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consolidating surveillance tests to the labworksResultsAll query (#386)
* consolidating surveillance tests to the labworksResultsAll query * Added Taqman Dataset
1 parent 93fab5f commit 9c6b8b3

14 files changed

Lines changed: 317 additions & 111 deletions

‎snprc_ehr/resources/data/reports.tsv‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ CycleDaily Reproductive Management query Cycle History true study CycleDaily
1010
activeAssignments Assignments and Groups query Active Assignments true study Assignment Active Assignments date false false qcstate/publicdata This report shows the active assignments for each animal
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assignmentHistory Assignments and Groups query Assignment History true study Assignment date false false qcstate/publicdata This report shows all assignments records for the animals
1212
biochemistry Lab Results query Biochemistry true study chemPivot date false false Contains results of chemistry panels. Can be displayed either by panel, or showing reference ranges
13-
clinPathRuns Lab Results query Requests true study clinpathRuns date false false qcstate/publicdata Contains all clinpath requests
13+
clinPathRuns Lab Results query Requests true study clinpathRunsALL date false false qcstate/publicdata Contains all clinpath requests
1414
hematology Lab Results query Hematology true study hematologyPivot date false false Contains hematology data showing cell subsets
1515
surveillance Lab Results query Surveillance true study surveillancePivot date false false Contains surveillance data
1616
urinalysis Lab Results query Urinalysis true study urinalysisPivot date false false Contains urinalysis results

‎snprc_ehr/resources/queries/spf_workflow/spfResults.query.xml‎

Lines changed: 1 addition & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -52,11 +52,6 @@
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<columnTitle>Ref Range</columnTitle>
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<isUnselectable>true</isUnselectable>
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<isHidden>false</isHidden>
55-
<!-- <fk>
56-
<fkDbSchema>study</fkDbSchema>
57-
<fkTable>labRefRange</fkTable>
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<fkColumnName>lsid</fkColumnName>
59-
</fk> -->
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</column>
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<column columnName="abnormal_flags">
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<columnTitle>Abnormal Flags</columnTitle>
@@ -74,29 +69,13 @@
7469
<column columnName="method">
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<nullable>true</nullable>
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<columnTitle>Method</columnTitle>
77-
<!--
78-
<fk>
79-
<fkDbSchema>ehr_lookups</fkDbSchema>
80-
<fkTable>chemistry_method</fkTable>
81-
<fkColumnName>value</fkColumnName>
82-
</fk> -->
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</column>
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8574
<column columnName="parentid">
86-
<!--<fk>-->
87-
<!--<fkDbSchema>study</fkDbSchema>-->
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<!--<fkTable>chemistryRuns</fkTable>-->
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<!--<fkColumnName>objectid</fkColumnName>-->
90-
<!--</fk>-->
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<nullable>true</nullable>
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</column>
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<column columnName="runid">
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<isHidden>true</isHidden>
95-
<fk>
96-
<fkDbSchema>study</fkDbSchema>
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<fkTable>ClinpathRuns</fkTable>
98-
<fkColumnName>objectid</fkColumnName>
99-
</fk>
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</column>
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<column columnName="diCreated">
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<isHidden>true</isHidden>
@@ -124,4 +103,4 @@
124103
</table>
125104
</tables>
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</metadata>
127-
</query>
106+
</query>

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

Lines changed: 3 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -53,11 +53,6 @@
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<columnTitle>Ref Range</columnTitle>
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<isUnselectable>true</isUnselectable>
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<isHidden>false</isHidden>
56-
<!-- <fk>
57-
<fkDbSchema>study</fkDbSchema>
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<fkTable>labRefRange</fkTable>
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<fkColumnName>lsid</fkColumnName>
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</fk> -->
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</column>
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<column columnName="abnormal_flags">
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<columnTitle>Abnormal Flags</columnTitle>
@@ -75,28 +70,17 @@
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<column columnName="method">
7671
<nullable>true</nullable>
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<columnTitle>Method</columnTitle>
78-
<!--
79-
<fk>
80-
<fkDbSchema>ehr_lookups</fkDbSchema>
81-
<fkTable>chemistry_method</fkTable>
82-
<fkColumnName>value</fkColumnName>
83-
</fk> -->
8473
</column>
8574

8675
<column columnName="parentid">
87-
<!--<fk>-->
88-
<!--<fkDbSchema>study</fkDbSchema>-->
89-
<!--<fkTable>chemistryRuns</fkTable>-->
90-
<!--<fkColumnName>objectid</fkColumnName>-->
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<!--</fk>-->
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<nullable>true</nullable>
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</column>
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<column columnName="runid">
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<isHidden>true</isHidden>
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<fk>
9781
<fkDbSchema>study</fkDbSchema>
98-
<fkTable>ClinpathRuns</fkTable>
99-
<fkColumnName>objectid</fkColumnName>
82+
<fkTable>assay_ClinpathRuns</fkTable>
83+
<fkColumnName>sampleid</fkColumnName>
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</fk>
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</column>
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<column columnName="diCreated">
@@ -125,4 +109,4 @@
125109
</table>
126110
</tables>
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</metadata>
128-
</query>
112+
</query>

‎snprc_ehr/resources/queries/study/clinpathRunsAll.sql‎

Lines changed: 38 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,10 +34,12 @@ select
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verifiedDate,
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datefinalized,
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remark,
37-
history
37+
history,
38+
objectid,
39+
lsid
3840
from study.clinpathRuns
3941

