hestia-earth-models 0.44.6__py3-none-any.whl → 0.44.7__py3-none-any.whl

hestia_earth/models/site/cationExchangeCapacityPerKgSoil.py

@@ -0,0 +1,75 @@
+from hestia_earth.schema import MeasurementStatsDefinition, MeasurementMethodClassification
+from hestia_earth.utils.model import find_term_match
+
+from hestia_earth.models.log import logRequirements, logShouldRun
+from hestia_earth.models.utils.measurement import _new_measurement, group_measurements_by_depth, measurement_value
+from . import MODEL
+
+REQUIREMENTS = {
+    "Site": {
+        "measurements": [
+            {"@type": "Measurement", "value": "", "term.@id": "clayContent"},
+            {"@type": "Measurement", "value": "", "term.@id": "soilPh"},
+            {"@type": "Measurement", "value": "", "term.@id": "organicCarbonPerKgSoil"}
+        ]
+    }
+}
+RETURNS = {
+    "Measurement": [{
+        "value": "",
+        "depthUpper": "",
+        "depthLower": "",
+        "statsDefinition": "modelled",
+        "methodClassification": "modelled using other physical measurements"
+    }]
+}
+TERM_ID = 'cationExchangeCapacityPerKgSoil'
+BIBLIO_TITLE = 'Contribution of Organic Matter and Clay to Soil Cation-Exchange Capacity as Affected by the pH of the Saturating Solution'  # noqa: E501
+
+
+def measurement(value: float, depthUpper: int = None, depthLower: int = None):
+    data = _new_measurement(TERM_ID, None, BIBLIO_TITLE)
+    data['value'] = [value]
+    if depthUpper is not None:
+        data['depthUpper'] = depthUpper
+    if depthLower is not None:
+        data['depthLower'] = depthLower
+    data['statsDefinition'] = MeasurementStatsDefinition.MODELLED.value
+    data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_PHYSICAL_MEASUREMENTS.value
+    return data
+
+
+def _run(measurements: list):
+    clayContent = find_term_match(measurements, 'clayContent')
+    clayContent_value = measurement_value(clayContent)
+    soilPh = measurement_value(find_term_match(measurements, 'soilPh'))
+    organicCarbonPerKgSoil = measurement_value(find_term_match(measurements, 'organicCarbonPerKgSoil'))
+
+    value = ((51 * soilPh - 59) * (organicCarbonPerKgSoil/10) + (30 + 4.4 * soilPh) * clayContent_value)/100
+
+    depthUpper = clayContent.get('depthUpper')
+    depthLower = clayContent.get('depthLower')
+
+    return measurement(value, depthUpper=depthUpper, depthLower=depthLower)
+
+
+def _should_run(site: dict, measurements: list):
+    clayContent = find_term_match(measurements, 'clayContent', None)
+    soilPh = find_term_match(measurements, 'soilPh', None)
+    organicCarbonPerKgSoil = find_term_match(measurements, 'organicCarbonPerKgSoil', None)
+
+    logRequirements(site, model=MODEL, term=TERM_ID,
+                    has_clayContent=clayContent is not None,
+                    has_soilPh=soilPh is not None,
+                    has_organicCarbonPerKgSoil=organicCarbonPerKgSoil is not None)
+
+    should_run = all([clayContent is not None, soilPh is not None, organicCarbonPerKgSoil is not None])
+    logShouldRun(site, MODEL, TERM_ID, should_run)
+    return should_run
+
+
+def run(site: dict):
+    grouped_measurements = list(group_measurements_by_depth(site.get('measurements', [])).values())
+    return [
+        _run(measurements) for measurements in grouped_measurements if _should_run(site, measurements)
+    ]

