25.11 fb blood processing clinical

onprc_ehr/resources/queries/study/processingSerology.sql

@@ -26,6 +26,12 @@ SELECT
   t.isPCRRequired,
   t.isPCRCurrent,
 
+  t.lastBchem,
+  t.daysSinceBchem,
+  t.isBchemRequired,
+  t.isBchemCurrent,
+
+
   CASE
     WHEN (t.isSRVRequired = true AND t.isSRVCurrent = false) THEN 4
     ELSE 0
@@ -36,6 +42,61 @@ SELECT
     ELSE 0
   END as PCRbloodVol,
 
+  CASE
+      WHEN  (t.isESPFRequired = true AND t.isESPFCurrent = false )  THEN 4
+      ELSE 0
+      END as ESPFbloodVol,
+
+  -----CBC
+  CASE
+      WHEN  (t.isCBCRequired1 = true AND t.isCBCCurrent1 = false ) OR  (t.isCBCRequired2 = true AND t.isCBCCurrent2 = false ) THEN 1
+      ELSE 0
+      END as CBCbloodVol1,
+
+
+  CASE
+      WHEN  (t.isCBCRequired3 = true AND t.isCBCCurrent3 = false )  THEN 1
+      ELSE 0
+      END as CBCbloodVol3,
+
+  CASE
+      WHEN  (t.isCBCRequired4 = true AND t.isCBCCurrent4 = false )  THEN 1
+      ELSE 0
+      END as CBCbloodVol4,
+
+  CASE
+      WHEN  (t.isCBCRequired5 = true AND t.isCBCCurrent5 = false )  THEN 1
+      ELSE 0
+      END as CBCbloodVol5,
+
+
+
+  -----Comprehensive Chemistry
+  CASE
+      WHEN  (t.isCChemRequired1 = true AND t.isCChemCurrent1 = false )  THEN 2
+      ELSE 0
+      END as CChembloodVol1,
+
+  CASE
+      WHEN  (t.isCChemRequired2 = true AND t.isCChemCurrent2 = false )  THEN 2
+      ELSE 0
+      END as CChembloodVol2,
+
+  CASE
+      WHEN  (t.isCChemRequired3 = true AND t.isCChemCurrent3 = false )  THEN 2
+      ELSE 0
+      END as CChembloodVol3,
+
+  CASE
+      WHEN  (t.isCChemRequired4 = true AND t.isCChemCurrent4 = false )  THEN 2
+      ELSE 0
+      END as CChembloodVol4,
+
+    -----Basic Chemistry
+  CASE
+      WHEN  (t.isBChemRequired = true AND t.isBChemCurrent = false )  THEN 2
+      ELSE 0
+      END as BchembloodVol,
 
