Udpate of onprc_ehr.xml to add update status to theeIACUC_PRIME_VIEW_…

…PROTOCOLS dataset
LabKey · Jul 24, 2024 · 41f2c11 · 41f2c11
1 parent feea40a
commit 41f2c11
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Showing 12 changed files with 273 additions and 8 deletions.
diff --git a/onprc_ehr/resources/etls/ProtocolMergefromeIACUC.xml b/onprc_ehr/resources/etls/ProtocolMergefromeIACUC.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--update of procedure to production for daily run-->
+<etl xmlns="http://labkey.org/etl/xml">
+
+    <name>InserteIACCUtoProtocol</name>
+    <description>Updates select columns into ehr Protocol extensible columns </description>
+<transforms>
+
+    <transform id="transform2">
+    <source schemaName="onprc_ehr" queryName="eIACUC_PRIME_VIEW_PROTOCOLS"/>
+    <destination schemaName="ehr" queryName="protocol" targetOption="merge">
+        <columnTransforms>
+            <column source="BaseProtocol" target="BaseProtocol"/>
+            <column source="RenewalNumber" target="RevisionNumber"/>
+            <column source="Protocol_State" target="Protocol_State"/>
+            <column source="last_modified" target="last_modified"/>
+        </columnTransforms>
+        <alternateKeys>
+            <!-- The pk of the target table is the "rowId" column. Use "OtherId" as an alternate match key -->
+            <column name="BaseProtocol"/>
+        </alternateKeys>
+
+    </destination>
+</transform>
+
+
+</transforms>
+</etl>
diff --git a/onprc_ehr/resources/etls/eIACUCtoPrimePhase1.xml b/onprc_ehr/resources/etls/eIACUCtoPrimePhase1.xml
@@ -0,0 +1,16 @@
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>eiACUCtoProtocolPhase1</name>
+    <description>Populates the extensible fields in Protocol</description>
+    <transforms>
+
+        <transform id="step1a">
+            <description>Transfer to Protocols</description>
+            <source queryName="eIACUCtoProtocolPhase1" schemaName="onprc_ehr"/>
+            <destination queryName="protocol" schemaName="ehr" targetOption="merge"/>
+        </transform>
+<!--//Need a query that has needed fields for BaseProtocol and revisionNumber and then inserts that into eIACUC_Prime_View_Protocols
+        Also only want latest data-->
+
+    </transforms>
+
+</etl>
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eAIACUCAppendProtocol.sql b/onprc_ehr/resources/queries/onprc_ehr/eAIACUCAppendProtocol.sql
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eIACUCtoPrimeUpdate.xml b/onprc_ehr/resources/queries/onprc_ehr/eIACUCtoPrimeUpdate.xml
@@ -0,0 +1,70 @@
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>eiACUCtoPrimeUpdate</name>
+    <description>Transfers from the eIACUC Import tables to the Prime tables in ONPRC_EHR</description>
+    <transforms>
+        <transform id="step1a">
+            <description>Transfer to eIACUC Animal Groups</description>
+            <source queryName="PRIME_VIEW_ANIMAL_GROUPS" schemaName="eIACUC"/>
+            <destination queryName="eIACUC_PRIME_VIEW_ANIMAL_GROUPS" schemaName="ONPRC_EHR" targetOption="truncate"/>
+        </transform>
+        <transform id="step2a">
+            <description>Transfer to IBX Numbers</description>
+            <source queryName="PRIME_VIEW_IBC_NUMBERS" schemaName="eIACUC"/>
+            <destination queryName="eIACUC_PRIME_VIEW_IBC_NUMBERS" schemaName="ONPRC_EHR" targetOption="truncate"/>
+        </transform>
+        <transform id="step3a">
+            <description>Transfer to Non Surgical Procedures</description>
+            <source queryName="PRIME_VIEW_NON_SURGICAL_PROCS" schemaName="eIACUC"/>
+            <destination queryName="eIACUC_PRIME_VIEW_NON_SURGICAL_PROCS" schemaName="ONPRC_EHR" targetOption="truncate"/>
+        </transform>
+        <transform id="step4a">
+            <description>Transfer to Protocols</description>
+            <source queryName="eIACUCwithBaseProtocol" schemaName="eIACUC"/>
+            <destination queryName="eIACUC_PRIME_VIEW_PROTOCOLS" schemaName="ONPRC_EHR" targetOption="truncate"/>
+        </transform>
+        <transform id="step5a">
+            <description>Transfer to Surgical Procedures</description>
+            <source queryName="PRIME_VIEW_SURGERIES" schemaName="eIACUC"/>
+            <destination queryName="eIACUC_PRIME_VIEW_SURGICAL_PROCS" schemaName="ONPRC_EHR" targetOption="truncate"/>