40-
union all
42+
union
4143

4244
select
4345
Id,
@@ -60,5 +62,37 @@ select
6062
verifiedDate,
6163
datefinalized,
6264
remark,
63-
history
64-
from study.assay_clinpathRuns
65+
history,
66+
sampleId as objectid,
67+
lsid
68+
from study.assay_clinpathRuns
69+
70+
union
71+
72+
select distinct
73+
tr.Id,
74+
tr.date,
75+
null enddate,
76+
'surveillance' as type,
77+
null as tissue,
78+
null as project,
79+
null as instructions,
80+
ls.serviceName,
81+
null as units,
82+
20000 as serviceId,
83+
null as collectedBy,
84+
null as sampleId,
85+
null as collectionMethod,
86+
null as method,
87+
null as sampleQuantity,
88+
null as quantityUnits,
89+
null as chargetype,
90+
tr.date as verifiedDate,
91+
tr.date as datefinalized,
92+
'From Excel import' as remark,
93+
tr.history as history,
94+
cast(tr.sequencenum as varchar) as objectid,
95+
tr.lsid
96+
from study.TaqmanResults as tr
97+
inner join snprc_ehr.labwork_services as ls on ls.serviceId = 20000
98+

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

Lines changed: 3 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
<query xmlns="http://labkey.org/data/xml/query">
22
<metadata>
33
<tables xmlns="http://labkey.org/data/xml">
4-
<table tableName="labworkResults" tableDbType="TABLE" useColumnOrder="true">
5-
<tableTitle>SNPRC Labwork Results</tableTitle>
4+
<table tableName="labworkResultsAll" tableDbType="NOT_IN_DB">
5+
<tableTitle>Consolidated Labwork Results</tableTitle>
66
<tableUrl/>
77
<insertUrl/>
88
<importUrl/>
@@ -54,11 +54,6 @@
5454
<columnTitle>Ref Range</columnTitle>
5555
<isUnselectable>true</isUnselectable>
5656
<isHidden>false</isHidden>
57-
<!-- <fk>
58-
<fkDbSchema>study</fkDbSchema>
59-
<fkTable>labRefRange</fkTable>
60-
<fkColumnName>lsid</fkColumnName>
61-
</fk> -->
6257
</column>
6358
<column columnName="abnormal_flags">
6459
<columnTitle>Abnormal Flags</columnTitle>
@@ -76,12 +71,6 @@
7671
<column columnName="method">
7772
<nullable>true</nullable>
7873
<columnTitle>Method</columnTitle>
79-
<!--
80-
<fk>
81-
<fkDbSchema>ehr_lookups</fkDbSchema>
82-
<fkTable>chemistry_method</fkTable>
83-
<fkColumnName>value</fkColumnName>
84-
</fk> -->
8574
</column>
8675
<column columnName="Id">
8776
<fk>
@@ -92,7 +81,6 @@
9281
</fk>
9382
</column>
9483
<column columnName="runid">
95-
<isHidden>true</isHidden>
9684
<fk>
9785
<fkDbSchema>study</fkDbSchema>
9886
<fkTable>ClinpathRuns</fkTable>
@@ -125,4 +113,4 @@
125113
</table>
126114
</tables>
127115
</metadata>
128-
</query>
116+
</query>

‎snprc_ehr/resources/queries/study/labworkResultsAll.sql‎

Lines changed: 29 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -39,10 +39,11 @@ select
3939
enddate,
4040
method,
4141
remark,
42-
history
42+
history,
43+
lsid
4344
from study.labworkResults
4445

45-
union all
46+
union
4647

4748
select
4849
Id,
@@ -62,5 +63,30 @@ select
6263
enddate,
6364
method,
6465
remark,
65-
history
66+
history,
67+
lsid
6668
from study.assay_labworkResults
69+
70+
union
71+
72+
select
73+
Id,
74+
date,
75+
project,
76+
serviceId,
77+
serviceTestId,
78+
testid,
79+
resultOORIndicator,
80+
value_type,
81+
result,
82+
units,
83+
qualresult,
84+
refRange,
85+
abnormal_flags,
86+
runid,
87+
enddate,
88+
method,
89+
remark,
90+
history,
91+
lsid
92+
from study.labworkTaqman

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

Lines changed: 17 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,21 @@
11
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
22
<columns>
3+
<column name="Id"/>
4+
<column name="Id/Demographics/species/arc_species_code">
5+
<properties>
6+
<property name="columnTitle" value="Species"/>
7+
</properties>
8+
</column>
9+
<column name="serviceTestId/serviceId/ServiceName">
10+
<properties>
11+
<property name="columnTitle" value="Service Name"/>
12+
</properties>
13+
</column>
14+
<column name="serviceTestId/serviceId/Dataset">
15+
<properties>
16+
<property name="columnTitle" value="Service Type"/>
17+
</properties>
18+
</column>
319
<column name="date"/>
420
<column name="testid"/>
521
<column name="value_type"/>
@@ -9,15 +25,12 @@
925
<column name="refRange"/>
1026
<column name="abnormal_flags"/>
1127
<column name="remark"/>
12-
<column name="runid"/>
13-
<column name="Id"/>
1428
<column name="resultNumber"/>
1529
<column name="resultInRange"/>
1630
<column name="qualresult"/>
1731
<column name="history"/>
18-
<!--<column name="taskid"/>-->
1932
</columns>
2033
<sorts>
2134
<sort column="Date" descending="true" />
2235
</sorts>
23-
</customView>
36+
</customView>

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