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[Feature] Sync Features from Client Repo (#425)

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- New PackageImporter
- Fix persisting Molfile on Structure creation
- Add NonPersistent Prediction
- Pathway View Options
- Edit Node Fix

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#425
This commit is contained in:
jebus
2026-07-16 07:50:46 +12:00
parent 2c2437e3f5
commit 72a63b4876
16 changed files with 733 additions and 627 deletions
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4
epdb/exceptions.py
View File

@ -4,3 +4,7 @@ class InvalidSMILESException(Exception):
class InvalidMolfileException(Exception):
pass
class PackageImportException(Exception):
pass

37
epdb/legacy_api.py
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@ -1635,24 +1635,10 @@ class PathwayNode(Schema):
# TODO
return []
@staticmethod
def resolve_engineered_intermediate(obj: Node):
# TODO
return False
@staticmethod
def resolve_image(obj: Node):
return f"{obj.default_node_label.url}?image=svg"
@staticmethod
def resolve_image_size(obj: Node):
return 400
@staticmethod
def resolve_proposed_intermediate(obj: Node):
# TODO
return []
class PathwaySchema(Schema):
aliases: List[str] = Field([], alias="aliases")
@ -2282,3 +2268,26 @@ def get_setting(request, setting_uuid):
return 403, {
"message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
}
########
# Util #
########
class NonPersistent(Schema):
smiles: str
setting_url: str = Field(..., alias="settingUri")
@router.post("/util", response={200: Any, 403: Error})
def predict(request, np: Form[NonPersistent]):
try:
from epdb.logic import SPathway
setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
spw.predict()
return spw.to_json()
except ValueError:
return 403, {
"message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
}

7
epdb/logic.py
View File

@ -1011,7 +1011,7 @@ class PackageManager(object):
add_import_timestamp=True,
trust_reviewed=False,
) -> Package:
importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
importer = PackageImporter(data, preserve_uuids)
imported_package = importer.do_import()
up = UserPackagePermission()
@ -1828,6 +1828,11 @@ class SPathway(object):
"to": to_indices,
}
if edge.rule:
e["rule"] = edge.rule.simple_json()
if edge.probability:
e["probability"] = edge.probability
edges.append(e)
return {

64
epdb/models.py
View File

@ -1241,8 +1241,12 @@ class CompoundStructure(
if description is not None:
cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
cs.smiles = smiles
cs.compound = compound
cs.smiles = smiles
# Check if molfile is present and valid
if molfile is not None and molfile.strip() != "":
cs.molfile = molfile
if "normalized_structure" in kwargs:
cs.normalized_structure = kwargs["normalized_structure"]
@ -2023,6 +2027,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
# add links start -> pseudo
new_link = {
"name": link["name"],
"plain_name": link["plain_name"],
"id": link["id"],
"url": link["url"],
"image": link["image"],
@ -2032,6 +2037,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
"source": node_url_to_idx[link["start_node_urls"][0]],
"target": pseudo_idx,
"app_domain": link.get("app_domain", None),
"to_pseudo": True,
}
adjusted_links.append(new_link)
@ -2039,6 +2045,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
for target in link["end_node_urls"]:
new_link = {
"name": link["name"],
"plain_name": link["plain_name"],
"id": link["id"],
"url": link["url"],
"image": link["image"],
@ -2049,6 +2056,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
"target": node_url_to_idx[target],
"app_domain": link.get("app_domain", None),
"multi_step": link["multi_step"],
"from_pseudo": True,
}
adjusted_links.append(new_link)
@ -2359,17 +2367,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
def _url(self):
return "{}/node/{}".format(self.pathway.url, self.uuid)
def get_name(self):
def get_name(self, include_suffix=True):
non_generic_name = True
if self.name == "no name":
if self.name is None or self.name == "no name":
non_generic_name = False
return (
self.name
if non_generic_name
else f"{self.default_node_label.name} (taken from underlying structure)"
)
if non_generic_name:
return self.name
else:
if include_suffix:
return f"{self.default_node_label.name} (taken from underlying structure)"
else:
return self.default_node_label.name
def d3_json(self):
app_domain_data = self.get_app_domain_assessment_data()
@ -2399,6 +2409,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
),
"image_type": "svg",
"name": self.get_name(),
"plain_name": self.get_name(include_suffix=False),
"smiles": self.default_node_label.smiles,
"scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
"app_domain": {
@ -2505,6 +2516,28 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
return res
def is_proposed_intermediate(self):
collected = defaultdict(dict)
for ai in self.additional_information.filter(
type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
scenario__isnull=False,
):
collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
if ai.type == "ProposedIntermediate":
collected[str(ai.scenario.uuid)]["proposed"] = True
if ai.type == "Confidence":
collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
if ai.type == "TransformationProductImportance":
collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
ai.get().importance.value
)
return list(collected.values())
class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
pathway = models.ForeignKey(
@ -2526,6 +2559,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
def d3_json(self):
edge_json = {
"name": self.get_name(),
"plain_name": self.get_name(include_suffix=False),
"id": self.url,
"url": self.url,
"image": self.url + "?image=svg",
@ -2640,17 +2674,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
return res
def get_name(self):
def get_name(self, include_suffix=True):
non_generic_name = True
if self.name == "no name":
non_generic_name = False
return (
self.name
if non_generic_name
else f"{self.edge_label.name} (taken from underlying reaction)"
)
if non_generic_name:
return self.name
else:
if include_suffix:
return f"{self.edge_label.name} (taken from underlying reaction)"
else:
return self.edge_label.name
class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):

39
epdb/views.py
View File

@ -775,13 +775,11 @@ def models(request):
}
if s.ENVIFORMER_PRESENT:
context["model_types"]["EnviFormer"] = (
{
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
},
)
context["model_types"]["EnviFormer"] = {
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
}
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():
@ -2102,12 +2100,14 @@ def package_pathways(request, package_uuid):
else:
prediction_setting = current_user.prediction_settings()
is_predict_mode = pw_mode in {"predict", "incremental"}
pw = Pathway.create(
current_package,
stand_smiles,
stand_smiles if is_predict_mode else smiles,
name=name,
description=description,
predicted=pw_mode in {"predict", "incremental"},
predicted=is_predict_mode,
)
# set mode
@ -2466,7 +2466,26 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
return JsonResponse({"success": current_node.url})
return HttpResponseBadRequest()
new_node_name = request.POST.get("node-name")
new_node_description = request.POST.get("node-description")
if any([new_node_name, new_node_description]):
if new_node_name is not None and new_node_name.strip() != "":
new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
current_node.name = new_node_name
if new_node_description is not None and new_node_description.strip() != "":
new_node_description = nh3.clean(
new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
).strip()
current_node.description = new_node_description
current_node.save()
return redirect(current_node.url)
return error(request, "Node update failed!", "No changes were made to the node")
else:
return HttpResponseNotAllowed(["GET", "POST"])