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[Fix] UI bugs, Registrations Mail, BTRules Popup, Legacy API fixes (#309)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#309
This commit is contained in:
jebus
2026-01-29 11:13:34 +13:00
parent ab0b5a5186
commit 5565b9cb9e
14 changed files with 391 additions and 154 deletions
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57
epdb/legacy_api.py
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@ -212,7 +212,7 @@ def get_user(request, user_uuid):
class GroupMember(Schema):
id: str = Field(None, alias="url")
id: str
identifier: str
name: str
@ -228,7 +228,7 @@ class GroupSchema(Schema):
members: List[GroupMember] = Field([], alias="members")
name: str = Field(None, alias="name")
ownerid: str = Field(None, alias="owner.url")
ownername: str = Field(None, alias="owner.name")
ownername: str = Field(None, alias="owner.get_name")
packages: List["SimplePackage"] = Field([], alias="packages")
readers: List[GroupMember] = Field([], alias="readers")
writers: List[GroupMember] = Field([], alias="writers")
@ -237,10 +237,10 @@ class GroupSchema(Schema):
def resolve_members(obj: Group):
res = []
for member in obj.user_member.all():
res.append(GroupMember(id=member.url, identifier="usermember", name=member.username))
res.append(GroupMember(id=member.url, identifier="usermember", name=member.get_name()))
for member in obj.group_member.all():
res.append(GroupMember(id=member.url, identifier="groupmember", name=member.name))
res.append(GroupMember(id=member.url, identifier="groupmember", name=member.get_name()))
return res
@ -374,7 +374,7 @@ class PackageSchema(Schema):
).values_list("user", flat=True)
).distinct()
return [{u.id: u.name} for u in users]
return [{u.id: u.get_name()} for u in users]
@staticmethod
def resolve_writers(obj: Package):
@ -384,7 +384,7 @@ class PackageSchema(Schema):
).values_list("user", flat=True)
).distinct()
return [{u.id: u.name} for u in users]
return [{u.id: u.get_name()} for u in users]
@staticmethod
def resolve_review_comment(obj):
@ -966,7 +966,12 @@ def create_package_simple_rule(
raise ValueError("Not yet implemented!")
else:
sr = SimpleAmbitRule.create(
p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
p,
r.name,
r.description,
r.smirks,
r.reactantFilterSmarts,
r.productFilterSmarts,
)
return redirect(sr.url)
@ -1119,7 +1124,7 @@ class ReactionSchema(Schema):
name: str = Field(None, alias="name")
pathways: List["SimplePathway"] = Field([], alias="related_pathways")
products: List["ReactionCompoundStructure"] = Field([], alias="products")
references: List[Dict[str, List[str]]] = Field([], alias="references")
references: Dict[str, List[str]] = Field({}, alias="references")
reviewStatus: str = Field(None, alias="review_status")
scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
smirks: str = Field("", alias="smirks")
@ -1135,8 +1140,12 @@ class ReactionSchema(Schema):
@staticmethod
def resolve_references(obj: Reaction):
# TODO
return []
rhea_refs = []
for rhea in obj.get_rhea_identifiers():
rhea_refs.append(f"{rhea.identifier_value}")
# TODO UniProt
return {"rheaReferences": rhea_refs, "uniprotCount": []}
@staticmethod
def resolve_medline_references(obj: Reaction):
@ -1715,7 +1724,7 @@ class EdgeSchema(Schema):
id: str = Field(None, alias="url")
identifier: str = "edge"
name: str = Field(None, alias="name")
reactionName: str = Field(None, alias="edge_label.name")
reactionName: str = Field(None, alias="edge_label.get_name")
reactionURI: str = Field(None, alias="edge_label.url")
reviewStatus: str = Field(None, alias="review_status")
scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
@ -1764,7 +1773,7 @@ class CreateEdge(Schema):
@router.post(
"/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
"/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge",
response={200: str | Any, 403: Error},
)
def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
@ -1783,10 +1792,26 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
if e.edgeAsSmirks:
for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
educts.append(
Node.objects.get(
pathway=pw,
default_node_label=CompoundStructure.objects.get(
compound__package=p, smiles=stand_ed
).compound.default_structure,
)
)
for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
stand_pr = FormatConverter.standardize(pr, remove_stereo=True)
products.append(
Node.objects.get(
pathway=pw,
default_node_label=CompoundStructure.objects.get(
compound__package=p, smiles=stand_pr
).compound.default_structure,
)
)
else:
for ed in e.educts.split(","):
educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
@ -1799,7 +1824,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
start_nodes=educts,
end_nodes=products,
rule=None,
name=e.name,
name=None,
description=e.edgeReason,
)
@ -1936,7 +1961,7 @@ def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
if pr.rule:
res["id"] = pr.rule.url
res["identifier"] = pr.rule.get_rule_identifier()
res["name"] = pr.rule.name
res["name"] = pr.rule.get_name()
res["reviewStatus"] = (
"reviewed" if pr.rule.package.reviewed else "unreviewed"
)