[bot] Fast-forward for 25.11.19

data/studies/Study001/study/export/data_states.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<studyqc xmlns="http://labkey.org/study/xml/qcStates">
+  <qcstates>
+    <qcstate name="First QC State" description="The first qc state description" public="false" color=""/>
+    <qcstate name="Second QC State" description="The second qc state description" public="false" color=""/>
+    <qcstate name="Third QC State" description="The third qc state description" public="false" color=""/>
+  </qcstates>
+  <showPrivateDataByDefault>true</showPrivateDataByDefault>
+  <blankQCStatePublic>true</blankQCStatePublic>
+  <requireCommentOnQCStateChange>false</requireCommentOnQCStateChange>
+  <pipelineImportDefault>First QC State</pipelineImportDefault>
+  <assayDataDefault>Second QC State</assayDataDefault>
+  <insertUpdateDefault>Third QC State</insertUpdateDefault>
+</studyqc>

data/studies/Study001/study/export/filebrowser_admin_config.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<PipelineOptions xmlns="http://labkey.org/data/xml">
+  <importEnabled>true</importEnabled>
+  <filePropertiesConfig>useDefault</filePropertiesConfig>
+  <inheritedTbarConfig>false</inheritedTbarConfig>
+</PipelineOptions>

data/studies/Study001/study/export/folder.xml

@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--Exported from LabKey Server at http://labkey.local:8011/labkey/StudyVerifyProject/Manually%20Created%20Study/project-begin.view by tchad">'>'"<script>alert('8(')</script> on Mon Nov 10 11:40:03 PST 2025-->
+<folder archiveVersion="25.007" label="Manually Created Study" type="normal" title="Manually Created Study" defaultDateFormat="dd-MMM-yyyy" defaultDateTimeFormat="dd-MMM-yyyy HH:mm" defaultNumberFormat="#.000" restrictedColumnsEnabled="true" xmlns="http://labkey.org/folder/xml">
+  <folderType name="Study">
+    <defaultModule>Core</defaultModule>
+    <modules>
+      <moduleName>Wiki</moduleName>
+      <moduleName>StudyDesign</moduleName>
+      <moduleName>Specimen</moduleName>
+      <moduleName>Study</moduleName>
+      <moduleName>Issues</moduleName>
+      <moduleName>Search</moduleName>
+      <moduleName>FileContent</moduleName>
+      <moduleName>Assay</moduleName>
+      <moduleName>Experiment</moduleName>
+      <moduleName>Query</moduleName>
+      <moduleName>Pipeline</moduleName>
+      <moduleName>API</moduleName>
+      <moduleName>Announcements</moduleName>
+      <moduleName>Core</moduleName>
+    </modules>
+  </folderType>
+  <missingValueIndicator>
+    <missingValueIndicator indicator="N" label="Data in this field has been marked as not usable."/>
+    <missingValueIndicator indicator="Q" label="Data currently under quality control review."/>
+  </missingValueIndicator>
+  <searchable>true</searchable>
+  <pages file="pages.xml"/>
+  <moduleProperties/>
+  <qcStates file="data_states.xml"/>
+  <fileBrowserConfig file="filebrowser_admin_config.xml"/>
+  <notifications>
+    <messagesDefault id="2" label="My conversations"/>
+    <filesDefault id="0" label="No Email"/>
+  </notifications>
+  <queries dir="queries"/>
+  <etls dir="etls"/>
+  <study dir="study"/>
+  <wikis dir="wikis"/>
+</folder>

data/studies/Study001/study/export/pages.xml

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pages xmlns="http://labkey.org/folder/xml">
+  <page index="4" name="study.DATA_ANALYSIS" propertyString="" hidden="false">
+    <webpart>
+      <name>Data Views</name>
+      <index>1</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+    <webpart>
+      <name>Study Data Tools</name>
+      <index>2</index>
+      <location>right</location>
+      <permanent>false</permanent>
+    </webpart>
+  </page>
+  <page index="2" name="Overview" propertyString="" hidden="false">
+    <webpart>
+      <name>Study Overview</name>
+      <index>1</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+  </page>
+  <page index="3" name="study.PARTICIPANTS" propertyString="" hidden="false">
+    <webpart>
+      <name>Search</name>
+      <index>1</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+    <webpart>
+      <name>Subject List</name>
+      <index>2</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+  </page>
+  <page index="6" name="Manage" propertyString="" hidden="false"/>
+  <page index="5" name="study.SPECIMENS" propertyString="" hidden="false">
+    <webpart>
+      <name>Specimen Search</name>
+      <index>1</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+    <webpart>
+      <name>Specimens</name>
+      <index>2</index>
+      <location>!content</location>
+      <permanent>false</permanent>
+    </webpart>
+    <webpart>
+      <name>Specimen Tools</name>
+      <index>3</index>
+      <location>right</location>
+      <permanent>false</permanent>
+    </webpart>
+  </page>
+</pages>