 FROM (
 
@@ -64,7 +125,158 @@ SELECT
   CASE
    WHEN (d.Id.age.ageInDays > 180 )  THEN true
     ELSE false
-    END as isPCRRequired
+    END as isPCRRequired,
+
+    espf.lastDate as lastESPF,
+    timestampdiff('SQL_TSI_DAY', espf.lastDate, now()) as daysSinceESPF,
+   CASE
+      WHEN (year(now()) = year(espf.lastDate) AND  (timestampdiff('SQL_TSI_DAY', espf.lastDate, now()) > 180) ) THEN false
+      ELSE true
+      END as isESPFCurrent,
+
+   CASE
+      WHEN (d.Id.age.ageInDays > 180 )  THEN true
+      ELSE false
+      END as isESPFRequired,
+
+
+    ------ All CBC Sections
+
+    cbc.lastDate as lastCBC1,
+    timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) as daysSinceCBC1,
+   CASE
+      WHEN (year(now()) = year(cbc.lastDate) AND (timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) > 165 )AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' ) ) THEN false
+      ELSE true
+      END as isCBCCurrent1,
+
+  CASE
+      WHEN (d.Id.age.ageInDays > 20 )  THEN true
+      ELSE false
+      END as isCBCRequired1,
+
+    cbc.lastDate as lastCBC2,
+    timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) as daysSinceCBC2,
+   CASE
+      WHEN (year(now()) = year(cbc.lastDate) AND (timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) > 340) AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' ) AND (flg.Id is not null) ) THEN false
+      ELSE true
+      END as isCBCCurrent2,
+
+   CASE
+      WHEN (d.Id.age.ageInDays > 180 )  THEN true
+      ELSE false
+      END as isCBCRequired2,
+
+    cbc.lastDate as lastCBC3,
+    timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) as daysSinceCBC3,
+   CASE
+      WHEN (year(now()) = year(cbc.lastDate) AND (timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) > 340) AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' )  ) THEN false
+      ELSE true
+      END as isCBCCurrent3,
+
+   CASE
+      WHEN (d.Id.age.ageInDays > 12 )  THEN true
+      ELSE false
+      END as isCBCRequired3,
+
+
+    cbc.lastDate as lastCBC4,
+    timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) as daysSinceCBC4,
+   CASE
+      WHEN ( cbc.lastDate is null AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' )  ) THEN false
+      ELSE true
+      END as isCBCCurrent4,
+
+   CASE
+      WHEN (d.Id.age.ageInDays > 6 )  THEN true
+      ELSE false
+      END as isCBCRequired4,
+
+
+    cbc.lastDate as lastCBC5,
+    timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) as daysSinceCBC5,
+   CASE
+      WHEN (year(now()) = year(cbc.lastDate) AND (timestampdiff('SQL_TSI_DAY', cbc.lastDate, now()) > 180)  AND (nts.Id is not null) )  THEN false
+      ELSE true
+      END as isCBCCurrent5,
+
+   CASE
+      WHEN (d.Id.age.ageInDays > 180 )  THEN true
+      ELSE false
+      END as isCBCRequired5,
+
+
+
+      ----- All Comp Chemistry sections
+
+
+    cchem.lastDate as lastCChem1,
+    timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) as daysSinceCChem1,
+  CASE
+      WHEN ( ( (year(now()) = year(cchem.lastDate) AND  (timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) > 165)) OR cchem.lastDate is null )   AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' )  ) THEN false
+      ELSE true
+      END as isCChemCurrent1,
+
+  CASE
+      WHEN (d.Id.age.ageInDays > 20 )  THEN true
+      ELSE false
+      END as isCChemRequired1,
+
+
+    cchem.lastDate as lastCChem2,
+        timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) as daysSinceCChem2,
+  CASE
+      WHEN ( ( (year(now()) = year(cchem.lastDate) AND  (timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) > 340) ) OR cchem.lastDate is null )   AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' ) AND (flg.Id is not null) ) THEN false
+      ELSE true
+      END as isCChemCurrent2,
+
+  CASE
+      WHEN (d.Id.age.ageInDays > 180 )  THEN true
+      ELSE false
+      END as isCChemRequired2,
+
+    cchem.lastDate as lastCChem3,
+        timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) as daysSinceCChem3,
+  CASE
+      WHEN ( year(now()) = year(cchem.lastDate) AND  (timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) > 180)  AND d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' )  ) THEN false
+      ELSE true
+      END as isCChemCurrent3,
+
+  CASE
+      WHEN (d.Id.age.ageInDays >= 18 )  THEN true
+      ELSE false
+      END as isCChemRequired3,
+
+    cchem.lastDate as lastCChem4,
+        timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) as daysSinceCChem4,
+  CASE
+      WHEN ( ( year(now()) = year(cchem.lastDate) AND  (timestampdiff('SQL_TSI_DAY', cchem.lastDate, now()) > 180 ))  AND (nts.Id is not null )  ) THEN false
+      ELSE true
+      END as isCChemCurrent4,
+
+  CASE
+      WHEN (d.Id.age.ageInDays > 180 )  THEN true
+      ELSE false
+      END as isCChemRequired4,
+
+
+    ------------- Basic Chemistry
+
+
+    bchem.lastDate as lastBChem,
+        timestampdiff('SQL_TSI_DAY', bchem.lastDate, now()) as daysSinceBChem,
+  CASE
+      WHEN ( ( year(now()) = year(bchem.lastDate) AND (timestampdiff('SQL_TSI_DAY', bchem.lastDate, now()) > 340 ) ) AND (d.Id.curLocation.area in ('Corrals', 'Shelters', 'PENS' ) )  ) THEN false
+      ELSE true
+      END as isBChemCurrent,
+
+  CASE
+      WHEN (d.Id.age.ageInDays >= 6 AND d.Id.age.ageInDays < 18 )  THEN true
+      ELSE false
+      END as isBChemRequired
+
+
+
+
 
