pyholos 0.0.1__py3-none-any.whl

pyholos/soil.py

@@ -0,0 +1,439 @@
+from enum import StrEnum, auto, unique
+
+from pyholos import common2
+from pyholos.common import Region, get_region
+from pyholos.config import PathsSlcData
+from pyholos.common2 import CanadianProvince
+from pyholos.utils import AutoNameEnum, keep_alphabetical_characters
+
+
+@unique
+class SoilTexture(StrEnum):
+    """Holos Source Code:
+    https://github.com/holos-aafc/Holos/blob/main/H.Core/Enumerations/SoilTexture.cs
+    """
+    Fine = auto()
+    Medium = auto()
+    Coarse = auto()
+    Unknown = auto()
+
+
+class SoilFunctionalCategory(AutoNameEnum):
+    NotApplicable = auto()
+    Brown = auto()
+    BrownChernozem = auto()
+    DarkBrown = auto()
+    DarkBrownChernozem = auto()
+    Black = auto()
+    BlackGrayChernozem = auto()
+    Organic = auto()
+    EasternCanada = auto()
+    All = auto()
+    Unknown = auto()
+    Grey = auto()
+    DarkGrey = auto()
+
+    def get_simplified_soil_category(self):
+        if self in [
+            self.__class__.Brown,
+            self.__class__.DarkBrown,
+            self.__class__.BrownChernozem,
+            self.__class__.DarkBrownChernozem
+        ]:
+            res = self.__class__.Brown
+        elif self in [
+            self.__class__.Black,
+            self.__class__.BlackGrayChernozem
+        ]:
+            res = SoilFunctionalCategory.Black
+        else:
+            # Other types cannot be reduced/simplified (i.e. Organic, Eastern Canada, etc.)
+            res = self
+
+        return res
+
+
+def convert_soil_texture_name(
+        name: str
+) -> SoilTexture:
+    """Returns a SoilTexture member as a function of the soil name.
+
+    Args:
+        name: soil name
+
+    Returns:
+        SoilTexture member
+
+    Holos source code:
+        https://github.com/holos-aafc/Holos/blob/768b3d8fe2565dad0ba01fb8490974f1047a114f/H.Core/Converters/SoilTextureStringConverter.cs#L9
+    """
+    match keep_alphabetical_characters(name=name):
+        case "fine":
+            return SoilTexture.Fine
+        case "coarse":
+            return SoilTexture.Coarse
+        case "medium":
+            return SoilTexture.Medium
+        case _:
+            # throw new Exception(string.Format(Resources.ExceptionUnknownSoilTextureString, input));
+            return SoilTexture.Unknown
+
+
+def convert_soil_functional_category_name(
+        name: str
+) -> SoilFunctionalCategory:
+    """Returns a SoilFunctionalCategory member as a function of the soil functional category name.
+
+    Args:
+        name: soil functional category name
+
+    Returns:
+        SoilFunctionalCategory member
+
+    Holos source code:
+        https://github.com/holos-aafc/Holos/blob/768b3d8fe2565dad0ba01fb8490974f1047a114f/H.Core/Converters/SoilFunctionalCategoryStringConverter.cs#L10
+    """
+    match keep_alphabetical_characters(name=name):
+        case "brownchernozem":
+            return SoilFunctionalCategory.BrownChernozem
+        case "darkbrownchernozem":
+            return SoilFunctionalCategory.DarkBrownChernozem
+        case "blackgraychernozem":
+            return SoilFunctionalCategory.BlackGrayChernozem
+        case "all":
+            return SoilFunctionalCategory.All
+        case "brown":
+            return SoilFunctionalCategory.Brown
+        case "darkbrown":
+            return SoilFunctionalCategory.DarkBrown
+        case "black":
+            return SoilFunctionalCategory.Black
+        case "organic":
+            return SoilFunctionalCategory.Organic
+        case "easterncanada" | "east":
+            return SoilFunctionalCategory.EasternCanada
+        case _:
+            # Trace.TraceError($"{nameof(SoilFunctionalCategoryStringConverter)}: Soil functional category '{input}' not mapped, returning default value.")
+            return SoilFunctionalCategory.NotApplicable
+
+
+class SoilGreatGroup:
+    def __init__(
+            self,
+            soil_great_group_type: str,
+            region: str,
+            soil_functional_category: str
+    ):
+        self.soil_great_group_type = soil_great_group_type
+        self.region = region
+        self.soil_functional_category = soil_functional_category
+
+
+def get_soil_great_group_table() -> list[SoilGreatGroup]:
+    return [
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.BrownChernozem.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.BrownChernozem.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DarkBrownChernozem.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.DarkBrown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DarkBrownChernozem.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.BlackChernozem.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Black),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.BlackChernozem.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DarkGrayChernozem.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Black),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DarkGrayChernozem.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Solonetz.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Solonetz.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.SolodizedSolonetz.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.SolodizedSolonetz.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Solod.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Solod.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.VerticSolonetz.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.VerticSolonetz.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.GrayBrownLuvisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.GrayBrownLuvisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.GrayLuvisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Black),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.GrayLuvisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.FerroHumicPodzol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.FerroHumicPodzol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumicPodzol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumicPodzol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumoFerricPodzol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumoFerricPodzol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.MelanicBrunisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.MelanicBrunisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.EutricBrunisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.EutricBrunisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.SombricBrunisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.SombricBrunisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DystricBrunisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.DystricBrunisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumicGleysol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.HumicGleysol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Gleysol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Brown),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Gleysol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.LuvicGleysol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Black),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.LuvicGleysol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Fibrisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Fibrisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Mesisol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Mesisol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.OrganicCryosol.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.OrganicCryosol.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.Organic),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.NotApplicable.name,
+            region=Region.WesternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.NotApplicable.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.NotApplicable),
+
+        SoilGreatGroup(
+            soil_great_group_type=common2.SoilGreatGroupNamesSlc.Unknown.name,
+            region=Region.EasternCanada,
+            soil_functional_category=SoilFunctionalCategory.EasternCanada),
+    ]
+
+
+def seek_soil_functional_category(
+        province: common2.CanadianProvince,
+        soil_great_group: str
+) -> str:
+    region = get_region(province=province)
+
+    for v in get_soil_great_group_table():
+        if all([v.soil_great_group_type == soil_great_group, v.region == region]):
+            return v.soil_functional_category
+
+
+def get_soil_functional_category(
+        province: common2.CanadianProvince,
+        soil_great_group: str
+) -> str:
+    soil_functional_category = seek_soil_functional_category(
+        province=province,
+        soil_great_group=soil_great_group)
+    return soil_functional_category if soil_functional_category is not None else SoilFunctionalCategory.Black
+
+
+def set_soil_texture_according_to_holos(
+        soil_texture_abbreviation_from_slc: str
+) -> str:
+    soil_name = common2.ParentMaterialTextureNamesSlc.get_name(abbreviation=soil_texture_abbreviation_from_slc)
+    if soil_name in ('Very Coarse', 'Coarse', 'Moderately Coarse'):
+        res = SoilTexture.Coarse.name
+    elif soil_name in ('Medium', 'Medium Skeletal'):
+        res = SoilTexture.Medium.name
+    elif soil_name in ('Moderately Fine', 'Fine', 'Very Fine', 'Fine Skeletal'):
+        res = SoilTexture.Fine.name
+    else:
+        res = SoilTexture.Medium.name
+    return res
+
+
+def set_soil_properties(
+        latitude: float,
+        longitude: float
+) -> dict:
+    """Calculates the soil properties required by Holos 4.0
+
+    Args:
+        latitude: (decimal degrees) latitude of the simulated site
+        longitude: (decimal degrees) longitude of the simulated site
+
+    Returns:
+        The following key-value pairs:
+            id_polygon (int): ID of the SLC polygon in which the site is located
+            province (str): The Canadian Province in which the site is located
+            ecodistrict_id (int): ID of the Ecodistrict within which the farm is located
+            soil_great_group (str): soil great group (e.g. "Regosol")
+            soil_functional_category (str): soil functional (e.g. "Black")
+            bulk_density (float): (g cm-3) soil bulk density
+            soil_texture (str): soil texture (e.g. "Fine")
+            soil_ph (float): (-) soil pH
+            top_layer_thickness (float): (mm) thickness of the soil top layer
+            sand_proportion (float): (between 0 and 1) fraction of sand in soil
+            clay_proportion (float): (between 0 and 1) fraction of clay in soil
+            organic_carbon_proportion (float): (between 0 and 100) percentage of soil organic carbon in soil
+
+    """
+    polygon_properties = common2.get_slc_polygon_properties(
+        latitude=latitude,
+        longitude=longitude,
+        geojson_data=common2.load_slc_data(
+            path_slc_geojson_file=PathsSlcData.geojson_file))
+    id_polygon = polygon_properties['POLY_ID']
+    dominant_component_properties = common2.get_dominant_component_properties(
+        id_polygon=id_polygon,
+        slc_components_table=common2.read_slc_csv(
+            path_file=PathsSlcData.cmp_file,
+            usecols=['POLY_ID', 'PROVINCE', 'PERCENT_', 'SOIL_ID']))
+    id_soil = dominant_component_properties['SOIL_ID']
+    soil_layer_table = common2.get_soil_layer_table(
+        id_soil=id_soil,
+        slc_soil_layer_table=common2.read_slc_csv(path_file=PathsSlcData.slt_file))
+    first_non_litter_layer = common2.get_first_non_litter_layer(
+        soil_layer_table=soil_layer_table)
+    soil_name_table = common2.get_soil_name_table(
+        soil_name_table=common2.read_slc_csv(
+            path_file=PathsSlcData.snt_file, usecols=['SOIL_ID', 'PMTEX1', 'G_GROUP3']),
+        id_soil=id_soil)
+
+    province = common2.CanadianProvince.get_name(abbreviation=dominant_component_properties['PROVINCE'])
+    soil_great_group = common2.SoilGreatGroupNamesSlc.get_name(
+        abbreviation=soil_name_table['G_GROUP3']).replace(' ', '')
+
+    return dict(
+        id_polygon=id_polygon,
+        province=province,
+        ecodistrict_id=polygon_properties['ECO_ID'],
+        soil_great_group=soil_great_group,
+        soil_functional_category=get_soil_functional_category(
+            province=getattr(CanadianProvince, province),
+            soil_great_group=soil_great_group),
+        bulk_density=first_non_litter_layer['BD'],
+        soil_texture=set_soil_texture_according_to_holos(
+            soil_texture_abbreviation_from_slc=soil_name_table['PMTEX1']),
+        soil_ph=round(first_non_litter_layer['PH2'], 1),
+        top_layer_thickness=first_non_litter_layer['LDEPTH'] * 10,
+        sand_proportion=first_non_litter_layer['TSAND'] / 100.,
+        clay_proportion=first_non_litter_layer['TCLAY'] / 100.,
+        organic_carbon_proportion=round(first_non_litter_layer['ORGCARB'], 2))
+
+    pass

