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bbimberbbimber
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Merge discvr-25.7 to develop
2 parents 23be554 + 9d2203c commit 4efe165

24 files changed

+615
-83
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 @@
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<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"/>
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<setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
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107107
<setting name="targetSchema" value="study"/>
@@ -155,6 +155,11 @@
155155
</settings>
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</taskref>
157157
</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: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,11 +6,14 @@
66
<column name="calculated_status"/>
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<column name="birth"/>
88
<column name="death"/>
9+
<column name="sivART/ageAtInfection"/>
910
<column name="projects/allStudies"/>
11+
<column name="projects/studyDescription"/>
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<column name="projects/subgroups"/>
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<column name="immunizations/immunizations"/>
1214
<column name="sivART/allInfections"/>
13-
<column name="sivART/allART"/>
15+
<column name="sivART/artInitiationDPI"/>
16+
<column name="interventions/allInterventions"/>
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<column name="outcomes/outcomes"/>
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</columns>
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<sorts>

‎SivStudies/resources/queries/study/demographics/Project Summary.qview.xml‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,8 +9,6 @@
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<column name="death"/>
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<column name="projects/allStudies"/>
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<column name="projects/categories"/>
12-
<column name="projects/rhCmvVaccines"/>
13-
<column name="projects/sivArt"/>
1412
</columns>
1513
<sorts>
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<sort column="Id" descending="false"/>

‎SivStudies/resources/queries/study/demographics/SIV and ART Info.qview.xml‎

Lines changed: 22 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,22 @@
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
2+
<columns>
3+
<column name="Id"/>
4+
<column name="sex"/>
5+
<column name="species"/>
6+
<column name="calculated_status"/>
7+
<column name="projects/categories"/>
8+
<column name="projects/allStudies"/>
9+
<column name="projects/subgroups"/>
10+
<column name="sivART/allInfections"/>
11+
<column name="sivART/artInitiationDate"/>
12+
<column name="sivART/artReleaseDate"/>
13+
<column name="sivART/artInitiationDPI"/>
14+
<column name="sivART/artReleaseWPI"/>
15+
<column name="pvlInfo/numPVL"/>
16+
<column name="pvlInfo/numPVLPostArtRelease"/>
17+
<column name="pvlInfo/lastPvlPostArtReleaseWeeks"/>
18+
</columns>
19+
<sorts>
20+
<sort column="Id" descending="false"/>
21+
</sorts>
22+
</customView>

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

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,12 +10,31 @@
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>
1721
<column columnName="infectionDate">
1822
<columnTitle>Infection Date</columnTitle>
23+
<formatString>Date</formatString>
24+
</column>
25+
<column columnName="artInitiationDate">
26+
<columnTitle>ART Initiation</columnTitle>
27+
<formatString>Date</formatString>
28+
</column>
29+
<column columnName="artInitiationDPI">
30+
<columnTitle>ART Initiation (DPI)</columnTitle>
31+
</column>
32+
<column columnName="artReleaseDate">
33+
<columnTitle>ART Release</columnTitle>
34+
<formatString>Date</formatString>
35+
</column>
36+
<column columnName="artReleaseWPI">
37+
<columnTitle>ART Release (WPI)</columnTitle>
1938
</column>
2039
</columns>
2140
<titleColumn>allInfections</titleColumn>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.sql‎

Lines changed: 33 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,35 @@
11
SELECT
2-
t.Id,
3-
group_concat(DISTINCT CASE
4-
WHEN t.category = 'SIV Infection' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
5-
ELSE NULL
6-
END, char(10)) as allInfections,
7-
group_concat(DISTINCT CASE
8-
WHEN t.category = 'ART' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
9-
ELSE NULL
10-
END, char(10)) as allART,
11-
min(CASE
12-
WHEN t.category = 'SIV Infection' THEN t.date
13-
ELSE NULL
14-
END) as infectionDate,
2+
t.*,
3+
TIMESTAMPDIFF('SQL_TSI_WEEK', t.infectionDate, t.artReleaseDate) as artReleaseWPI
4+
FROM (
5+
SELECT
6+
t.Id,
7+
group_concat(DISTINCT CASE
8+
WHEN t.category = 'SIV Infection' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
9+
ELSE NULL
10+
END, char(10)) as allInfections,
11+
min(floor(age(t.DataSets.Demographics.birth, CASE WHEN t.category = 'SIV Infection' THEN t.date ELSE NULL END))) AS ageAtInfection,
1512

16-
FROM study.treatments t
17-
GROUP BY t.Id
13+
group_concat(DISTINCT CASE
14+
WHEN t.category = 'ART' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
15+
ELSE NULL
16+
END, char(10)) as allART,
17+
min(CASE
18+
WHEN t.category = 'SIV Infection' THEN t.date
19+
ELSE NULL
20+
END) as infectionDate,
21+
min(CASE
22+
WHEN t.category = 'ART' THEN t.date
23+
ELSE NULL
24+
END) as artInitiationDate,
25+
min(CASE
26+
WHEN t.category = 'ART' THEN t.timePostSivChallenge.daysPostInfection
27+
ELSE NULL
28+
END) as artInitiationDPI,
29+
min(CASE
30+
WHEN t.category = 'ART' THEN t.artInformation.artRelease
31+
ELSE NULL
32+
END) as artReleaseDate
33+
FROM study.treatments t
34+
GROUP BY t.Id
35+
) t

‎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>
1822
<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

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
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<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

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