22.3 fb hl7 demographics (#422)

* New queries and ETLs for Orchard demographics ETL

* Additional HL7 changes

* 1. Changed .sql file encoding to UTF-8
2. Removed un-needed files

* reformatted and changed line endings

* reformatted and changed line endings

Author: spamhurts

snprc_ehr/resources/etls/DemographicsHL7.xml

@@ -0,0 +1,25 @@
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>DemographicsHL7</name>
+    <description>Export Demographics Data to Orchard Harvest</description>
+    <transforms>
+        <transform id="step1" type="org.labkey.di.pipeline.TransformTask">
+            <description>Copy to target</description>
+            <source schemaName="study" queryName="DemographicsHL7" />
+            <destination schemaName="LISExport" queryName="DemographicsHL7Staging" bulkLoad="true" targetOption="append">
+                <alternateKeys>
+                    <column name="objectid"/>
+                </alternateKeys>
+            </destination>
+        </transform>
+        <transform id="step2" type="StoredProcedure">
+            <description>Kick off HL7 processing</description>
+            <source schemaName="study" queryName="DemographicsHL7" />
+            <procedure schemaName="LISExport" procedureName="p_load_demographics">
+            </procedure>
+        </transform>
+    </transforms>
+        <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" />
+    <schedule>
+        <poll interval="60m" />
+    </schedule>
+</etl>

snprc_ehr/resources/queries/study/DemographicsHL7.sql

@@ -0,0 +1,15 @@
+SELECT
+    d.Id,
+    d.gender,
+    d.species.arc_species_code.Common_name as species,
+    d.species.arc_species_code as breed,
+    d.birth as birthDate,
+    d.death as deathDate,
+    case when d.calculated_status.code = 'Alive' then 'Y' when d.calculated_status.code = 'Dead' then 'N' else Null end as isAlive,
+    d.dam,
+    d.sire,
+    d.objectId,
+    d.modifiedBy.DisplayName as modifiedBy,
+    d.modified
+FROM demographics as d
+where len(d.id) <= 6

snprc_ehr/resources/source_queries/Create_LIS_DemographicsHL7Staging.sql

@@ -0,0 +1,39 @@
+USE animal
+GO 
+
+-- Create TAC schema if not exists
+IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
+BEGIN
+    -- The schema must be run in its own batch!
+EXEC( 'CREATE SCHEMA LIS' );
+END
+
+DROP TABLE IF EXISTS LIS.DemographicsHL7Staging;
+
+CREATE TABLE LIS.DemographicsHL7Staging
+(
+    RowId INT IDENTITY,
+    Id VARCHAR(6) NOT NULL,
+    Gender CHAR(1) NULL,
+    BirthDate DATETIME NULL,
+    DeathDate DATETIME NULL,
+    Breed VARCHAR(2) NULL,  -- arc_species_code
+    Species VARCHAR(MAX) NULL, -- common name
+    isAlive Varchar(1) NULL, -- Y/N/NULL
+    Sire VARCHAR(6) NULL,
+    Dam VARCHAR(6) NULL,
+    Modified DATETIME NULL,
+    ModifiedBy VARCHAR(MAX) NULL,
+    Processed INT DEFAULT 0 NOT NULL, -- will be 0 when data is exported, and stored procedure will update it to 1 when processed
+    ObjectId UNIQUEIDENTIFIER DEFAULT NEWID() NOT NULL,
+    CONSTRAINT PK_TAC_DemographicsHL7Staging
+        PRIMARY KEY CLUSTERED (RowId ASC)
+)
+
+GO
+
+-- Table permissions
+GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.DemographicsHL7Staging TO z_labkey;
+GRANT VIEW DEFINITION ON LIS.DemographicsHL7Staging TO z_labkey;
+
+GO

