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Prima cassette project (#1332)
* Prima cassette project * Prima cassette project updated with the queries.
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‎onprc_ehr/resources/etls/PrimaToPrime.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<!--Copy Prima tables into Prime. Runs daily at 3AM -->
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<!--Added By Kollil, 7/26/2021 -->
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<!--Copy Prima tables into Prime. Runs daily at 9am and 5pm, Refer to tkt #11937 -->
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<!--Added By Kollil, 7/26/2021 , Modified by Kollil, 03-02-2025-->
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<!--NOTES: The source DB name is "Prima" in production and "PrimaTest" on other servers -->
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<etl xmlns="http://labkey.org/etl/xml">
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<name>PrimatoPrime</name>
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<description>Transfers data from the Prima tables to the Prime tables in ONPRC_EHR</description>
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<description>Transfers data from the Prima tables to the Prime in ONPRC_EHR</description>
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<transforms>
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<transform id="step1a">
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<description>Transfer to UserPersons</description>
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<source queryName="UserPersons" schemaName="Prima"/>
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<destination queryName="Prima_UserPersons" schemaName="ONPRC_EHR" targetOption="truncate"/>
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<description>Transfer CassetteBases into onprc_ehr table</description>
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<source queryName="CassetteBases" schemaName="Prima"/>
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<destination queryName="Prima_CassetteBases" schemaName="onprc_ehr" targetOption="truncate"/>
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</transform>
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<transform id="step2a">
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<description>Transfer to SurgicalWheels</description>
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<source queryName="SurgicalWheels" schemaName="Prima"/>
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<destination queryName="Prima_SurgicalWheels" schemaName="ONPRC_EHR" targetOption="truncate"/>
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<description>Transfer to TissueCollections</description>
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<source queryName="TissueCollections" schemaName="Prima"/>
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<destination queryName="Prima_TissueCollections" schemaName="onprc_ehr" targetOption="truncate"/>
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</transform>
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<transform id="step3a">
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<description>Transfer to StainTests</description>
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<source queryName="StainTests" schemaName="Prima"/>
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<destination queryName="Prima_StainTests" schemaName="ONPRC_EHR" targetOption="truncate"/>
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<description>Transfer to Animals</description>
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<source queryName="Animals" schemaName="Prima"/>
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<destination queryName="Prima_Animals" schemaName="onprc_ehr" targetOption="truncate"/>
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</transform>
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<transform id="step4a">
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<description>Transfer to SlideBases</description>
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<source queryName="SlideBases" schemaName="Prima"/>
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<destination queryName="Prima_SlideBases" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step5a">
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<description>Transfer to CaseBase</description>
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<source queryName="CaseBase" schemaName="Prima"/>
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<destination queryName="Prima_CaseBase" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step6a">
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<description>Transfer to CassetteEvents</description>
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<source queryName="CassetteEvents" schemaName="Prima"/>
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<destination queryName="Prima_CassetteEvents" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step7a">
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<description>Transfer to CassetteEventLocations</description>
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<source queryName="CassetteEventLocations" schemaName="Prima"/>
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<destination queryName="Prima_CassetteEventLocations" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step8a">
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<description>Transfer to CassetteBases</description>
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<source queryName="CassetteBases" schemaName="Prima"/>
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<destination queryName="Prima_CassetteBases" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step9a">
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<description>Transfer to LabstationTypes</description>
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<source queryName="LabstationTypes" schemaName="Prima"/>
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<destination queryName="Prima_LabstationTypes" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step10a">
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<description>Transfer to SlideEvents</description>
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<source queryName="SlideEvents" schemaName="Prima"/>
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<destination queryName="Prima_SlideEvents" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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<transform id="step11a">
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<description>Transfer to SlideEventLoctions</description>
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<source queryName="SlideEventLocations" schemaName="Prima"/>
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<destination queryName="Prima_SlideEventLocations" schemaName="ONPRC_EHR" targetOption="truncate"/>
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</transform>
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</transforms>
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<schedule>
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<!--Runs daily 3AM-->
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<cron expression="0 50 03 * * ?"/>
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<!--Runs daily 9Am and 5pm-->
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<cron expression="0 0 9,17 * * ?"/>
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</schedule>
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</etl>

