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[Fix] Catch Exception for Adding Structures / Show PubChem Substances (#168)

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Fixes #163
Fixes #165

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#168
This commit is contained in:
jebus
2025-10-22 01:13:06 +13:00
parent 376fd65785
commit 819a94aced
3 changed files with 36 additions and 8 deletions
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13
epdb/models.py
View File

@ -310,7 +310,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="ChEBI"),
"placeholder": "ChEBI ID without prefix e.g. 12345",
"placeholder": "ChEBI ID without prefix e.g. 10576",
},
],
"structure": [
@ -328,7 +328,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="ChEBI"),
"placeholder": "ChEBI ID without prefix e.g. 12345",
"placeholder": "ChEBI ID without prefix e.g. 10576",
},
],
"reaction": [
@ -342,7 +342,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="UniProt"),
"placeholder": "Query ID for UniPro e.g. rhea:12345",
"placeholder": "Query ID for UniProt e.g. rhea:12345",
},
],
}
@ -477,7 +477,7 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
return self.add_external_identifier("CAS", cas_number)
def get_pubchem_identifiers(self):
return self.get_external_identifier("PubChem Compound") or self.get_external_identifier(
return self.get_external_identifier("PubChem Compound") | self.get_external_identifier(
"PubChem Substance"
)
@ -3043,6 +3043,7 @@ class EnviFormer(PackageBasedModel):
@cached_property
def model(self):
from enviformer import load
ckpt = os.path.join(s.MODEL_DIR, "enviformer", str(self.uuid), f"{self.uuid}.ckpt")
mod = load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt)
return mod
@ -3062,7 +3063,9 @@ class EnviFormer(PackageBasedModel):
start = datetime.now()
products_list = self.model.predict_batch(canon_smiles)
end = datetime.now()
logger.info(f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}")
logger.info(
f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}"
)
results = []
for products in products_list:

11
epdb/views.py
View File

@ -1251,7 +1251,16 @@ def package_compound_structures(request, package_uuid, compound_uuid):
structure_smiles = request.POST.get("structure-smiles")
structure_description = request.POST.get("structure-description")
cs = current_compound.add_structure(structure_smiles, structure_name, structure_description)
try:
cs = current_compound.add_structure(
structure_smiles, structure_name, structure_description
)
except ValueError:
return error(
request,
"Adding structure failed!",
"The structure could not be added as normalized structures don't match!",
)
return redirect(cs.url)

20
templates/objects/compound.html
View File

@ -183,7 +183,7 @@
</div>
<div id="compound-external-identifier" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% if compound.get_pubchem_identifiers %}
{% if compound.get_pubchem_compound_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
@ -193,12 +193,28 @@
</h4>
</div>
<div id="compound-pubchem-identifier" class="panel-collapse collapse in">
{% for eid in compound.get_pubchem_identifiers %}
{% for eid in compound.get_pubchem_compound_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">CID{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
{% if compound.get_pubchem_substance_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="compound-pubchem-identifier-link" data-toggle="collapse"
data-parent="#compound-external-identifier"
href="#compound-pubchem-identifier">PubChem Substance Identifier</a>
</h4>
</div>
<div id="compound-pubchem-identifier" class="panel-collapse collapse in">
{% for eid in compound.get_pubchem_substance_identifiers %}
<a class="list-group-item"
href="{{ eid.external_url }}">SID{{ eid.identifier_value }}</a>
{% endfor %}
</div>
{% endif %}
{% if compound.get_chebi_identifiers %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">