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[Feature] Biotransformer in enviPath (#364)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#364
This commit is contained in:
jebus
2026-04-10 00:00:13 +12:00
parent 5029a8cda5
commit 964574c700
13 changed files with 793 additions and 56 deletions
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54
epdb/views.py
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@ -33,6 +33,7 @@ from .models import (
APIToken,
Compound,
CompoundStructure,
ClassifierPluginModel,
Edge,
EnviFormer,
EnzymeLink,
@ -774,16 +775,16 @@ def models(request):
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():
context["model_types"][v().display()] = {
context["model_types"][v.display()] = {
"type": k,
"requires_rule_packages": True,
"requires_data_packages": True,
"requires_rule_packages": v.requires_rule_packages(),
"requires_data_packages": v.requires_data_packages(),
}
for k, v in s.PROPERTY_PLUGINS.items():
context["model_types"][v().display()] = {
context["model_types"][v.display()] = {
"type": k,
"requires_rule_packages": v().requires_rule_packages,
"requires_data_packages": v().requires_data_packages,
"requires_rule_packages": v.requires_rule_packages(),
"requires_data_packages": v.requires_data_packages(),
}
# Context for paginated template
@ -914,16 +915,19 @@ def package_models(request, package_uuid):
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():
context["model_types"][v().display()] = {
context["model_types"][v.display()] = {
"type": k,
"requires_rule_packages": True,
"requires_data_packages": True,
"requires_rule_packages": v.requires_rule_packages(),
"requires_data_packages": v.requires_data_packages(),
"additional_parameters": v.Config.__name__.lower()
if v.Config.__name__ != ""
else None,
}
for k, v in s.PROPERTY_PLUGINS.items():
context["model_types"][v().display()] = {
context["model_types"][v.display()] = {
"type": k,
"requires_rule_packages": v().requires_rule_packages,
"requires_data_packages": v().requires_data_packages,
"requires_rule_packages": v.requires_rule_packages(),
"requires_data_packages": v.requires_data_packages(),
}
return render(request, "collections/models_paginated.html", context)
@ -986,20 +990,34 @@ def package_models(request, package_uuid):
mod = RuleBasedRelativeReasoning.create(**params)
elif s.FLAGS.get("PLUGINS", False) and model_type in s.CLASSIFIER_PLUGINS:
pass
elif s.FLAGS.get("PLUGINS", False) and model_type in s.PROPERTY_PLUGINS:
params["plugin_identifier"] = model_type
impl = s.PROPERTY_PLUGINS[model_type]
inst = impl()
impl = s.CLASSIFIER_PLUGINS[model_type]
if inst.requires_rule_packages():
if impl.requires_rule_packages():
params["rule_packages"] = [
PackageManager.get_package_by_url(current_user, p) for p in rule_packages
]
else:
params["rule_packages"] = []
if not inst.requires_data_packages():
if not impl.requires_data_packages():
params["data_packages"] = []
params["config"] = impl.parse_config(request.POST.dict())
mod = ClassifierPluginModel.create(**params)
elif s.FLAGS.get("PLUGINS", False) and model_type in s.PROPERTY_PLUGINS:
params["plugin_identifier"] = model_type
impl = s.PROPERTY_PLUGINS[model_type]
if impl.requires_rule_packages():
params["rule_packages"] = [
PackageManager.get_package_by_url(current_user, p) for p in rule_packages
]
else:
params["rule_packages"] = []
if not impl.requires_data_packages():
del params["data_packages"]
mod = PropertyPluginModel.create(**params)