hestia-earth-models 0.70.0__py3-none-any.whl → 0.70.2__py3-none-any.whl

hestia_earth/models/{site → hestia}/rainfallAnnual.py

@@ -3,7 +3,7 @@ from hestia_earth.utils.tools import flatten, non_empty_list
 
 from hestia_earth.models.log import logRequirements, logShouldRun
 from hestia_earth.models.utils.measurement import _new_measurement
-from .utils import _slice_by_year
+from .utils import slice_by_year
 from . import MODEL
 
 REQUIREMENTS = {
@@ -26,7 +26,7 @@ MEASUREMENT_ID = 'rainfallMonthly'
 
 
 def _measurement(value: float, start_date: str, end_date: str):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = [value]
     data['startDate'] = start_date
     data['endDate'] = end_date
@@ -38,7 +38,7 @@ def _run(measurement: dict):
     values = measurement.get('value', [])
     dates = measurement.get('dates', [])
     term_id = measurement.get('term', {}).get('@id')
-    results = _slice_by_year(term_id, dates, values)
+    results = slice_by_year(term_id, dates, values)
     return [_measurement(value, start_date, end_date) for (value, start_date, end_date) in results]
 
 

hestia_earth/models/{site → hestia}/rainfallMonthly.py

@@ -3,7 +3,7 @@ from hestia_earth.utils.tools import flatten, non_empty_list
 
 from hestia_earth.models.log import logRequirements, logShouldRun
 from hestia_earth.models.utils.measurement import _new_measurement
-from .utils import _group_by_month
+from .utils import group_by_month
 from . import MODEL
 
 REQUIREMENTS = {
@@ -25,7 +25,7 @@ MEASUREMENT_ID = 'rainfallDaily'
 
 
 def _measurement(value: list, dates: list):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = value
     data['dates'] = dates
     data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_MEASUREMENTS.value
@@ -36,7 +36,7 @@ def _run(measurement: dict):
     values = measurement.get('value', [])
     dates = measurement.get('dates', [])
     term_id = measurement.get('term', {}).get('@id')
-    result = _group_by_month(term_id, dates, values)
+    result = group_by_month(term_id, dates, values)
     return _measurement(result[0], result[1]) if len(result[0]) > 0 else None
 
 

hestia_earth/models/{cycle → hestia}/readyToCookWeightPerHead.py

@@ -36,7 +36,7 @@ TERM_ID = 'readyToCookWeightPerHead'
 
 
 def _property(value: float):
-    prop = _new_property(TERM_ID)
+    prop = _new_property(TERM_ID, MODEL)
     prop['value'] = value
     return prop
 

hestia_earth/models/{cycle → hestia}/residueBurnt.py

@@ -25,7 +25,7 @@ TERM_ID = 'residueBurnt'
 
 
 def _practice(value: float):
-    practice = _new_practice(TERM_ID)
+    practice = _new_practice(TERM_ID, MODEL)
     practice['value'] = [value]
     return practice
 

hestia_earth/models/{cycle → hestia}/residueIncorporated.py

@@ -35,7 +35,7 @@ TERM_ID = 'residueIncorporated'
 
 
 def _practice(value: float):
-    practice = _new_practice(TERM_ID)
+    practice = _new_practice(TERM_ID, MODEL)
     practice['value'] = [value]
     return practice
 

hestia_earth/models/{cycle → hestia}/residueLeftOnField.py

@@ -25,7 +25,7 @@ TERM_ID = 'residueLeftOnField'
 
 
 def _practice(value: float):
-    practice = _new_practice(TERM_ID)
+    practice = _new_practice(TERM_ID, MODEL)
     practice['value'] = [value]
     return practice
 

hestia_earth/models/hestia/residueRemoved.py

@@ -1,5 +1,5 @@
 from hestia_earth.schema import TermTermType
-from hestia_earth.utils.model import filter_list_term_type
+from hestia_earth.utils.model import filter_list_term_type, find_term_match
 from hestia_earth.utils.tools import list_sum
 
