W3C home > Mailing lists > Public > public-prov-wg@w3.org > February 2013

Re: PROV-XML element ordering

From: Stephan Zednik <zednis@rpi.edu>
Date: Thu, 7 Feb 2013 13:30:38 -0700
Cc: Luc Moreau <l.moreau@ecs.soton.ac.uk>, "public-prov-wg@w3.org" <public-prov-wg@w3.org>
Message-Id: <E7878EC1-D7A9-40AB-B288-062185C9AC26@rpi.edu>
To: Curt Tilmes <Curt.Tilmes@nasa.gov>
I have committed change to prov-core.xsd to use ordered elements for prov attributes.

https://dvcs.w3.org/hg/prov/rev/3f1e31b0df28

I have also updated a few prov-xml test files in eg-40 to conform with the new required ordering of elements

https://dvcs.w3.org/hg/prov/rev/f95aa1566db7

--Stephan

On Feb 7, 2013, at 1:10 PM, Stephan Zednik <zednis@rpi.edu> wrote:

> 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 20:31:31 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 16:51:30 UTC