ADF MAGE-ML Tool XML Schema Documentation

Table of Contents

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Schema Document Properties

Target Namespace http://www.ebi.ac.uk/ADFConverter
Element and Attribute Namespaces
  • Global element and attribute declarations belong to this schema's target namespace.
  • By default, local element declarations belong to this schema's target namespace.
  • By default, local attribute declarations have no namespace.

Declared Namespaces

Prefix Namespace
xml http://www.w3.org/XML/1998/namespace
ADFConv http://www.ebi.ac.uk/ADFConverter
xs http://www.w3.org/2001/XMLSchema
Schema Component Representation
<xs:schema targetNamespace="http://www.ebi.ac.uk/ADFConverter" elementFormDefault="qualified" attributeFormDefault="unqualified">
...
</xs:schema>
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Global Declarations

Element: documentStructure

Name documentStructure
Type ADFConv:documentStructureType
Nillable no
Abstract no
Documentation data structure in a or several files
XML Instance Representation
<ADFConv:documentStructure>
<ADFConv:files> [1] ?
<ADFConv:file> ADFConv:FileType </ADFConv:file> [1..*]
</ADFConv:files>
</ADFConv:documentStructure>
Schema Component Representation
<xs:element name="documentStructure" type="ADFConv:documentStructureType"/>
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Element: filer

Name filer
Type ADFConv:FileType
Nillable no
Abstract no
Documentation data file strucuture definition
XML Instance Representation
<ADFConv:filer
extension="xs:string [1]"
name="xs:string [0..1]"
fileFormat="ADFConv:fileFormatType [1]">
<ADFConv:dataSet> [1] ?
<ADFConv:data> ADFConv:DataType </ADFConv:data> [1..*]
</ADFConv:dataSet>
</ADFConv:filer>
Schema Component Representation
<xs:element name="filer" type="ADFConv:FileType"/>
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Element: header

Name header
Type ADFConv:headerType
Nillable no
Abstract no
Documentation list of header item of data table contained in a file
XML Instance Representation
<ADFConv:header>
<ADFConv:items> [1] ?
<ADFConv:item> ADFConv:ItemType </ADFConv:item> [1..*]
</ADFConv:items>
</ADFConv:header>
Schema Component Representation
<xs:element name="header" type="ADFConv:headerType"/>
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Element: itemTemp

Name itemTemp
Type ADFConv:ItemType
Nillable no
Abstract no
XML Instance Representation
<ADFConv:itemTemp
name="xs:ID [1]"
element="xs:string [0..1]">
<ADFConv:relaxCheckRules> [0..1] ?
<ADFConv:relaxCheck> ADFConv:CheckRuleType </ADFConv:relaxCheck> [1..*]
</ADFConv:relaxCheckRules>
<ADFConv:strictCheck> ADFConv:CheckRuleType </ADFConv:strictCheck> [1] ?
<ADFConv:itemType> xs:string </ADFConv:itemType> [1] ?
<ADFConv:exactName> xs:string </ADFConv:exactName> [1] ?
<ADFConv:fieldValueType> ADFConv:FieldType </ADFConv:fieldValueType> [1] ?
<ADFConv:cardinality> ADFConv:CardinalityType </ADFConv:cardinality> [1] ?
<ADFConv:fieldCardinality> ADFConv:CardinalityType </ADFConv:fieldCardinality> [1] ?
<ADFConv:location> ADFConv:LocationType </ADFConv:location> [1] ?
<ADFConv:multiplicity> xs:boolean </ADFConv:multiplicity> [0..1] ?
<ADFConv:valueFieldSeparator> xs:string </ADFConv:valueFieldSeparator> [0..1] ?
<ADFConv:innerValueFieldSeparator> xs:string </ADFConv:innerValueFieldSeparator> [0..1] ?
<ADFConv:fieldDependence> [0..1] ?
<ADFConv:itemref> xs:IDREF </ADFConv:itemref> [1..*]
</ADFConv:fieldDependence>
<ADFConv:subNames> [0..1]
<ADFConv:subName> ADFConv:SubNameType </ADFConv:subName> [1..*]
</ADFConv:subNames>
<ADFConv:simpleMicroarrayLayoutRelatedItem> xs:IDREF </ADFConv:simpleMicroarrayLayoutRelatedItem> [0..1]
</ADFConv:itemTemp>
Schema Component Representation
<xs:element name="itemTemp" type="ADFConv:ItemType"/>
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Global Definitions