hestia_earth/models/site/organicCarbonPerHa.py

@@ -0,0 +1,82 @@
+from hestia_earth.schema import MeasurementStatsDefinition, MeasurementMethodClassification
+from hestia_earth.utils.model import find_term_match
+
+from hestia_earth.models.log import logRequirements, logShouldRun
+from hestia_earth.models.utils.measurement import _new_measurement, group_measurements_by_depth, measurement_value
+from . import MODEL
+
+REQUIREMENTS = {
+    "Site": {
+        "measurements": [
+            {"@type": "Measurement", "value": "", "term.@id": "soilBulkDensity", "depthUpper": "", "depthLower": ""},
+            {"@type": "Measurement", "value": "", "term.@id": "organicCarbonPerKgSoil", "depthUpper": "", "depthLower": ""}  # noqa: E501
+        ]
+    }
+}
+RETURNS = {
+    "Measurement": [{
+        "value": "",
+        "depthUpper": "",
+        "depthLower": "",
+        "statsDefinition": "modelled",
+        "methodClassification": "modelled using other physical measurements"
+    }]
+}
+TERM_ID = 'organicCarbonPerHa'
+BIBLIO_TITLE = 'Soil organic carbon sequestration rates in vineyard agroecosystems under different soil management practices: A meta-analysis'  # noqa: E501
+
+
+def measurement(value: float, depthUpper: int, depthLower: int):
+    data = _new_measurement(TERM_ID, None, BIBLIO_TITLE)
+    data['value'] = [value]
+    data['depthUpper'] = depthUpper
+    data['depthLower'] = depthLower
+    data['statsDefinition'] = MeasurementStatsDefinition.MODELLED.value
+    data['methodClassification'] = MeasurementMethodClassification.MODELLED_USING_OTHER_PHYSICAL_MEASUREMENTS.value
+    return data
+
+
+def _run(measurements: list):
+    soilBulkDensity = measurement_value(find_term_match(measurements, 'soilBulkDensity'))
+    organicCarbonPerKgSoil = find_term_match(measurements, 'organicCarbonPerKgSoil')
+    organicCarbonPerKgSoil_value = measurement_value(organicCarbonPerKgSoil)
+
+    value = (
+        organicCarbonPerKgSoil.get('depthLower') - organicCarbonPerKgSoil.get('depthUpper')
+    ) * soilBulkDensity * (organicCarbonPerKgSoil_value/10) * 1000
+
+    depthUpper = organicCarbonPerKgSoil.get('depthUpper')
+    depthLower = organicCarbonPerKgSoil.get('depthLower')
+
+    return measurement(value, depthUpper, depthLower)
+
+
+def _should_run(site: dict, measurements: list):
+    soilBulkDensity = find_term_match(measurements, 'soilBulkDensity', None)
+    has_soilBulkDensity_depthLower = (soilBulkDensity or {}).get('depthLower') is not None
+    has_soilBulkDensity_depthUpper = (soilBulkDensity or {}).get('depthUpper') is not None
+    organicCarbonPerKgSoil = find_term_match(measurements, 'organicCarbonPerKgSoil', None)
+    has_organicCarbonPerKgSoil_depthLower = (organicCarbonPerKgSoil or {}).get('depthLower') is not None
+    has_organicCarbonPerKgSoil_depthUpper = (organicCarbonPerKgSoil or {}).get('depthUpper') is not None
+
+    logRequirements(site, model=MODEL, term=TERM_ID,
+                    has_soilBulkDensity=soilBulkDensity is not None,
+                    has_soilBulkDensity_depthLower=has_soilBulkDensity_depthLower,
+                    has_soilBulkDensity_depthUpper=has_soilBulkDensity_depthUpper,
+                    has_organicCarbonPerKgSoil=organicCarbonPerKgSoil is not None,
+                    has_organicCarbonPerKgSoil_depthLower=has_organicCarbonPerKgSoil_depthLower,
+                    has_organicCarbonPerKgSoil_depthUpper=has_organicCarbonPerKgSoil_depthUpper)
+
+    should_run = all([
+        soilBulkDensity is not None, has_soilBulkDensity_depthLower, has_soilBulkDensity_depthUpper,
+        organicCarbonPerKgSoil is not None, has_organicCarbonPerKgSoil_depthLower, has_organicCarbonPerKgSoil_depthUpper
+    ])
+    logShouldRun(site, MODEL, TERM_ID, should_run)
+    return should_run
+
+
+def run(site: dict):
+    grouped_measurements = list(group_measurements_by_depth(site.get('measurements', [])).values())
+    return [
+        _run(measurements) for measurements in grouped_measurements if _should_run(site, measurements)
+    ]

