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Re: PROV-XML element ordering

From: Stephan Zednik <zednis@rpi.edu>
Date: Thu, 7 Feb 2013 13:10:49 -0700
Cc: Luc Moreau <l.moreau@ecs.soton.ac.uk>, "public-prov-wg@w3.org" <public-prov-wg@w3.org>
Message-Id: <B6C83F69-C8C7-4573-9578-D1D6D1E03A04@rpi.edu>
To: Curt Tilmes <Curt.Tilmes@nasa.gov>
Sounds good.  I will commit the change.

--Stephan

On Feb 7, 2013, at 1:06 PM, Curt Tilmes <Curt.Tilmes@nasa.gov> wrote:

> I was going to suggest the order from PROV-DM section 5.7.2 and table 8,
> which appears to be alphabetical...
> 
> Curt
> 
> On 02/07/2013 01:39 PM, Stephan Zednik wrote:
>> How about alphabetical?
>> 
>> --Stephan
>> 
>> On Feb 7, 2013, at 9:57 AM, Stephan Zednik <zednis@rpi.edu> wrote:
>> 
>>> Now I think it is time to determine what ordering we want to have.  Should we use alphabetic ordering?  order by expectations of usage?  I don't have a preference except that we are consistent.
>>> 
>>> --Stephan
>>> 
>>> 
>>> On Feb 7, 2013, at 4:12 AM, Curt Tilmes <Curt.Tilmes@nasa.gov> wrote:
>>> 
>>>> Agreed.  If we just explain clearly in the doc what the order is, anyone implementing can do it that way.
>>>> Most people will be using other tools to output the XML so the tool will hide the need for order from them
>>>> anyway.
>>>> 
>>>> Curt
>>>> 
>>>> On 2/7/13 4:40 AM, Stephan Zednik wrote:
>>>>> 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
>>>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Curt Tilmes, Ph.D.
>>>> U.S. Global Change Research Program
>>>> 1717 Pennsylvania Avenue, NW, Suite 250
>>>> Washington, D.C. 20006, USA
>>> 
>> 
> 
> 
> -- 
> 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


Received on Thursday, 7 February 2013 20:11:27 UTC

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