Sla weaning project

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>

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,

sla/resources/schemas/dbscripts/sqlserver/sla-23.002-23.003.sql

@@ -0,0 +1,185 @@
+-- =================================================================================================
+--Created by Kollil
+--These tables and stored proc was created to enter weaning data into SLA tables
+--Refer to ticket #11233
+-- =================================================================================================
+
+--Drop table if exists
+EXEC core.fn_dropifexists 'weaning','sla','TABLE';
+--Drop Stored proc if exists
+EXEC core.fn_dropifexists 'SLAWeaningDataTransfer', 'onprc_ehr', 'PROCEDURE';
+GO
+
+CREATE TABLE sla.weaning (
+    rowid int IDENTITY(1,1) NOT NULL,
+    investigator varchar(250),
+    date DATETIME,  -- Pup's DOB
+    project varchar(200),
+    vendorLocation varchar(200),
+    DOB DATETIME,   --Dam's DOB
+    DOM DATETIME,   --Date of Mating
+    species varchar(100),
+    sex varchar(100),
+    strain varchar (200),
+    numAlive INTEGER,
+    numDead INTEGER,
+    totalPups INTEGER,
+    dateofTransfer DATETIME,    --The date of transfer into SLA tables
+    createdBy USERID,
+    created DATETIME,
+    modifiedBy USERID,
+    modified DATETIME,
+
+    CONSTRAINT PK_weaning PRIMARY KEY (rowid)
+);
+
+GO
+
+/****** Object:  StoredProcedure  sla.SLAWeaningDataTransfer   Script Date: 8/24/2024 *****/
+-- ==========================================================================================
+-- Author: Lakshmi Kolli
+-- Create date: 8/24/2024
+-- Description: Create a stored proc to check for any rodents with age >= 21 days and enter
+-- the data into SLA tables
+-- ==========================================================================================
+
+CREATE PROCEDURE [onprc_ehr].[SLAWeaningDataTransfer]
+AS
+
+DECLARE
+    @WCount			        int,
+    @alias			        varchar(100),
+    @purchaseId		        entityid,
+    @center_project         int,
+	@center_project2        int,
+    @counter		        int,
+	@counter2				int,
+	@DOT					DATETIME,
+	@DOT2					DATETIME
+
+BEGIN
+    --Check if any rodents age is 21 days and above and not transferred into SLA tables
+    Select @WCount = COUNT(*) From sla.weaning Where numAlive > 0 And dateofTransfer is null And DateDiff(dd, date, GETDATE()) >= 21
+
+    --Found entries, so, insert those records into SLA.purchase and SLA.purchasedetails tables
+    If @WCount > 0 -- start if, 1
+    Begin
+        --Create a local temp table to process the weaning data. The table drops automatically at the end of the session
+        CREATE TABLE #TempWeaning (
+          rowid int IDENTITY(1,1) NOT NULL,
+          orig_weaning_rowid INTEGER,
+          investigator varchar(250),
+          date DATETIME,
+          project varchar(200),
+          vendorLocation varchar(200),
+          DOB DATETIME,
+          DOM DATETIME,
+          species varchar(100),
+          sex varchar(100),
+          strain varchar (200),
+          numAlive INTEGER,
+          dateofTransfer DATETIME,
+          created DATETIME
+        );
+
+        --Move the weaning entries into a temp table
+        INSERT INTO #TempWeaning (orig_weaning_rowid, investigator, date, project, vendorlocation, DOB, DOM, species, sex, strain, numAlive, created)
+        Select rowid, investigator, date, project, vendorlocation, date, DOM, species,
+            CASE
+            WHEN sex = 'F' THEN 'Female'
+            WHEN sex = 'M' THEN 'Male'
+            ELSE 'Male or Female'
+        END AS sex,
+        strain, numAlive, GETDATE() From sla.weaning Where numAlive > 0 And dateofTransfer is null And DateDiff(dd, date, GETDATE()) >= 21
+
+         --Set the counter seed value
+        Select top 1 @counter = rowid from #TempWeaning order by rowid asc
+
+        WHILE @counter <= @WCount -- start 1st while
+        BEGIN
+            /* Requestorid - (Kati Marshall ) - 7B3F1ED1-4CD9-4D9A-AFF4-FE0618D49C4B
+            Userid - (Kati Marshall) - 1294
+            vendor - (ONPRC Weaning - SLA) - E1EE1B64-B7BE-1035-BFC4-5107380AE41E
+            container - (SLA) - 4831D09C-4169-1034-BAD2-5107380A9819
+            created - (onprc-is) - 1003
+            */
+
+            Select @DOT = dateofTransfer From #TempWeaning Where rowid = @counter
+            If @DOT IS NULL --start @DOT
+            Begin
+                -- Get projectid, PI and account
+                Select @center_project = project, @alias = account From ehr.project Where name = (Select project From #TempWeaning Where rowid = @counter)
+
+                -- Check if the row is already transferred into the main SLA tables. If DOT is null means the row hasn't been transferred yet.
+                --Insert weaning data into sla.purchase table as a pending order