snprc_ehr/resources/source_queries/Create_LIS_HL7ExportErrorLog.sql

@@ -0,0 +1,35 @@
+USE animal
+GO 
+/*
+	Error log for demographics export errors
+*/
+-- Create TAC schema if not exists
+IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
+BEGIN
+    -- The schema must be run in its own batch!
+EXEC( 'CREATE SCHEMA LIS' );
+END
+
+DROP TABLE IF EXISTS LIS.HL7ExportErrorLog;
+
+CREATE TABLE LIS.HL7ExportErrorLog
+(
+	[RowId] [NUMERIC](18, 0) IDENTITY(1,1) NOT NULL,
+	[ObjectId] [VARCHAR](50) NOT NULL,
+	[ProcessedDateTm] [DATETIME] NULL,
+	[MessageControlId] [VARCHAR](50) NULL,
+	[PatientId] [VARCHAR](20) NULL,
+	[ErrorMsg] [VARCHAR](MAX) NULL,
+	[UserName] [VARCHAR](128) NOT NULL,
+	[EntryDateTm] [DATETIME] NOT NULL,
+    CONSTRAINT PK_TAC_HL7ExportErrorLog
+        PRIMARY KEY CLUSTERED (RowId ASC)
+)
+
+GO
+
+-- Table permissions
+GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.HL7ExportErrorLog TO z_labkey;
+GRANT VIEW DEFINITION ON LIS.HL7ExportErrorLog TO z_labkey;
+
+GO

snprc_ehr/resources/source_queries/Create_LIS_HL7ImportLog.sql

@@ -0,0 +1,40 @@
+USE animal
+GO 
+/*
+	Import log for results from Orchard Harvest
+*/
+-- Create TAC schema if not exists
+IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'LIS')
+BEGIN
+    -- The schema must be run in its own batch!
+EXEC( 'CREATE SCHEMA LIS' );
+END
+
+DROP TABLE IF EXISTS LIS.HL7ImportLog;
+
+CREATE TABLE LIS.HL7ImportLog
+(
+	[RowId] [NUMERIC](18, 0) IDENTITY(1,1) NOT NULL,
+	[MessageId] [VARCHAR](50) NOT NULL,
+	[ObservationDateTm] [DATETIME] NULL,
+	[MessageControlId] [VARCHAR](50) NULL,
+	[ImportStatus] [INT] NOT NULL,
+	[ResultStatis] [VARCHAR](10) NULL,
+	[PatientId] [VARCHAR](20) NULL,
+	[Species] [VARCHAR](50) NULL,
+	[HL7MessageText] [VARCHAR](MAX) NULL,
+	[ImportText] [VARCHAR](MAX) NULL,
+	[UserName] [VARCHAR](128) NOT NULL,
+	[EntryDateTm] [DATETIME] NOT NULL,
+	[TIMESTAMP] [TIMESTAMP] NULL,
+    CONSTRAINT PK_TAC_HL7ImportLog
+        PRIMARY KEY CLUSTERED (RowId ASC)
+)
+
+GO
+
+-- Table permissions
+GRANT DELETE, INSERT, REFERENCES, SELECT, UPDATE ON LIS.HL7ImportLog TO z_labkey;
+GRANT VIEW DEFINITION ON LIS.HL7ImportLog TO z_labkey;
+
+GO

snprc_ehr/resources/source_queries/Create_LIS_f_format_hl7_date.sql

@@ -0,0 +1,41 @@
+USE
+[TAC_HL7_staging]
+GO
+/****** Object:  UserDefinedFunction [dbo].[f_format_hl7_date]    Script Date: 3/23/2022 11:14:18 AM ******/
+SET ANSI_NULLS ON
+GO
+SET QUOTED_IDENTIFIER ON
+GO
+-- =============================================
+-- Author:		Terry Hawkins
+-- Create date: 1/30/2014
+-- Description:	Converts a date and time string into MSSQL datetime format
+-- =============================================
+CREATE FUNCTION [dbo].[f_format_hl7_date]
+(
+	-- Add the parameters for the function here
+	@date_str VARCHAR(50)
+)
+RETURNS DATETIME
+
+AS
+BEGIN
+	DECLARE
+@ret_date DATETIME
+	IF LEN(@date_str) = 8
+BEGIN
+		--20140117
+		SET
+@ret_date = CAST(SUBSTRING(@date_str, 1,4)+ '-' + SUBSTRING(@date_str, 5,2) + '-' + SUBSTRING(@date_str,7,2) AS DATETIME)
+END
+ELSE
+BEGIN
+		--201401171008
+		SET
+@ret_date = CAST(SUBSTRING(@date_str, 1,4)+ '-' + SUBSTRING(@date_str, 5,2) + '-' + SUBSTRING(@date_str,7,2) +
+			' ' + SUBSTRING(@date_str, 9,2) + ':' + SUBSTRING(@date_str, 11,2) AS DATETIME)
+END
+
+RETURN @ret_date
+
+END