Skip to content

Commit e6d27d0

Browse files
spamhurtsspamhurts
authored
Updates to lab work reports and animalDemographics & acq_disp queries (#358)
* 1. Added CulturePivot query and meta-data for CULTURE and SUSCEPTIBILITY data 2. Refined ParasitologyPivot queries 3. Added CulturePivot to reports.tsv * 1. fixed logic errors in acq_disp queries 2. changed animalDemographics.sql to a parameterized query to select animals on a specific date 3. tweaked CulturePivot.sql
1 parent f341b4e commit e6d27d0

11 files changed

Lines changed: 124 additions & 34 deletions

‎snprc_ehr/resources/data/reports.tsv‎

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -16,10 +16,10 @@ surveillance Lab Results query Surveillance true study surveillancePivot date
1616
urinalysis Lab Results query Urinalysis true study urinalysisPivot date false false Contains urinalysis results
1717
miscTests Lab Results query Misc Tests true study miscPivot date false false qcstate/publicdata This report contains the misc lab results not represented in the other reports
1818
surgery Surgery js Surgeries true study underDevelopment Surgeries date false false qcstate/publicdata This report contains one record for each encounter with each animal, including surgeries, exams, procedures, etc.
19-
Animal events Clinical query Animal Events true study encounters encountersHistory date false false qcstate/publicdata
20-
Admission History Clinical query Adm History true study cases admHistory date false false qcstate/publicdata
21-
procedures Clinical query Procedures true study procedure proceduresByEncounter date false false qcstate/publicdata
22-
proceduresBeforeDisposition Clinical js Procedures Before Disposition true study proceduresBeforeDisposition ProceduresBeforeDisposition date false false qcstate/publicdata
19+
Animal events Clinical query Animal Events true study encounters encountersHistory date false false qcstate/publicdata
20+
Admission History Clinical query Adm History true study cases admHistory date false false qcstate/publicdata
21+
procedures Clinical query Procedures true study procedure proceduresByEncounter date false false qcstate/publicdata
22+
proceduresBeforeDisposition Clinical js Procedures Before Disposition true study proceduresBeforeDisposition ProceduresBeforeDisposition date false false qcstate/publicdata
2323
procedureHistory Surgery query Procedure Summary true study proceduresPerYear date false false qcstate/publicdata This report contains one record for each encounter with each animal, including surgeries, exams, procedures, etc.
2424
DailyObs Clinical query Daily Obs true study DailyObs date false false Contains daily observations
2525
clinObsBsu Behavior js Observations true study underDevelopment BSU Observations date false false qcstate/publicdata This report contains one record for each encounter with each animal, including surergies, exams, procedures, etc.
@@ -52,14 +52,15 @@ blood General query Blood Draw History true study Blood Draws date false fals
5252
idHistory General query ID History true study idHistory id_date false false This report contains a summary of the identifiers that have been assigned for each animal
5353
generalTb General query TB Test Results true study tb date false false TB Test results
5454
demographics General query Demographics true study demographics By Location false false qcstate/publicdata This report displays the demographics data about each animal including species, gender and birth
55-
reproSummary Reproductive Management js Reproductive Summary true study underDevelopment date false false qcstate/publicdata
56-
menses Reproductive Management js Menses true study underDevelopment date false false qcstate/publicdata
57-
freezerworks General query Freezer/Sample Data true study Freezerworks date false false qcstate/publicdata
55+
reproSummary Reproductive Management js Reproductive Summary true study underDevelopment date false false qcstate/publicdata
56+
menses Reproductive Management js Menses true study underDevelopment date false false qcstate/publicdata
57+
freezerworks General query Freezer/Sample Data true study Freezerworks date false false qcstate/publicdata
5858
currentBlood General js Current Blood true study currentBlood date false false This report contains a summary of the current available blood for each animal
59-
Obscan Reproductive Management query Obscan true study ObScan date false false qcstate/publicdata
59+
Obscan Reproductive Management query Obscan true study ObScan date false false qcstate/publicdata
6060
blood Type General query Blood Type true study BloodType date false false Contains blood type.
6161
ParasitologyPivot Lab Results query Parasitology (Non O&P) true study ParasitologyPivot date false false Parasitology data.
62-
ParasitologyPivot Lab Results query Parasitology O&P true study ParasitologyPivotOP date false false O&P Parasitology data.
62+
ParasitologyPivot2 Lab Results query Parasitology O&P true study ParasitologyPivotOP date false false O&P Parasitology data.
63+
CulturePivot Lab Results query Cultures true study CulturePivot date false false Culture data.
6364
Notes General query Notes true study Notes date false false Contains Misc. Notes
6465
Flags Colony Management query Animal Attributes (flags) true study flags StartDate false false qcstate/publicdata Animal attribute flags
6566
FileRepository General js File Repository true study FileRepository false false qcstate/publicdata File Repository for uploading and viewing animal related files
@@ -70,4 +71,4 @@ Procedure History Exposures query Procedure History true study ExpProcedureHist
7071
Research Treatments Exposures query Research Treatments true study ExpResearchTreatments Date false false qcstate/publicdata Research Treatments data
7172
Abnormal Behavior Behavior query Abnormal Behavior true study BehaviorAbnormalSummary Date false false qcstate/publicdata Abnormal behavoir detail data
7273
Vaccines Exposures query Vaccines true study ExpVaccines Date false false qcstate/publicdata Exposure vaccines data
73-
Body Condition Score Clinical query Body Condition Score true study BodyConditionScores
74+
Body Condition Score Clinical query Body Condition Score true study BodyConditionScores