pyholos/utils.py

@@ -0,0 +1,83 @@
+import re
+from enum import StrEnum
+from pathlib import Path
+from typing import Callable, Iterable
+
+from pandas import DataFrame, read_csv
+
+from pyholos.core_constants import CoreConstants
+
+
+class AutoNameEnum(StrEnum):
+    """Allows automatically setting the member value identical to the member name."""
+
+    def _generate_next_value_(self, start, count, last_values):
+        return self
+
+
+def read_holos_resource_table(
+        path_file: Path | str,
+        **kwargs
+) -> DataFrame:
+    return read_csv(path_file, sep=',', decimal='.', comment='#', **kwargs
+                    ).replace({
+        'NotApplicable': CoreConstants.NotApplicable,
+        float('nan'): None})
+
+
+def get_local_args(kwargs: dict) -> dict:
+    return {k: v for k, v in kwargs.items() if not any([k.startswith('_'), k == 'self'])}
+
+
+def convert_camel_case_to_space_delimited(s: str) -> str:
+    return re.sub("([a-z])([A-Z])", r"\g<1> \g<2>", s)
+
+
+def concat_lists(*args) -> list:
+    return [v for ls in args for v in ls]
+
+
+def keep_alphabetical_characters(name: str) -> str:
+    return ''.join(s for s in name if s.isalpha()).lower()
+
+
+def calc_average(values: Iterable[int | float]) -> float:
+    values = list(values)
+    return sum(values) / len(list(values))
+
+
+def clean_string(
+        input_string: str,
+        characters_to_remove: str | list[str] = (',', ' ', ';'),
+        is_remove_text_between_parentheses: bool = True,
+        is_remove_text_between_brackets: bool = True
+) -> str:
+    if not isinstance(characters_to_remove, (str, tuple)):
+        characters_to_remove = [characters_to_remove]
+
+    for s in characters_to_remove:
+        input_string = input_string.replace(s, '')
+
+    if is_remove_text_between_parentheses:
+        input_string = re.sub("[(].*?[)]", "", input_string)
+
+    if is_remove_text_between_brackets:
+        input_string = re.sub("[[].*?[]]", "", input_string)
+
+    return input_string
+
+
+def calc_vector_percentage(vector: int | float | Iterable) -> list:
+    if not isinstance(vector, Iterable):
+        vector = [vector]
+    assert all([v >= 0 for v in vector]), "Negative values are not allowed when calculating a vector's percentage"
+    assert sum(vector) > 0, "At least on item must be greater than 0 when calculating a vector's percentage"
+
+    return [v / sum(vector) * 100 for v in vector]
+
+
+def print_holos_msg(
+        is_print_message: bool,
+        holos_message: str
+) -> Callable | None:
+    return print(holos_message) if is_print_message else None

pyholos-0.0.1.dist-info/METADATA

@@ -0,0 +1,16 @@
+Metadata-Version: 2.4
+Name: pyholos
+Version: 0.0.1
+Summary: A Python package for running the HOLOS 4.0 CLI.
+Project-URL: Homepage, https://github.com/Mon-Systeme-Fourrager/pyholos
+Project-URL: Issues, https://github.com/Mon-Systeme-Fourrager/pyholos/issues
+Author-email: Rami ALBASHA <ralbasha@msfourrager.com>
+License-File: LICENSE
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+
+# Welcome to PyHolos, the Python wrapper for Holos CLI! (and beyond)
+Description in progress
+

pyholos-0.0.1.dist-info/RECORD

@@ -0,0 +1,55 @@
+pyholos/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyholos/common.py,sha256=JOnsBjlxWAmzyGLkuNoTACEfuVAuCg8EqwnAcFNOQT4,4822
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