+        </transform>
+        <!--
+
+                    <!–Need to update to change the processes and document each one–>
+                    <transform id="Stored_ProcStep10" type="StoredProcedure">
+                        <description>Runs a stored procedure tocapture information from the eIACUC Protocol Table.</description>
+                        <procedure schemaName="ONPRC_EHR" procedureName="etlStep1eIACUCtoPRIMEProcessing">
+                        </procedure>
+                    </transform>
+
+
+                    <transform id="Stored_ProcStep20" type="StoredProcedure">
+                        <description>Runs a stored procedure to process records from eIACUC to temp to ehr.protocol.</description>
+                        <procedure schemaName="ONPRC_EHR" procedureName="etlStep2eIACUCtoPublicAction">
+                        </procedure>
+                    </transform>
+
+                    <transform id="Stored_ProcStep30" type="StoredProcedure">
+                        <description>Runs a stored procedure identify record updated from eIACUC2 to ehrProtocol ending ehrProtocol Record.</description>
+                        <procedure schemaName="ONPRC_EHR" procedureName="etlStep3update_ehrProtocol">
+                        </procedure>
+                    </transform>
+
+                    <transform id="Stored_ProcStep40" type="StoredProcedure">
+                        <description>Runs a stored procedure to insert new and updated records from eIACUC to ehrProtocol and update log.</description>
+                        <procedure schemaName="ONPRC_EHR" procedureName="etlStep4insertToEhr_Protocol">
+                        </procedure>
+                    </transform>
+
+
+
+
+
+
+            -->
+    </transforms>
+    <!--	<schedule>
+
+              <poll interval="12h"/>
+
+          </schedule>-->
+</etl>
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eIACUCwithBaseProtocol.sql b/onprc_ehr/resources/queries/onprc_ehr/eIACUCwithBaseProtocol.sql
@@ -0,0 +1,26 @@
+SELECT p.Protocol_ID,
+       Case when len(p.protocol_id) > 10 then substring(p.protocol_id, 6,15)
+            else p.protocol_id
+           End as BaseProtocol,
+       Case when len(p.protocol_id) > 10 then substring(p.protocol_id, 1,4)
+            else 'Original'
+           End as RevisionNumber,
+
+       p.Date_Modified,
+       p.Template_OID,
+       p.OID,
+       p.Protocol_Title,
+       p.Protocol_State,
+       p.PI_ID,
+       p.PI_First_Name,
+       p.PI_Last_Name,
+       p.PI_Email,
+       p.PI_Phone,
+       p.USDA_Level,
+       p.PPQ_Numbers,
+       p.Approval_date,
+       p.Annual_Update_Last_Approved,
+       p.Annual_Update_Due,
+       p.Three_Year_Expiration,
+       p.Last_Modified
+FROM PRIME_VIEW_PROTOCOLS p
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eIACUFiedlUpdateforProtocol.sql b/onprc_ehr/resources/queries/onprc_ehr/eIACUFiedlUpdateforProtocol.sql
@@ -0,0 +1,8 @@
+Select p.baseProtocol,
+        p.RevisionNumber,
+        p.Protocol_State,
+        p.PPQ_Numbers,
+        p.Last_Modified,
+        p.USDA_Level
+ from  onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p
+ --where p.last_Modified = (Select Max(p1.Last_Modified) from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p1 where p1.BaseProtocol = p.BaseProtocol))
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eIACUProtocolReview.sql b/onprc_ehr/resources/queries/onprc_ehr/eIACUProtocolReview.sql
@@ -0,0 +1,21 @@
+SELECT e.rowid,
+       e.Protocol_ID,
+       e.Template_OID,
+       e.Protocol_OID,
+       e.Protocol_Title,
+       e.USDA_Level,
+       e.Approval_Date,
+       e.Annual_Update_Due,
+       e.Three_year_Expiration,
+       e.Last_Modified,
+       e.PROTOCOL_State,
+       e.BaseProtocol,
+       e.RevisionNumber,
+       Case
+           When p.external_id is Null then 'No Longer in Prime'
+           When (p.enddate is null and e.Protocol_State != 'Approved')then 'Still Active in Prime'
+           when (p.enddate is not null and p.external_id is not null) then 'Active in Prime'
+           End as ProtocolStatus,
+       p.external_ID,
+       p.enddate
+FROM eIACUC_PRIME_VIEW_PROTOCOLS e left join ehr.protocol p on e.BaseProtocol = p.external_id
diff --git a/onprc_ehr/resources/queries/onprc_ehr/eiACUCtoProtocolPhase1.sql b/onprc_ehr/resources/queries/onprc_ehr/eiACUCtoProtocolPhase1.sql