‎snprc_ehr/resources/queries/study/CulturePivot.query.xml‎

Lines changed: 31 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
1+
<query xmlns="http://labkey.org/data/xml/query">
2+
<metadata>
3+
<tables xmlns="http://labkey.org/data/xml">
4+
<table tableName="CulturePivot" tableDbType="TABLE">
5+
<tableTitle>Culture Pivot</tableTitle>
6+
<columns>
7+
<column columnName="Id">
8+
<fk>
9+
<fkDbSchema>study</fkDbSchema>
10+
<fkTable>animal</fkTable>
11+
<fkColumnName>Id</fkColumnName>
12+
</fk>
13+
</column>
14+
<column columnName="panelName">
15+
<columnTitle>Panel Name</columnTitle>
16+
<displayWidth>105</displayWidth>
17+
</column>
18+
<column columnName="runId">
19+
<isHidden>true</isHidden>
20+
<shownInDetailsView>false</shownInDetailsView>
21+
<fk>
22+
<fkDbSchema>study</fkDbSchema>
23+
<fkTable>ClinpathRuns</fkTable>
24+
<fkColumnName>message_id</fkColumnName>
25+
</fk>
26+
</column>
27+
</columns>
28+
</table>
29+
</tables>
30+
</metadata>
31+
</query>

‎snprc_ehr/resources/queries/study/CulturePivot.sql‎

Lines changed: 41 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,41 @@
1+
/*
2+
* Copyright (c) 2019 LabKey Corporation
3+
*
4+
* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
7+
*
8+
* http://www.apache.org/licenses/LICENSE-2.0
9+
*
10+
* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*/
16+
/******************************************************************************
17+
Non Ova & Parasite (O&P) result set.
18+
srr 04.02.2019
19+
20+
******************************************************************************/
21+
SELECT
22+
p.runid,
23+
p.Id,
24+
p.date,
25+
p.serviceTestId.testName as TestName,
26+
p.runId.serviceRequested as PanelName,
27+
GROUP_CONCAT(p.qualresult) as QResults
28+
29+
FROM study.labworkResults as p
30+
inner join snprc_ehr.labwork_panels as lt
31+
on p.serviceTestid = lt.rowId
32+
and lt.ServiceId.Dataset='Culture'
33+
34+
where p.id is not null
35+
group by p.runid, p.Id, p.date,p.serviceTestId.testName, p.runId.serviceRequested
36+
PIVOT QResults by TestName IN
37+
(select t.testName from snprc_ehr.labwork_panels t
38+
where t.includeInPanel = true
39+
and t.ServiceId.Dataset = 'Culture'
40+
order by t.TestName asc
41+
);

‎snprc_ehr/resources/queries/study/CulturePivot/.qview.xml‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
2+
<sorts>
3+
<sort column="date" descending="true" />
4+
<sort column="Id" descending="true" />
5+
<sort column="PanelName" />
6+
</sorts>
7+
</customView>

‎snprc_ehr/resources/queries/study/ParasitologyPivot.query.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
</column>
1414
<column columnName="panelName">
1515
<columnTitle>Parasitology Panel Name</columnTitle>
16-
<displayWidth>20</displayWidth>
16+
<displayWidth>80</displayWidth>
1717
</column>
1818
<column columnName="runId">
1919
<isHidden>true</isHidden>
@@ -28,4 +28,4 @@
2828
</table>
2929
</tables>
3030
</metadata>
31-
</query>
31+
</query>

