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Merge discvr-24.7 to develop
2 parents 4468bc4 + 9e30f1c commit d08b7b4

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Lines changed: 1427 additions & 114 deletions

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‎MccColony/resources/queries/study/departure/.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All">
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<columns>
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<column name="Id"/>
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<column name="Id/mccAlias/externalAlias"/>
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<column name="date"/>
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<column name="source"/>
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<column name="destination"/>
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<column name="mccTransfer"/>
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<column name="remark"/>
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<column name="qcstate" />
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</columns>
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<sorts>
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<sort column="date" descending="true"/>
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</sorts>
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</customView>

‎mcc/resources/data/source.tsv‎

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code meaning
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SNPRC SNPRC
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WNPRC WNPRC
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UCSD UCSD
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JHU JHU

‎mcc/resources/etls/mcc.xml‎

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</destination>
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</transform>
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<transform type="SimpleQueryTransformStep" id="departure">
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<description>Copy to target</description>
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<source schemaName="mcc" queryName="aggregatedDepartures" >
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>source</column>
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<column>destination</column>
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<column>mccTransfer</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="departure" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
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</destination>
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</transform>
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</transforms>
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<schedule>
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<!--11PM-->

‎mcc/resources/folderTypes/MCC NIH Dashboard.folderType.xml‎

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<folderType xmlns="http://labkey.org/data/xml/folderType">
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<name>MCC NIH Dashboard</name>
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<description>The default folder layout for the MCC NIH/U24 Overview</description>
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<preferredWebParts>
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<webPart>
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<name>MCC Menu</name>
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<location>menu</location>
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</webPart>
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</preferredWebParts>
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<folderTabs>
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<folderTab>
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<name>u24</name>
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<caption>U24 Dashboard</caption>
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<selectors>
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<selector>
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<regex>u24</regex>
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</selector>
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</selectors>
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<requiredWebParts>
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</requiredWebParts>
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<preferredWebParts>
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<webPart>
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<name>MCC U24 Dashboard Webpart</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>mcc</name>
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<caption>National Dashboard</caption>
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<selectors>
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<selector>
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<regex>overview</regex>
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</selector>
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</selectors>
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<requiredWebParts>
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</requiredWebParts>
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<preferredWebParts>
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<webPart>
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<name>MCC Dashboard Webpart</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>animalData</name>
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<caption>Animal List</caption>
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<selectors>
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<selector>
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<view>animalData</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>MCC U24 Demographics</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>census</name>
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<caption>Census Data</caption>
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<selectors>
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<selector>
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<view>census</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>MCC Census</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>requests</name>
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<caption>MCC Requests</caption>
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<selectors>
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<selector>
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<view>request</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>MCC Request Summary</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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<permissions>
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<permission name="org.labkey.mcc.security.MccViewRequestsPermission"/>
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</permissions>
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</folderTab>
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</folderTabs>
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<modules>
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<moduleName>MCC</moduleName>
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<moduleName>Study</moduleName>
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<moduleName>Query</moduleName>
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<moduleName>Pipeline</moduleName>
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<moduleName>Core</moduleName>
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</modules>
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<defaultModule>Core</defaultModule>
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</folderType>

‎mcc/resources/queries/study/demographics/.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView">
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<columns>
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<column name="colony"/>
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<column name="u24_status"/>
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<column name="Id"/>
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<column name="gender"/>
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<column name="Id/age/yearAndDays"/>
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<property name="columnTitle" value="Status"/>
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</properties>
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</column>
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<column name="dam"/>
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<column name="sire"/>
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<column name="u24_status"/>
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<column name="birth"/>
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<column name="death"/>
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<column name="MostRecentWeightGrams">
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<properties>
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<property name="columnTitle" value="Current Weight (g)"/>
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<column name="usage_future"/>
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<column name="date_of_observations"/>
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<column name="litterId"/>
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<column name="history" />
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>

MccColony/resources/queries/study/demographics/U24 Assigned.qview.xml renamed to mcc/resources/queries/study/demographics/Available For Transfer.qview.xml

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<customView xmlns="http://labkey.org/data/xml/queryCustomView">
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<filters>
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<filter column="u24_status" operator="eq" value="true"/>
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<filter column="availability" operator="eq" value="available for transfer"/>
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</filters>
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<sorts>
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<sort column="Id" descending="false"/>

‎mcc/resources/queries/study/demographics/With Parent Gender.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="true">
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<columns>
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<column name="colony"/>
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<column name="Id"/>
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<column name="gender"/>
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<column name="Id/age/yearAndDays"/>
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<column name="calculated_status">
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<properties>
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<property name="columnTitle" value="Status"/>
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</properties>
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</column>
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<column name="u24_status"/>
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<column name="birth"/>
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<column name="dam"/>
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<column name="dam/demographics/gender">
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<properties>
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<property name="columnTitle" value="Dam Sex"/>
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</properties>
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</column>
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<column name="sire"/>
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<column name="sire/demographics/gender">
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<properties>
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<property name="columnTitle" value="Sire Sex"/>
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</properties>
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</column>
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<column name="litterId"/>
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<column name="history" />
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>
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</sorts>
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</customView>

‎mcc/resources/queries/study/demographicsGenomicData.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="demographicsGenomicData" tableDbType="NOT_IN_DB">
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<tableTitle>Genomic Data Summary</tableTitle>
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<description>Genomic Data Summary</description>
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<columns>
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<column columnName="Id">
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<isKeyField>true</isKeyField>
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<isHidden>true</isHidden>
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</column>
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<column columnName="datatypes">
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<columnTitle>Data Types</columnTitle>
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<url>/query/executeQuery.view?
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schemaName=study&amp;
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query.queryName=genomicDatasets&amp;
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query.Id~eq=${Id}
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</url>
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</column>
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<column columnName="sra_accession">
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<columnTitle>SRA Accession(s)</columnTitle>
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</column>
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</columns>
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<titleColumn>datatypes</titleColumn>
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</table>
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</tables>
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</metadata>
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</query>

‎mcc/resources/queries/study/demographicsGenomicData.sql‎

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SELECT
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d.Id,
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GROUP_CONCAT(distinct d.datatype, ',') as datatypes,
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GROUP_CONCAT(distinct d.sra_accession, chr(10)) as sra_accession,
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FROM study.genomicDatasets d
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WHERE d.qcstate.publicdata = true
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GROUP BY d.Id

‎mcc/resources/queries/study/demographicsLittermates.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<description>Littermates of Any Animal</description>
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="demographicsLittermates" tableDbType="NOT_IN_DB">
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<tableTitle>Littermates</tableTitle>
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<description>Littermates of Any Animal</description>
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<columns>
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<column columnName="Id">
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</column>
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<column columnName="litterMates">
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<columnTitle>Littermate(s)</columnTitle>
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<url>/query/executeQuery.view?
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schemaName=study&amp;
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query.queryName=demographics&amp;
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query.litterId~eq=${litterId}
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</url>
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</column>
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</columns>
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<titleColumn>Relationship</titleColumn>
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<titleColumn>litterMates</titleColumn>
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</table>
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</tables>
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</metadata>

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