[Animl-develop] Summary of changes to core schema and request for help

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

Hi again (Mark Bean here from home)

 I think it is time for a phone conference, ASAP please.


This note documents in detail changes Maren and I made (below).   Please
search for HELP if you are conversant with XML Schema.  At this point we are
lacking needed expertise and the HELP tags areas where we have questions.
Maren's 1.3 version validates in VisualStudio.Net and XMLSpy.

(1)  There is a proposal on the board to allow multiple VectorSets.  No
answer from Mark Mullins or anyone else yet as to whether that is a good
option.



(2) Before that, Vector.Length.  There is none!  I remember in our
discussions that we felt we should omit lengths unless they were needed, and
I felt pretty sure that any Base65 conversion algorithm would provide a
length for array dimensioning.  Here is the C# conversion code:

// Decode a GAML-type XData or YData Base64 string to array of doubles
public double[] B64ToDblArr(string crdString)
{
        return ByteToDouble(Convert.FromBase64String(crdString));
}

As you can see, the array is dimensioned and filled without needing to know
the length.  I don't know if other algorithms work the same way, but it is
possible.  What we wanted to avoid was having to parse the XML file to find
the length and then reparse it to obtain the values.  As a result, VectorSet
has Length but Vector does not.



(2) LCMS reports have summed spectra from multiple regions.  Maren suggested
using a timeline with the first data point of each region.  I had actually
thought to use the "peak retention time", but am not sure that is generally
applicable.  What do you think?



(4) AnIML Schema Changes up to version 1.3   Line numbers in v. 1.0 in
brown.  1.03 version in red

lines 2  MF (unnecessary XMLSPY entries)
<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by Maren Fiege
(Creon·Lab·Control AG) -->
<!-- edited with XMLSpy v2005 U (http://www.xmlspy.com) by Maren Fiege
(Waters) -->


line 316  MF (HELP no explanation yet -see letter of Nov 26)
removed the following from v.1.0
        <xs:keyref name="vectorIDRef" refer="vectorID">
                <xs:selector xpath="."/>
                <xs:field xpath="@vector"/>
        </xs:keyref>


line 606 (MFB XMLSpy validation error:  "Not a valid restriction since its
"maxOccurs" value <unbounded> is greater than "1".)
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.
    <xs:choice>
changed to
    <xs:choice maxOccurs="unbounded">


----------------------------------------------------------------------------
-
line 165  MB  HELP.  I don't think my fix is quite right yet.  (XMLSpy:
"The complex type "no name" has multiple Attribute Definitions (e.g.
"templateid") whose type defintions is derived from "ID").  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.   "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. "

added to element name Template
        <xs:unique name="templateIdKey">
                <xs:selector xpath="." />
                <xs:field xpath="@templateId" />
        </xs:unique>


and also line 144  MB
        <xs:attribute name="templateUsed" type="xs:IDREF" use="optional"/>
changed to
        <xs:attribute name="templateUsed" type="xs:string" use="optional" />



and also line 162 MB
        <xs:attribute name="templateId" type="xs:ID" use="required"/>
changed to
        <xs:attribute name="templateId" type="xs:string" use="required" />

----------------------------------------------------------------------------
-



MAJOR CHANGES TO derivation from  by restriction (ExperimentStepType and
TemplateType).  The problem is that derivation by restriction must contain
all the original tags and no others, being able only to restrict the
original value ranges.  Derivation by extension might be better, but I
couldn't get it to work so opted simply to create a new <xs:complexType
name="Technique">.  HELP needed to derive by extension
----------------------------------------------------------------------------
------

line 450...459
removed the following from v. 1.0
        <xs:keyref name="sampleIDUsage" refer="sampleID">
                <xs:selector xpath="."/>
                <xs:field xpath="@sampleID"/>
        </xs:keyref>
and moved it to outside the ComplexType but still inside SamplesUsed element
        <xs:keyref name="sampleIDUsage" refer="sampleID">
                <xs:selector xpath=".//SamplesUsed" />
                <xs:field xpath="SampleRef/@sampleID" />
        </xs:keyref>


