XML Schema : CLI.xsd
Target namespace: http://www.openmicroscopy.org/XMLschemas/CLI/RC1/CLI.xsd
Schema Comments: Open Microscopy Environment Command Line Interface XML Schema Author: Josiah Johnston Generated by Turbo XML 2.3.1.100. Conforms to w3c http://www.w3.org/2001/XMLSchema
Imports namespace:http://www.w3.org/XML/1998/namespace schemaLocation: http://www.w3.org/2001/xml.xsd
Processing Instructions
Schema has: 39element definitions,  2 global attribute definitions,  31 element attribute definitions,  0 datatype definitions.
Possible root elements: ExecutionInstructions, Output, pat, PixelOutput, PixelsInput, TempFile

Element list

Element AutoIterate
 
diagram
description Iterates a dimension over its entire range. Produces outputs.
uses elements OutputTo
 
used by elementstheT, theW, theZ
content sequence
 
source
-<element name="AutoIterate">
-<annotation>
 <documentation>Iterates a dimension over its entire range. Produces outputs.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:OutputTo" maxOccurs="unbounded" />
 </sequence>
 </complexType>
 </element>

Element BitsPerPixel
 
diagram
description Specifies an input data location for populating the semantic element
uses attributes BitsPerPixel/Location
 
used by elementsPixelOutput
content sequence (default)
 
Attribute Datatype Use Values Default Comments
Location string required This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"
 
source
-<element name="BitsPerPixel">
-<annotation>
 <documentation>Specifies an input data location for populating the semantic element</documentation>
 </annotation>
-<complexType>
-<attribute name="Location" use="required" type="string">
-<annotation>
 <documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</documentation>
 </annotation>
 </attribute>
 </complexType>
 </element>

Element CommandLine
 
diagram
description This describes the string that will be passed to a command line program via command line parameters. The command line handler will perform basic variable substitution on sub elements of this. Example: when you use the program, you type: /OME/bin/OME_Image_XYZ_stats Path=[path to repository file] Dims=[X],[Y],[Z],[W],[T],[BytesPerPix] XML specification of the command line parameters is: <CommandLine>Path=<RawImageFilePath/> Dims=<sizeX/>,<sizeY/>,<sizeZ/>,<sizeW/>,<sizeT/>,<BPP/></CommandLine>
uses elements Parameter
 
used by elementsExecutionInstructions
content sequence
 
source
-<element name="CommandLine">
-<annotation>
 <documentation>This describes the string that will be passed to a command line program via command line parameters. The command line handler will perform basic variable substitution on sub elements of this. Example: when you use the program, you type: /OME/bin/OME_Image_XYZ_stats Path=[path to repository file] Dims=[X],[Y],[Z],[W],[T],[BytesPerPix] XML specification of the command line parameters is: <CommandLine>Path=<RawImageFilePath/> Dims=<sizeX/>,<sizeY/>,<sizeZ/>,<sizeW/>,<sizeT/>,<BPP/></CommandLine> </documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:Parameter" minOccurs="0" maxOccurs="unbounded" />
 </sequence>
 </complexType>
-<unique name="CommandLine_XYPlaneID">
 <selector xpath=".//CLI:XYPlane" />
 <field xpath="@XYPlaneID" />
 </unique>
-<keyref name="CommandLine_XYPlaneID_Ref" refer="CLI:CommandLine_XYPlaneID">
 <selector xpath=".//CLI:Match" />
 <field xpath="@XYPlaneID" />
 </keyref>
 </element>

Element CustomRecord
 
diagram
description Used to construct an arbitrarily formatted record. Not currently supported. email Josiah <siah@nih.gov> if you need this implemented.
uses elements InputSubString
 
used by elementsInputRecord
content sequence
 
source
-<element name="CustomRecord">
-<annotation>
 <documentation>Used to construct an arbitrarily formatted record. Not currently supported. email Josiah <siah@nih.gov> if you need this implemented.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:InputSubString" maxOccurs="unbounded" />
 </sequence>
 </complexType>
 </element>

Element DelimitedRecord
 
diagram
description Use this to construct a Delimited Record. (i.e. tab delimitted, comma delimitted, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.
uses elements Input
uses attributes DelimitedRecord/FieldDelimiter, DelimitedRecord/RecordDelimiter
 
used by elementsInputRecord
content sequence
 
Attribute Datatype Use Values Default Comments
FieldDelimiter string required This string will be used to separate fields in this record.
RecordDelimiter string optional (default) \n This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).
 
source
-<element name="DelimitedRecord">
-<annotation>
 <documentation>Use this to construct a Delimited Record. (i.e. tab delimitted, comma delimitted, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:Input" maxOccurs="unbounded" />
 </sequence>
-<attribute name="FieldDelimiter" use="required" type="string">
-<annotation>
 <documentation>This string will be used to separate fields in this record.</documentation>
 </annotation>
 </attribute>
-<attribute name="RecordDelimiter" default="\n" type="string">
-<annotation>
 <documentation>This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).</documentation>
 </annotation>
 </attribute>
 </complexType>
 </element>