hestia_earth/models/utils/measurement.py

@@ -1,8 +1,10 @@
+from functools import reduce
 from dateutil import parser
 from statistics import mode, mean
 from hestia_earth.schema import SchemaType
 from hestia_earth.utils.api import download_hestia
 from hestia_earth.utils.model import linked_node
+from hestia_earth.utils.tools import non_empty_list
 
 from . import _term_id, _include_method, _include_source
 from .term import get_lookup_value
@@ -59,3 +61,21 @@ def most_relevant_measurement(measurements: list, term_id: str, date: str):
 def most_relevant_measurement_value(measurements: list, term_id: str, date: str, default=None):
     measurement = most_relevant_measurement(measurements, term_id, date)
     return measurement_value(measurement) if measurement else default
+
+
+def _group_measurement_key(measurement: dict):
+    keys = non_empty_list([
+        str(measurement.get('depthUpper', '')),
+        str(measurement.get('depthLower', '')),
+        measurement.get('startDate'),
+        measurement.get('endDate')
+    ])
+    return '-'.join(keys) if len(keys) > 0 else 'default'
+
+
+def group_measurements_by_depth(measurements: list):
+    def group_by(group: dict, measurement: dict):
+        key = _group_measurement_key(measurement)
+        return group | {key: group.get(key, []) + [measurement]}
+
+    return reduce(group_by, measurements, {})

hestia_earth/models/version.py

@@ -1 +1 @@
-VERSION = '0.44.6'
+VERSION = '0.44.7'

{hestia_earth_models-0.44.6.dist-info → hestia_earth_models-0.44.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hestia-earth-models
-Version: 0.44.6
+Version: 0.44.7
 Summary: Hestia's set of modules for filling gaps in the activity data using external datasets (e.g. populating soil properties with a geospatial dataset using provided coordinates) and internal lookups (e.g. populating machinery use from fuel use). Includes rules for when gaps should be filled versus not (e.g. never gap fill yield, gap fill crop residue if yield provided etc.).
 Home-page: https://gitlab.com/hestia-earth/hestia-engine-models
 Author: Hestia Team

{hestia_earth_models-0.44.6.dist-info → hestia_earth_models-0.44.7.dist-info}/RECORD

