- From: Stephan Zednik <zednis@rpi.edu>
- Date: Thu, 7 Feb 2013 13:10:49 -0700
- To: Curt Tilmes <Curt.Tilmes@nasa.gov>
- 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>
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