Element End
 
diagram
description Specifies an end point of iteration. Not currently supported.
uses attribute groups InputLocation
 
used by elementsIterateRange
content sequence (default)
 
source
-<element name="End">
-<annotation>
 <documentation>Specifies an end point of iteration. Not currently supported. </documentation>
 </annotation>
-<complexType>
 <attributeGroup ref="CLI:InputLocation" />
 </complexType>
 </element>

Element ExecutionInstructions
 
diagram
description Tied to DB. Table PROGRAMS Column EXECUTION
uses elements CommandLine, STDIN, STDOUT
uses attributes ExecutionInstructions/ExecutionPoint, ExecutionInstructions/MakesNewFeature
 
substitution hierarchy ExecutionInstructions
content sequence
 
Attribute Datatype Use Values Default Comments
ExecutionPoint {} required possible values: executeGlobal | startDataset | startImage | startFeature | finishFeature | finishImage | finishDataset Assigns a execution point for the analysis.
MakesNewFeature boolean optional (default) false
 
source
-<element name="ExecutionInstructions">
-<annotation>
 <documentation>Tied to DB. Table PROGRAMS Column EXECUTION </documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:CommandLine" minOccurs="0" />
 <element ref="CLI:STDIN" minOccurs="0" />
 <element ref="CLI:STDOUT" minOccurs="0" />
 </sequence>
-<attribute name="ExecutionPoint" use="required">
-<annotation>
 <documentation>Assigns a execution point for the analysis. </documentation>
 </annotation>
-<simpleType>
-<restriction base="string">
 <enumeration value="executeGlobal" />
 <enumeration value="startDataset" />
 <enumeration value="startImage" />
 <enumeration value="startFeature" />
 <enumeration value="finishFeature" />
 <enumeration value="finishImage" />
 <enumeration value="finishDataset" />
 </restriction>
 </simpleType>
 </attribute>
 <attribute name="MakesNewFeature" default="false" type="boolean" />
 </complexType>
 </element>

Element Index
 
diagram
description This specifies what semantic elements of the attributes should be used to merge them into records. Every formalInput in a record should be included in this. For records with multiple indexes, (Stack Statistics for example has theT and theC), specify two indexes. The records will be sorted based on the index order. This means a stack statistics record that specifies theC as an index before theT will be sorted first on theC, then on theT.
uses elements Input
 
used by elementsInputRecord
content sequence
 
source
-<element name="Index">
-<annotation>
 <documentation>This specifies what semantic elements of the attributes should be used to merge them into records. Every formalInput in a record should be included in this. For records with multiple indexes, (Stack Statistics for example has theT and theC), specify two indexes. The records will be sorted based on the index order. This means a stack statistics record that specifies theC as an index before theT will be sorted first on theC, then on theT. </documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:Input" maxOccurs="unbounded" />
 </sequence>
 </complexType>
 </element>

Element Input
 
diagram
description References a particular column in a FormalInput. Used for variable substitution.
uses attributes Input/DivideBy, Input/MultiplyBy
uses attribute groups InputLocation
 
used by elementsDelimitedRecord, Index, InputSubString
content sequence (default)
 
Attribute Datatype Use Values Default Comments
DivideBy string optional (default)
MultiplyBy string optional (default)
 
source
-<element name="Input">
-<annotation>
 <documentation>References a particular column in a FormalInput. Used for variable substitution.</documentation>
 </annotation>
-<complexType>
 <attributeGroup ref="CLI:InputLocation" />
 <attribute name="DivideBy" type="string" />
 <attribute name="MultiplyBy" type="string" />
 </complexType>
 </element>

Element InputRecord
 
diagram
description Groups a set of inputs into records.
uses elements CustomRecord, DelimitedRecord, Index
 
used by elementsSTDIN
content sequence
 
source
-<element name="InputRecord">
-<annotation>
 <documentation>Groups a set of inputs into records.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:Index" maxOccurs="unbounded" />
-<choice>
 <element ref="CLI:DelimitedRecord" />
 <element ref="CLI:CustomRecord" />
 </choice>
 </sequence>
 </complexType>
-<unique name="InputRecord_XYPlaneID">
 <selector xpath=".//CLI:XYPlane" />
 <field xpath="@XYPlaneID" />
 </unique>
-<keyref name="InputRecord_XYPlaneID_Ref" refer="CLI:InputRecord_XYPlaneID">
 <selector xpath=".//CLI:Match" />
 <field xpath="@XYPlaneID" />
 </keyref>
 </element>

