- From: Stephan Zednik <zednis@rpi.edu>
- Date: Thu, 7 Feb 2013 02:40:48 -0700
- To: Luc Moreau <l.moreau@ecs.soton.ac.uk>
- Cc: Curt Tilmes <Curt.Tilmes@nasa.gov>, "public-prov-wg@w3.org" <public-prov-wg@w3.org>
- Message-Id: <2B9ABF2D-FA0F-4942-A233-32ACAE5BEF67@rpi.edu>
Ok. I am on-board with updating the schema to enforce element ordering on prov attributes. I like the idea of using jax bindings + simplify plugin but I think that is too complex a solution.
--Stephan
On Feb 7, 2013, at 1:47 AM, Luc Moreau <l.moreau@ecs.soton.ac.uk> wrote:
> Hi Stephan,
>
> Response interleaved.
>
> On 07/02/2013 04:08, Stephan Zednik wrote:
>>
>> On Feb 6, 2013, at 4:58 PM, Luc Moreau <L.Moreau@ecs.soton.ac.uk> wrote:
>>
>>
>>> Hi Stephan and Curt,
>>>
>>> It is good to keep choice in documentElement. You both introduced it. Let's not remove it.
>>>
>> I agree, but the choice in documentElement will lead to the same problem with JAXB that a choice in attributes does.
>>
>
> I don't think the situation is the same.
> A bundle/document has a containment relationship with respect to documentElements, whereas prov attributes, we want them
> to appear as instance variables (with associated setters and getters). I am therefore fine, with all documentElments being
> amalgamated in a single list.
>> Both Document and Bundle classes generated by JAXB's xjc use a single list for all available elements in a documentElement.
>>
>> The generated code looks like the following:
>>
>> protected List<JAXBElement<?>> entityOrActivityOrWasGeneratedBy;
>>
>> /**
>> * Gets the value of the entityOrActivityOrWasGeneratedBy property.
>> *
>> * <p>
>> * This accessor method returns a reference to the live list,
>> * not a snapshot. Therefore any modification you make to the
>> * returned list will be present inside the JAXB object.
>> * This is why there is not a <CODE>set</CODE> method for the entityOrActivityOrWasGeneratedBy property.
>> *
>>
>
>
> We can easily improve on this, as I did in the provtoolbox:
> See http://openprovenance.org/java/site/prov/apidocs/org/openprovenance/prov/xml/Document.html#getEntityOrActivityOrWasGeneratedBy()
>
>
>> * <p>
>> * For example, to add a new item, do as follows:
>> * <pre>
>> * getEntityOrActivityOrWasGeneratedBy().add(newItem);
>> * </pre>
>> *
>> *
>> * <p>
>> * Objects of the following type(s) are allowed in the list
>> * {@link JAXBElement }{@code <}{@link Association }{@code >}
>> * {@link JAXBElement }{@code <}{@link EmptyCollection }{@code >}
>> * {@link JAXBElement }{@code <}{@link Specialization }{@code >}
>> * {@link JAXBElement }{@code <}{@link Removal }{@code >}
>> * {@link JAXBElement }{@code <}{@link Dictionary }{@code >}
>> * {@link JAXBElement }{@code <}{@link Organization }{@code >}
>> * {@link JAXBElement }{@code <}{@link EmptyDictionary }{@code >}
>> * {@link JAXBElement }{@code <}{@link Plan }{@code >}
>> * {@link JAXBElement }{@code <}{@link Start }{@code >}
>> * {@link JAXBElement }{@code <}{@link Agent }{@code >}
>> * {@link JAXBElement }{@code <}{@link Collection }{@code >}
>> * {@link JAXBElement }{@code <}{@link Mention }{@code >}
>> * {@link JAXBElement }{@code <}{@link Generation }{@code >}
>> * {@link JAXBElement }{@code <}{@link SoftwareAgent }{@code >}
>> * {@link JAXBElement }{@code <}{@link Derivation }{@code >}
>> * {@link JAXBElement }{@code <}{@link KeyValuePair }{@code >}
>> * {@link JAXBElement }{@code <}{@link Object }{@code >}
>> * {@link JAXBElement }{@code <}{@link Communication }{@code >}
>> * {@link JAXBElement }{@code <}{@link Attribution }{@code >}
>> * {@link JAXBElement }{@code <}{@link Delegation }{@code >}
>> * {@link JAXBElement }{@code <}{@link Entity }{@code >}
>> * {@link JAXBElement }{@code <}{@link Influence }{@code >}
>> * {@link JAXBElement }{@code <}{@link Usage }{@code >}
>> * {@link JAXBElement }{@code <}{@link Alternate }{@code >}
>> * {@link JAXBElement }{@code <}{@link Membership }{@code >}
>> * {@link JAXBElement }{@code <}{@link Bundle }{@code >}
>> * {@link JAXBElement }{@code <}{@link End }{@code >}
>> * {@link JAXBElement }{@code <}{@link Insertion }{@code >}
>> * {@link JAXBElement }{@code <}{@link Activity }{@code >}
>> * {@link JAXBElement }{@code <}{@link Invalidation }{@code >}
>> * {@link JAXBElement }{@code <}{@link Person }{@code >}
>> * {@link JAXBElement }{@code <}{@link Revision }{@code >}
>> * {@link JAXBElement }{@code <}{@link Quotation }{@code >}
>> * {@link JAXBElement }{@code <}{@link PrimarySource }{@code >}
>> * {@link JAXBElement }{@code <}{@link DictionaryMembership }{@code >}
>> *
>> *
>> */
>> public List<JAXBElement<?>> getEntityOrActivityOrWasGeneratedBy() {
>> if (entityOrActivityOrWasGeneratedBy == null) {
>> entityOrActivityOrWasGeneratedBy = new ArrayList<JAXBElement<?>>();
>> }
>> return this.entityOrActivityOrWasGeneratedBy;
>> }
>>
>>
>>> My concern about choice in prov attributes is that they lead, by default, to non natural object mapping with jaxb. I believe jaxb matters because jaxb is a community standard reaching well beyond the java community.
