Merge 24.11 to 25.1

onprc_ehr/resources/etls/SLAWeaning.xml

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--Created By: Kollil, 9/25/2024.
+ Create an ETL process for SLA weaning data: Based on the alive pups DOB, create an ETL process that runs daily and checks if there are any pups
+ that’s 21 days old, load them into SLA purchase & purchase details datasets as pending orders (Confirmation num is null & dateCanceled is null).
+ Once the data is moved, the “dateofTransfer” field will be set marking the pups are moved into SLA purchase datasets and will be excluded
+ from the future daily checks.
+ Refer to ticket # 11233 for more details.
+-->
+<etl xmlns="http://labkey.org/etl/xml">
+
+    <name>SLAWeaning</name>
+
+    <description>Executes stored procedure to populate the SLA purchase datasets</description>
+
+    <transforms>
+        <transform id="Stored_Proc" type="StoredProcedure">
+            <description>Runs the stored procedure to process and update the weaning data from sla.TempWeaning table to sla.purchase and sla.purchasedetails tables in prime</description>
+            <procedure schemaName="onprc_ehr" procedureName="SLAWeaningDataTransfer"> </procedure>
+        </transform>
+    </transforms>
+
+    <schedule>
+        <!-- Runs daily at 11pm -->
+        <cron expression="0 0 23 * * ?"/>
+<!--        <poll interval="15m" />&lt;!&ndash; For testing only - runs every 15 mins &ndash;&gt;-->
+    </schedule>
+
+</etl>

onprc_ehr/resources/etls/UpdateEhrProtocols.xml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<etl xmlns="http://labkey.org/etl/xml">
+
+    <name>Update Protocols in EHR</name>
+
+    <description>Runs stored procedures to update the protocol table in schema ehr.</description>
+
+    <transforms>
+
+        <transform id="UpdateBaseProtocol" type="StoredProcedure">
+            <description>Determines and populates BaseProtocol and RevisionNumber data for the protocol table in schema onprc_ehr.</description>
+            <procedure schemaName="onprc_ehr" procedureName="BaseProtocol">
+            </procedure>
+        </transform>
+
+        <transform id="enddateExpiredProtocolsProtocol" type="StoredProcedure">
+            <description>Adds enddate data to the protocol table in ehr.</description>
+            <procedure schemaName="onprc_ehr" procedureName="ExpiredProtocolUpdate">
+            </procedure>
+        </transform>
+
+    </transforms>
+
+    <!--
+    <schedule>
+        <cron expression="0 50 04 * * "/>
+     </schedule>
+     -->
+
+</etl>
+
+
+
+

onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.001-24.002.sql

@@ -0,0 +1,7 @@
+--added to allow insert of calculated fields from eIACUC
+
+--2024-12-13 In development need to use a drop if exists statement for these to run
+
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS ADD [BaseProtocol] varchar(100) Null;
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS ADD [RevisionNumber] varchar(100) Null;
+ALTER TABLE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS ADD [NewestRecord] INT Null;

onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.002-24.003.sql

@@ -0,0 +1,34 @@
+CREATE PROCEDURE onprc_ehr.BaseProtocol
+AS
+BEGIN
+    -- Create a Common Table Expression (CTE) named BaseProtocol
+    WITH BaseProtocol AS
+             (
+                 SELECT
+                     RowID,
+                     Protocol_id,
+                     -- Determine the BaseProtocol based on the length of the Protocol_id
+                     CASE
+                         WHEN LEN(Protocol_id) > 10 THEN SUBSTRING(Protocol_id, 6, 15)
+                         ELSE Protocol_id
+                         END AS BaseProtocol,
+                     -- Determine the RevisionNumber based on the length of the Protocol_id
+                     CASE
+                         WHEN LEN(Protocol_id) > 10 THEN SUBSTRING(Protocol_id,1, 5)
+                         ELSE 'Original'
+                         END AS RevisionNumber,
+                     approval_date,
+                     Three_Year_Expiration,
+                     last_modified,
+                     Protocol_State
+                 FROM onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS
+             )
+
+    -- Update the onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS table with BaseProtocol and RevisionNumber from the CTE
+    UPDATE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS
+    SET BaseProtocol = BaseProtocol.BaseProtocol,
+        RevisionNumber = BaseProtocol.RevisionNumber
+    FROM BaseProtocol
+    WHERE onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS.RowID = BaseProtocol.RowID;
+END
+GO

onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.004-24.005.sql

@@ -0,0 +1,48 @@
+GO
+/****** Object:  StoredProcedure [onprc_ehr].[ExpiredProtocolUpdate]    Script Date: 12/20/2024 9:09:09 AM ******/
+SET ANSI_NULLS ON
+GO
+SET QUOTED_IDENTIFIER ON
+GO
+CREATE PROCEDURE [onprc_ehr].[ExpiredProtocolUpdate]
+    AS
+BEGIN
+
+WITH ApprovedProtocols AS (
+    SELECT
+        BaseProtocol,
+        MAX(Approval_Date) AS maxApprovalDate
+    FROM
+        onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS
+    WHERE
+        Protocol_State IN ('approved','expired', 'terminated')
+    GROUP BY
+        BaseProtocol
+),
+
+
+     DistinctProtocols AS (
+         SELECT DISTINCT
+             p.rowID,
+             p.BaseProtocol,
+             p.RevisionNumber,
+             p.Protocol_State,
+             p.Approval_Date,
+             p.Last_Modified,
+             p.Three_Year_Expiration
+         FROM
+             onprc_ehr.eIACUC_PRIME_VIEW_PROTOCOLS p
+                 INNER JOIN ApprovedProtocols ap ON p.BaseProtocol = ap.BaseProtocol
+                                AND p.Approval_Date = ap.maxApprovalDate),
+     ExpiredProtocol AS (
+         Select
+             d.*,
+             p.protocol,
+             p.enddate
+         from DistinctProtocols d inner join ehr.protocol p on d.BaseProtocol = p.external_ID
+            where d.Protocol_State != 'Approved' and p.enddate is Null)
+
+Update p
+    Set p.enddate = getDate()
+    from ehr.protocol p inner join expiredProtocol e on p.external_id = e.BaseProtocol
+END

onprc_ehr/resources/schemas/onprc_ehr.xml

@@ -735,6 +735,9 @@
             <column columnName="PROTOCOL_State"/>
             <column columnName="PPQ_Numbers"/>
             <column columnName="Description"/>
+            <column columnName="BaseProtocol"/>
+            <column columnName="RevisionNumber"/>
+            <column columnName="NewestRecord"/>
         </columns>
     </table>
     <table tableName="PotentialDam_source" tableDbType="TABLE">

onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java

@@ -126,7 +126,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 23.016;
+        return 24.005;
     }
 
     @Override

sla/resources/queries/sla/ProtocolProjectsAndBreedingInfo.query.xml

@@ -37,7 +37,7 @@
                         <columnTitle>Species</columnTitle>
                     </column>
                     <column columnName="Gender">
-                        <columnTitle>Gender</columnTitle>
+                        <columnTitle>Sex</columnTitle>
                     </column>
                     <column columnName="Strain">
                         <columnTitle>Strain</columnTitle>

sla/resources/queries/sla/ProtocolProjectsAndBreedingInfo.sql

@@ -8,7 +8,7 @@ SELECT
     a.title As Title,
     i.LastName || ', ' || i.FirstName As PIName,
     aa.Species,
-    aa.Gender,
+    aa.Gender as Sex,
     aa.Strain,
     aa.Allowed As NumAllowed,
     aa.StartDate,

sla/resources/queries/sla/ProtocolProjectsUsage.query.xml

@@ -35,7 +35,7 @@
                         <columnTitle>Species</columnTitle>
                     </column>
                     <column columnName="Gender">
-                        <columnTitle>Gender</columnTitle>
+                        <columnTitle>Sex</columnTitle>
                     </column>
                     <column columnName="Strain">
                         <columnTitle>Strain</columnTitle>

sla/resources/queries/sla/ProtocolProjectsUsage.sql

@@ -13,7 +13,7 @@ SELECT
     y.grantNumber as OGAGrantNumber,
     y.fiscalAuthorityName As FiscalAuthorityName,
     aa.Species,
-    aa.Gender,
+    aa.Gender as Sex,
     aa.Strain,
     aa.Allowed AS NumAllowed,
     calc.NumUsed,

sla/resources/queries/sla/allowableSLA.sql

@@ -4,7 +4,7 @@
 SELECT a.protocol,
        c.protocol_id as eIACUC_protocol_name,
        a.species,
-       a.gender,
+       a.gender as Sex,
        a.strain,
        a.age,
        a.allowed,

sla/resources/queries/sla/weaning/.qview.xml

@@ -0,0 +1,18 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <columns>
+        <column name="rowid"/>
+        <column name="investigator"/>
+        <column name="date"/>
+        <column name="project"/>
+        <column name="vendorlocation"/>
+        <column name="DOB"/>
+        <column name="DOM"/>
+        <column name="species"/>
+        <column name="sex"/>
+        <column name="strain"/>
+        <column name="numAlive"/>
+        <column name="numDead"/>
+        <column name="totalPups"/>
+        <column name="dateofTransfer"/>
+    </columns>
+</customView>

sla/resources/queries/sla_public/PurchaseOrderDetails.sql

@@ -10,7 +10,7 @@ p.requestorid,
 p.requestor,
 p.vendor,
 pd.species,
-pd.gender,
+pd.gender as Sex,
 pd.strain,
 pd.weight,
 pd.gestation,

sla/resources/queries/sla_public/PurchaseOrderDetailsAdmin.sql

@@ -11,7 +11,7 @@ p.requestorid,
 p.requestor,
 p.vendor,
 pd.species,
-pd.gender,
+pd.gender As Sex,
 pd.strain,
 pd.weight,
 pd.gestation,