 from hestia_earth.models.log import logRequirements, logShouldRun, log_as_table
@@ -11,14 +11,20 @@ from . import MODEL
 REQUIREMENTS = {
     "Cycle": {
         "completeness.cropResidue": "False",
-        "practices": [{
-            "@type": "Practice",
-            "term.@id": [
-                "residueIncorporated",
-                "residueIncorporatedLessThan30DaysBeforeCultivation",
-                "residueIncorporatedMoreThan30DaysBeforeCultivation"
+        "or": {
+            "practices": [{
+                "@type": "Practice",
+                "term.@id": [
+                    "residueIncorporated",
+                    "residueIncorporatedLessThan30DaysBeforeCultivation",
+                    "residueIncorporatedMoreThan30DaysBeforeCultivation"
+                ]
+            }],
+            "products": [
+                {"@type": "Product", "term.@id": "aboveGroundCropResidueTotal", "value": "> 0"},
+                {"@type": "Product", "term.@id": "aboveGroundCropResidueRemoved", "value": "> 0"}
             ]
-        }],
+        },
         "none": {
             "practices": [{
                 "@type": "Practice",
@@ -45,14 +51,57 @@ def _practice(value: float):
     return practice
 
 
-def _should_run(cycle: dict):
+def _run_by_products(cycle: dict):
+    products = cycle.get('products', [])
+    aboveGroundCropResidueTotal = list_sum(find_term_match(products, 'aboveGroundCropResidueTotal').get('value'))
+    aboveGroundCropResidueRemoved = list_sum(find_term_match(products, 'aboveGroundCropResidueRemoved').get('value'))
+    return [_practice(aboveGroundCropResidueRemoved / aboveGroundCropResidueTotal * 100)]
+
+
+def _should_run_by_products(cycle: dict):
+    crop_residue_incomplete = _is_term_type_incomplete(cycle, TermTermType.CROPRESIDUE)
+    products = cycle.get('products', [])
+    aboveGroundCropResidueTotal = list_sum(find_term_match(products, 'aboveGroundCropResidueTotal').get('value', [0]))
+    has_aboveGroundCropResidueTotal = aboveGroundCropResidueTotal > 0
+    aboveGroundCropResidueRemoved = list_sum(
+        find_term_match(products, 'aboveGroundCropResidueRemoved').get('value', [0]))
+    has_aboveGroundCropResidueRemoved = aboveGroundCropResidueRemoved > 0
+
+    logRequirements(cycle, model=MODEL, term=TERM_ID,
+                    term_type_cropResidue_incomplete=crop_residue_incomplete,
+                    has_aboveGroundCropResidueTotal=has_aboveGroundCropResidueTotal,
+                    has_aboveGroundCropResidueRemoved=has_aboveGroundCropResidueRemoved)
+
+    should_run = all([crop_residue_incomplete, has_aboveGroundCropResidueTotal, has_aboveGroundCropResidueRemoved])
+    logShouldRun(cycle, MODEL, TERM_ID, should_run)
+    return should_run
+
+
+def _is_incorporated_practice(practice: dict):
+    return all([
+        practice.get('term', {}).get('@id').startswith('residueIncorporated'),
+        practice.get('term', {}).get('termType') == TermTermType.CROPRESIDUEMANAGEMENT.value,
+        not is_from_model(practice)
+    ])
+
+
+def _run_by_practices(cycle: dict):
+    incorporated_value = list_sum([
+        list_sum(p.get('value'))
+        for p in cycle.get('practices', [])
+        if _is_incorporated_practice(p)
+    ])
+    return [_practice(100 - (incorporated_value or 0))]
+
+
+def _should_run_by_practices(cycle: dict):
     crop_residue_incomplete = _is_term_type_incomplete(cycle, TermTermType.CROPRESIDUE)
 
     practices = filter_list_term_type(cycle.get('practices', []), TermTermType.CROPRESIDUEMANAGEMENT)
     incorporated_practices = [
         {'id': p.get('term', {}).get('@id'), 'value': list_sum(p.get('value'), None)}
         for p in practices
-        if p.get('term', {}).get('@id').startswith('residueIncorporated') and not is_from_model(p)
+        if _is_incorporated_practice(p)
     ]
     has_other_practices = any([
         not p.get('term', {}).get('@id').startswith('residueIncorporated')
@@ -68,9 +117,12 @@ def _should_run(cycle: dict):
 
     should_run = all([crop_residue_incomplete, incorporated_value, not has_other_practices])
     logShouldRun(cycle, MODEL, TERM_ID, should_run)
-    return should_run, 100 - (incorporated_value or 0)
+    return should_run
 