data/studies/Study001/study/export/queries/Hidden.query.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<query name="Hidden" hidden="true" schemaName="core" xmlns="http://labkey.org/data/xml/query">
+  <metadata>
+    <tables xmlns="http://labkey.org/data/xml">
+      <table tableName="Hidden" tableDbType="NOT_IN_DB">
+        <columns>
+    </columns>
+      </table>
+    </tables>
+  </metadata>
+</query>

data/studies/Study001/study/export/queries/Hidden.sql

@@ -0,0 +1,6 @@
+SELECT APIKeys.CreatedBy,
+APIKeys.Created,
+APIKeys.Expiration,
+APIKeys.LastUsed,
+APIKeys.Description
+FROM APIKeys

data/studies/Study001/study/export/queries/Inherit & Hidden.query.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<query name="Inherit &amp; Hidden" hidden="true" inherit="true" schemaName="core" xmlns="http://labkey.org/data/xml/query">
+  <metadata>
+    <tables xmlns="http://labkey.org/data/xml">
+      <table tableName="Inherit &amp; Hidden" tableDbType="NOT_IN_DB">
+        <columns>
+    </columns>
+      </table>
+    </tables>
+  </metadata>
+</query>

data/studies/Study001/study/export/queries/Inherit & Hidden.sql

@@ -0,0 +1,6 @@
+SELECT APIKeys.CreatedBy,
+APIKeys.Created,
+APIKeys.Expiration,
+APIKeys.LastUsed,
+APIKeys.Description
+FROM APIKeys

data/studies/Study001/study/export/queries/Inherit.query.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<query name="Inherit" inherit="true" schemaName="core" xmlns="http://labkey.org/data/xml/query">
+  <metadata>
+    <tables xmlns="http://labkey.org/data/xml">
+      <table tableName="Inherit" tableDbType="NOT_IN_DB">
+        <columns>
+    </columns>
+      </table>
+    </tables>
+  </metadata>
+</query>

data/studies/Study001/study/export/queries/Inherit.sql

@@ -0,0 +1,6 @@
+SELECT APIKeys.CreatedBy,
+APIKeys.Created,
+APIKeys.Expiration,
+APIKeys.LastUsed,
+APIKeys.Description
+FROM APIKeys

data/studies/Study001/study/export/queries/Normal.query.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<query name="Normal" schemaName="core" xmlns="http://labkey.org/data/xml/query">
+  <metadata>
+    <tables xmlns="http://labkey.org/data/xml">
+      <table tableName="Normal" tableDbType="NOT_IN_DB">
+        <columns>
+    </columns>
+      </table>
+    </tables>
+  </metadata>
+</query>

data/studies/Study001/study/export/queries/Normal.sql

@@ -0,0 +1,6 @@
+SELECT APIKeys.CreatedBy,
+APIKeys.Created,
+APIKeys.Expiration,
+APIKeys.LastUsed,
+APIKeys.Description
+FROM APIKeys

data/studies/Study001/study/export/study/assaySchedule/assayspecimen.tsv

@@ -0,0 +1 @@
+RowId	AssayName	Description	LocationId	DataSet	Source	TubeType	Lab	SampleType	SampleQuantity	SampleUnits

data/studies/Study001/study/export/study/assaySchedule/assayspecimenvisit.tsv

@@ -0,0 +1 @@
+RowId	VisitId	AssaySpecimenId	Container	Created	CreatedBy	Modified	ModifiedBy	visitId.sequenceNumMin

data/studies/Study001/study/export/study/assaySchedule/studydesignassays.tsv

@@ -0,0 +1 @@
+Name	Label	Description	Inactive	Type	Platform	Category	TargetFunction	LeadContributor	Contact	Summary	Keywords	TargetType	TargetSubtype	Editorial	AlternateName	Lab	LabPI

data/studies/Study001/study/export/study/assaySchedule/studydesignlabs.tsv

@@ -0,0 +1 @@
+Name	Label	Inactive	PI	Description	Summary	Institution

data/studies/Study001/study/export/study/assaySchedule/studydesignsampletypes.tsv