Complex Type: CardinalityType

Super-types: None
Sub-types: None
Name CardinalityType
Abstract no
Documentation Cardinality of an item or value in a field Represent by a minimal occur and a maximal
XML Instance Representation
<...
lowerBound="xs:nonNegativeInteger [1]"
upperBound="xs:int [0..1]"/>
Schema Component Representation
<xs:complexType name="CardinalityType">
<xs:attribute name="lowerBound" type="xs:nonNegativeInteger" use="required"/>
<xs:attribute name="upperBound" type="xs:int" default="-1"/>
<-- integer from 0 to 126789 shoulb enough-->
<--<xs:restriction base="xs:string"> <xs:pattern value="\d\.\.\d{1,}"/> </xs:restriction>-->
</xs:complexType>
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Complex Type: CheckRuleType

Super-types: None
Sub-types: None
Name CheckRuleType
Abstract no
Documentation Rule for checking: using pattern to identify items
XML Instance Representation
<...>
<ADFConv:regex> xs:string (pattern = [^/].+[^/]) </ADFConv:regex> [1] ?
<ADFConv:description> xs:string </ADFConv:description> [0..1] ?
</...>
Schema Component Representation
<xs:complexType name="CheckRuleType">
<xs:sequence>
<xs:element name="regex">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:pattern value="[^/].+[^/]"/>
<xs:pattern value="/.+/"/>
<-- <xs:pattern value="\slash .+\slash"/>-->
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="description" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
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Complex Type: ConstraintType

Super-types: None
Sub-types: None
Name ConstraintType
Abstract no
XML Instance Representation
<...>
<ADFConv:rule> ADFConv:CheckRuleType </ADFConv:rule> [1]
<ADFConv:curatedValue> xs:string </ADFConv:curatedValue> [0..1]
</...>
Schema Component Representation
<xs:complexType name="ConstraintType">
<xs:sequence>
<xs:element name="rule" type="ADFConv:CheckRuleType"/>
<xs:element name="curatedValue" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
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Complex Type: DataType

Super-types: None
Sub-types: None
Name DataType
Abstract no
Documentation structure of data: can be composed of several table
XML Instance Representation
<...
name="xs:string [0..1]"
tableDelimiter="xs:string [0..1]"
dataFormat="ADFConv:dataFormatType [1]">
<ADFConv:tables> [1] ?
<ADFConv:table> ADFConv:tableType </ADFConv:table> [1..*]
</ADFConv:tables>
</...>
Schema Component Representation
<xs:complexType name="DataType">
<xs:sequence>
<xs:element name="tables">
<xs:complexType>
<xs:sequence>
<xs:element name="table" type="ADFConv:tableType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="name" type="xs:string"/>
<xs:attribute name="tableDelimiter" type="xs:string"/>
<xs:attribute name="dataFormat" type="ADFConv:dataFormatType" use="required"/>
</xs:complexType>
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Complex Type: FieldType

Super-types: None
Sub-types: None
Name FieldType
Abstract no
Documentation Specifies the field value type and constraints
XML Instance Representation
<...>
<ADFConv:typeName> ADFConv:fieldTypeName </ADFConv:typeName> [1]
<ADFConv:constraints> [0..1]
<ADFConv:constraint> ADFConv:ConstraintType </ADFConv:constraint> [1..*]
</ADFConv:constraints>
</...>
Schema Component Representation
<xs:complexType name="FieldType">
<xs:sequence>
<xs:element name="typeName" type="ADFConv:fieldTypeName"/>
<xs:element name="constraints" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="constraint" type="ADFConv:ConstraintType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
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Complex Type: FileType

Super-types: None
Sub-types: None
Name FileType
Abstract no
Documentation definition of a file
XML Instance Representation
<...
extension="xs:string [1]"
name="xs:string [0..1]"
fileFormat="ADFConv:fileFormatType [1]">
<ADFConv:dataSet> [1] ?
<ADFConv:data> ADFConv:DataType </ADFConv:data> [1..*]
</ADFConv:dataSet>
</...>
Schema Component Representation
<xs:complexType name="FileType">
<xs:sequence>
<xs:element name="dataSet">
<xs:complexType>
<xs:sequence>
<xs:element name="data" type="ADFConv:DataType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="extension" type="xs:string" use="required"/>
<xs:attribute name="name" type="xs:string" default=""/>
<xs:attribute name="fileFormat" type="ADFConv:fileFormatType" use="required"/>
</xs:complexType>
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Complex Type: ItemType