 
 def run(cycle: dict):
-    should_run, value = _should_run(cycle)
-    return [_practice(value)] if should_run else []
+    return (
+        _run_by_products(cycle) if _should_run_by_products(cycle) else
+        _run_by_practices(cycle) if _should_run_by_practices(cycle) else
+        []
+    )

hestia_earth/models/{site → hestia}/salineWater.py

@@ -22,7 +22,7 @@ TERM_ID = 'salineWater'
 
 
 def _measurement():
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = [True]
     data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_MEASUREMENTS.value
     return data

hestia_earth/models/{site → hestia}/soilMeasurement.py

@@ -32,7 +32,7 @@ STANDARD_DEPTHS = {(0, 30), (0, 50)}
 
 
 def _measurement(value: float, date: str, term_id: str, standard_fields: dict):
-    data = _new_measurement(term=term_id)
+    data = _new_measurement(term_id, MODEL)
     data["value"] = [value]
     data["depthUpper"] = standard_fields["depthUpper"]
     data["depthLower"] = standard_fields["depthLower"]

hestia_earth/models/{cycle → hestia}/stockingDensityAnimalHousingAverage.py

@@ -28,7 +28,7 @@ TERM_ID = 'stockingDensityAnimalHousingAverage'
 
 
 def _practice(value: float):
-    practice = _new_practice(TERM_ID)
+    practice = _new_practice(TERM_ID, MODEL)
     practice['value'] = [round(value, 7)]
     return practice
 

hestia_earth/models/{site → hestia}/temperatureAnnual.py

@@ -3,7 +3,7 @@ from hestia_earth.utils.tools import flatten, non_empty_list
 
 from hestia_earth.models.log import logRequirements, logShouldRun
 from hestia_earth.models.utils.measurement import _new_measurement
-from .utils import _slice_by_year
+from .utils import slice_by_year
 from . import MODEL
 
 REQUIREMENTS = {
@@ -26,7 +26,7 @@ MEASUREMENT_ID = 'temperatureMonthly'
 
 
 def _measurement(value: float, start_date: str, end_date: str):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = [value]
     data['startDate'] = start_date
     data['endDate'] = end_date
@@ -38,7 +38,7 @@ def _run(measurement: dict):
     values = measurement.get('value', [])
     dates = measurement.get('dates', [])
     term_id = measurement.get('term', {}).get('@id')
-    results = _slice_by_year(term_id, dates, values)
+    results = slice_by_year(term_id, dates, values)
     return [_measurement(value, start_date, end_date) for (value, start_date, end_date) in results]
 
 

hestia_earth/models/{site → hestia}/temperatureMonthly.py

@@ -3,7 +3,7 @@ from hestia_earth.utils.tools import flatten, non_empty_list
 
 from hestia_earth.models.log import logRequirements, logShouldRun
 from hestia_earth.models.utils.measurement import _new_measurement
-from .utils import _group_by_month
+from .utils import group_by_month
 from . import MODEL
 
 REQUIREMENTS = {
@@ -25,7 +25,7 @@ MEASUREMENT_ID = 'temperatureDaily'
 
 
 def _measurement(value: list, dates: list):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = value
     data['dates'] = dates
     data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_MEASUREMENTS.value
@@ -36,7 +36,7 @@ def _run(measurement: dict):
     values = measurement.get('value', [])
     dates = measurement.get('dates', [])
     term_id = measurement.get('term', {}).get('@id')
-    result = _group_by_month(term_id, dates, values)
+    result = group_by_month(term_id, dates, values)
     return _measurement(result[0], result[1]) if len(result[0]) > 0 else None
 
 

hestia_earth/models/{site → hestia}/totalNitrogenPerKgSoil.py

@@ -25,7 +25,7 @@ BIBLIO_TITLE = 'Reducing food’s environmental impacts through producers and co
 
 
 def _measurement(site: dict, value: float):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = [value]
     data['depthUpper'] = 0
     data['depthLower'] = 50

hestia_earth/models/{cycle → hestia}/unknownPreSeasonWaterRegime.py

@@ -28,7 +28,7 @@ TERM_ID = 'unknownPreSeasonWaterRegime'
 
 
 def _practice():
-    practice = _new_practice(TERM_ID)
+    practice = _new_practice(TERM_ID, MODEL)
     practice['value'] = [100]
     return practice
 

hestia_earth/models/hestia/utils.py

@@ -1,6 +1,11 @@
+from functools import reduce
 from hestia_earth.schema import TermTermType
+from hestia_earth.utils.tools import non_empty_list
+from hestia_earth.utils.date import DAY
 
