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Missing property descriptor for attribute exception handling #184

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merged 2 commits into from
Mar 21, 2024
Merged

Missing property descriptor for attribute exception handling #184

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a589021
Added exception handling for the case when a property descriptor is n…
spamhurts Mar 20, 2024
13ecf39
Refactored insertExpObjectProperties() in SNDManager.java to ensure t…
spamhurts Mar 20, 2024
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18 changes: 11 additions & 7 deletions src/org/labkey/snd/SNDManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2300,14 +2300,13 @@ private String insertExpObjectProperties(Container c, User u, Event event, Event

for (AttributeData attributeData : eventData.getAttributes())
{
if (attributeData.getPropertyName() != null)
{
propertyDescriptor = OntologyManager.getPropertyDescriptor(PackageDomainKind.getDomainURI(
SNDSchema.NAME, PackageDomainKind.getPackageKindName(), c, u) + "-" + pkgId + "#" + attributeData.getPropertyName(), c);
}
else
propertyDescriptor = OntologyManager.getPropertyDescriptor(attributeData.getPropertyId());

if (propertyDescriptor == null)
{
propertyDescriptor = OntologyManager.getPropertyDescriptor(attributeData.getPropertyId());
propertyDescriptor = OntologyManager.getPropertyDescriptor(PackageDomainKind.getDomainURI(
SNDSchema.NAME, PackageDomainKind.getPackageKindName(), c, u) + "-" + pkgId + "#" +
attributeData.getPropertyName().replaceAll("\\s", "+"), c);
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PageFlowUtil.encode(attributeData.getPropertyName())

Might need to do a quick test on this, but this should handle how these names are expected to be encoded.

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Hi Marty,

Thanks for looking at the PR. Unfortunately, your suggestion is not going to work. The PageFlowUtil.encode() method replaces the space with a %20, resulting in, for example, body%20part. In the attribute data, the propertyURI replaces the space with a +. Here is the propertyURI for the body part attribute:

urn:lsid:txbiomed.org:package-snd.Folder-6:Package-62#body+part

Both the + and the %20 are proper URL encodings for the space, but the OntologyManager.getPropertyDescriptor() function is doing a key/value lookup in the property descriptor cache, with the propertyURI as the key, and it is failing when the encoding doesn’t match.

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Sorry I didn't do enough investigation into that. Here is the function that is being used when those are first encoded. Let me know if that works for you.

Lsid.encodePart(attributeData.getPropertyName())

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That does the trick! I'll submit a new PR for the change. Thanks!

}

if (propertyDescriptor != null)
Expand All @@ -2327,6 +2326,11 @@ private String insertExpObjectProperties(Container c, User u, Event event, Event
OntologyManager.insertProperties(c, u, null, objectProperty);
}
}
else
{
// property descriptor not found
throw new ValidationException("Property descriptor not found for attribute: " + attributeData.getPropertyName());
}
}

return objectURI;
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