Eco updates from review

hawc/apps/eco/autocomplete.py

@@ -26,13 +26,20 @@ class EcoregionAutocomplete(BaseAutocomplete):
     search_fields = ["value"]
 
     def get_queryset(self):
-        return super().get_queryset().filter(category=constants.VocabCategories.ECOREGION)
+        return (
+            super()
+            .get_queryset()
+            .filter(category=constants.VocabCategories.ECOREGION, deprecated_on__isnull=True)
+        )
 
 
 @register
 class NestedTermAutocomplete(BaseAutocomplete):
     model = models.NestedTerm
     search_fields = ("id", "name")
 
+    def get_queryset(self):
+        return super().get_queryset().filter(deprecated_on__isnull=True)
+
     def get_result_label(self, obj):
         return f"{obj.label()} ({obj.id})"

hawc/apps/eco/filterset.py

@@ -19,6 +19,10 @@ class Meta:
         }
         main_field = "name__contains"
 
+    def filter_queryset(self, queryset):
+        queryset = super().filter_queryset(queryset)
+        return queryset.filter(deprecated_on__isnull=True)
+
     @property
     def has_query(self) -> bool:
         return self.data.get("name__contains", "") != ""

hawc/apps/eco/fixtures/nestedterms_2.json

@@ -0,0 +1 @@
+[{"parents": ["Air", "Physical"], "fields": {"name": "acid rain", "type": "CE"}}, {"parents": ["Air", "Physical", "climate"], "fields": {"name": "storms/hurricanes", "type": "CE"}}, {"parents": ["Air", "Physical"], "fields": {"name": "excess energy", "type": "CE"}}, {"parents": ["Air", "Physical", "excess energy"], "fields": {"name": "light pollution", "type": "CE"}}, {"parents": ["Air", "Physical", "excess energy"], "fields": {"name": "noise pollution", "type": "CE"}}, {"parents": ["Air", "Physical", "excess energy"], "fields": {"name": "thermal pollution", "type": "CE"}}, {"parents": ["Air", "Physical"], "fields": {"name": "transportation and service corridors- flight paths", "type": "CE"}}, {"parents": ["Land", "Biological", "Birds"], "fields": {"name": "behavior", "type": "CE"}}, {"parents": ["Land", "Biological", "Birds"], "fields": {"name": "physiology/condition", "type": "CE"}}, {"parents": ["Land", "Biological", "Birds"], "fields": {"name": "reproduction/fecundity", "type": "CE"}}, {"parents": ["Land", "Biological"], "fields": {"name": "Resource use", "type": "CE"}}, {"parents": ["Land", "Biological", "Resource use"], "fields": {"name": "Hunting and collecting terrestrial animals", "type": "CE"}}, {"parents": ["Land", "Biological", "Resource use"], "fields": {"name": "Gathering terrestrial plants", "type": "CE"}}, {"parents": ["Land", "Biological", "Resource use"], "fields": {"name": "Logging and wood harvesting", "type": "CE"}}, {"parents": ["Land", "Biological"], "fields": {"name": "Terrestrial invasive species", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover"], "fields": {"name": "residential/commercial development", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "residential/commercial development"], "fields": {"name": "housing and urban areas", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "residential/commercial development"], "fields": {"name": "commercial and industrial areas", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "residential/commercial development"], "fields": {"name": "tourism and recreational areas", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "agriculture"], "fields": {"name": "annual and perennial non-timber crops", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "agriculture"], "fields": {"name": "wood and pulp plantations", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "agriculture"], "fields": {"name": "livestock farming and ranching", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover"], "fields": {"name": "energy production and mining", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "energy production and mining"], "fields": {"name": "oil and gas drilling", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "energy production and mining"], "fields": {"name": "mining and quarrying", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "energy production and mining"], "fields": {"name": "renewable energy", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover"], "fields": {"name": "transportation and service corridors", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "transportation and service corridors"], "fields": {"name": "roads and railroads", "type": "CE"}}, {"parents": ["Land", "Physical", "Land use/land cover", "transportation and service corridors"], "fields": {"name": "utility and service lines", "type": "CE"}}, {"parents": ["Land", "Physical"], "fields": {"name": "Geological events", "type": "CE"}}, {"parents": ["Land", "Physical", "Geological events"], "fields": {"name": "Volcanoes", "type": "CE"}}, {"parents": ["Land", "Physical", "Geological events"], "fields": {"name": "Earthquakes/tsunamis", "type": "CE"}}, {"parents": ["Land", "Physical", "Geological events"], "fields": {"name": "Avalanches/landslides", "type": "CE"}}, {"parents": ["Water", "Biological"], "fields": {"name": "Corals", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "abundance", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "biochemical", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals", "biochemical"], "fields": {"name": "enzyme", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals", "biochemical"], "fields": {"name": "stoichiometry", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "community structure", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals", "community structure"], "fields": {"name": "diversity", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals", "community structure"], "fields": {"name": "multimetric index", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals", "community structure"], "fields": {"name": "richness", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "genetic", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "growth/size/biomass", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "mortality", "type": "CE"}}, {"parents": ["Water", "Biological", "Corals"], "fields": {"name": "population structure", "type": "CE"}}, {"parents": ["Water", "Biological"], "fields": {"name": "Resource use", "type": "CE"}}, {"parents": ["Water", "Biological", "Resource use"], "fields": {"name": "Fishing and harvesting aquatic resources", "type": "CE"}}, {"parents": ["Water", "Physical", "Effluent"], "fields": {"name": "agricultural and forestry", "type": "CE"}}, {"parents": ["Water", "Physical", "Effluent"], "fields": {"name": "domestic and urban wastewater", "type": "CE"}}, {"parents": ["Water", "Physical", "Effluent"], "fields": {"name": "garbage and solid waste", "type": "CE"}}, {"parents": ["Water", "Physical", "Effluent"], "fields": {"name": "industrial and military", "type": "CE"}}, {"parents": ["Water", "Physical", "Hydrology"], "fields": {"name": "sea level rise", "type": "CE"}}, {"parents": ["Water", "Physical"], "fields": {"name": "Transportation and service corridors- shipping lanes", "type": "CE"}}]