<xs:complexType name="ExperimentStepType">
line 491... MFB
commented out derivation by extension (note that <!-- .... --> comments out
all enclosed XML)
        <!--xs:element name="Technique" minOccurs="0">
                <xs:annotation>
                        <xs:documentation>Reference to Technique used in
this Experiment.</xs:documentation>
                </xs:annotation>
                <xs:complexType>
                        <xs:sequence>
                                <xs:element name="Extension" minOccurs="0"
maxOccurs="unbounded">
                                        <xs:annotation>
                                                <xs:documentation>Reference
to Extension to amend Technique.</xs:documentation>
                                        </xs:annotation>
                                        <xs:complexType>
                                                <xs:attribute name="uri"
type="xs:anyURI" use="required">
                                                        <xs:annotation>

<xs:documentation>URI where Extension file can be
fetched.</xs:documentation>
                                                        </xs:annotation>
                                                </xs:attribute>
                                                <xs:attribute name="name"
type="xs:token" use="required">
                                                        <xs:annotation>

<xs:documentation>Name of Extension to be used. Must match Name given in
Extension Definition file.</xs:documentation>
                                                        </xs:annotation>
                                                </xs:attribute>
                                        </xs:complexType>
                                </xs:element>
                        </xs:sequence>
                        <xs:attributeGroup ref="SignableItemWithName"/>
                        <xs:attribute name="uri" type="xs:anyURI"
use="required">
                                <xs:annotation>
                                        <xs:documentation>URI where
Technique Definition file can be fetched.</xs:documentation>
                                </xs:annotation>
                        </xs:attribute>
                </xs:complexType>
        </xs:element-->


<xs:complexType name="TemplateType">
line 496...MFB
commented out derivation by extension same as above
<!--xs:element name="Technique" minOccurs="0">
    <xs:annotation>
        <xs:documentation>Reference to Technique used in this
Experiment.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
        <xs:sequence>
            <xs:element name="Extension" minOccurs="0"
maxOccurs="unbounded">
                <xs:annotation>
                    <xs:documentation>Reference to Extension to amend
Technique.</xs:documentation>
                </xs:annotation>
                <xs:complexType>
                    <xs:attribute name="uri" type="xs:anyURI"
use="required">
                        <xs:annotation>
                            <xs:documentation>URI where Extension file can
be fetched.</xs:documentation>
                        </xs:annotation>
                    </xs:attribute>
                    <xs:attribute name="name" type="xs:token"
use="required">
                        <xs:annotation>
                            <xs:documentation>Name of Extension to be used.
Must match Name given in Extension Definition
file.</xs:documentation>
                        </xs:annotation>
                    </xs:attribute>
                </xs:complexType>
            </xs:element>
         </xs:sequence>
         <xs:attributeGroup ref="SignableItemWithName"/>
             <xs:attribute name="uri" type="xs:anyURI" use="required">
                 <xs:annotation>
                     <xs:documentation>URI where Technique Definition file
can be fetched.</xs:documentation>
                </xs:annotation>
            </xs:attribute>

    </xs:complexType>
</xs:element-->



line 544 (remaining close tags also commented out - some are extraneous)
        <!--xs:complexContent-->
        <!--xs:restriction base="ExperimentStepType"-->
        <!--/xs:restriction-->
        <!--/xs:complexContent-->


line 893
MFB Added <xs:complexType name="Technique">

        <xs:complexType name="Technique">
                <xs:annotation>
                        <xs:documentation>Reference to Technique used in
this Experiment.</xs:documentation>
                </xs:annotation>
                <xs:sequence>
                        <xs:element name="Extension" minOccurs="0"
maxOccurs="unbounded">
                                <xs:annotation>
                                        <xs:documentation>Reference to
Extension to amend Technique.</xs:documentation>
                                </xs:annotation>
                                <xs:complexType>
                                        <xs:attribute name="uri"
type="xs:anyURI" use="required">
                                                <xs:annotation>

<xs:documentation>URI where Extension file can be
fetched.</xs:documentation>
                                                </xs:annotation>
                                        </xs:attribute>
                                        <xs:attribute name="name"
type="xs:token" use="required">
                                                <xs:annotation>

<xs:documentation>Name of Extension to be used. Must match Name given in
Extension Definition file.</xs:documentation>
                                                </xs:annotation>
                                        </xs:attribute>
                                </xs:complexType>
                        </xs:element>
                </xs:sequence>
                <xs:attributeGroup ref="SignableItemWithName" />
                <xs:attribute name="uri" type="xs:anyURI" use="required">
                        <xs:annotation>
                                <xs:documentation>URI where Technique
Definition file can be fetched.</xs:documentation>
                        </xs:annotation>
                </xs:attribute>
        </xs:complexType>

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