 FROM study.demographics d
 
@@ -78,6 +290,16 @@ LEFT JOIN (
 
 ) srv ON (srv.id = d.id)
 
+LEFT JOIN (
+    SELECT
+        k.id,
+        max(k.date) as lastDate
+    FROM study.blood k
+    WHERE (k.additionalservices = 'ESPF Surveillance - Semiannual')
+    GROUP BY k.id
+
+) espf ON (espf.id = d.id)
+
 LEFT JOIN (
     SELECT
         b.id,
@@ -88,6 +310,60 @@ LEFT JOIN (
 
 ) pcr ON (pcr.id = d.id)
 
+LEFT JOIN (
+    SELECT
+        j.id,
+        max(j.date) as lastDate
+    FROM study.blood j
+    WHERE j.additionalservices like  'CBC with automated differential'
+    GROUP BY j.id
+
+) cbc ON (cbc.id = d.id)
+
+LEFT JOIN (
+    SELECT
+        m.id,
+        max(m.date) as lastDate
+    FROM study.blood m
+    WHERE m.additionalservices like  'Comprehensive Chemistry panel in-house'
+    GROUP BY m.id
+
+) cchem ON (cchem.id = d.id)
+
+
+LEFT JOIN (
+    SELECT
+        t.id,
+        max(t.date) as lastDate
+    FROM study.blood t
+    WHERE t.additionalservices like  'Basic Chemistry Panel'
+    GROUP BY t.id
+
+) bchem ON (bchem.id = d.id)
+
+LEFT JOIN (
+    SELECT
+        n.id,
+        max(n.date) as lastDate
+    FROM study.flags n
+    WHERE n.category ='Behavior Flag' And n.value = 'Socially important'
+    And n.enddate is null
+    GROUP BY n.id
+
+) flg ON (flg.id = d.id)
+
+
+LEFT JOIN (
+    SELECT
+        p.id,
+        max(p.date) as lastDate
+    FROM study.flags p
+    WHERE p.flag.category ='Notes Pertaining to DAR' And p.flag.value = 'Assignment pool'
+    And p.enddate is null
+    GROUP BY p.id
+
+) nts ON (nts.id = d.id)
+
 
 WHERE d.calculated_status = 'Alive'
 

onprc_reports/resources/queries/study/processingBloodDraws.query.xml

@@ -22,12 +22,24 @@
                     <column columnName="PCRBloodVolume">
                         <columnTitle>PCR PTT (mL)</columnTitle>
                     </column>
+                    <column columnName="ESPFbloodVol">
+                        <columnTitle>ESPF PTT (mL)</columnTitle>
+                    </column>
                     <column columnName="dnaBloodDrawVol">
                         <columnTitle>DNA Pink/PTT (mL)</columnTitle>
                     </column>
                     <column columnName="serologyBloodVol">
                         <columnTitle>Serology RTT (mL)</columnTitle>
                     </column>
+                    <column columnName="totalCBCVol">
+                        <columnTitle>CBC PTT (mL)</columnTitle>
+                    </column>
+                    <column columnName="totalCompChemBloodVol">
+                        <columnTitle>COMP Chem RTT (mL)</columnTitle>
+                    </column>
+                    <column columnName="BasicChemBloodVol">
+                        <columnTitle>BASIC Chem RTT (mL)</columnTitle>
+                    </column>
                     <column columnName="geneticsBloodVol">
                         <columnTitle>Genetics Blood Vol (mL)</columnTitle>
                     </column>

