XML Schema "study.xsd"

Target Namespace:

Defined Components:

1 global element, 19 local elements, 2 complexTypes, 4 simpleTypes

Default Namespace-Qualified Form:

Local Elements: qualified; Local Attributes: unqualified

Schema Location:

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

Imported by Schema:

folder.xsd [src]

Annotation

Describes a file-based study. This is the top-level file in the /study subfolder of a folder archive. It defines the top-level study settings and points to the other files in the archive.

XML Source

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

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

<xs:annotation>

<xs:documentation xml:lang="en">

Describes a file-based study. This is the top-level file in the /study subfolder of a folder archive. It
defines the top-level study settings and points to the other files in the archive.

</xs:documentation>

</xs:annotation>

<xs:element name="study">

<xs:complexType>

<xs:all>

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

<xs:complexType>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation xml:lang="en">

Indicates the "file" (string) that lists the study's visits. The file must follow the visit map XML format.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:attribute name="showPrivateDataByDefault" type="xs:boolean">

<xs:annotation>

<xs:documentation>

This setting determines whether users see non-public data by default. Users can
always explicitly choose to see data in any QC state.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file that stores qc state configuration information.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:attribute name="mode" type="cohortMode">

<xs:annotation>

<xs:documentation>

Indicates the mode of assignment.
"SIMPLE": Subjects are assigned to a single cohort throughout the study.
"ADVANCED": Subjects may change cohorts mid-study. Note that advanced cohort
management requires automatic assignment via a study dataset.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="type" type="cohortType">

<xs:annotation>

<xs:documentation xmlns="http://www.w3.org/1999/xhtml">

Indicates the method of cohort assignment used in the study.
Can either be "AUTOMATIC" or "MANUAL". See

<a href="https://www.labkey.org/Documentation/wiki-page.view?name=manageCohorts" target="_top">Manage Cohorts</a>

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="datasetId" type="xs:int">

<xs:annotation>

<xs:documentation>

If the "AUTOMATIC" method of cohort assignment is used the datasetID indicates
the dataset used to describe cohorts.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="datasetProperty" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the column used to assign cohorts in the dataset indicated by the datasetID
for "AUTOMATIC" cohort assignment.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the XML file that records how cohorts are assigned if the "MANUAL" method of
cohort assignment is used.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:attribute name="datasetId" type="xs:int" use="required">

<xs:annotation>

<xs:documentation>

The name of the dataset that contains the participant/alias mapping information.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="sourceProperty" type="xs:string" use="required">

<xs:annotation>

<xs:documentation>

The name of the column/field in the dataset that contains the "source" value for the alias.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="aliasProperty" type="xs:string" use="required">

<xs:annotation>

<xs:documentation>

The name of the column/field in the dataset that contains the value of the participant's alias.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:annotation>

<xs:documentation>

Provides information on the files that contain and describe the datasets in the study.

</xs:documentation>

</xs:annotation>

<xs:complexType>

<xs:all>

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

<xs:complexType>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file where the schema can be found. The file can follow either
the new, XML format, or the old, schema.tsv format.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="labelColumn" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the column where labels are found.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="typeNameColumn" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the column where type names are found.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="typeIdColumn" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the column where type IDs are found.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

<xs:element name="definition">

<xs:complexType>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file that determines what happens during study reload (e.g.,
whether to replace or delete datasets). Typically named STUDYNAME.dataset,
where STUDYNAME is the shortened label of the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

</xs:all>

<xs:attribute name="dir" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the directory that stores the relevant file.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file manifest for datasets.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:annotation>

<xs:documentation>

Provides information on the files that describe the specimens in the study.

</xs:documentation>

</xs:annotation>

<xs:complexType>

<xs:attribute name="dir" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the directory that contains the specimen data and settings.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file that stores specimen data.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="settings" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file that stores specimen settings information.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:attribute name="dir" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the folder that stores study specific views.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="settings" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the file that stores view settings information.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:attribute name="participantCommentDatasetId" type="xs:int">

<xs:annotation>

<xs:documentation>

The ID of the dataset that includes comments about participants.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="participantCommentDatasetProperty" type="xs:string">

<xs:annotation>

<xs:documentation>

The property name that includes the participant comments.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="participantVisitCommentDatasetId" type="xs:int">

<xs:annotation>

<xs:documentation>

The ID of the dataset that includes comments about participant visits.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="participantVisitCommentDatasetProperty" type="xs:string">

<xs:annotation>

<xs:documentation>

The property name that includes the participant visit comments.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

<xs:element minOccurs="0" name="protocolDocs" type="exportDirType"/>

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

<xs:complexType>

<xs:sequence>

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

<xs:annotation>

<xs:documentation>

The descriptive text for this study.

</xs:documentation>

</xs:annotation>

</xs:element>

</xs:sequence>

<xs:attribute name="rendererType" type="xs:string">

<xs:annotation>

<xs:documentation>

The render type of the description (HTML, wiki, or text).

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:annotation>

<xs:documentation>

The description of the assay plan for the study.

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element minOccurs="0" name="treatmentData" type="exportDirType">

<xs:annotation>

<xs:documentation>

The directory that contains the export data for Treatment data.

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element minOccurs="0" name="assaySchedule" type="exportDirType">

<xs:annotation>

<xs:documentation>

The directory that contains the export data for Assay schedule information.