>>>
>> I agree. Would having a section in the FAQ which analyzes the problem in the context of a specific ORM technology and provides possible solutions (hints and/or alternate schemas) for that technology be satisfiable?
>>
>>
>
> alternate schemas is challenging, since you want any xml compatible with prov-xml to be readable by a jaxb-friendly schema.
>> Also, looking at the JAXB generated class I think the manner in which the schema defines and uses prov:ref will result in a mapping that is not natural.
>>
>> The following components from the schema
>>
>> <xs:complexType name="Generation">
>> <xs:sequence>
>> <xs:element name="entity" type="prov:IDRef"/>
>> <xs:element name="activity" type="prov:IDRef" minOccurs="0"/>
>> <xs:element name="time" type="xs:dateTime" minOccurs="0"/>
>> <xs:choice minOccurs="0" maxOccurs="unbounded">
>> <xs:element ref="prov:location"/>
>> <xs:element ref="prov:role"/>
>> <xs:element ref="prov:label"/>
>> <xs:element ref="prov:type"/>
>> <xs:any namespace="##other"/>
>> </xs:choice>
>> </xs:sequence>
>> <xs:attribute ref="prov:id"/>
>> </xs:complexType>
>>
>> <!-- note, this is not xs:IDREF -->
>> <xs:complexType name="IDRef">
>> <xs:attribute ref="prov:ref" use="required" />
>> </xs:complexType>
>>
>> result in class members with type IDRef
>>
>> protected IDRef entity;
>> protected IDRef activity;
>>
>> Whose class is defined like so:
>>
>>
>
> Here, provtoolbox maps as follows:
>
> http://openprovenance.org/java/site/prov/apidocs/org/openprovenance/prov/xml/Entity.html#getId()
>
> public QName getId()
>
> So, i think this works ok.
>
> Luc
>
>
>> @XmlAccessorType(XmlAccessType.FIELD)
>> @XmlType(name = "IDRef")
>> public class IDRef {
>>
>> @XmlAttribute(name = "ref", namespace = MailScanner has detected a possible fraud attempt from "www.w3.org" claiming to be "http://www.w3.org/ns/prov#", required = true)
>> protected QName ref;
>>
>> /**
>> * Gets the value of the ref property.
>> *
>> * @return
>> * possible object is
>> * {@link QName }
>> *
>> */
>> public QName getRef() {
>> return ref;
>> }
>>
>> /**
>> * Sets the value of the ref property.
>> *
>> * @param value
>> * allowed object is
>> * {@link QName }
>> *
>> */
>> public void setRef(QName value) {
>> this.ref = value;
>> }
>>
>> }
>>
>> I think our modeling of prov:ref will likewise cause confusion among ORM generated classes.
>>
>> --Stephan
>>
>>
>>> Now, I am not expert in jaxb. There may well be standard jaxb annotations that allow us To support a natural object mapping with an xsd choice. If so, we should go for xsd:choice.
>>>
>>> Curt's suggestion of a plugin (-simple) is a good, as long as plugin is maintained, which with my jaxb experience, is not encouraging, especially.
>>>
>>>
>>> In the absence of standard jaxb annotations that lead to natural jaxb mappings, my preference is to be conservative and go for ordered prov attributes.