@@ -2,7 +2,7 @@ hestia_earth/__init__.py,sha256=G-d438vPx7m_ks5e9XTtM3u7LDRO5dSSukibukWmyPM,56
 hestia_earth/models/__init__.py,sha256=qEFeq3yuf3lQKVseALmL8aPM8fpCS54B_5pry00M3hk,76
 hestia_earth/models/log.py,sha256=rOgKa-gSrcS-Y1gO9eJXJaA3ofxcQW_45hGly2Lf00Y,2444
 hestia_earth/models/requirements.py,sha256=znNZJAhwX2iYiKcAQXPftY7z_1MsNa0QxCXkXyHm_U0,17363
-hestia_earth/models/version.py,sha256=taeVh2_WgbOJy1VoS9mf7Yd35BQxdqpZcIFdshvWnD0,19
+hestia_earth/models/version.py,sha256=siXWAyoDG_AIMVLULiR25FA-JVP5ErxJNeP4ZVU5pwI,19
 hestia_earth/models/agribalyse2016/__init__.py,sha256=WvK0qCQbnYtg9oZxrACd1wGormZyXibPtpCnIQeDqbw,415
 hestia_earth/models/agribalyse2016/fuelElectricity.py,sha256=ztMnY6XTwsJD-lp62jJyzN2AUODvFHIs5d5CaFrlVGI,3567
 hestia_earth/models/agribalyse2016/machineryInfrastructureDepreciatedAmountPerCycle.py,sha256=10XV1fz_yBYlqmNJ3cxmT2I2Vp_0w7nT4zMIuBw2wCY,3294
@@ -315,7 +315,7 @@ hestia_earth/models/lcImpactCertainEffectsInfinite/damageToTerrestrialEcosystems
 hestia_earth/models/linkedImpactAssessment/__init__.py,sha256=x6xsPu-Rwh-7HKsvHuKmgM1YML6fQy2z9Hsy9_BeO2Y,3565
 hestia_earth/models/mocking/__init__.py,sha256=Y39V6yj_3M1q8v9ShCHwPeJOstypOVIvb_FldMEbF7g,766
 hestia_earth/models/mocking/mock_search.py,sha256=ysPhzvMGvsHKqQXKRFi8ZqohcnyKutBlNqT_j0OH8L4,1983
-hestia_earth/models/mocking/search-results.json,sha256=2OtWvfsZjgMVDQHmlMUHZMcsjIu6IaBub8vz492JnQ4,29411
+hestia_earth/models/mocking/search-results.json,sha256=OxONqG0icjhfpsx9abPt-4FQDnOD2OQFHJot1eJNX_8,29671
 hestia_earth/models/pooreNemecek2018/__init__.py,sha256=nPboL7ULJzL5nJD5q7q9VOZt_fxbKVm8fmn1Az5YkVY,417
 hestia_earth/models/pooreNemecek2018/aboveGroundCropResidueTotal.py,sha256=trQBxjc8V77q96sxvK4Y9HfpD64zgyGuB5o5_o0lHts,2189
 hestia_earth/models/pooreNemecek2018/belowGroundCropResidue.py,sha256=do9zHHR8VuqFcWNLnql5t3tV478SCVc7tC3mEs5cdUk,2184
@@ -401,8 +401,10 @@ hestia_earth/models/schererPfister2015/pToGroundwaterSoilFlux.py,sha256=Gt3YdTCu
 hestia_earth/models/schererPfister2015/pToSurfaceWaterSoilFlux.py,sha256=bzgtCAtX0D5cRqoL24Ukg2IDr00Up7Ji4m1QQ9fJ-9w,2741
 hestia_earth/models/schererPfister2015/utils.py,sha256=LEvz9guqto0kuF5rXcQjgYsD3CvEmORvJQqRA1f7uMI,3130
 hestia_earth/models/site/__init__.py,sha256=aQRep10EVnCIY97xAxTFQ_AFJNNoZtPvb50mIu_HmQo,342
+hestia_earth/models/site/cationExchangeCapacityPerKgSoil.py,sha256=TOc5u1r0-wOXjdmNunz0QErexNRQc2n9i3fMykvFu60,3153
 hestia_earth/models/site/flowingWater.py,sha256=ZPeXd2tNYgG24kYOGQZM9lrUzCi9nZsabvHJsaH0hy4,1796
 hestia_earth/models/site/netPrimaryProduction.py,sha256=mwoQcjYkCbHxzZ8PhFN7RtjwKa5igqkICpNVJq08lYc,1901
+hestia_earth/models/site/organicCarbonPerHa.py,sha256=_duLpVHx-rx0f1I5IzreDp9LulC0JULrX63bm2W_tcM,3905
 hestia_earth/models/site/organicCarbonPerKgSoil.py,sha256=zY9QUho9jhaQK-X0x_DszZOoj-Ol8NzNcASk-Ix_qEk,1870
 hestia_earth/models/site/organicCarbonPerM3Soil.py,sha256=r-rDBLr-h10__csvlWreoe2MVBpMT5MMmokZVLRJ7Iw,1870
 hestia_earth/models/site/organicMatterPerKgSoil.py,sha256=VXXLt9lBWkNR8xY4tGOi9DmiaRBKydbevwJ_HL2JNf0,1870
@@ -464,7 +466,7 @@ hestia_earth/models/utils/inorganicFertiliser.py,sha256=zJpNvDNaEsZ2T_V4APAQy4rm