‎onprc_ehr/resources/queries/onprc_ehr/PrimaCassetteDataWithAnimalIds.sql‎

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/*
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Added by Kollil April, 2025
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This query will join the cassette data with EHR data. Refer to tkt #11937
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*/
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Select
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sd.id, -- ONPRC AnimalId
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pc.CassetteAccessionNumber,
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pc.TissueType,
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pc.TissueTypeAbbreviation,
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pc.TissueAlternateIdentifier
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From PrimatoPrimeCassetteData pc, study.Demographics sd
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Where pc.id = sd.id

‎onprc_ehr/resources/queries/onprc_ehr/PrimaToPrimeCassetteData.sql‎

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/*
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Added by Kollil April, 2025
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This query will extract the cassette data from the ETLed db tables from Prima db. Refer to tkt #11937
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*/
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SELECT
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an.Identifier as Id,
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--an.AlternateIdentifier as AnimalAlternateIdentifier,
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ctb.SavedIdentifier as CassetteAccessionNumber,
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ctb.AlternateIdentifier as TissueAlternateIdentifier,
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tc.Title as TissueType,
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tc.Abbreviation as TissueTypeAbbreviation
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--cb.Id as CaseId
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FROM Prima_CassetteBases as ctb
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join Prima_TissueCollections tc on ctb.TissueCollectionId = tc.Id
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join Prima_CaseBase cb on cb.Id = ctb.CaseBaseId
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Join Prima_Animals an on cb.AnimalId = an.Id
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Where ctb.SavedIdentifier NOT LIKE 'IPC%'
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And ctb.SavedIdentifier NOT LIKE '19[0-9][0-9]%'
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And ctb.SavedIdentifier NOT LIKE '20[0-9][0-9]%'

