XML Schema "study.xsd"
Target Namespace:
http://labkey.org/study/xml
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: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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