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labkey-teamcitylabkey-teamcity
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Merge 22.4 to develop
2 parents 37b8bbf + 3ceb8ad commit b42b738

9 files changed

Lines changed: 593 additions & 6 deletions

‎snprc_ehr/resources/etls/DemographicsHL7.xml‎

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<etl xmlns="http://labkey.org/etl/xml">
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<name>DemographicsHL7</name>
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<description>Export Demographics Data to Orchard Harvest</description>
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<transforms>
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<transform id="step1" type="org.labkey.di.pipeline.TransformTask">
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<description>Copy to target</description>
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<source schemaName="study" queryName="DemographicsHL7" />
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<destination schemaName="LISExport" queryName="DemographicsHL7Staging" bulkLoad="true" targetOption="append">
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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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<transform id="step2" type="StoredProcedure">
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<description>Kick off HL7 processing</description>
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<source schemaName="study" queryName="DemographicsHL7" />
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<procedure schemaName="LISExport" procedureName="p_load_demographics">
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</procedure>
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</transform>
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</transforms>
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<incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" />
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<schedule>
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<poll interval="60m" />
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</schedule>
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</etl>

‎snprc_ehr/resources/queries/study/DemographicsHL7.sql‎

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SELECT
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d.Id,
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d.gender,
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d.species.arc_species_code.Common_name as species,
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d.species.arc_species_code as breed,
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d.birth as birthDate,
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d.death as deathDate,
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case when d.calculated_status.code = 'Alive' then 'Y' when d.calculated_status.code = 'Dead' then 'N' else Null end as isAlive,
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d.dam,
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d.sire,
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d.objectId,
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d.modifiedBy.DisplayName as modifiedBy,
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d.modified
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FROM demographics as d
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where len(d.id) <= 6

‎snprc_ehr/resources/queries/study/diet.query.xml‎

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<nullable>false</nullable>
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<columnTitle>Diet</columnTitle>
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<fk>
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<fkDbSchema>ehr_lookups</fkDbSchema>
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<fkTable>snomed</fkTable>
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<fkColumnName>code</fkColumnName>
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<fkDbSchema>snprc_ehr</fkDbSchema>
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<fkTable>validDiet</fkTable>
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<fkColumnName>SnomedCode</fkColumnName>
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</fk>
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</column>
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<column columnName="diCreated">

‎snprc_ehr/resources/queries/study/dietHistory.query.xml‎

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<nullable>false</nullable>
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<columnTitle>Diet</columnTitle>
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<fk>
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<fkDbSchema>ehr_lookups</fkDbSchema>
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<fkTable>snomed</fkTable>
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<fkColumnName>code</fkColumnName>
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<fkDbSchema>snprc_ehr</fkDbSchema>
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<fkTable>validDiet</fkTable>
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<fkColumnName>SnomedCode</fkColumnName>
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</fk>
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</column>
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<column columnName="duration">

‎snprc_ehr/resources/source_queries/Create_LIS_DemographicsHL7Staging.sql‎

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USE animal
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GO
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-- Create TAC schema if not exists
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IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
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BEGIN
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-- The schema must be run in its own batch!
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EXEC( 'CREATE SCHEMA LIS' );
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END
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DROP TABLE IF EXISTS LIS.DemographicsHL7Staging;
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CREATE TABLE LIS.DemographicsHL7Staging
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(
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RowId INT IDENTITY,
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Id VARCHAR(6) NOT NULL,
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Gender CHAR(1) NULL,
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BirthDate DATETIME NULL,
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DeathDate DATETIME NULL,
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Breed VARCHAR(2) NULL, -- arc_species_code
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Species VARCHAR(MAX) NULL, -- common name
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isAlive Varchar(1) NULL, -- Y/N/NULL
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Sire VARCHAR(6) NULL,
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Dam VARCHAR(6) NULL,
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Modified DATETIME NULL,
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ModifiedBy VARCHAR(MAX) NULL,
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Processed INT DEFAULT 0 NOT NULL, -- will be 0 when data is exported, and stored procedure will update it to 1 when processed
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ObjectId UNIQUEIDENTIFIER DEFAULT NEWID() NOT NULL,
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CONSTRAINT PK_TAC_DemographicsHL7Staging
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PRIMARY KEY CLUSTERED (RowId ASC)
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)
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GO
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-- Table permissions
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GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.DemographicsHL7Staging TO z_labkey;
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GRANT VIEW DEFINITION ON LIS.DemographicsHL7Staging TO z_labkey;
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GO