onprc_reports/resources/queries/study/processingBloodDraws.sql

@@ -10,15 +10,37 @@ SELECT
  End as PCRBloodVolume,
 
   s.srvBloodVol as serologyBloodVol,
+
+  Case when (a.Id IS NOT NULL)  And (s.ESPFBloodVol > 0 ) then 4
+       ELSE
+           0
+      End as ESPFBloodVol,
+
+
+ ( coalesce(s.CBCbloodVol1,0) +   coalesce(s.CBCbloodVol3,0) +  coalesce(s.CBCbloodVol4,0) +  coalesce(s.CBCbloodVol5,0) ) as totalCBCVol,
+ (coalesce(s.CChembloodVol1,0) + coalesce(s.CChembloodVol2,0) + coalesce(s.CChembloodVol3,0) + coalesce(s.CChembloodVol4,0) )  as totalCompChemBloodVol,
+ (coalesce(s.BChembloodVol,0) )  as BasicChemBloodVol,
+
   g.parentageBloodDrawVol,
   g.mhcBloodDrawVol,
   g.dnaBloodDrawVol,
   g.totalBloodDrawVol as geneticsBloodVol,
 
-  coalesce(s.srvBloodVol, 0) +  Case when (a.Id IS NOT NULL)   And (s.pcrbloodVol > 0 )  then 2
+
+
+  coalesce(s.srvBloodVol, 0) +
+  Case when (a.Id IS NOT NULL)   And (s.pcrbloodVol > 0 )  then 2
    ELSE
      0
-   End + coalesce(g.totalBloodDrawVol, 0) as totalBloodDrawVol,
+   End +
+  Case when (a.Id IS NOT NULL)  And (s.ESPFBloodVol > 0 ) then 4
+  ELSE
+      0
+  End +
+  coalesce(s.CBCbloodVol1,0) +   coalesce(s.CBCbloodVol3,0) +  coalesce(s.CBCbloodVol4,0) +  coalesce(s.CBCbloodVol5,0) +
+  coalesce(s.CChembloodVol1,0) + coalesce(s.CChembloodVol2,0) + coalesce(s.CChembloodVol3,0) + coalesce(s.CChembloodVol4,0) +
+  coalesce(s.BChembloodVol,0) +
+  coalesce(g.totalBloodDrawVol, 0) as totalBloodDrawVol,
 
     (select k.room  from study.housing k where k.Id =d.Id And k.enddate is null) as currentlocationroom,
     (select coalesce(k.cage, ' ') from study.housing k where k.Id =d.Id And k.enddate is null) as currentlocationcage,
@@ -34,3 +56,5 @@ FROM study.assignment a
 WHERE a.isActive = true and a.project.name = javaConstant('org.labkey.onprc_ehr.ONPRC_EHRManager.U42_PROJECT')
 GROUP BY a.Id
     ) a ON (a.Id = d.Id)
+
+

onprc_reports/resources/queries/study/processingBloodDraws/.qview.xml

@@ -8,6 +8,10 @@
     <column name="spfStatus"/>
     <column name="PCRBloodVolume"/>
     <column name="serologyBloodVol"/>
+    <column name="ESPFbloodVol"/>
+    <column name="totalCompChemBloodVol"/>
+    <column name="totalCBCVol"/>
+    <column name="BasicChemBloodVol"/>
     <column name="parentageBloodDrawVol"/>
     <column name="mhcBloodDrawVol"/>
     <column name="dnaBloodDrawVol"/>