Element InputSubString
 
diagram
description
uses elements Input, RawImageFilePath, RawText, XYPlane
 
used by elementsCustomRecord, Parameter
content choice
 
source
-<element name="InputSubString">
-<complexType>
-<choice>
 <element ref="CLI:Input" />
 <element ref="CLI:XYPlane" />
 <element ref="CLI:RawImageFilePath" />
 <element ref="CLI:RawText" />
 </choice>
 </complexType>
 </element>

Element IterateRange
 
diagram
description Iterate this dimension over a range of values. Produces outputs.
uses elements End, OutputTo, Start
 
used by elementstheT, theW, theZ
content sequence
 
source
-<element name="IterateRange">
-<annotation>
 <documentation>Iterate this dimension over a range of values. Produces outputs.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:Start" />
 <element ref="CLI:End" />
 <element ref="CLI:OutputTo" maxOccurs="unbounded" />
 </sequence>
 </complexType>
 </element>

Element Match
 
diagram
description Used to reference the index method used by another XYplane. Effectively syncs the planes on certain dimensions. Use with caution. Unsynced dimensions need to be compatible.
uses attributes Match/XYPlaneID
 
used by elementstheT, theW, theZ
content sequence (default)
 
Attribute Datatype Use Values Default Comments
XYPlaneID string required References another Plane.
 
source
-<element name="Match">
-<annotation>
 <documentation>Used to reference the index method used by another XYplane. Effectively syncs the planes on certain dimensions. Use with caution. Unsynced dimensions need to be compatible.</documentation>
 </annotation>
-<complexType>
-<attribute name="XYPlaneID" use="required" type="string">
-<annotation>
 <documentation>References another Plane.</documentation>
 </annotation>
 </attribute>
 </complexType>
 </element>

Element Output
 
diagram
description References a particular column of a FormalOutput.
uses elements OutputTo
uses attributes Output/AccessBy
 
content sequence
 
Attribute Datatype Use Values Default Comments
AccessBy integer required Describes how to access information extracted using a regular expression. Examples are 1, 2, 3, ...
 
source
-<element name="Output">
-<annotation>
 <documentation>References a particular column of a FormalOutput.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:OutputTo" maxOccurs="unbounded" />
 </sequence>
-<attribute name="AccessBy" use="required" type="integer">
-<annotation>
 <documentation>Describes how to access information extracted using a regular expression. Examples are 1, 2, 3, ...</documentation>
 </annotation>
 </attribute>
 </complexType>
 </element>

Element OutputRecord
 
diagram
description Groups a set of outputs into records.
uses attributes OutputRecord/RepeatCount, OutputRecord/TerminateAt
 
used by elementsSTDOUT
content sequence (default)
 
Attribute Datatype Use Values Default Comments
RepeatCount positiveInteger optional (default) RepeatCount specifies how many times to read a record. If it is not specified, reading will continue until it reaches the end of the output stream. If used in conjuction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first.
TerminateAt string optional (default) TerminateAt specifies a regular expression. When a match to this is found, reading will stop. If used in conjuction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first.
 
source
-<element name="OutputRecord">
-<annotation>
 <documentation>Groups a set of outputs into records.</documentation>
 </annotation>
-<complexType>
-<attribute name="RepeatCount" type="positiveInteger">
-<annotation>
 <documentation>RepeatCount specifies how many times to read a record. If it is not specified, reading will continue until it reaches the end of the output stream. If used in conjuction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first. </documentation>
 </annotation>
 </attribute>
-<attribute name="TerminateAt" type="string">
-<annotation>
 <documentation>TerminateAt specifies a regular expression. When a match to this is found, reading will stop. If used in conjuction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first. </documentation>
 </annotation>
 </attribute>
 </complexType>
 </element>

Element OutputTo
 
diagram
description Specifies location to write output. One data chunk that the Output element references may be written to one or more places.
uses attribute groups OutputLocation
 
used by elementsAutoIterate, IterateRange, Output, TempFile
content sequence (default)
 
source
-<element name="OutputTo">
-<annotation>
 <documentation>Specifies location to write output. One data chunk that the Output element references may be written to one or more places.</documentation>
 </annotation>
-<complexType>
 <attributeGroup ref="CLI:OutputLocation" />
 </complexType>
 </element>

Element Parameter
 
diagram
description All Formal Inputs referenced within this scope should have a count of 0 or 1.
uses elements InputSubString
 
used by elementsCommandLine
content sequence
 
source
-<element name="Parameter">
-<annotation>
 <documentation>All Formal Inputs referenced within this scope should have a count of 0 or 1.</documentation>
 </annotation>
-<complexType>
-<sequence>
 <element ref="CLI:InputSubString" maxOccurs="unbounded" />
 </sequence>
 </complexType>
 </element>

Element pat
 
diagram
description Contains a regular expression. Checked for compilation when the module is imported.