‎snprc_ehr/resources/source_queries/Create_LIS_HL7ExportErrorLog.sql‎

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USE animal
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GO
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/*
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Error log for demographics export errors
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*/
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-- Create TAC schema if not exists
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IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
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BEGIN
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-- The schema must be run in its own batch!
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EXEC( 'CREATE SCHEMA LIS' );
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END
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DROP TABLE IF EXISTS LIS.HL7ExportErrorLog;
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CREATE TABLE LIS.HL7ExportErrorLog
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(
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[RowId] [NUMERIC](18, 0) IDENTITY(1,1) NOT NULL,
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[ObjectId] [VARCHAR](50) NOT NULL,
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[ProcessedDateTm] [DATETIME] NULL,
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[MessageControlId] [VARCHAR](50) NULL,
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[PatientId] [VARCHAR](20) NULL,
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[ErrorMsg] [VARCHAR](MAX) NULL,
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[UserName] [VARCHAR](128) NOT NULL,
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[EntryDateTm] [DATETIME] NOT NULL,
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CONSTRAINT PK_TAC_HL7ExportErrorLog
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PRIMARY KEY CLUSTERED (RowId ASC)
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)
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GO
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-- Table permissions
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GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.HL7ExportErrorLog TO z_labkey;
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GRANT VIEW DEFINITION ON LIS.HL7ExportErrorLog TO z_labkey;
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GO

‎snprc_ehr/resources/source_queries/Create_LIS_HL7ImportLog.sql‎

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USE animal
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GO
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/*
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Import log for results from Orchard Harvest
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*/
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-- Create TAC schema if not exists
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IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
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BEGIN
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-- The schema must be run in its own batch!
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EXEC( 'CREATE SCHEMA LIS' );
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END
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DROP TABLE IF EXISTS LIS.HL7ImportLog;
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CREATE TABLE LIS.HL7ImportLog
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(
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[RowId] [NUMERIC](18, 0) IDENTITY(1,1) NOT NULL,
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[MessageId] [VARCHAR](50) NOT NULL,
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[ObservationDateTm] [DATETIME] NULL,
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[MessageControlId] [VARCHAR](50) NULL,
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[ImportStatus] [INT] NOT NULL,
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[ResultStatis] [VARCHAR](10) NULL,
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[PatientId] [VARCHAR](20) NULL,
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[Species] [VARCHAR](50) NULL,
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[HL7MessageText] [VARCHAR](MAX) NULL,
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[ImportText] [VARCHAR](MAX) NULL,
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[UserName] [VARCHAR](128) NOT NULL,
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[EntryDateTm] [DATETIME] NOT NULL,
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[TIMESTAMP] [TIMESTAMP] NULL,
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CONSTRAINT PK_TAC_HL7ImportLog
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PRIMARY KEY CLUSTERED (RowId ASC)
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)
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GO
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-- Table permissions
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GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.HL7ImportLog TO z_labkey;
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GRANT VIEW DEFINITION ON LIS.HL7ImportLog TO z_labkey;
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GO

‎snprc_ehr/resources/source_queries/Create_LIS_f_format_hl7_date.sql‎

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USE
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[TAC_HL7_staging]
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GO
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/****** Object: UserDefinedFunction [dbo].[f_format_hl7_date] Script Date: 3/23/2022 11:14:18 AM ******/
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SET ANSI_NULLS ON
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GO
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SET QUOTED_IDENTIFIER ON
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GO
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-- =============================================
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-- Author: Terry Hawkins
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-- Create date: 1/30/2014
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-- Description: Converts a date and time string into MSSQL datetime format
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-- =============================================
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CREATE FUNCTION [dbo].[f_format_hl7_date]
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(
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-- Add the parameters for the function here
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@date_str VARCHAR(50)
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)
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RETURNS DATETIME
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AS
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BEGIN
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DECLARE
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@ret_date DATETIME
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IF LEN(@date_str) = 8
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BEGIN
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--20140117
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SET
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@ret_date = CAST(SUBSTRING(@date_str, 1,4)+ '-' + SUBSTRING(@date_str, 5,2) + '-' + SUBSTRING(@date_str,7,2) AS DATETIME)
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END
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ELSE
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BEGIN
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--201401171008
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SET
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@ret_date = CAST(SUBSTRING(@date_str, 1,4)+ '-' + SUBSTRING(@date_str, 5,2) + '-' + SUBSTRING(@date_str,7,2) +
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' ' + SUBSTRING(@date_str, 9,2) + ':' + SUBSTRING(@date_str, 11,2) AS DATETIME)
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END
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RETURN @ret_date
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END

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