hawc/apps/eco/fixtures/vocab_2.jsonl

@@ -0,0 +1,34 @@
+{"pk": 203, "model": "eco.Vocab", "fields": {"category": 2, "value": "Freshwater aquatic"}}
+{"pk": 204, "model": "eco.Vocab", "fields": {"category": 2, "parent": 203, "value": "Rivers and streams biome"}}
+{"pk": 205, "model": "eco.Vocab", "fields": {"category": 2, "parent": 203, "value": "Artificial wetlands biome"}}
+{"pk": 206, "model": "eco.Vocab", "fields": {"category": 2, "parent": 203, "value": "Lakes biome"}}
+{"pk": 207, "model": "eco.Vocab", "fields": {"category": 2, "value": "Freshwater aquatic/Marine"}}
+{"pk": 208, "model": "eco.Vocab", "fields": {"category": 2, "value": "Marine"}}
+{"pk": 209, "model": "eco.Vocab", "fields": {"category": 2, "parent": 208, "value": "Marine shelf biome"}}
+{"pk": 210, "model": "eco.Vocab", "fields": {"category": 2, "parent": 208, "value": "Pelagic ocean waters biome"}}
+{"pk": 211, "model": "eco.Vocab", "fields": {"category": 2, "parent": 208, "value": "Deep sea floors biome"}}
+{"pk": 212, "model": "eco.Vocab", "fields": {"category": 2, "parent": 208, "value": "Anthropogenic marine biome"}}
+{"pk": 213, "model": "eco.Vocab", "fields": {"category": 2, "value": "Marine/Terrestrial"}}
+{"pk": 214, "model": "eco.Vocab", "fields": {"category": 2, "parent": 213, "value": "Shorelines biome"}}
+{"pk": 215, "model": "eco.Vocab", "fields": {"category": 2, "parent": 213, "value": "Supralittoral coastal biome"}}
+{"pk": 216, "model": "eco.Vocab", "fields": {"category": 2, "parent": 213, "value": "Anthropogenic shorelines biome"}}
+{"pk": 217, "model": "eco.Vocab", "fields": {"category": 2, "value": "Marine/Freshwater/Terrestrial"}}
+{"pk": 218, "model": "eco.Vocab", "fields": {"category": 2, "parent": 217, "value": "Brackish tidal biome"}}
+{"pk": 219, "model": "eco.Vocab", "fields": {"category": 2, "value": "Terrestrial"}}
+{"pk": 220, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Tropical-subtropical forests biome"}}
+{"pk": 221, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Temperate-boreal forests and woodlands biome"}}
+{"pk": 222, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Shurblands and shrubby woodlands biome"}}
+{"pk": 223, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Savannas and grasslands biome"}}
+{"pk": 224, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Deserts and semi-deserts biome"}}
+{"pk": 225, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Polar/alpine (cryogenic) biome"}}
+{"pk": 226, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Intensive land-use biome (crops)"}}
+{"pk": 227, "model": "eco.Vocab", "fields": {"category": 2, "parent": 219, "value": "Intensive land-use biome (urban)"}}
+{"pk": 228, "model": "eco.Vocab", "fields": {"category": 2, "value": "Terrestrial/Freshwater"}}
+{"pk": 229, "model": "eco.Vocab", "fields": {"category": 2, "parent": 228, "value": "Palustrine wetlands biome"}}
+{"pk": 230, "model": "eco.Vocab", "fields": {"category": 2, "value": "Subterranean"}}
+{"pk": 231, "model": "eco.Vocab", "fields": {"category": 2, "parent": 230, "value": "Lithic biome"}}
+{"pk": 232, "model": "eco.Vocab", "fields": {"category": 2, "parent": 230, "value": "Anthropogenic voids biome"}}
+{"pk": 233, "model": "eco.Vocab", "fields": {"category": 2, "value": "Subterranean/Freshwater"}}
+{"pk": 234, "model": "eco.Vocab", "fields": {"category": 2, "parent": 233, "value": "Anthropogenic"}}
+{"pk": 235, "model": "eco.Vocab", "fields": {"category": 2, "value": "Subterranean/Marine"}}
+{"pk": 236, "model": "eco.Vocab", "fields": {"category": 2, "parent": 235, "value": "Tidal biome"}}

