#26 Improve Annotation handling

[Richard Adams]

Suggested by Chris Myers:

The getAnnotation method returns a list of Annotations even though there is only one Annotation on each object. This function is marked as deprecated, so I suspect that you know this, but I cannot find a replacement.
I assume addAnnotation should also be deprecated and setAnnotation should take a single item. It would also be nice to have some functions to help build and parse annotations. See getSEDBaseAnnotation in the attached as an example.

[Richard Adams]

Ticket moved from /p/jlibsedml/bugs/6/

[Richard Adams]

I've committed in some improved methods to set Annotation, to add top-level elements and also an AnnotationValidator that will complain if you add > 1 top level element with same namespace, as per the SBML spec's recommendations. Please Can you add your attachment here in a comment so I can have a look and see what else you were looking to do?
Thanks Richard

[Chris Myers]

Here is the getSEDBaseAnnotation method I wrote.

public static String getSEDBaseAnnotation(SEDBase sedBase, String name, String attribute, String defaultValue)
{
    List<Annotation> annotations = sedBase.getAnnotation();
    for (int i = 0; i < annotations.size(); i++)
    {
        Annotation annotation = annotations.get(i);
        List<Element> elements = annotation.getAnnotationElementsList();
        for (Element element : elements) {
            if (!element.getNamespaceURI().equals("http://www.async.ece.utah.edu/iBioSim")) continue;
            if (element.getName().equals(name)) {
                if (element.getAttributeValue(attribute)!=null) {
                    return element.getAttributeValue(attribute);
                } else {
                    return defaultValue;
                }
            }
        }
    }
    return defaultValue;
}

On Aug 3, 2016, at 2:59 PM, Richard Adams otter606@users.sf.net wrote:

I've committed in some improved methods to set Annotation, to add top-level elements and also an AnnotationValidator that will complain if you add > 1 top level element with same namespace, as per the SBML spec's recommendations. Please Can you add your attachment here in a comment so I can have a look and see what else you were looking to do?
Thanks Richard

[feature-requests:#26] Improve Annotation handling

Status: open
Group: 2.3
Created: Wed Jul 13, 2016 08:50 PM UTC by Richard Adams
Last Updated: Wed Jul 13, 2016 08:51 PM UTC
Owner: nobody

Suggested by Chris Myers:

The getAnnotation method returns a list of Annotations even though there is only one Annotation on each object. This function is marked as deprecated, so I suspect that you know this, but I cannot find a replacement.
I assume addAnnotation should also be deprecated and setAnnotation should take a single item. It would also be nice to have some functions to help build and parse annotations. See getSEDBaseAnnotation in the attached as an example.

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[Chris Myers]

Here is the function modified with your changes;

public static String getSEDBaseAnnotation(SEDBase sedBase, String name, String attribute, String defaultValue)
{
    Annotation annotation = sedBase.getAnnotation();
    if (annotation!=null) {
        List<Element> elements = annotation.getAnnotationElementsList();
        for (Element element : elements) {
            if (!element.getNamespaceURI().equals("http://www.async.ece.utah.edu/iBioSim")) continue;
            if (element.getName().equals(name)) {
                if (element.getAttributeValue(attribute)!=null) {
                    return element.getAttributeValue(attribute);
                } else {
                    return defaultValue;
                }
            }
        }
    }
    return defaultValue;
}

I’m also still getting this warning, not sure why:

17:04:23 [AWT-EventQueue-0] WARN org.jlibsedml.SEDMLReader - Unexpected [Element: <annotation [namespace:="" <a="" href="http://sed-ml.org/sed-ml/level1/version2">http://sed-ml.org/sed-ml/level1/version2]/>]</annotation>
17:04:23 [AWT-EventQueue-0] WARN org.jlibsedml.SEDMLReader - Unexpected [Element: <annotation [namespace:="" <a="" href="http://sed-ml.org/sed-ml/level1/version2">http://sed-ml.org/sed-ml/level1/version2]/>]</annotation>

On Aug 4, 2016, at 4:46 PM, Chris Myers ccmyers@users.sf.net wrote:

Here is the getSEDBaseAnnotation method I wrote.
public static String getSEDBaseAnnotation(SEDBase sedBase, String name, String attribute, String defaultValue)
{
List<annotation> annotations = sedBase.getAnnotation();
for (int i = 0; i < annotations.size(); i++)
{
Annotation annotation = annotations.get(i);
List<element> elements = annotation.getAnnotationElementsList();
for (Element element : elements) {
if (!element.getNamespaceURI().equals("http://www.async.ece.utah.edu/iBioSim")) continue;
if (element.getName().equals(name)) {
if (element.getAttributeValue(attribute)!=null) {
return element.getAttributeValue(attribute);
} else {
return defaultValue;
}
}
}
}
return defaultValue;
}
On Aug 3, 2016, at 2:59 PM, Richard Adams otter606@users.sf.net otter606@users.sf.net wrote:</element></annotation>

I've committed in some improved methods to set Annotation, to add top-level elements and also an AnnotationValidator that will complain if you add > 1 top level element with same namespace, as per the SBML spec's recommendations. Please Can you add your attachment here in a comment so I can have a look and see what else you were looking to do?
Thanks Richard

[feature-requests:#26] Improve Annotation handling

Status: open
Group: 2.3
Created: Wed Jul 13, 2016 08:50 PM UTC by Richard Adams
Last Updated: Wed Jul 13, 2016 08:51 PM UTC
Owner: nobody

Suggested by Chris Myers:

The getAnnotation method returns a list of Annotations even though there is only one Annotation on each object. This function is marked as deprecated, so I suspect that you know this, but I cannot find a replacement.
I assume addAnnotation should also be deprecated and setAnnotation should take a single item. It would also be nice to have some functions to help build and parse annotations. See getSEDBaseAnnotation in the attached as an example.

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[feature-requests:#26] Improve Annotation handling

Status: accepted
Group: 2.3
Created: Wed Jul 13, 2016 08:50 PM UTC by Richard Adams
Last Updated: Wed Aug 03, 2016 09:00 PM UTC
Owner: Richard Adams

Suggested by Chris Myers:

The getAnnotation method returns a list of Annotations even though there is only one Annotation on each object. This function is marked as deprecated, so I suspect that you know this, but I cannot find a replacement.
I assume addAnnotation should also be deprecated and setAnnotation should take a single item. It would also be nice to have some functions to help build and parse annotations. See getSEDBaseAnnotation in the attached as an example.

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jlibsedml/feature-requests/26/ https://sourceforge.net/p/jlibsedml/feature-requests/26/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/ https://sourceforge.net/auth/subscriptions/