@@ -0,0 +1 @@
+Name	PrimaryType	ShortSampleCode	Inactive

data/studies/Study001/study/export/study/assaySchedule/studydesignunits.tsv

@@ -0,0 +1 @@
+Name	Label	Inactive

data/studies/Study001/study/export/study/cohorts.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cohorts xmlns="http://labkey.org/study/xml"/>

data/studies/Study001/study/export/study/datasets/Manually.dataset

@@ -0,0 +1,19 @@
+# default group can be used to avoid repeating definitions for each dataset
+#
+# action=[REPLACE,APPEND,DELETE] (default:REPLACE)
+# deleteAfterImport=[TRUE|FALSE] (default:FALSE)
+
+default.action=REPLACE
+default.deleteAfterImport=FALSE
+
+# map a source tsv column (right side) to a property name or full propertyURI (left)
+# predefined properties: ParticipantId, SiteId, VisitId, Created
+default.property.ParticipantId=ptid
+default.property.Created=dfcreate
+
+# use to map from filename->datasetid
+# NOTE: if there are NO explicit import definitions, we will try to import all files matching pattern
+# NOTE: if there are ANY explicit mapping, we will only import listed datasets
+
+default.filePattern=dataset(\\d*).tsv
+default.importAllMatches=TRUE

data/studies/Study001/study/export/study/datasets/Study.dataset

@@ -0,0 +1,19 @@
+# default group can be used to avoid repeating definitions for each dataset
+#
+# action=[REPLACE,APPEND,DELETE] (default:REPLACE)
+# deleteAfterImport=[TRUE|FALSE] (default:FALSE)
+
+default.action=REPLACE
+default.deleteAfterImport=FALSE
+
+# map a source tsv column (right side) to a property name or full propertyURI (left)
+# predefined properties: ParticipantId, SiteId, VisitId, Created
+default.property.ParticipantId=ptid
+default.property.Created=dfcreate
+
+# use to map from filename->datasetid
+# NOTE: if there are NO explicit import definitions, we will try to import all files matching pattern
+# NOTE: if there are ANY explicit mapping, we will only import listed datasets
+
+default.filePattern=dataset(\\d*).tsv
+default.importAllMatches=TRUE

data/studies/Study001/study/export/study/datasets/dataset5001.tsv

@@ -0,0 +1,2 @@
+ParticipantId	SequenceNum	date	QCStateLabel	TestInt	TestString	TestDate	TestDateTime	Location
+PTID123	1.0000		First QC State	999	ABC	2013-10-29 00:00:00.0	2013-10-28 01:23:00.0	

data/studies/Study001/study/export/study/datasets/datasets_manifest.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<datasets metaDataFile="datasets_metadata.xml" xmlns="http://labkey.org/study/xml">
+  <datasets>
+    <dataset name="TestDataset" id="5001" type="Standard">
+      <tags/>
+    </dataset>
+  </datasets>
+</datasets>