‎onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.007-24.008.sql‎

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-- =======================================================================================================================================
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-- Author: Lakshmi Kolli
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-- Create date: 2025-03-04
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-- Description: Db tables creation for Prima cassette project. Created all the Prima tables in Prime onprc_ehr schema folder.
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-- Refer to tkt #11937
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-- =======================================================================================================================================
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--Drop if exists. We are using these 4 tables for the Cassette Project
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EXEC core.fn_dropifexists 'Prima_Animals','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_CassetteBases','onprc_ehr','TABLE'; -- Drop this table and create again
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EXEC core.fn_dropifexists 'Prima_TissueCollections','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_CaseBase','onprc_ehr','TABLE'; -- Drop this table and create again
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--Drop these tables permanently. We are not using these tables in onprc_ehr.
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EXEC core.fn_dropifexists 'Prima_VeterinaryResearchCase','onprc_ehr','TABLE'; --This table doesn't exist anymore in Prima DB
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EXEC core.fn_dropifexists 'Prima_CassetteEvents','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_CassetteEventLocations','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_LabstationTypes','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_SlideBases','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_SlideEvents','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_SlideEventLocations','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_StainTests','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_SurgicalWheels','onprc_ehr','TABLE';
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EXEC core.fn_dropifexists 'Prima_UserPersons','onprc_ehr','TABLE';
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GO
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--Create tables
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--1. Animals table
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/****** Object: Table [onprc_ehr].[Prima_Animals] ******/
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CREATE TABLE [onprc_ehr].[Prima_Animals](
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[Id] [int] NOT NULL,
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[AlternateIdentifier] [nvarchar](63) NULL,
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[BreedId] [int] NULL,
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[DateOfBirth] [datetime] NULL,
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[FecesId] [int] NULL,
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[Gender] [tinyint] NOT NULL,
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[GeneTarget] [nvarchar](127) NULL,
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[GeneticLine] [nvarchar](127) NULL,
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[Genotype] [nvarchar](127) NULL,
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[Identifier] [nvarchar](127) NULL,
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[MannerOfDeathId] [int] NULL,
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[RoomNumber] [nvarchar](9) NULL,
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[SpeciesId] [int] NOT NULL,
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[StomachContentsId] [int] NULL,
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[StrainId] [int] NULL,
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[DateOfDeath] [datetime] NULL,
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[Created] [datetimeoffset](7) NOT NULL,
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[OwnerId] [int] NULL,
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[Perfuse] [bit] NOT NULL,
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[SampleType] [tinyint] NOT NULL
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)
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;
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--2. TissueCollections table
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/****** Object: Table [onprc_ehr].[Prima_TissueCollections] ******/
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CREATE TABLE [onprc_ehr].[Prima_TissueCollections](
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[Id] [int] NOT NULL,
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[Constant] [tinyint] NULL,
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[IsWholeAnimal] [bit] NOT NULL,
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[SpeciesId] [int] NOT NULL,
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[SpecimenType] [int] NOT NULL,
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[CreatedByUserId] [int] NOT NULL,
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[Deleted] [datetimeoffset](7) NULL,
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[DeletedByUserId] [int] NULL,
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[NextVersionId] [int] NULL,
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[PreviousVersionId] [int] NULL,
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[Title] [nvarchar](127) NOT NULL,
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[Created] [datetimeoffset](7) NOT NULL,
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[LastModified] [timestamp] NOT NULL,
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[Abbreviation] [nvarchar](127) NULL
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)
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;
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--3. CaseBase table
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/****** Object: Table [onprc_ehr].[Prima_CaseBase] ******/
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CREATE TABLE [onprc_ehr].[Prima_CaseBase](
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[Id] [int] NOT NULL,
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[DifferentialDiagnosisId] [int] NULL,
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[PathologistId] [int] NULL,
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[PriorityLevelId] [int] NOT NULL,
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[ResidentPathologistId] [int] NULL,
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[SerialNumber] [int] NOT NULL,
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[SurgeryDate] [datetime] NULL,
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[SurgicalWheelId] [int] NOT NULL,
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[Created] [datetimeoffset](7) NOT NULL,
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[ResearcherId] [int] NULL,
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[StudyId] [int] NULL,
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[Discriminator] [nvarchar](128) NULL,
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[StudyPhaseId] [int] NULL,
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[CohortId] [int] NULL,
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[SavedIdentifier] [nvarchar](max) NULL,
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[Status] [tinyint] NOT NULL,
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[AlternateIdentifier] [nvarchar](24) NULL,
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[SurgeryLocationId] [int] NULL,
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[ResearchPatientId] [int] NULL,
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[AnimalId] [int] NULL,
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[ClinicalPatientId] [int] NULL,
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[SurgeryAge] [nvarchar](31) NULL
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)
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;
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--4. CassetteBases table
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/****** Object: Table [onprc_ehr].[Prima_CassetteBases] ******/
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CREATE TABLE [onprc_ehr].[Prima_CassetteBases](
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[Id] [bigint] NOT NULL,
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[CassetteColorId] [int] NOT NULL,
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[EmbeddingInstructionId] [int] NOT NULL,
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[HasTissue] [bit] NOT NULL,
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[ProtocolCassetteId] [int] NULL,
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[SpecimenBaseId] [bigint] NOT NULL,
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[TissueCollectionId] [int] NULL,
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[TissueProcessorProgramId] [int] NULL,
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[TissueQuantity] [smallint] NOT NULL,
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[CaseBaseId] [int] NOT NULL,
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[PriorityLevelId] [int] NOT NULL,
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[QcStatus] [tinyint] NOT NULL,
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[SurgicalSerialPart] [smallint] NOT NULL,
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[Created] [datetimeoffset](7) NOT NULL,
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[OrderedStatus] [tinyint] NOT NULL,
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[SavedIdentifier] [nvarchar](24) NULL,
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[BarcodeContent] [nvarchar](72) NULL,
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[AlternateIdentifier] [nvarchar](63) NULL,
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[PrintStatus] [tinyint] NOT NULL,
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[ItemStatus] [smallint] NOT NULL,
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[Hazard] [tinyint] NOT NULL,
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[CurrentContainerId] [int] NULL
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)
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;
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GO

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