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Expand ETL/presentation of SIV data
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13 files changed

+384
-9
lines changed

13 files changed

+384
-9
lines changed

‎SivStudies/resources/etls/idr-data.xml‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -100,8 +100,8 @@
100100
<setting name="dataSourceSchema" value="bimber_data"/>
101101
<setting name="dataSourceQuery" value="vacc"/>
102102
<setting name="dataSourceSubjectColumn" value="Rh"/>
103-
<setting name="dataSourceColumns" value="Rh,vacc_date,name,route,dose,ag_source"/>
104-
<setting name="dataSourceColumnMapping" value="Rh=Id,vacc_date=date,name=treatment,dose=quantity,ag_source=category"/>
103+
<setting name="dataSourceColumns" value="Rh,vacc_date,name,route,dose,ag_source,backbone,vc_vector_id,orf"/>
104+
<setting name="dataSourceColumnMapping" value="Rh=Id,vacc_date=date,name=treatment,dose=quantity,ag_source=category,vc_vector_id=vectorId,orf=antigens"/>
105105
<setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
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107107
<setting name="targetSchema" value="study"/>
@@ -155,6 +155,11 @@
155155
</settings>
156156
</taskref>
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</transform>
158+
<transform id="subjects" type="TaskRefTransformStep">
159+
<taskref ref="org.labkey.sivstudies.etl.PerformManualIdrStepsTask">
160+
161+
</taskref>
162+
</transform>
158163
</transforms>
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<schedule>
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<cron expression="0 30 20 * * ?"/>

‎SivStudies/resources/queries/study/demographics/Expanded.qview.xml‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,8 @@
1010
<column name="projects/subgroups"/>
1111
<column name="immunizations/immunizations"/>
1212
<column name="sivART/allInfections"/>
13-
<column name="sivART/allART"/>
13+
<column name="sivART/artInitiationDate"/>
14+
<column name="interventions/interventions"/>
1415
<column name="outcomes/outcomes"/>
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</columns>
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<sorts>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.query.xml‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,13 +10,20 @@
1010
</column>
1111
<column columnName="allInfections">
1212
<columnTitle>SIV Infection</columnTitle>
13+
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=SIV Infection</url>
14+
<urlTarget>_blank</urlTarget>
1315
</column>
1416
<column columnName="allART">
1517
<columnTitle>ART</columnTitle>
18+
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=ART</url>
19+
<urlTarget>_blank</urlTarget>
1620
</column>
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<column columnName="infectionDate">
1822
<columnTitle>Infection Date</columnTitle>
1923
</column>
24+
<column columnName="artInitiationDate">
25+
<columnTitle>ART Initiation (WPI)</columnTitle>
26+
</column>
2027
</columns>
2128
<titleColumn>allInfections</titleColumn>
2229
</table>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.sql‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,9 @@ SELECT
1212
WHEN t.category = 'SIV Infection' THEN t.date
1313
ELSE NULL
1414
END) as infectionDate,
15-
15+
min(CASE
16+
WHEN t.category = 'ART' THEN t.timePostSivChallenge.daysPostInfection
17+
ELSE NULL
18+
END) as artInitiationDate
1619
FROM study.treatments t
1720
GROUP BY t.Id

‎SivStudies/resources/queries/study/demographicsImmunizations.query.xml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,13 @@
1010
</column>
1111
<column columnName="immunizations">
1212
<columnTitle>Immunizations</columnTitle>
13+
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=immunizations&amp;query.Id~eq=${Id}</url>
14+
<urlTarget>_blank</urlTarget>
1315
</column>
1416
<column columnName="immunizationTypes">
1517
<columnTitle>Immunization Types</columnTitle>
18+
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=immunizations&amp;query.Id~eq=${Id}</url>
19+
<urlTarget>_blank</urlTarget>
1620
</column>
1721
</columns>
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<titleColumn>immunizations</titleColumn>