 hestia_earth/models/utils/input.py,sha256=CsoMC_Jjnifl5mjPWhWOBhiHmNI5IGWRfPjshOV1Ipg,6798
 hestia_earth/models/utils/liveAnimal.py,sha256=u_Lym0hVinncCZMYF_KscCA3vuelWmlyHn4I-jVRDs4,1505
 hestia_earth/models/utils/lookup.py,sha256=Y9ekB_AGpmZKZI7NnYodvvF2pFHlkFHkryMk1SVWp60,5307
-hestia_earth/models/utils/measurement.py,sha256=jeX82DPwVQHFBMe5V0yGvQEDDv4ymMtiMsMbOwgM9oU,2607
+hestia_earth/models/utils/measurement.py,sha256=FPH1yPOztLe2J5dwGbrHMDFiEPe7aBVYKHvRUY8Cd2c,3266
 hestia_earth/models/utils/pesticideAI.py,sha256=KQNXos2oG-TbDARxg3ksJAfAAYeiaQIZ5e3V2S0A-fA,1329
 hestia_earth/models/utils/practice.py,sha256=tNadOzsrNlCEt801B815XaruJXzZ5yPASam7B3sWpXE,1091
 hestia_earth/models/utils/product.py,sha256=OFzxe2mFdqUfhQ7tfXkhd-sYMqIxPLIgKJFq65oNrQE,8605
@@ -860,8 +862,10 @@ tests/models/schererPfister2015/test_pToDrainageWaterSoilFlux.py,sha256=57MVRyiE
 tests/models/schererPfister2015/test_pToGroundwaterSoilFlux.py,sha256=lOTL-ue6hEbQsKIss6VsN7bJME5UCB3pTbqbLtMp9rk,1064
 tests/models/schererPfister2015/test_pToSurfaceWaterSoilFlux.py,sha256=1VJo9q-Kb2OboK2RMp3-bkP6lXfkFbqMz1ACJC75FWw,1441
 tests/models/site/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/models/site/test_cationExchangeCapacityPerKgSoil.py,sha256=FOtllJ_E4Ld4MngPn__CsQXXeHhZ5fNB-ruSd8DUgFQ,963
 tests/models/site/test_flowingWater.py,sha256=q7ktHV7sffIUBf0SgIhbkL_U_c7RTHYv6oWhXY4A6io,1274
 tests/models/site/test_netPrimaryProduction.py,sha256=FaC5TEwHnR56_QrXkIB5u3mgSLOcSmBRbL8vzqaZwk0,1056
+tests/models/site/test_organicCarbonPerHa.py,sha256=m392fH_aEt_tI6dVhAzOVHKpeuztNgP5p6yNiLTs4Mw,983
 tests/models/site/test_organicCarbonPerKgSoil.py,sha256=fqPe2JbrZwwMK497Qnb2WPx4-n2vda4PW-S3tQa_CGI,1035
 tests/models/site/test_organicCarbonPerM3Soil.py,sha256=8fOwtcBAFH1fSduIXXtYOdL83oYAVxC4f6BAZpY5X_w,1035
 tests/models/site/test_organicMatterPerKgSoil.py,sha256=EvZ6HknxjUjhdmdYostB9eCc_WowpRWpmssWM2vT_NU,1035
@@ -921,8 +925,8 @@ tests/models/utils/test_site.py,sha256=deEIYptl2MHEklSfHbZV9qA59YKqZLQr8y5rWYiD4
 tests/models/utils/test_term.py,sha256=-Wn2C1jyOLfkvhcKmKWT-Jms7yqLwx5ok91gYJNcGWc,2028
 tests/models/webbEtAl2012AndSintermannEtAl2012/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/models/webbEtAl2012AndSintermannEtAl2012/test_nh3ToAirOrganicFertiliser.py,sha256=qi2FNXS5Af2WDtm7nq_FsprH3BfCF0XxnE0XHmC4aIY,2244
-hestia_earth_models-0.44.6.dist-info/LICENSE,sha256=EFSZhfUdZCTsCIYdHzTGewMKfRfp7X9t1s2aaKxm8O0,1154
-hestia_earth_models-0.44.6.dist-info/METADATA,sha256=sZ1RfX1WGhbTlTP_40S7dwt1QBruRa52MSpOWiZmD-w,3192
-hestia_earth_models-0.44.6.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-hestia_earth_models-0.44.6.dist-info/top_level.txt,sha256=1dqA9TqpOLTEgpqa-YBsmbCmmNU1y56AtfFGEceZ2A0,19
-hestia_earth_models-0.44.6.dist-info/RECORD,,
+hestia_earth_models-0.44.7.dist-info/LICENSE,sha256=EFSZhfUdZCTsCIYdHzTGewMKfRfp7X9t1s2aaKxm8O0,1154
+hestia_earth_models-0.44.7.dist-info/METADATA,sha256=FVLQ7WFHs3bn6q2b2j-Dzjanz9_fRIlt1fL2ms6MBsM,3192
+hestia_earth_models-0.44.7.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+hestia_earth_models-0.44.7.dist-info/top_level.txt,sha256=1dqA9TqpOLTEgpqa-YBsmbCmmNU1y56AtfFGEceZ2A0,19
+hestia_earth_models-0.44.7.dist-info/RECORD,,