‎snprc_ehr/resources/queries/study/ParasitologyPivot.sql‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,6 @@ SELECT
2424
p.date,
2525
p.serviceTestId.testName as TestName,
2626
p.runId.serviceRequested as PanelName,
27-
--p.TestName,
2827
GROUP_CONCAT(p.qualresult) as QResults
2928

3029
FROM study.labworkResults as p

‎snprc_ehr/resources/queries/study/ParasitologyPivotOP.query.xml‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
<metadata>
33
<tables xmlns="http://labkey.org/data/xml">
44
<table tableName="ParasitologyPivotOP" tableDbType="TABLE">
5-
<tableTitle>Parasitology OP Pivot </tableTitle>
5+
<tableTitle>Parasitology OP Pivot</tableTitle>
66
<columns>
77
<column columnName="Id">
88
<fk>
@@ -16,6 +16,7 @@
1616
</column>
1717
<column columnName="panelName">
1818
<columnTitle>Parasitology Panel Name</columnTitle>
19+
<displayWidth>80</displayWidth>
1920
</column>
2021
<column columnName="COMMENTS::QResults">
2122
<displayWidth>500</displayWidth>
@@ -33,4 +34,4 @@
3334
</table>
3435
</tables>
3536
</metadata>
36-
</query>
37+
</query>

‎snprc_ehr/resources/queries/study/ParasitologyPivotOP.sql‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -20,12 +20,11 @@ srr 04.02.2019
2020
******************************************************************************/
2121

2222
SELECT
23-
--p.runid,
23+
p.runid,
2424
p.Id,
2525
p.date,
2626
p.serviceTestId.testName as TestName,
27-
-- p.runId.serviceRequested as PanelName,
28-
--p.TestName,
27+
p.runId.serviceRequested as PanelName,
2928
GROUP_CONCAT(p.qualresult) as QResults
3029

3130
FROM study.labworkResults as p
@@ -34,13 +33,11 @@ FROM study.labworkResults as p
3433
and lt.ServiceId.Dataset='Parasitology'
3534

3635
where p.id is not null
37-
--and p.runId.serviceRequested in ('OVA & PARASITES' ) --,'OVA & PARASITES, URINE')
38-
group by p.runid, p.Id, p.date,p.serviceTestId.testName--, p.runId.serviceRequested
36+
and p.runId.serviceRequested in ('OVA & PARASITES' ,'OVA & PARASITES, URINE')
37+
group by p.runid, p.Id, p.date, p.serviceTestId.testName, p.runId.serviceRequested
3938
PIVOT QResults by TestName IN
4039
(select TestName from snprc_ehr.labwork_panels t
4140
where t.includeInPanel = true
4241
and t.ServiceId.Dataset = 'Parasitology'
4342
and t.ServiceId.ServiceName in ('OVA & PARASITES', 'OVA & PARASITES, URINE')
44-
45-
)
46-
;
43+
);

‎snprc_ehr/resources/queries/study/acq_disp.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -31,9 +31,9 @@ d.dispositionType.value as disp_code,
3131
d.dispositionType
3232
FROM arrival a
3333
LEFT OUTER JOIN departure d
34-
on d.id = a.id and a.date < ifnull(d.date,now())
34+
on d.id = a.id and a.date <= ifnull(d.date,now())
3535

36-
where a.date < ifnull(d.date,now())
37-
and ( d.date = (select min(z.date) from departure z where z.id = d.id and z.date > a.date)
36+
where a.date <= ifnull(d.date,now())
37+
and ( d.date = (select min(z.date) from departure z where z.id = d.id and z.date >= a.date)
3838
or
39-
d.date is NULL)
39+
d.date is NULL)

‎snprc_ehr/resources/queries/study/acq_dispHistory.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -27,9 +27,9 @@ a.id as id, a.date as acq_date,
2727

2828
FROM arrival a
2929
LEFT OUTER JOIN departure d
30-
on d.id = a.id and a.date < ifnull(d.date, now())
30+
on d.id = a.id and a.date <= ifnull(d.date, now())
3131

32-
where a.date < ifnull(d.date, now())
33-
and ( d.date = (select min(z.date) from departure z where z.id = d.id and z.date > a.date)
32+
where a.date <= ifnull(d.date, now())
33+
and ( d.date = (select min(z.date) from departure z where z.id = d.id and z.date >= a.date)
3434
or
35-
d.date is NULL)
35+
d.date is NULL)

0 commit comments

Comments
 (0)