+from hestia_earth.models.utils import _omit, first_day_of_month, last_day_of_month
 from hestia_earth.models.utils.term import get_lookup_value
+from hestia_earth.models.utils.measurement import _new_measurement, measurement_value, has_all_months
 from . import MODEL
 
 IPCC_LAND_USE_CATEGORY_ANNUAL = "Annual crops"
@@ -45,3 +50,91 @@ def crop_ipcc_land_use_category(
         column='IPCC_LAND_USE_CATEGORY',
         model=MODEL
     )
+
+
+def get_liveAnimal_term_id(product: dict, **log_ars):
+    term_id = get_lookup_value(product.get('term', {}), 'liveAnimalTermId', model=MODEL, **log_ars)
+    return term_id.split(';')[0] if term_id else None
+
+
+def _value_func(data: dict, apply_func, key: str = 'value'):
+    values = data.get(key, data.get('value', []))
+    return list(map(apply_func, values))
+
+
+def copy_measurement(term_id: str, data: dict):
+    measurement = _new_measurement(term_id, MODEL)
+    return _omit(data, ['description', 'method']) | measurement
+
+
+def slice_by_year(term_id: str, dates: list, values: list):
+    def group_values(group: dict, index: int):
+        try:
+            date = dates[index]
+            value = values[index]
+            month = dates[index][0:4]
+            group[month] = group.get(month, []) + [(date, value)]
+        except IndexError:
+            pass
+        return group
+
+    def iterate_values(data: list):
+        return (
+            measurement_value({
+                'term': {
+                    '@id': term_id,
+                    'termType': TermTermType.MEASUREMENT.value
+                },
+                'value': non_empty_list([v for (_d, v) in data])
+            }, is_larger_unit=True),
+            data[0][0],
+            data[-1][0]
+        ) if has_all_months([d for (d, _v) in data]) else None
+
+    values_by_month = reduce(group_values, range(0, len(dates)), {})
+    return non_empty_list(map(iterate_values, values_by_month.values()))
+
+
+def _extract_year_month(date: str):
+    try:
+        year = int(date[0:4])
+        month = int(date[5:7])
+        return year, month
+    except Exception:
+        return None, None
+
+
+def group_by_month(term_id: str, dates: list, values: list):
+    def group_values(group: dict, index: int):
+        date = dates[index]
+        value = values[index]
+        month = dates[index][0:7]
+        group[month] = group.get(month, []) + [(date, value)]
+        return group
+
+    def map_to_month(data: list, year: int, month: int):
+        # make sure we got all the necessary days
+        difference = last_day_of_month(year, month) - first_day_of_month(year, month)
+        days_in_month = round(difference.days + difference.seconds / DAY, 1) + 1
+
+        return measurement_value({
+            'term': {
+                '@id': term_id,
+                'termType': TermTermType.MEASUREMENT.value
+            },
+            'value': non_empty_list([v for (_d, v) in data])
+        }, is_larger_unit=True) if len(data) == days_in_month else None
+
+    values_by_month = reduce(group_values, range(0, len(dates)), {}) if len(dates) == len(values) else {}
+
+    values = []
+    dates = []
+    for month, data in values_by_month.items():
+        year, m = _extract_year_month(data[0][0])
+        # date might not contain a year or a month, cannot handle it
+        value = map_to_month(data, year, m) if year and m else None
+        if value is not None:
+            dates.append(month)
+            values.append(value)
+
+    return values, dates

hestia_earth/models/{site → hestia}/waterDepth.py

@@ -25,7 +25,7 @@ SITE_TYPE_TO_DEPTH = {
 
 
 def _measurement(site: dict, value: float):
-    data = _new_measurement(TERM_ID)
+    data = _new_measurement(TERM_ID, MODEL)
     data['value'] = [value]
     data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_MEASUREMENTS.value
     return data | get_source(site, BIBLIO_TITLE)