>>>
>>>
>>> Professor Luc Moreau
>>> Electronics and Computer Science
>>> University of Southampton
>>> Southampton SO17 1BJ
>>> United Kingdom
>>>
>>> On 6 Feb 2013, at 20:08, "Stephan Zednik" <zednis@rpi.edu> wrote:
>>>
>>>
>>>> After having played around with JAB and gaining a better understanding of the problem I am more amenable to the idea of requiring element ordering for properties.
>>>>
>>>> I am still not sold on the idea of element ordering in documentElements and without that the generated class methods for Bundle will be a 'bag of hurt'.
>>>>
>>>> An alternate idea is a to have a section in the FAQ dedicated to providing ORM implementation-specific tips on how to generate 'nice' mappings.
>>>>
>>>> The plugin Curt has mentioned could be mentioned in a FAQ entry and we could provide an example of how to use external hints to JAXB. The FAQ could also contain links to a modified schema that uses ordered elements and is only intended to be used as a source for ORM mappings, but not as a schema to validate against.
>>>>
>>>> I think I like the second option best as it allows us to respond to ORM-mapping issues after the WG activity has completed and is a natural way to talk about implementation specific ORM issues.
>>>>
>>>> --Stephan
>>>>
>>>> On Feb 5, 2013, at 11:56 AM, Curt Tilmes <Curt.Tilmes@nasa.gov> wrote:
>>>>
>>>>
>>>>> Luc,
>>>>>
>>>>> I haven't tested this yet, but is it possible that the jaxb
>>>>> "Simplify" plugin could address this problem with jaxb?
>>>>>
>>>>> http://confluence.highsource.org/display/J2B/Simplify+Plugin
>>>>>
>>>>> It seems (again, untested), that you could use it and specify
>>>>> some application hints for jaxb ("simplify:as-element-property")
>>>>> for the attributes that would instruct jaxb to model
>>>>> each attribute family (type, location, label, etc.) with
>>>>> its own list rather than bundling them together as it
>>>>> does by default with choices.
>>>>>
>>>>> Curt
>>>>>
>>>>> On 02/05/2013 01:37 AM, Luc Moreau wrote:
>>>>>
>>>>>> Hi Curt,
>>>>>>
>>>>>> Does the schema now impose an order on prov "attributes"?
>>>>>>
>>>>>> Without order, I have failed to define an object mapping (with jaxb)
>>>>>>
>>>>> that is useful from an OO perspective. Likewise, i have not managed to
>>>>> define a meaningful ORM mapping. Now, this is my experience with these
>>>>> tools, maybe somebody has succeeded.
>>>>>
>>>>>> In summary, The problem I encountered is as follows. If there is a
>>>>>>
>>>>> choice (instead of sequence) between say, prov:type, prov:location,
>>>>> prov:label, all these elements are mapped to a single java method or a
>>>>> single sql column. This results in non natural code or SQL queries.
>>>>>
>>>>>> Because of this, my preference is to keep these in a sequence. It does
>>>>>>
>>>>> not at all reduce expressivity, I think.
>>>>>
>>>>>>
>>>>>> Professor Luc Moreau
>>>>>> Electronics and Computer Science
>>>>>> University of Southampton
>>>>>> Southampton SO17 1BJ
>>>>>> United Kingdom
>>>>>>
>>>>>> On 5 Feb 2013, at 01:17, "Curt Tilmes" <Curt.Tilmes@nasa.gov> wrote:
>>>>>>
>>>>>>
>>>>>>> Last week, we also briefly mentioned the PROV-XML element
>>>>>>> ordering issue, described here:
>>>>>>>
>>>>>>> https://www.w3.org/2011/prov/track/issues/572
>>>>>>>
>>>>>>> Are there strong opinions about changing anything (either
>>>>>>> arguments, or attributes or anything else from the way it
>>>>>>> is now?
>>>>>>>
>>>>>>> Tracker, this is ISSUE-572.
>>>>>>>
>>>>>>> Curt
>>>>>>>
>>>>>>>
>>>>>
>>>>> --
>>>>> Curt Tilmes, Ph.D.
>>>>> U.S. Global Change Research Program
>>>>> 1717 Pennsylvania Avenue NW, Suite 250
>>>>> Washington, D.C. 20006, USA
>>>>>
>>>>> +1 202-419-3479 (office)
>>>>> +1 443-987-6228 (cell)
>>>>> globalchange.gov
>>>>>
>>>>>
>>>>>
>
> --
> Professor Luc Moreau
> Electronics and Computer Science tel: +44 23 8059 4487
> University of Southampton fax: +44 23 8059 2865
> Southampton SO17 1BJ email: l.moreau@ecs.soton.ac.uk
> United Kingdom http://www.ecs.soton.ac.uk/~lavm
>
Received on Thursday, 7 February 2013 09:41:40 UTC