‎SivStudies/resources/queries/study/demographicsImmunizations.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
SELECT
22
s.Id,
3-
group_concat(DISTINCT s.treatment, char(10)) as immunizations,
3+
group_concat(DISTINCT COALESCE(s.backbone, s.treatment), char(10)) as immunizations,
44
group_concat(DISTINCT s.category, char(10)) as immunizationTypes,
55

66
FROM study.immunizations s

‎SivStudies/resources/queries/study/demographicsInterventions.query.xml‎

Lines changed: 30 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
1+
<query xmlns="http://labkey.org/data/xml/query">
2+
<metadata>
3+
<tables xmlns="http://labkey.org/data/xml">
4+
<table tableName="" tableDbType="NOT_IN_DB">
5+
<tableTitle>Interventions/Treatments Summary</tableTitle>
6+
<columns>
7+
<column columnName="Id">
8+
<isKeyField>true</isKeyField>
9+
<isHidden>true</isHidden>
10+
</column>
11+
<column columnName="allInterventions">
12+
<columnTitle>Interventions/Treatments</columnTitle>
13+
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=Intervention</url>
14+
<urlTarget>_blank</urlTarget>
15+
</column>
16+
<column columnName="firstInterventionDate">
17+
<columnTitle>Date of First Intervention</columnTitle>
18+
</column>
19+
<column columnName="firstInterventionDPI">
20+
<columnTitle>First Intervention (DPI)</columnTitle>
21+
</column>
22+
<column columnName="firstInterventionWPI">
23+
<columnTitle>First Intervention (WPI)</columnTitle>
24+
</column>
25+
</columns>
26+
<titleColumn>allInterventions</titleColumn>
27+
</table>
28+
</tables>
29+
</metadata>
30+
</query>

‎SivStudies/resources/queries/study/demographicsInterventions.sql‎

Lines changed: 20 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
1+
SELECT
2+
t.Id,
3+
group_concat(DISTINCT CASE
4+
WHEN t.category = 'Intervention' THEN (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')')
5+
ELSE NULL
6+
END, char(10)) as allInterventions,
7+
min(CASE
8+
WHEN t.category = 'Intervention' THEN t.date
9+
ELSE NULL
10+
END) as firstInterventionDate,
11+
min(CASE
12+
WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.daysPostInfection
13+
ELSE NULL
14+
END) as firstInterventionDPI,
15+
min(CASE
16+
WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.weeksPostInfection
17+
ELSE NULL
18+
END) as firstInterventionWPI
19+
FROM study.treatments t
20+
GROUP BY t.Id

‎SivStudies/resources/queries/study/immunizations.query.xml‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,12 @@
1515
<column columnName="treatment">
1616
<columnTitle>Treatment</columnTitle>
1717
</column>
18+
<column columnName="backbone">
19+
<columnTitle>Vector Backbone</columnTitle>
20+
</column>
21+
<column columnName="antigens">
22+
<columnTitle>Antigens</columnTitle>
23+
</column>
1824
<column columnName="route">
1925
<columnTitle>Route</columnTitle>
2026
</column>
@@ -27,6 +33,12 @@
2733
<column columnName="reason">
2834
<columnTitle>Reason</columnTitle>
2935
</column>
36+
<column columnName="vectorId">
37+
<columnTitle>Vector ID</columnTitle>
38+
</column>
39+
<column columnName="isMock">
40+
<columnTitle>Is Mock?</columnTitle>
41+
</column>
3042
<column columnName="comments">
3143
<columnTitle>Comments</columnTitle>
3244
<inputType>textarea</inputType>

‎SivStudies/resources/queries/study/immunizations/.qview.xml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,10 @@
77
<column name="route"/>
88
<column name="quantity"/>
99
<column name="quantity_units"/>
10+
<column name="backbone"/>
11+
<column name="antigens"/>
12+
<column name="vectorId"/>
13+
<column name="isMock"/>
1014
<column name="comments"/>
1115
<column name="dataSource"/>
1216
</columns>

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