initialize HyDAMO class from GeoPackage
+
+        Parameters
+        ----------
+        file_path : path-string
+            Path-string to the hydamo GeoPackage
+        check_columns : bool, optional
+            Check if all required columns are present in the GeoDataFrame.
+            The default is True.
+        check_geotype : bool, optional
+            Check if the geometry is of the required type. The default is True.
+
+        Returns
+        -------
+        hydamo : HyDAMO
+            HyDAMO object initialized with content of GeoPackage
+
+        """
+        hydamo = cls(version=version)
+        for layer in fiona.listlayers(file_path):
+            if layer in hydamo.layers:
+                hydamo_layer = getattr(hydamo, layer)
+                hydamo_layer.set_data(
+                    gpd.read_file(file_path, layer=layer),
+                    check_columns=check_columns,
+                    check_geotype=check_geotype,
+                )
+        return hydamo