+                INSERT INTO sla.purchase
+                (project, account, requestorid, vendorid, hazardslist, dobrequired, comments, confirmationnum, housingconfirmed,
+                 iacucconfirmed, requestdate, orderdate, orderedby, objectid, container, createdby, created, modifiedby, modified, DARComments, VendorContact)
+                Select @center_project, @alias ,'7B3F1ED1-4CD9-4D9A-AFF4-FE0618D49C4B','E1EE1B64-B7BE-1035-BFC4-5107380AE41E','',0,'',null,null,null,null,null,'',NEWID(),
+                '4831D09C-4169-1034-BAD2-5107380A9819',1003,GETDATE(),null,null,'',''
+
+                --Get the newly created purchaseid from sla.purchase
+                Select top 1 @purchaseid = objectid From sla.purchase order by created desc
+
+                --Insert data into purchasedetails with the newly created purchaseid above
+                INSERT INTO sla.purchaseDetails
+                (purchaseid, species, age, weight, weight_units, gestation, gender, strain, room, animalsordered, animalsreceived, boxesquantity, costperanimal, shippingcost,
+                 totalcost, housingInstructions, requestedarrivaldate, expectedarrivaldate, receiveddate, receivedby, cancelledby, datecancelled,
+                 objectid, container, createdby, created, modifiedby, modified, sla_DOB, vendorLocation)
+                Select @purchaseid, species, CONVERT(VARCHAR, DateDiff(dd, date, GETDATE())) + ' days', '','','',sex, strain,'',numAlive,null,null,'','',
+                '','',DateAdd(dd, 21, date), DateAdd(dd, 21, date),null,'','',null,
+                NewId(),'4831D09C-4169-1034-BAD2-5107380A9819',1003,GETDATE(),null,null,date,vendorLocation
+                From #TempWeaning Where rowid = @counter
+
+                --Update the sla.weaning row with the date of transfer date set for the transferred weaning row
+                Update sla.weaning
+                Set dateofTransfer = GETDATE() Where rowid = (Select orig_weaning_rowid from #TempWeaning Where rowid = @counter)
+
+                Update #TempWeaning
+                Set dateofTransfer = GETDATE() Where rowid = @counter
+
+                --Find if there are any rows with the same center project. Then create them under the same purchaseId
+                --set the new counter
+                SET @counter2 = @counter + 1;
+                WHILE @counter2 <= @Wcount -- start 2nd while
+                BEGIN
+                    Select @DOT2 = dateofTransfer From #TempWeaning Where rowid = @counter2
+                    If @DOT2 IS NULL
+                    Begin
+                        --Get projectid of the next row
+                        Select @center_project2 = project From ehr.project Where name = (Select project From #TempWeaning Where rowid = @counter2)
+
+                        --If they are same projects, then use the the same purchaseid when creating the purchase details record
+                        If (@center_project = @center_project2) -- start if, 2
+                        Begin
+                            INSERT INTO sla.purchaseDetails
+                            (purchaseid, species, age, weight, weight_units, gestation, gender, strain, room, animalsordered, animalsreceived, boxesquantity, costperanimal, shippingcost,
+                             totalcost, housingInstructions, requestedarrivaldate, expectedarrivaldate, receiveddate, receivedby, cancelledby, datecancelled,
+                             objectid, container, createdby, created, modifiedby, modified, sla_DOB, vendorLocation)
+                             Select @purchaseid, species, CONVERT(VARCHAR, DateDiff(dd, date, GETDATE())) + ' days', '','','',sex, strain, '',numAlive,null,null,'','',
+                             '','',DateAdd(dd, 21, date), DateAdd(dd, 21, date),null,'','',null,
+                             NewId(),'4831D09C-4169-1034-BAD2-5107380A9819',1003,GETDATE(),null,null,date,vendorLocation
+                            From #TempWeaning Where rowid = @counter2
+
+                            Update sla.weaning
+                            Set dateofTransfer = GETDATE() Where rowid = (Select orig_weaning_rowid from #TempWeaning Where rowid = @counter2)
+
+                            Update #TempWeaning
+                            Set dateofTransfer = GETDATE() Where rowid = @counter2
+                        End -- end if, 2
+                    End --end DOT2
+                    SET @counter2 = @counter2 + 1;
+                END -- end, 2nd while
+
+            End --end @DOT
+        SET @counter = @counter + 1;
+        END -- end, 1st while
+    End -- end if, 1
+
+    --Drop the temp table incase it exists...
+    IF EXISTS (SELECT * FROM tempdb.sys.tables WHERE name = '#TempWeaning')
+    BEGIN
+        DROP TABLE #TempWeaning;
+    END;
+END
+Go

sla/resources/schemas/sla.xml

@@ -461,4 +461,60 @@
         </columns>
     </table>
 
-</tables>
+    <table tableName="Weaning" tableDbType="TABLE" useColumnOrder="true">
+        <tableTitle>Weaning</tableTitle>
+        <auditLogging>DETAILED</auditLogging>
+        <importUrl></importUrl>
+        <insertUrl></insertUrl>
+        <updateUrl></updateUrl>
+        <deleteUrl></deleteUrl>
+
+        <columns>
+            <column columnName="rowid" />
+            <column columnName="investigator">
+                <columnTitle>PI</columnTitle>
+            </column>
+            <column columnName="date">
+                <columnTitle>Date</columnTitle>
+            </column>
+            <column columnName="project">
+                <columnTitle>Center Project</columnTitle>
+            </column>
+            <column columnName="vendorLocation">
+                <columnTitle>Vendor Location</columnTitle>
+            </column>
+            <column columnName="DOB">
+                <columnTitle>DOB</columnTitle>
+            </column>
+            <column columnName="DOM">
+                <columnTitle>DOM</columnTitle>
+            </column>
+            <column columnName="species">
+                <columnTitle>Species</columnTitle>
+            </column>
+            <column columnName="sex">
+                <columnTitle>Sex</columnTitle>
+            </column>
+            <column columnName="strain">
+                <columnTitle>Strain</columnTitle>
+            </column>
+            <column columnName="numAlive">
+                <columnTitle>Alive Pups</columnTitle>
+            </column>
+            <column columnName="numDead">
+                <columnTitle>Dead Pups</columnTitle>
+            </column>
+            <column columnName="totalPups">
+                <columnTitle>Total Pups</columnTitle>
+            </column>
+            <column columnName="dateofTransfer">
+                <columnTitle>Date moved to SLA pending orders</columnTitle>
+            </column>
+            <column columnName="createdby" />
+            <column columnName="created" />
+            <column columnName="modifiedby" />
+            <column columnName="modified" />
+        </columns>
+    </table>
+
+  </tables>

sla/resources/views/SLA_LandingPage.html

@@ -5,23 +5,27 @@ <h2><span style="font-size: large;"><b>SLA Purchase </b></span></h2>
 <p>Click the link below to view the SLA groups & breeding information for the protocols. This information is retrieved daily from the eIACUC database.</p>
 <p><strong><a href="/query/ONPRC/SLA/executeQuery.view?schemaName=ehrSLA&query.queryName=ProtocolProjectsAndBreedingInfo">SLA Groups & Breeding Information</a>&nbsp</strong></p>
 <br>
+<h2><span style="font-size: large;"><b>SLA Weaning </b></span></h2>
+<p>SLA weaning module is used by SLAU staff to record the rodent births and documenting the number of animals weaned.<br> Weaned mice are entered into SLA purchase module as they need to be subtracted from the protocol's SLA allowance numbers.</p>
+<!--<p><strong><a href="http://localhost:8080/labkey/ldk/ONPRC/SLA/updateQuery.view?schemaName=sla&query.queryName=Weaning">Click here to view/upload the weaning data</a>&nbsp</strong></p>-->
+<p><strong><a href="/ldk/ONPRC/SLA/updateQuery.view?schemaName=sla&query.queryName=Weaning">Click here to view/upload the weaning data</a>&nbsp</strong></p>
+<br>
 <h2><span style="font-size: large;"><b>SLA Census </b></span></h2>
 <p>SLA census module is used by SLAU staff to maintain rodent demographic and location data and billing. Please click on the links below for specific operations.</p>
-<br>
-<h3><span style="font-size: large;">Entering Animals</span></h3>
+<h3><span style="font-size: large;"><b><i>Entering Animals:</i></b></span></h3>
 <address>
     <p><strong><a href="/ehr/ONPRC/SLA/dataEntryForm.view?formType=SLA%20Census">SLA Census - Entry Screen</a></strong></p>
     <p><strong><a href="/ehr/onprc/sla/enterData.view">SLA Census - Edit&nbsp;Previous Record Menu</a>&nbsp;</strong>&nbsp;- Choose "All Tasks" navigational tab and click the mouse on the task id to edit a record.</p>
     <p><strong><a href="/sla/ONPRC/SLA/censusBulkEdit.view?">SLA Census - Bulk Editing Grid</a>&nbsp; -&nbsp;</strong>Allows editing more than one Census records.</p>
     <p><strong><a href="/EHR/ONPRC/EHR/dataEntryForm.view?formType=arrival">SLA - Entry Grid for Rabbits / Guinea Pigs</a>&nbsp; -&nbsp;</strong>Web link to enter new Rabbits and Guinea Pig records.</p>
 </address>
-<h3><span style="font-size: large;">Entering Charges</span></h3>
+<h3><span style="font-size: large;"><b><i>Entering Charges:</i></b></span></h3>
 <address>
     <p><strong><a href="/query/ONPRC/EHR/executeQuery.view?schemaName=onprc_billing&amp;query.queryName=miscChargesFees">Misc Charges - Grid</a>&nbsp;-&nbsp;</strong>This format is best for export to Excel.</p>
     <p><strong><a href="/ehr/ONPRC/EHR/dataEntryForm.view?formType=miscCharges">Misc Charges - Entry Form</a></strong></p>
     <p><strong><a href="/onprc_ehr/onprc/ehr/enterData.view">Return to "My Task/All Task" Page</a><a href="/ehr/ONPRC/EHR/dataEntryForm.view?formType=miscCharges">&nbsp;</a></strong></p>
 </address>
-<h3><span style="font-size: large;">Reports</span></h3>
+<h3><span style="font-size: large;"><b><i>Reports:</i></b></span></h3>
 <address>
     <p><strong><a href="/EHR/ONPRC/SLA/executeQuery.view?schemaName=sla&amp;query.queryName=census">SLA Census - Grid</a></strong></p>
     <p><strong><a href="https://pcdbssrsprd1.ohsu.edu/ReportServer/Pages/ReportViewer.aspx?%2fPrime+Reports%2fSLA+Reports%2fSLACensusMainReport_Project&amp;rs:Command=Render">SLA Census - Printed Report</a>&nbsp;-&nbsp;</strong>Center Project &amp; Date Range required.</p>