hawc/apps/eco/migrations/0002_load_fixtures.py

@@ -8,8 +8,8 @@ def load_fixture(apps, schema_editor):
     here = Path(__file__).parent
     fixtures = (here / "../fixtures").resolve()
     call_command("loaddata", str(fixtures / "states.json"), app_label="eco")
-    call_command("loaddata", str(fixtures / "vocab.json"), app_label="eco")
-    call_command("loaddata", str(fixtures / "nestedterms.jsonl"), app_label="eco")
+    call_command("loaddata", str(fixtures / "vocab_1.json"), app_label="eco")
+    call_command("loaddata", str(fixtures / "nestedterms_1.jsonl"), app_label="eco")
 
 
 def unload_fixture(apps, schema_editor):

hawc/apps/eco/migrations/0006_update_vocab.py

@@ -0,0 +1,129 @@
+import json
+from pathlib import Path
+
+import django.db.models.deletion
+from django.core.management import call_command
+from django.db import migrations, models
+from django.utils import timezone
+
+here = Path(__file__).parent
+fixtures = (here / "../fixtures").resolve()
+
+
+def load_vocab(apps, schema_editor):
+    now = timezone.now()
+
+    # deprecate existing
+    vocab = apps.get_model("eco", "Vocab")
+    vocab.objects.filter(category=2).exclude(id__in=[197, 198]).update(deprecated_on=now)
+
+    # load new values
+    call_command("loaddata", str(fixtures / "vocab_2.jsonl"), app_label="eco")
+
+
+def load_nested_terms(apps, schema_editor):
+    now = timezone.now()
+
+    # load the "real model" since we to use Treebeard manager methods
+    from hawc.apps.eco.models import NestedTerm
+
+    # rename
+    NestedTerm.objects.filter(id=457).update(name="fire and fire suppression")
+    NestedTerm.objects.filter(id=60).update(name="Water withdrawal/abstraction")
+
+    # fmt: off
+    # mark as deprecated
+    NestedTerm.objects.filter(
+        id__in=[
+            37, 38, 39, 434, 435, 436, 437, 438, 439, 440, 456, 461, 468, 537, 538, 539, 593, 595
+        ]
+    ).update(deprecated_on=now)
+    # fmt: on
+
+    # load new terms. We can't use a django fixture because Treebeard reorders nodes and
+    # may change the `path` of nodes based on name (for this model)
+    additions = json.loads((fixtures / "nestedterms_2.json").read_text())
+    for addition in additions:
+        for i, parent_name in enumerate(addition["parents"]):
+            if i == 0:
+                parent = NestedTerm.objects.get(depth=1, name=parent_name)
+            else:
+                for child in parent.get_children():
+                    if child.name == parent_name:
+                        parent = child
+                        break
+        parent.add_child(**addition["fields"])
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("eco", "0005_remove_restraints"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="nestedterm",
+            name="deprecated_on",
+            field=models.DateTimeField(blank=True, default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name="vocab",
+            name="deprecated_on",
+            field=models.DateTimeField(blank=True, default=None, null=True),
+        ),
+        migrations.AlterField(
+            model_name="design",
+            name="climates",
+            field=models.ManyToManyField(
+                help_text='Select one or more <a rel="noopener noreferrer" target="_blank" href="http://koeppen-geiger.vu-wien.ac.at/present.htm">Koppen climate classifications</a> to which the evidence applies',
+                limit_choices_to={"category": 11, "deprecated_on": None},
+                related_name="designs_by_climate",
+                to="eco.vocab",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="design",
+            name="design",
+            field=models.ForeignKey(
+                help_text="Select study design",
+                limit_choices_to={"category": 0, "deprecated_on": None},
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="designs_by_type",
+                to="eco.vocab",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="design",
+            name="ecoregions",
+            field=models.ManyToManyField(
+                blank=True,
+                help_text='Select one or more <a rel="noopener noreferrer" target="_blank" href="https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states">Level III Ecoregions</a> from the continental US, if known',
+                limit_choices_to={"category": 12, "deprecated_on": None},
+                related_name="designs_by_ecoregion",
+                to="eco.vocab",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="design",
+            name="habitats",
+            field=models.ManyToManyField(
+                help_text='Select one or more <a rel="noopener noreferrer" target="_blank" href="https://global-ecosystems.org/">IUCN Global Ecosystems</a> to which the evidence applies.',
+                limit_choices_to={"category": 2, "deprecated_on": None},
+                related_name="designs_by_habitat",
+                to="eco.vocab",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="design",
+            name="study_setting",
+            field=models.ForeignKey(
+                help_text="Select the setting in which evidence was generated",
+                limit_choices_to={"category": 1, "deprecated_on": None},
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="designs_by_setting",
+                to="eco.vocab",
+            ),
+        ),
+        migrations.RunPython(load_vocab, reverse_code=migrations.RunPython.noop),
+        migrations.RunPython(load_nested_terms, reverse_code=migrations.RunPython.noop),
+    ]