Super-types: None
Sub-types: None
Name ItemType
Abstract no
Documentation an header item with characteristic of it for checking
XML Instance Representation
<...
name="xs:ID [1]"
element="xs:string [0..1]">
<ADFConv:relaxCheckRules> [0..1] ?
<ADFConv:relaxCheck> ADFConv:CheckRuleType </ADFConv:relaxCheck> [1..*]
</ADFConv:relaxCheckRules>
<ADFConv:strictCheck> ADFConv:CheckRuleType </ADFConv:strictCheck> [1] ?
<ADFConv:itemType> xs:string </ADFConv:itemType> [1] ?
<ADFConv:exactName> xs:string </ADFConv:exactName> [1] ?
<ADFConv:fieldValueType> ADFConv:FieldType </ADFConv:fieldValueType> [1] ?
<ADFConv:cardinality> ADFConv:CardinalityType </ADFConv:cardinality> [1] ?
<ADFConv:fieldCardinality> ADFConv:CardinalityType </ADFConv:fieldCardinality> [1] ?
<ADFConv:location> ADFConv:LocationType </ADFConv:location> [1] ?
<ADFConv:multiplicity> xs:boolean </ADFConv:multiplicity> [0..1] ?
<ADFConv:valueFieldSeparator> xs:string </ADFConv:valueFieldSeparator> [0..1] ?
<ADFConv:innerValueFieldSeparator> xs:string </ADFConv:innerValueFieldSeparator> [0..1] ?
<ADFConv:fieldDependence> [0..1] ?
<ADFConv:itemref> xs:IDREF </ADFConv:itemref> [1..*]
</ADFConv:fieldDependence>
<ADFConv:subNames> [0..1]
<ADFConv:subName> ADFConv:SubNameType </ADFConv:subName> [1..*]
</ADFConv:subNames>
<ADFConv:simpleMicroarrayLayoutRelatedItem> xs:IDREF </ADFConv:simpleMicroarrayLayoutRelatedItem> [0..1]
</...>
Schema Component Representation
<xs:complexType name="ItemType">
<xs:sequence>
<xs:element name="relaxCheckRules" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="relaxCheck" type="ADFConv:CheckRuleType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="strictCheck" type="ADFConv:CheckRuleType"/>
<xs:element name="itemType" type="xs:string"/>
<xs:element name="exactName" type="xs:string"/>
<xs:element name="fieldValueType" type="ADFConv:FieldType"/>
<xs:element name="cardinality" type="ADFConv:CardinalityType"/>
<xs:element name="fieldCardinality" type="ADFConv:CardinalityType"/>
<xs:element name="location" type="ADFConv:LocationType"/>
<xs:element name="multiplicity" type="xs:boolean" default="false" minOccurs="0"/>
<xs:element name="valueFieldSeparator" type="xs:string" default=";" minOccurs="0"/>
<xs:element name="innerValueFieldSeparator" type="xs:string" minOccurs="0"/>
<xs:element name="fieldDependence" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="itemref" type="xs:IDREF" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<-- <xs:key name="itemUnique"> <xs:selector xpath="."/> <xs:field xpath="@name"/> </xs:key>-->
</xs:element>
<xs:element name="subNames" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="subName" type="ADFConv:SubNameType" maxOccurs="unbounded"/>
<-- for now, only one is handle by the application -->
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="simpleMicroarrayLayoutRelatedItem" type="xs:IDREF" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="name" type="xs:ID" use="required"/>
<xs:attribute name="element" type="xs:string" default="default"/>
</xs:complexType>
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Complex Type: LocationType

Super-types: None
Sub-types: None
Name LocationType
Abstract no
Documentation type of the field value : : a free text, a controlled vocabulary, a date...
XML Instance Representation
<...>
Start Choice [1]
<ADFConv:columNumber> xs:int </ADFConv:columNumber> [1]
<ADFConv:previousColumns> [1]
<ADFConv:previousColumn> xs:IDREF </ADFConv:previousColumn> [1..*]
</ADFConv:previousColumns>
End Choice
</...>
Schema Component Representation
<xs:complexType name="LocationType">
<xs:choice>
<xs:element name="columNumber" type="xs:int"/>
<xs:element name="previousColumns">
<xs:complexType>
<xs:sequence>
<xs:element name="previousColumn" type="xs:IDREF" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:choice>
</xs:complexType>
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Complex Type: SubNameType

