Repair all uncertainty distributions. Fixes #104.

ocelot/transformations/parameterization/__init__.py

@@ -10,11 +10,13 @@
     replace_reserved_words,
 )
 from .recalculation import recalculate
+from .uncertainty import repair_all_uncertainty_distributions
 from .validation import variable_names_are_unique
 
 fix_ecoinvent_parameters = Collection(
     fix_specific_ecoinvent_issues,
     replace_implicit_references,
+    repair_all_uncertainty_distributions,
     fix_known_bad_formula_strings,
     lowercase_all_parameters,
     fix_math_formulas,

ocelot/transformations/parameterization/uncertainty.py

@@ -0,0 +1,17 @@
+# -*- coding: utf-8 -*-
+from ..uncertainty import get_uncertainty_class
+from ..utils import iterate_all_uncertainties
+import logging
+
+
+def repair_all_uncertainty_distributions(data):
+    """Repair all uncertainty distributions.
+
+    Uses distribution-specific ``repair`` methods."""
+    for ds in data:
+        for obj in iterate_all_uncertainties(ds):
+            if not obj.get('uncertainty'):
+                continue
+            # TODO: Add detailed log message
+            obj = get_uncertainty_class(obj).repair(obj)
+    return data

ocelot/transformations/utils.py

@@ -106,6 +106,22 @@ def iterate_all_parameters(dataset):
             yield parameter
 
 
+def iterate_all_uncertainties(dataset):
+    """Generator that returns all objects with an uncertainty distribution."""
+    for exc in dataset['exchanges']:
+        if "uncertainty" in exc:
+            yield exc
+        pv = exc.get("production volume", {})
+        if "uncertainty" in pv:
+            yield pv
+        for prop in exc.get('properties', []):
+            if "uncertainty" in prop:
+                yield prop
+    for parameter in dataset.get('parameters', []):
+        if "uncertainty" in parameter:
+            yield parameter
+
+
 def get_biggest_pv_to_exchange_ratio(dataset):
     """Return the largest ration of production volume to exchange amount.
 

tests/parameterization/parameterizaton_uncertainty.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+from ocelot.transformations.parameterization.uncertainty import repair_all_uncertainty_distributions as repair
+import numpy as np
+
+
+def test_repair():
+    given = [{
+        'exchanges': [{
+            'amount': -4,
+            'uncertainty': {
+                'type': 'lognormal',
+                'variance with pedigree uncertainty': 0.7
+            },
+            'pedigree matrix': {}
+        }, {
+            'amount': 0,
+            'uncertainty': {'type': 'lognormal'}
+        }]
+    }]
+    expected = [{
+        'exchanges': [{
+            'amount': -4,
+            'pedigree matrix': {},
+            'uncertainty': {
+                'type': 'lognormal',
+                'mean': 4,
+                'mu': np.log(4),
+                'negative': True,
+                'variance': 0.7,
+                'variance with pedigree uncertainty': 0.7
+            },
+        }, {
+            'amount': 0
+        }]
+    }]
+    assert repair(given) == expected

tests/transformations/transformations_utils.py

@@ -328,6 +328,44 @@ def test_iterate_all_parameters(parameterized_ds):
     assert next(generator) == parameterized_ds['parameters'][0]
     assert next(generator) == parameterized_ds['parameters'][1]
 
+@pytest.fixture(scope="function")
+def uncertain_ds():
+    return {
+        'exchanges': [{
+            'amount': 3.1415926535,
+            'uncertainty': '',
+            'production volume': {  # Nonsensical but should work
+                'uncertainty': '',
+                'amount': 42
+            },
+            'properties': [{
+                'uncertainty': '',
+                'amount': 17
+            }]
+        }, {
+            'uncertainty': '',
+            'properties': [{
+                'uncertainty': '',
+            }]
+        }],
+        'parameters': [{
+            'uncertainty': '',
+        }, {
+            'uncertainty': '',
+            'amount': 1
+        }]
+    }
+
+def test_iterate_all_uncertainties(uncertain_ds):
+    generator = iterate_all_uncertainties(uncertain_ds)
+    assert next(generator) == uncertain_ds['exchanges'][0]
+    assert next(generator) == uncertain_ds['exchanges'][0]['production volume']
+    assert next(generator) == uncertain_ds['exchanges'][0]['properties'][0]
+    assert next(generator) == uncertain_ds['exchanges'][1]
+    assert next(generator) == uncertain_ds['exchanges'][1]['properties'][0]
+    assert next(generator) == uncertain_ds['parameters'][0]
+    assert next(generator) == uncertain_ds['parameters'][1]
+
 def test_activity_hash():
     given = {
         'name': 'a',