@@ -0,0 +1,9 @@
+SELECT
+e.BaseProtocol,
+e.RenewalNumber,
+e.Protocol_state,
+e.LatestRenewal,
+p.protocol
+
+from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS e join  ehr.protocol p on e.BaseProtocol = p.external_id
+where e.latestRenewal = true
diff --git a/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.002-24.003.sql b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.002-24.003.sql
@@ -0,0 +1,81 @@
+================================================
+-- Template generated from Template Explorer using:
+-- Create Procedure (New Menu).SQL
+--
+-- Use the Specify Values for Template Parameters
+-- command (Ctrl-Shift-M) to fill in the parameter
+-- values below.
+--
+-- This block of comments will not be included in
+-- the definition of the procedure.
+-- ================================================
+SET ANSI_NULLS ON
+GO
+SET QUOTED_IDENTIFIER ON
+GO
+-- =============================================
+-- Author:		Jonesga
+-- Create date: 2024/07/18
+-- Description:	Iniitial Stage of update of eIACUC to protocol processing
+-- =============================================
+
+CREATE PROCEDURE onprc_ehr.eIACUCBaseProtocol
+
+    AS
+BEGIN
+	-- SET NOCOUNT ON added to prevent extra result sets from
+	-- interfering with SELECT statements.
+	SET NOCOUNT ON;
+--Drop Temporary Table
+DROP TABLE #eIACUCBaseProtocol
+-- Insert statements for procedure here
+cREATE tABLE #eIACUCBaseProtocol
+(BaseProtocol varchar(50) Not Null,
+ RevisionNumber varchar(20) Not Null,
+ Protocol_Id varchar(50) Not Null,
+ Last_Modified varchar(30) not null ,
+ LatestInstance varchar (30) Not Null);
+
+--Populate the temporary table from query
+Insert INTO #eIACUCBaseProtocol(BaseProtocol,RevisionNumber,Protocol_id,Last_Modified,LatestInstance)
+Select
+
+    Case when len(p.protocol_id) > 10 then substring(p.protocol_id, 6,15)
+         else p.protocol_id
+        End as BaseProtocol,
+    Case when len(p.protocol_id) > 10 then substring(p.protocol_id, 1,4)
+         else 'Original'
+        End as RevisionNumber,
+    protocol_id,
+    Last_Modified,
+    ' ' as LatestInstance
+
+from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p
+
+Update p1
+Set p1.BaseProtocol = e.BaseProtocol
+
+    from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p1 join #eIACUCUpdate e on p1.protocol_id = e.Protocol_Id
+
+Update p1
+Set p1.RevisionNumber = e.RevisionNumber
+
+    from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p1 join #eIACUCUpdate e on p1.protocol_id = e.Protocol_Id
+
+
+
+--Now will limit the records to be inserted to most recent record
+
+
+update p
+Set p.updateStatus = 'Update'
+
+    from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p
+where (p.BaseProtocol is not null and p.last_Modified = (Select Max(p1.Last_Modified) from onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p1 where p1.BaseProtocol = p.BaseProtocol))
+
+
+
+
+
+END
+GO
diff --git a/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.003-24.004.sql b/onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.003-24.004.sql
@@ -0,0 +1,8 @@
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS DROP COLUMN IF EXISTS BaseProtocol;
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS DROP COLUMN IF EXISTS RevisionNumber;
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS DROP COLUMN IF EXISTS UpdateStatus;
+
+
+ALTER TABLE [onprc_ehr].[eIACUC_PRIME_VIEW_PROTOCOLS] ADD  BaseProtocol varchar(50) ;
+ALTER TABLE [onprc_ehr].[eIACUC_PRIME_VIEW_PROTOCOLS] ADD  RenewalNumber varchar(50) ;
+ALTER TABLE [onprc_ehr].[eIACUC_PRIME_VIEW_PROTOCOLS] ADD  LatestRenewal Bit ;
diff --git a/onprc_ehr/resources/schemas/onprc_ehr.xml b/onprc_ehr/resources/schemas/onprc_ehr.xml
@@ -710,7 +710,6 @@
             <column columnName="Surgery_Name"/>
         </columns>
     </table>
-
     <table tableName="eIACUC_PRIME_VIEW_PROTOCOLS" tableDbType="TABLE">
         <columns>
             <column columnName="rowid"/>
@@ -735,6 +734,9 @@
             <column columnName="PROTOCOL_State"/>
             <column columnName="PPQ_Numbers"/>
             <column columnName="Description"/>
+            <column columnName="BaseProtocol"/>
+            <column columnName="RevisionNumber"/>
+            <column columnName="UpdateStatus"/>
         </columns>
     </table>
     <table tableName="PotentialDam_source" tableDbType="TABLE">

diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java b/onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java
@@ -126,7 +126,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 23.013;
+        return 24.004;
     }
 
     @Override
@@ -219,9 +219,6 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         //Added Oct 3rd, 2023 Kollil
         ns.registerNotification(new TreatmentAlertsMPANotification(this));
 
-        //Added June 28th, 2024 Kollil
-        ns.registerNotification(new LongTermMedsNotification(this));
-
         //Added 8-7-2018 R.Blasa
         ns.registerNotification(new BirthHousingMismatchNotification(this));
 
@@ -230,7 +227,6 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
 
         //Added 6-4-2019 Additional Scheduled for 5pm
         ns.registerNotification(new TreatmentAlertsPostOpsNotificationThird(this));
-
         //Added 5-9-2024 Additional to validate Available Draw Feed Values
         ns.registerNotification(new AvailableBloodVolumeNotification(this));
 
@@ -407,10 +403,10 @@ public String toString()
         }
 
 
-        //Modified: 7-2-2024  R.Blasa
+        //Modified: 9-7-2023  R.Blasa
         try
         {
-            EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Clinical Pathology Test Results for Environmental Assessment Summary Report", this, new URLHelper("https://pcdbssrsprd1.ohsu.edu/ReportServer/Pages/ReportViewer.aspx?%2fPrime+Reports%2fClinPath%2fPrimeLaboratory_AssessmentReport&rs:Command=Render")
+            EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.moreReports, "Clinical Pathology CPL Surface Sanitation Summary Report", this, new URLHelper("https://pcdbssrsprd1.ohsu.edu/ReportServer/Pages/ReportViewer.aspx?%2fPrime+Reports%2fClinPath%2fPrimeLaboratory_AssessmentReport&rs:Command=Render")
             {
                 // SSRS is picky about the URI-encoding of the query parameters
                 @Override