[Feature] PEPPER in enviPath (#332)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#332
2026-03-06 22:11:22 +13:00
parent 6e00926371
commit c6ff97694d
43 changed files with 3793 additions and 371 deletions
--- a/epdb/migrations/0018_auto_20260220_1203.py
+++ b/epdb/migrations/0018_auto_20260220_1203.py
@ -0,0 +1,132 @@
+# Generated by Django 5.2.7 on 2026-02-20 12:03
+
+from django.db import migrations
+
+
+def get_additional_information(scenario):
+    from envipy_additional_information import registry
+    from envipy_additional_information.parsers import TypeOfAerationParser
+
+    for k, vals in scenario.additional_information.items():
+        if k == "enzyme":
+            continue
+
+        if k == "SpikeConentration":
+            k = "SpikeConcentration"
+
+        if k == "AerationType":
+            k = "TypeOfAeration"
+
+        for v in vals:
+            # Per default additional fields are ignored
+            MAPPING = {c.__name__: c for c in registry.list_models().values()}
+            try:
+                inst = MAPPING[k](**v)
+            except Exception:
+                if k == "TypeOfAeration":
+                    toa = TypeOfAerationParser()
+                    inst = toa.from_string(v["type"])
+
+            # Add uuid to uniquely identify objects for manipulation
+            if "uuid" in v:
+                inst.__dict__["uuid"] = v["uuid"]
+
+            yield inst
+
+
+def forward_func(apps, schema_editor):
+    Scenario = apps.get_model("epdb", "Scenario")
+    ContentType = apps.get_model("contenttypes", "ContentType")
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    bulk = []
+    related = []
+    ctype = {o.model: o for o in ContentType.objects.all()}
+    parents = Scenario.objects.prefetch_related(
+        "compound_set",
+        "compoundstructure_set",
+        "reaction_set",
+        "rule_set",
+        "pathway_set",
+        "node_set",
+        "edge_set",
+    ).filter(parent__isnull=True)
+
+    for i, scenario in enumerate(parents):
+        print(f"{i + 1}/{len(parents)}", end="\r")
+        if scenario.parent is not None:
+            related.append(scenario.parent)
+            continue
+
+        for ai in get_additional_information(scenario):
+            bulk.append(
+                AdditionalInformation(
+                    package=scenario.package,
+                    scenario=scenario,
+                    type=ai.__class__.__name__,
+                    data=ai.model_dump(mode="json"),
+                )
+            )
+
+    print("\n", len(bulk))
+
+    related = Scenario.objects.prefetch_related(
+        "compound_set",
+        "compoundstructure_set",
+        "reaction_set",
+        "rule_set",
+        "pathway_set",
+        "node_set",
+        "edge_set",
+    ).filter(parent__isnull=False)
+
+    for i, scenario in enumerate(related):
+        print(f"{i + 1}/{len(related)}", end="\r")
+        parent = scenario.parent
+        # Check to which objects this scenario is attached to
+        for ai in get_additional_information(scenario):
+            rel_objs = [
+                "compound",
+                "compoundstructure",
+                "reaction",
+                "rule",
+                "pathway",
+                "node",
+                "edge",
+            ]
+            for rel_obj in rel_objs:
+                for o in getattr(scenario, f"{rel_obj}_set").all():
+                    bulk.append(
+                        AdditionalInformation(
+                            package=scenario.package,
+                            scenario=parent,
+                            type=ai.__class__.__name__,
+                            data=ai.model_dump(mode="json"),
+                            content_type=ctype[rel_obj],
+                            object_id=o.pk,
+                        )
+                    )
+
+    print("Start creating additional information objects...")
+    AdditionalInformation.objects.bulk_create(bulk)
+    print("Done!")
+    print(len(bulk))
+
+    Scenario.objects.filter(parent__isnull=False).delete()
+    # Call ai save to fix urls
+    ais = AdditionalInformation.objects.all()
+    total = ais.count()
+
+    for i, ai in enumerate(ais):
+        print(f"{i + 1}/{total}", end="\r")
+        ai.save()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0017_additionalinformation"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]