data/studies/Study001/study/export/study/datasets/datasets_metadata.xml

@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tables xmlns="http://labkey.org/data/xml">
+  <table tableName="TestDataset" tableDbType="TABLE">
+    <description>Contains up to one row of TestDataset data for each Participant/Visit combination.</description>
+    <columns>
+      <column columnName="ParticipantId">
+        <datatype>varchar</datatype>
+        <columnTitle>Participant ID</columnTitle>
+        <description>Subject identifier</description>
+        <propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
+        <nullable>false</nullable>
+        <url replaceMissing="blankValue">/study-participant.view?participantId=${ParticipantId}</url>
+        <importAliases>
+          <importAlias>ptid</importAlias>
+          <importAlias>participantid</importAlias>
+        </importAliases>
+        <fk>
+          <fkDbSchema>study</fkDbSchema>
+          <fkTable>Participant</fkTable>
+          <fkColumnName>ParticipantId</fkColumnName>
+        </fk>
+        <scale>32</scale>
+      </column>
+      <column columnName="SequenceNum">
+        <datatype>double</datatype>
+        <columnTitle>Sequence Num</columnTitle>
+        <propertyURI>http://cpas.labkey.com/Study#SequenceNum</propertyURI>
+        <nullable>false</nullable>
+        <importAliases>
+          <importAlias>visit</importAlias>
+          <importAlias>visitid</importAlias>
+        </importAliases>
+      </column>
+      <column columnName="date">
+        <datatype>timestamp</datatype>
+        <columnTitle>Date</columnTitle>
+        <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
+        <formatString>Date</formatString>
+      </column>
+      <column columnName="TestInt">
+        <datatype>integer</datatype>
+        <columnTitle>TestInt</columnTitle>
+        <rangeURI>http://www.w3.org/2001/XMLSchema#int</rangeURI>
+        <defaultValueType>FIXED_EDITABLE</defaultValueType>
+        <validators>
+          <validator>
+            <name>numberValidator</name>
+            <description>numberValidator</description>
+            <typeURI>urn:lsid:labkey.com:PropertyValidator:range</typeURI>
+            <expression>~eq=999</expression>
+            <errorMessage>TestInt must equals '999'.</errorMessage>
+            <property>
+              <name>failOnMatch</name>
+              <value>false</value>
+            </property>
+          </validator>
+        </validators>
+      </column>
+      <column columnName="TestString">
+        <datatype>varchar</datatype>
+        <columnTitle>TestRequiredString</columnTitle>
+        <rangeURI>http://www.w3.org/2001/XMLSchema#string</rangeURI>
+        <required>true</required>
+        <defaultValueType>FIXED_EDITABLE</defaultValueType>
+        <scale>4000</scale>
+      </column>
+      <column columnName="TestDate">
+        <datatype>timestamp</datatype>
+        <columnTitle>TestDate</columnTitle>
+        <rangeURI>http://www.w3.org/2001/XMLSchema#dateTime</rangeURI>
+        <defaultValueType>FIXED_EDITABLE</defaultValueType>
+      </column>
+      <column columnName="TestDateTime">
+        <datatype>timestamp</datatype>
+        <columnTitle>TestDateTime</columnTitle>
+        <rangeURI>http://www.w3.org/2001/XMLSchema#dateTime</rangeURI>
+        <defaultValueType>FIXED_EDITABLE</defaultValueType>
+      </column>
+      <column columnName="Location">
+        <datatype>integer</datatype>
+        <columnTitle>Location</columnTitle>
+        <rangeURI>http://www.w3.org/2001/XMLSchema#int</rangeURI>
+        <fk>
+          <fkDbSchema>study</fkDbSchema>
+          <fkTable>Location</fkTable>
+          <fkColumnName>RowId</fkColumnName>
+        </fk>
+        <defaultValueType>FIXED_EDITABLE</defaultValueType>
+      </column>
+    </columns>
+    <tableTitle>TestDataset</tableTitle>
+  </table>
+</tables>

data/studies/Study001/study/export/study/properties/objective.tsv

@@ -0,0 +1 @@
+RowId	Label	Type	Description	DescriptionRendererType

data/studies/Study001/study/export/study/properties/personnel.tsv

@@ -0,0 +1 @@
+RowId	Label	Role	URL	UserId	userId.displayName

data/studies/Study001/study/export/study/properties/study.tsv

@@ -0,0 +1,3 @@
+Label	StartDate	EndDate	TimepointType	SubjectNounSingular	SubjectNounPlural	SubjectColumnName	Grant	Investigator	Species	ParticipantAliasDatasetId	ParticipantAliasProperty	ParticipantAliasSourceProperty	AssayPlan	Description	DescriptionRendererType	DateBased	LSID	cust_string	cust_integer	cust_dateTime	cust_double	cust_multiline
+Study Properties	2025-11-10 00:00:00.0		VISIT	Participant	Participants	ParticipantId	Grantland	Dr. Strangelove	Human					study description	TEXT_WITH_LINKS	false	urn:lsid:labkey.com:Study.Folder-68:68	custom string	2	2014-03-26 00:00:00.0	3.14	"custom multiline
+custom multiline"