tests/models/site/test_cationExchangeCapacityPerKgSoil.py

@@ -0,0 +1,31 @@
+from unittest.mock import patch
+import json
+from tests.utils import fixtures_path, fake_new_measurement
+
+from hestia_earth.models.site.cationExchangeCapacityPerKgSoil import MODEL, TERM_ID, run, _should_run
+
+class_path = f"hestia_earth.models.{MODEL}.{TERM_ID}"
+fixtures_folder = f"{fixtures_path}/{MODEL}/{TERM_ID}"
+
+
+@patch(f"{class_path}.find_term_match")
+def test_should_run(mock_find):
+    # no measurement => no run
+    mock_find.return_value = None
+    assert not _should_run({}, [])
+
+    # with measurement => run
+    mock_find.return_value = {'value': [10]}
+    assert _should_run({}, []) is True
+
+
+@patch(f"{class_path}._new_measurement", side_effect=fake_new_measurement)
+def test_run(*args):
+    with open(f"{fixtures_folder}/site.jsonld", encoding='utf-8') as f:
+        site = json.load(f)
+
+    with open(f"{fixtures_folder}/result.jsonld", encoding='utf-8') as f:
+        expected = json.load(f)
+
+    value = run(site)
+    assert value == expected

tests/models/site/test_organicCarbonPerHa.py

@@ -0,0 +1,31 @@
+from unittest.mock import patch
+import json
+from tests.utils import fixtures_path, fake_new_measurement
+
+from hestia_earth.models.site.organicCarbonPerHa import MODEL, TERM_ID, run, _should_run
+
+class_path = f"hestia_earth.models.{MODEL}.{TERM_ID}"
+fixtures_folder = f"{fixtures_path}/{MODEL}/{TERM_ID}"
+
+
+@patch(f"{class_path}.find_term_match")
+def test_should_run(mock_find):
+    # no measurement => no run
+    mock_find.return_value = {}
+    assert not _should_run({}, [])
+
+    # with measurement => run
+    mock_find.return_value = {'value': [10], 'depthUpper': 0, 'depthLower': 10}
+    assert _should_run({}, []) is True
+
+
+@patch(f"{class_path}._new_measurement", side_effect=fake_new_measurement)
+def test_run(*args):
+    with open(f"{fixtures_folder}/site.jsonld", encoding='utf-8') as f:
+        site = json.load(f)
+
+    with open(f"{fixtures_folder}/result.jsonld", encoding='utf-8') as f:
+        expected = json.load(f)
+
+    value = run(site)
+    assert value == expected