XML Schema "assayProvider.xsd"

Target Namespace:

Defined Components:

2 global elements, 19 local elements, 2 complexTypes

Default Namespace-Qualified Form:

Local Elements: qualified; Local Attributes: unqualified

Schema Location:

C:\dev\labkey\labkeyHome\server\modules\platform\assay\schemas\assayProvider.xsd, see XML source

Imports Schema:

expTypes.xsd [src]

XML Source

<?xml version="1.0" encoding="UTF-8"?>

<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://labkey.org/study/assay/xml" xmlns:ap="http://labkey.org/study/assay/xml" xmlns:exp="http://cpas.fhcrc.org/exp/xml" xmlns:xs="http://www.w3.org/2001/XMLSchema">

<xs:import namespace="http://cpas.fhcrc.org/exp/xml" schemaLocation="../../api/schemas/expTypes.xsd"/>

<xs:element name="provider" type="ap:ProviderType"/>

<xs:complexType name="ProviderType">

<xs:sequence>

<xs:element maxOccurs="1" minOccurs="0" name="name" type="xs:string"/>

<xs:element maxOccurs="1" minOccurs="0" name="description" type="xs:string"/>

<xs:element maxOccurs="1" minOccurs="0" name="requiredModules">

<xs:annotation>

<xs:documentation>

If provided, this set of modules will always be active in a given folder when an instance of this assay is present.
This could be useful if the assay depends on a user schema or other resources present in the module.

</xs:documentation>

</xs:annotation>

<xs:complexType>

<xs:sequence>

<xs:element maxOccurs="unbounded" minOccurs="0" name="moduleName" type="xs:string"/>

</xs:sequence>

</xs:complexType>

</xs:element>

<xs:element maxOccurs="unbounded" minOccurs="0" name="inputDataFileSuffix" type="xs:string">

<xs:annotation>

<xs:documentation>

Deprecated (use inputDataFile/fileSuffixes instead). File extension that should be offered the option to import into designs of this type

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="primaryDataFileType" type="ap:AssayDataType">

<xs:annotation>

<xs:documentation>

Information about the files to be used as inputs to this assay.

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="unbounded" minOccurs="0" name="relatedDataFileType" type="ap:AssayDataType">

<xs:annotation>

<xs:documentation>

If there are related data files available on the server's file system
(ones that share the same base file name, with different suffixes/file extensions), they are
attached to the run at import time. If they happen to match up with a <relatedDataFile>
element, they will be added using the associated namespace prefix and role.

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="fieldKeys">

<xs:annotation>

<xs:documentation>

Contains field keys (column names, potentially with lookups) used to resolve various values

</xs:documentation>

</xs:annotation>

<xs:complexType>

<xs:sequence>

<xs:element maxOccurs="1" minOccurs="0" name="participantId" type="xs:string">

<xs:annotation>

<xs:documentation>

Field key relative to the data/results table that gives the ParticipantID for a given row of data

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="visitId" type="xs:string">

<xs:annotation>

<xs:documentation>

Field key relative to the data/results table that gives the VisitID for a given row of data

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="date" type="xs:string">

<xs:annotation>

<xs:documentation>

Field key relative to the data/results table that gives the date for a given row of data

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="specimenId" type="xs:string">

<xs:annotation>

<xs:documentation>

Field key relative to the data/results table that gives the SpecimenID for a given row of data

</xs:documentation>

</xs:annotation>

</xs:element>

</xs:sequence>

</xs:complexType>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="transformScripts">

<xs:annotation>

<xs:documentation>

Ordered list of transformation/validation scripts that must be run as data is
imported. The scripts themselves should be in the assay's ./scripts subdirectory.
Scripts will be executed in the order given here. Any scripts in the ./script subdirectory
that are not listed here will be executed in alphabetical order after all of the scripts
listed here.

</xs:documentation>

</xs:annotation>

<xs:complexType>

<xs:sequence>

<xs:element maxOccurs="unbounded" minOccurs="0" name="transformScript">

<xs:complexType>

<xs:sequence>

<xs:element maxOccurs="1" minOccurs="1" name="fileName" type="xs:string">

<xs:annotation>

<xs:documentation>

Simple file name (no path) of the script. If a script engine associated
with the script's file extension isn't registered in the Admin Console,
the import attempt will fail.

</xs:documentation>

</xs:annotation>

</xs:element>

</xs:sequence>

</xs:complexType>

</xs:element>

</xs:sequence>

</xs:complexType>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="saveHandler" type="xs:string">

<xs:annotation>

<xs:documentation>

Class name of the custom save handler for this assay type.

</xs:documentation>

</xs:annotation>

</xs:element>

</xs:sequence>

<xs:attribute default="false" name="plateBased" type="xs:boolean">

<xs:annotation>

<xs:documentation>Not used.</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute default="true" name="canCopyToStudy" type="xs:boolean">

<xs:annotation>

<xs:documentation>Deprecated. Not used anymore.</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

<xs:element name="domain" type="exp:DomainDescriptorType"/>

<xs:complexType name="AssayDataType">

<xs:sequence>

<xs:element maxOccurs="1" minOccurs="0" name="namespacePrefix" type="xs:string">

<xs:annotation>

<xs:documentation>

Namespace prefix to be used when creating the LSID for the input data file

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="1" minOccurs="0" name="role" type="xs:string">

<xs:annotation>

<xs:documentation>

The role name to be used for the file when it is used as the input to an assay run

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element maxOccurs="unbounded" minOccurs="1" name="fileSuffix">

<xs:complexType>

<xs:simpleContent>

<xs:annotation>

<xs:documentation>

The file name suffixes (such as file extensions) to be matched for potential input files to the assay. Typical usages include ".tsv" or ".jpg"

</xs:documentation>

</xs:annotation>

<xs:extension base="xs:string">

<xs:attribute default="false" name="default" type="xs:boolean">

<xs:annotation>

<xs:documentation>

Indicates which of the file suffixes should be used as the default. If multiple are set, the one will be used.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:extension>

</xs:simpleContent>

</xs:complexType>

</xs:element>

</xs:sequence>

</xs:complexType>

</xs:schema>

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