</xs:documentation>

</xs:annotation>

</xs:element>

<xs:element minOccurs="0" name="properties" type="exportDirType">

<xs:annotation>

<xs:documentation>

The directory that contains the export data for study properties.

</xs:documentation>

</xs:annotation>

</xs:element>

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

<xs:complexType>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation xml:lang="en">

Indicates the "file" (string) that contains the study security policy. The file must follow the study security policy (studySecurityPolicy.xsd) XML format.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

</xs:all>

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

<xs:annotation>

<xs:documentation>

Allow this study to be imported into a Dataspace project. Warning! This does not support all study configurations.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="importDelay" type="xs:int">

<xs:annotation>

<xs:documentation>

For testing/debugging purposes only. The number of seconds to delay the import after the job has started.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="archiveVersion" type="xs:double">

<xs:annotation>

<xs:documentation>

The version number of the LabKey Server that produced this archive.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="label" type="xs:string">

<xs:annotation>

<xs:documentation>

The label used for naming the study in the UI.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="subjectNounSingular" type="xs:string">

<xs:annotation>

<xs:documentation>

The singular noun used to identify subjects. Examples include "Participant", "Mouse", or "Yeast".

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="subjectNounPlural" type="xs:string">

<xs:annotation>

<xs:documentation>

The plural noun used to identify subjects. Examples include "Participants", "Mice", or "Yeasts".

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="subjectColumnName" type="xs:string">

<xs:annotation>

<xs:documentation>

The column header for subject IDs. Examples include "ParticipantId", "MouseId", or "YeastId".

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="dateBased" type="xs:boolean">

<xs:annotation>

<xs:documentation>

Deprecated in favor of 'timepointType' attribute.
Indicates whether this study is date-based (vs. time-based).

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="timepointType" type="timepointType">

<xs:annotation>

<xs:documentation>

The timepoint type of the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="startDate" type="xs:date">

<xs:annotation>

<xs:documentation>

The start date of the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="endDate" type="xs:date">

<xs:annotation>

<xs:documentation>

The end date of the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="defaultTimepointDuration" type="xs:int">

<xs:annotation>

<xs:documentation>

For date-based studies, the default duration for timepoints, in days.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="securityType" type="securityType">

<xs:annotation>

<xs:documentation>

Indicates the type of security used for the study. Must be one of the following four options:
"BASIC_READ", "BASIC_WRITE", "ADVANCED_READ" or "ADVANCED_WRITE".

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="description" type="xs:string">

<xs:annotation>

<xs:documentation>

The descriptive text for this study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="descriptionRendererType" type="xs:string">

<xs:annotation>

<xs:documentation>

The render type of the description (HTML, wiki, or text).

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="investigator" type="xs:string">

<xs:annotation>

<xs:documentation>

The investigator for the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="grant" type="xs:string">

<xs:annotation>

<xs:documentation>

The grant associated with the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="species" type="xs:string">

<xs:annotation>

<xs:documentation>

The species of the subjects in the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="alternateIdPrefix" type="xs:string">

<xs:annotation>

<xs:documentation>

The alternate ID prefix for the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="alternateIdDigits" type="xs:int">

<xs:annotation>

<xs:documentation>

The number of digits with which to generate an alternate ID for the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="failForUndefinedTimepoints" type="xs:boolean">

<xs:annotation>

<xs:documentation>

Indicates whether new timepoints can be created automatically when data is imported into the study.

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:anyAttribute processContents="lax"/>

</xs:complexType>

</xs:element>

<xs:simpleType name="timepointType">

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

<xs:enumeration value="VISIT"/>

<xs:enumeration value="DATE"/>

<xs:enumeration value="CONTINUOUS"/>

</xs:restriction>

</xs:simpleType>

<xs:simpleType name="securityType">

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

<xs:enumeration value="BASIC_READ"/>

<xs:enumeration value="BASIC_WRITE"/>

<xs:enumeration value="ADVANCED_READ"/>

<xs:enumeration value="ADVANCED_WRITE"/>

</xs:restriction>

</xs:simpleType>

<xs:simpleType name="cohortType">

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

<xs:enumeration value="AUTOMATIC"/>

<xs:enumeration value="MANUAL"/>

</xs:restriction>

</xs:simpleType>

<xs:simpleType name="cohortMode">

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

<xs:enumeration value="ADVANCED"/>

<xs:enumeration value="SIMPLE"/>

</xs:restriction>

</xs:simpleType>

<xs:complexType name="exportDirType">

<xs:attribute name="dir" type="xs:string">

<xs:annotation>

<xs:documentation>

Names the directory that contains exported resource.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

<xs:complexType name="missingValueIndicatorsType">

<xs:sequence maxOccurs="unbounded" minOccurs="0">

<xs:element name="missingValueIndicator">

<xs:complexType>

<xs:attribute name="indicator" type="xs:string">

<xs:annotation>

<xs:documentation>

The indicator to use for a certain type of missing values (e.g., "N").

</xs:documentation>

</xs:annotation>

</xs:attribute>

<xs:attribute name="label" type="xs:string">

<xs:annotation>

<xs:documentation>

The text to use in association with this indicator in the UI
(e.g., "Required field marked by site as 'data not available'.").

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="file" type="xs:string">

<xs:annotation>

<xs:documentation>

The file that contains the list of missing value indicators.

</xs:documentation>

</xs:annotation>

</xs:attribute>

</xs:complexType>

</xs:schema>

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