Super-types: None
Sub-types: None
Name SubNameType
Abstract no
Documentation Definition for the subname of the item
XML Instance Representation
<...
prefixDelimiter="xs:string [1]"
suffixDelimiter="xs:string [0..1]">
<ADFConv:type> ADFConv:SubNameTypeName </ADFConv:type> [0..1]
<ADFConv:constraints> [0..1]
<ADFConv:constraint> ADFConv:ConstraintType </ADFConv:constraint> [1..*]
</ADFConv:constraints>
</...>
Schema Component Representation
<xs:complexType name="SubNameType">
<xs:sequence>
<xs:element name="type" type="ADFConv:SubNameTypeName" minOccurs="0"/>
<xs:element name="constraints" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="constraint" type="ADFConv:ConstraintType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="prefixDelimiter" type="xs:string" use="required"/>
<xs:attribute name="suffixDelimiter" type="xs:string"/>
</xs:complexType>
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Complex Type: documentStructureType

Super-types: None
Sub-types: None
Name documentStructureType
Abstract no
Documentation definition of a data document: can contain several data table (in several files)
XML Instance Representation
<...>
<ADFConv:files> [1] ?
<ADFConv:file> ADFConv:FileType </ADFConv:file> [1..*]
</ADFConv:files>
</...>
Schema Component Representation
<xs:complexType name="documentStructureType">
<xs:sequence>
<xs:element name="files">
<xs:complexType>
<xs:sequence>
<xs:element name="file" type="ADFConv:FileType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
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Complex Type: headerType

Super-types: None
Sub-types: None
Name headerType
Abstract no
Documentation Header list Structure: contains item
XML Instance Representation
<...>
<ADFConv:items> [1] ?
<ADFConv:item> ADFConv:ItemType </ADFConv:item> [1..*]
</ADFConv:items>
</...>
Schema Component Representation
<xs:complexType name="headerType">
<xs:sequence>
<xs:element name="items">
<xs:complexType>
<xs:sequence>
<xs:element name="item" type="ADFConv:ItemType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<-- <xs:key name="ID"> <xs:selector xpath="item"/> <xs:field xpath="@mame"/> </xs:key> <xs:keyref name="IDREF" refer="ID"> <xs:selector xpath="item/itemDependence/itemref|item/itemDependence/location/previousColumns/previousColumn"/> <xs:field xpath="@ref"/> </xs:keyref>-->
</xs:element>
</xs:sequence>
</xs:complexType>
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Complex Type: tableType

Super-types: None
Sub-types: None
Name tableType
Abstract no
Documentation structure of datatable: can have a header
XML Instance Representation
<...
name="xs:string [0..1]"
sheetNumber="xs:int [0..1]"
dataDelimiter="xs:string [0..1]"
orientation="ADFConv:TableOrientationType [0..1]"
haveHeader="xs:boolean [0..1]">
<ADFConv:header> ADFConv:headerType </ADFConv:header> [0..1]
</...>
Schema Component Representation
<xs:complexType name="tableType">
<xs:sequence>
<xs:element name="header" type="ADFConv:headerType" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="name" type="xs:string"/>
<xs:attribute name="sheetNumber" type="xs:int"/>
<xs:attribute name="dataDelimiter" type="xs:string" default=""/>
<xs:attribute name="orientation" type="ADFConv:TableOrientationType" default="horizontal"/>
<xs:attribute name="haveHeader" type="xs:boolean" default="true"/>
</xs:complexType>
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Simple Type: SubNameTypeName

Super-types: xs:string < SubNameTypeName (by restriction)
Sub-types: None
Name SubNameTypeName
Content
  • Base XSD Type: string
  • value comes from list: {'Database Tag'|'Group Tag'|'Other'}
Documentation type of the subname of a header item : a database tag, a group tag, e...
Schema Component Representation
<xs:simpleType name="SubNameTypeName">
<xs:restriction base="xs:string">
<xs:enumeration value="Database Tag"/>
<xs:enumeration value="Group Tag"/>
<xs:enumeration value="Other"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: TableOrientationType

Super-types: xs:string < TableOrientationType (by restriction)
Sub-types: None
Name TableOrientationType
Content
  • Base XSD Type: string
  • value comes from list: {'horizontal'|'vertical'}
Documentation Orientation of the data table : horizontal (default) - vertical
Schema Component Representation
<xs:simpleType name="TableOrientationType">
<xs:restriction base="xs:string">
<xs:enumeration value="horizontal"/>
<xs:enumeration value="vertical"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: dataFormatType

Super-types: xs:string < dataFormatType (by restriction)
Sub-types: None
Name dataFormatType
Content
  • Base XSD Type: string