hawc/apps/eco/models.py

@@ -28,6 +28,7 @@ class NestedTerm(MP_Node):
     created = models.DateTimeField(auto_now_add=True)
     last_updated = models.DateTimeField(auto_now=True)
     notes = models.TextField(blank=True)
+    deprecated_on = models.DateTimeField(blank=True, default=None, null=True)
 
     node_order_by = ["name"]
 
@@ -76,6 +77,7 @@ class Vocab(models.Model):
         related_name="children",
         related_query_name="children",
     )
+    deprecated_on = models.DateTimeField(blank=True, default=None, null=True)
 
     class Meta:
         verbose_name = "Controlled vocabulary"
@@ -95,14 +97,14 @@ class Design(models.Model):
     name = models.CharField(max_length=128, help_text="Name to refer to this study design")
     design = models.ForeignKey(
         Vocab,
-        limit_choices_to={"category": VocabCategories.TYPE},
+        limit_choices_to={"category": VocabCategories.TYPE, "deprecated_on": None},
         on_delete=models.CASCADE,
         help_text="Select study design",
         related_name="designs_by_type",
     )
     study_setting = models.ForeignKey(
         Vocab,
-        limit_choices_to={"category": VocabCategories.SETTING},
+        limit_choices_to={"category": VocabCategories.SETTING, "deprecated_on": None},
         on_delete=models.CASCADE,
         help_text="Select the setting in which evidence was generated",
         related_name="designs_by_setting",
@@ -118,14 +120,14 @@ class Design(models.Model):
     ecoregions = models.ManyToManyField(
         Vocab,
         blank=True,
-        limit_choices_to={"category": VocabCategories.ECOREGION},
-        help_text=f"Select one or more {new_window_a('https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states', 'Level III Ecoregions')}, if known",
+        limit_choices_to={"category": VocabCategories.ECOREGION, "deprecated_on": None},
+        help_text=f"Select one or more {new_window_a('https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states', 'Level III Ecoregions')} from the continental US, if known",  # noqa: S608
         related_name="designs_by_ecoregion",
     )
     habitats = models.ManyToManyField(
         Vocab,
-        limit_choices_to={"category": VocabCategories.HABITAT},
-        help_text="Select one or more habitats to which the evidence applies.",
+        limit_choices_to={"category": VocabCategories.HABITAT, "deprecated_on": None},
+        help_text=f"Select one or more {new_window_a('https://global-ecosystems.org/', 'IUCN Global Ecosystems')} to which the evidence applies.",
         related_name="designs_by_habitat",
     )
     habitats_as_reported = models.TextField(
@@ -135,7 +137,7 @@ class Design(models.Model):
     )
     climates = models.ManyToManyField(
         Vocab,
-        limit_choices_to={"category": VocabCategories.CLIMATE},
+        limit_choices_to={"category": VocabCategories.CLIMATE, "deprecated_on": None},
         help_text=f"Select one or more {new_window_a('http://koeppen-geiger.vu-wien.ac.at/present.htm', 'Koppen climate classifications')} to which the evidence applies",
         related_name="designs_by_climate",
     )