hestia_earth/models/hestia/waterSalinity.py

@@ -0,0 +1,78 @@
+from hestia_earth.schema import MeasurementMethodClassification, TermTermType
+from hestia_earth.utils.model import filter_list_term_type
+from hestia_earth.utils.tools import safe_parse_float
+
+from hestia_earth.models.log import logRequirements, logShouldRun, log_as_table
+from hestia_earth.models.utils.measurement import _new_measurement
+from hestia_earth.models.utils.site import related_cycles
+from hestia_earth.models.utils.blank_node import get_lookup_value
+from . import MODEL
+
+REQUIREMENTS = {
+    "Site": {
+        "related": {
+            "Cycle": {
+                "@type": "Cycle",
+                "products": [{
+                    "@type": "Product",
+                    "primary": "True",
+                    "term.termType": "liveAquaticSpecies"
+                }]
+            }
+        }
+    }
+}
+RETURNS = {
+    "Measurement": [{
+        "value": "",
+        "startDate": "",
+        "endDate": "",
+        "methodClassification": "expert opinion"
+    }]
+}
+LOOKUPS = {
+    "liveAquaticSpecies": "defaultSalinity"
+}
+TERM_ID = 'waterSalinity'
+
+
+def _measurement(value: float, start_date: str = None, end_date: str = None):
+    data = _new_measurement(TERM_ID, MODEL)
+    data['value'] = [value]
+    data['endDate'] = end_date
+    if start_date:
+        data['startDate'] = start_date
+    data['methodClassification'] = MeasurementMethodClassification.EXPERT_OPINION.value
+    return data
+
+
+def _should_run(site: dict):
+    cycles = related_cycles(site)
+    relevant_products = [
+        {
+            'product-id': product.get('term', {}).get('@id'),
+            'lookup-value': safe_parse_float(
+                get_lookup_value(product.get('term', {}), LOOKUPS['liveAquaticSpecies']), default=None
+            ),
+            'start-date': product.get('startDate') or cycle.get('startDate'),
+            'end-date': product.get('endDate') or cycle.get('endDate')
+        }
+        for cycle in cycles
+        for product in filter_list_term_type(cycle.get('products', []), TermTermType.LIVEAQUATICSPECIES)
+    ]
+    has_valid_products = any([product.get('lookup-value') for product in relevant_products])
+
+    logRequirements(site, model=MODEL, term=TERM_ID,
+                    live_aquatic_products=log_as_table(relevant_products))
+
+    should_run = all([has_valid_products])
+    logShouldRun(site, MODEL, TERM_ID, should_run)
+    return should_run, relevant_products
+
+
+def run(site: dict):
+    should_run, values = _should_run(site)
+    return [
+        _measurement(value.get('lookup-value'), value.get('start-date'), value.get('end-date'))
+        for value in values if value.get('lookup-value') is not None
+    ] if should_run else []

hestia_earth/models/ipcc2019/aboveGroundBiomass.py

@@ -568,7 +568,7 @@ def _measurement(
         "dates": [f"{year}-12-31" for year in timestamps],
         "methodClassification": _METHOD_CLASSIFICATION
     }
-    measurement = _new_measurement(TERM_ID) | {
+    measurement = _new_measurement(TERM_ID, MODEL) | {
         key: value for key, value in update_dict.items() if value
     }
     return measurement

hestia_earth/models/ipcc2019/belowGroundBiomass.py

@@ -551,7 +551,7 @@ def _measurement(
         "dates": [f"{year}-12-31" for year in timestamps],
         "methodClassification": _METHOD_CLASSIFICATION
     }
-    measurement = _new_measurement(TERM_ID) | {
+    measurement = _new_measurement(TERM_ID, MODEL) | {
         key: value for key, value in update_dict.items() if value
     }
     measurement["depthUpper"] = _DEPTH_UPPER

hestia_earth/models/ipcc2019/biomass_utils.py

@@ -1,7 +1,7 @@
 from enum import Enum
 from functools import reduce
 from math import isclose
-from numpy import random
+from numpy import inf, random
 from numpy.typing import NDArray
 from typing import Callable, Optional, Union
 
@@ -393,9 +393,7 @@ def sample_plus_minus_error(
 ) -> NDArray:
     """Randomly sample a model parameter with a truncated normal distribution described using plus/minus error."""
     sd = value * (error / 200)
-    low = value - (value * (error / 100))
-    high = value + (value * (error / 100))
-    return truncated_normal_1d(shape=(1, iterations), mu=value, sigma=sd, low=low, high=high, seed=seed)
+    return truncated_normal_1d(shape=(1, iterations), mu=value, sigma=sd, low=0, high=inf, seed=seed)
 
 
 def sample_constant(*, iterations: int, value: float, **_) -> NDArray: