LabKey · spamhurts · Aug 16, 2022 · Jun 2, 2022 · Jun 14, 2022 · Jun 14, 2022
diff --git a/snprc_ehr/resources/etls/SqlmedMsh.xml b/snprc_ehr/resources/etls/SqlmedMsh.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>Sqlmed MSH data</name>
+    <description>Sqlmed MSH Data (Synthetic)</description>
+    <transforms>
+        <transform id="step1" type="org.labkey.di.pipeline.TransformTask">
+            <description>Copy to target</description>
+            <source schemaName="snprcSrc" queryName="v_Sqlmed_msh" />
+            <destination schemaName="snprc_ehr" queryName="HL7_MSH" bulkLoad="true" batchSize="10000" targetOption="merge">
+                <alternateKeys>
+                    <column name="object_id"/>
+                </alternateKeys>
+            </destination>
+        </transform>
+    </transforms>
+    <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="timestamp">
+        <deletedRowsSource schemaName="snprcSrc" queryName="v_delete_clinpathruns" timestampColumnName="entry_date_tm" deletedSourceKeyColumnName="objectid" targetKeyColumnName="OBJECT_ID"/>
+    </incrementalFilter>
+    <schedule>
+        <poll interval="60m" />
+    </schedule>
+</etl>
diff --git a/snprc_ehr/resources/etls/SqlmedObr.xml b/snprc_ehr/resources/etls/SqlmedObr.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>Sqlmed OBR data</name>
+    <description>Clinical Pathology OBR data</description>
+    <transforms>
+        <transform id="step1" type="org.labkey.di.pipeline.TransformTask">
+            <description>Copy to target</description>
+            <source schemaName="snprcSrc" queryName="v_Sqlmed_obr" />
+            <destination schemaName="snprc_ehr" queryName="HL7_OBR" bulkLoad="true" batchSize="10000" targetOption="merge">
+                <alternateKeys>
+                    <column name="OBJECT_ID"/>
+                </alternateKeys>
+            </destination>
+        </transform>
+    </transforms>
+    <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="timestamp">
+        <deletedRowsSource schemaName="snprcSrc" queryName="v_delete_clinpathruns" timestampColumnName="entry_date_tm" deletedSourceKeyColumnName="objectid" targetKeyColumnName="OBJECT_ID"/>
+    </incrementalFilter>
+    <schedule>
+        <poll interval="60m" />
+    </schedule>
+</etl>
diff --git a/snprc_ehr/resources/queries/pdl_workflow/pdlResults.query.xml b/snprc_ehr/resources/queries/pdl_workflow/pdlResults.query.xml
@@ -52,11 +52,6 @@
                         <columnTitle>Ref Range</columnTitle>
                         <isUnselectable>true</isUnselectable>
                         <isHidden>false</isHidden>
-                        <!-- <fk>
-                            <fkDbSchema>study</fkDbSchema>
-                            <fkTable>labRefRange</fkTable>
-                            <fkColumnName>lsid</fkColumnName>
-                        </fk> -->
                     </column>
                     <column columnName="abnormal_flags">
                         <columnTitle>Abnormal Flags</columnTitle>
@@ -74,27 +69,16 @@
                     <column columnName="method">
                         <nullable>true</nullable>
                         <columnTitle>Method</columnTitle>
-                        <!--
-                        <fk>
-                            <fkDbSchema>ehr_lookups</fkDbSchema>
-                            <fkTable>chemistry_method</fkTable>
-                            <fkColumnName>value</fkColumnName>
-                        </fk> -->
                     </column>
 
                     <column columnName="parentid">
-                        <!--<fk>-->
-                        <!--<fkDbSchema>study</fkDbSchema>-->
-                        <!--<fkTable>chemistryRuns</fkTable>-->
-                        <!--<fkColumnName>objectid</fkColumnName>-->
-                        <!--</fk>-->
                         <nullable>true</nullable>
                     </column>
                     <column columnName="runid">
                         <isHidden>true</isHidden>
                         <fk>
                             <fkDbSchema>study</fkDbSchema>
-                            <fkTable>ClinpathRuns</fkTable>
+                            <fkTable>ClinpathRunsAll</fkTable>
                             <fkColumnName>objectid</fkColumnName>
                         </fk>
                     </column>

diff --git a/snprc_ehr/resources/queries/pdl_workflow/pdlResults.sql b/snprc_ehr/resources/queries/pdl_workflow/pdlResults.sql
@@ -17,28 +17,18 @@
   Purpose: ETL from SPF assay tables to assay_labworkResults and ultimately SurveillancePivot
   Author: Charles Peterson, Texas Biomedical Research Institute, October 17, 2018
  */
--- noinspection SqlNoDataSourceInspection
 select distinct
-  case when d.snprc_id is NULL then
-    d.pdl_animal_id
-    else d.snprc_id end as Id,
+  COALESCE(d.snprc_id, d.pdl_animal_id) as Id,
   d.sample_date as date,
   d.procedure_name as panelName,
   NULL as serviceTestId,
   d.procedure_id as serviceId,
   d.test_id as testid,
   d.test_name as test_name,
-/*  d.Run as runId, */
   NULL as runId,
   NULL as result,
   'ST' as value_type,
   d.results as qualresult,
   d.file_name as remark,
   d.sample as sampleId
-
-/*  ServiceName debugging hack
-  ,d.test_id as refRange,
-  d.procedure_id as abnormal_flags,
-  d.test_name as resultOORIndicator */
-
 from pdl_workflow.data as d
diff --git a/snprc_ehr/resources/queries/pdl_workflow/pdlWorkflow.sql b/snprc_ehr/resources/queries/pdl_workflow/pdlWorkflow.sql
@@ -18,9 +18,7 @@
   Author: Charles Peterson, Texas Biomedical Research Institute, September 20, 2018
  */
   select distinct
-    case when d.snprc_id is NULL then
-      d.pdl_animal_id
-    else d.snprc_id end as Id,
+    COALESCE(d.snprc_id, d.pdl_animal_id) as Id,
     d.sample_date as date,
     d.report_date as datefinalized,
     d.procedure_id as serviceId,

diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7BiochemistryPivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Biochemistry Results Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.sql
@@ -0,0 +1,25 @@
+SELECT
+    obr.ANIMAL_ID as id,
+    obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+WHERE obr.PROCEDURE_ID.Dataset = 'Biochemistry'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.SET_ID, obr.PROCEDURE_NAME, obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName as TEST_NAME from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Biochemistry'
+    )
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot/.qview.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot/.qview.xml
@@ -0,0 +1,6 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7CulturePivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Culture and Sensitivity Results Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql
@@ -0,0 +1,25 @@
+SELECT
+    obr.ANIMAL_ID as id,
+    obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+WHERE obr.PROCEDURE_ID.Dataset = 'Culture'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.SET_ID, obr.PROCEDURE_NAME, obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName as TEST_NAME from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Culture'
+    )
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot/.qview.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot/.qview.xml
@@ -0,0 +1,6 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7HematologyPivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Hematology Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.sql
@@ -0,0 +1,25 @@
+SELECT
+    obr.ANIMAL_ID as id,
+    obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+WHERE obr.PROCEDURE_ID.Dataset = 'Hematology'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.SET_ID, obr.PROCEDURE_NAME, obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName as TEST_NAME from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Hematology'
+    )
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot/.qview.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot/.qview.xml
@@ -0,0 +1,6 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7HistologyPivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Histology Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.sql
@@ -0,0 +1,24 @@
+SELECT obr.ANIMAL_ID as id,
+       obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+WHERE obr.PROCEDURE_ID.Dataset = 'Histology'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Histology'
+    )
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot/.qview.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot/.qview.xml
@@ -0,0 +1,6 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7MiscPivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Misc Tests Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql
@@ -0,0 +1,24 @@
+SELECT obr.ANIMAL_ID as id,
+       obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+WHERE obr.PROCEDURE_ID.Dataset = 'Misc Tests'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Misc Tests'
+    )
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot/.qview.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot/.qview.xml
@@ -0,0 +1,6 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.query.xml b/snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.query.xml
@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="HL7ParasitologyPivot" tableDbType="NOT_IN_DB">
+                <tableTitle>Parasitology Pivot</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.sql b/snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.sql
@@ -0,0 +1,24 @@
+SELECT obr.ANIMAL_ID as id,
+       obr.OBSERVATION_DATE_TM as date,
+    obr.MESSAGE_ID,
+    COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
+    obr.PROCEDURE_ID,
+    nte.COMMENT,
+    COALESCE (lp.TestName, obx.TEST_NAME) as TestName,
+    MAX(obx.ABNORMAL_FLAGS) AS ABNORMAL_FLAGS,
+    COALESCE(MAX(obx.RESULT), MAX(obx.QUALITATIVE_RESULT)) as RESULT
+
+FROM snprc_ehr.HL7_OBR obr
+    LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
+    LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
+WHERE obr.PROCEDURE_ID.Dataset = 'Parasitology'
+
+GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
+    PIVOT RESULT, ABNORMAL_FLAGS BY TestName
+
+    IN
+    (
+    select TestName from snprc_ehr.labwork_panels t
+    where t.includeInPanel = true AND t.ServiceId.Dataset='Parasitology'
+    )