[Animl-develop] animl-core 1.01.xsd now validates in XMLSpy

[Mark F. B. <sa...@co...>]

Hi everyone

(Mark Bean here writing from home)


Nice to see some of you again in the AnIML business meeting in Somerset.  I
finally got CVS working today and checked in a revised version into CVS
schema animl-core 1.01.xsd.   I also checked in a new folder under AnIML
called base64_converters and in that added a C#Converters.cs file with a
bunch of conversion routines, a few of which are relevant to AnIML and
C#.Net implementers.  If you don't have access to the CVS except in
browsing, here's how I managed it.  I followed a link provided by Maren
Fiege, but used TortoiseCVS instead of WinCVS and have to recommend
TortoiseCVS as easy to use (you check in and out from Windows Explorer).
You can get TortoiseCVS from Sourceforge.

To install the required client software for using AnIML CVS, follow the
instructions here:
http://sourceforge.net/docman/display_doc.php?docid=766&group_id=1


I also downloaded the latest enterprise version of XMLSpy and ran into a
number of invalid faults in the AnIML core schema.  The faults I find at
work and at home are not the same using Microsoft VisualStudio.Net, but
perhaps I have different versions of MSXML.  I also am behind a firewall at
work and that probably makes it impossible for the validator to access the
schemaLocation="http://www.w3.org/TR/xmldsig-core/xmldsig-core-schema.xsd"
for digital signatures.  I suspect if I modified that to a local reference
some of those errors would disappear.

Anyway, here are the errors I found and what I did to "fix" them.  Fix is in
quotes because I don't really know XML Schema or AnIML and may have created
more problems than I fixed.  I believe that except for the first error, I
commented out the old tags and added new tags just before it, so you can see
what I did.



  1.. XMLSpy:  “Not a valid restriction since its “maxOccurs” value
<unbounded> is greater than “1”.  “
<xs:complexType name="VectorValueType">

<xs:annotation>

                                <xs:documentation>Elements for
IndividualValueSets in Vectors.</xs:documentation>

                                                <xs:documentation>Elements
for values in Vectors.</xs:documentation>

                                </xs:annotation>


<xs:complexContent>

                                                <xs:restriction
base="ParameterValueType">


<xs:choice maxOccurs="unbounded">



This is because the base complex type "ParameterValueType" has no such
maxOccurs.  The rule is that in order to define by restriction from a base
complex type, one must only restrict, not extend.  I fixed this by setting
the base xs:choice to unbounded as well.





  2.. XMLSpy:  “The complex type “ no name” has multiple Attribute
Definitions (e.g. “templateid”) whose type definitions is derived from “ID””
<xs:element name="Template">

<xs:annotation>

                                <xs:documentation>ExperimentStep
templates</xs:documentation>

                                <xs:documentation>Represents a container for
ExperementStep templates</xs:documentation>

                </xs:annotation>

                <xs:complexType>

                                <xs:complexContent>

                                                <xs:extension
base="TemplateType">


<xs:attributeGroup ref="SignableItem"/>


<xs:attribute name="templateId" type="xs:ID" use="required"/>

                                                </xs:extension>

                                </xs:complexContent>

                </xs:complexType>

</xs:element>

ID attributes are required to be unique.  I believe the problem here is that
the attributeGroup "SignableItem" has an attribute whose name is ID and type
is xs:ID and that this Template element has this group by reference as well
as another atrribute of the same type.



Perhaps we should pay attention to what MSDN has to say about use of IDs and
IDREFs and replace them with KEY and KEYREFs.  Why you should favor
key/keyref/unique over ID/IDREF for identity constraints

DTDs provide a mechanism for specifying that an attribute has a type ID,
meaning that its value will be unique within the document and that it
matches the Name production in XML 1.0. IDs in XML 1.0 can also be
referenced by attributes of type IDREF or IDREFS. For compatibility with
DTDs, W3C XML Schema has the xs:ID, xs:IDREF and xs:IDREFS types.

W3C XML Schema identity constraints are used for specifying unique values,
keys or references to keys using XPath expressions defined within the scope
of an element declaration. Comparing feature for feature, the identity
constraint mechanisms offer more than their ID/IDREF counterparts do.  For
one, there is no limitation on the values or types that can be used as part
of an identity constraint, whereas IDs can only be one of a specific range
of values (for example, 7 is not a valid ID). A more important benefit of
the schema identity constraints over ID/IDREF is that, while the latter have
to be unique within the document, the former do not.  In other words, the
symbol space for unique IDs is the entire document, while for unique keys it
is the target scope of the XPath.  This is particularly useful if uniqueness
is needed in two overlapping value spaces with different scopes in the same
XML document.  An example of this would be an XML document that contained
room numbers and table numbers for a hotel.  It is likely that some of the
numbers overlap (i.e. there is a room 18 and a table 18), but they should
not overlap within either value space.

Note   The W3C XML Schema family of ID types are not exactly compatible with
the DTD ID types. For one, the xs:ID, xs:IDREF and xs:IDREFS types can be
applied to both elements and attributes in the W3C XML Schema, although they
can only apply to attributes in their DTD equivalents. Secondly, there is no
restriction on how many attributes of type xs:ID can appear on an element,
although such a restriction exists for ID attributes in the DTD equivalents.



I added the following key and commented out the old one.  I feel sure I
broke something somewhere.



<xs:unique name="templateIdKey">

                <xs:selector xpath=".//Template"/>

                <xs:field xpath=" templateId"/>

</xs:unique>





  3.. XMLSpy:  “Type Definition “Technique is no valid derivation of Type
Definition “Technique. “”
<xs:complexType name="TemplateType">

<xs:complexContent>

                                <xs:restriction base="ExperimentStepType">

                                                <xs:sequence>

                                                                <xs:element
name="Author" type="UserInformationType" minOccurs="0">


</xs:element>

                                                                <xs:element
ref="Timestamp" minOccurs="0"/>

                                                                <xs:element
name="Technique" minOccurs="0">



I notice that there are two definitions of the element named Technique.  One
in ExperimentStepType and one in TemplateType.  They look identical to me.
I created a new complexType called Technique and then referred to it in both
ExperimentStepType and TemplateType.



The resultant xml schema animl-core 1.01.xsd now validated correctly.  I
then used the schema to generate a sample XML file for manual filling.  I
used the XMLSpy title bar menu item “DTD/Schema:Generate Sample XML File”
and checked all boxes.  However, I was unable to save it as it itself was
invalid!  Let’s go through those errors:



  4.. XMLSpy:  “The <keyfef> Identity Constraint Definition “VectorIDRef”
did not match any elements or attributes within the scope of element
“IndexRef”
<MeasurementData id="ID000006">

                <Template id="ID000007">

                                <PageSet id="ID000013">

                                                <Page id="ID000014"
name="token">

                                                                <References
id="ID000015">

                                                <IndexRef index="1"
refWidth="1" id="ID000016" name="token" vectorID="String"/>



I gave up at this point but would appreciate some help in completing the
task of obtaining a valid XML file.  By the way the bruker_quinine sample
also had validation errors against new or old schema using XMLSpy - and that
is without taking the technique validation into consideration!



Microsoft has a good discussion of XML Schema design recommendations.  It
would be great if AnIML core were simpler.

W3C XML Schema Design Patterns: Avoiding Complexity
Dare Obasanjo, Microsoft Corporation

http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnxml/html/
xmlschemacomplex.asp

regards, Mark