Merge discvr-25.3 to develop

IDR/resources/queries/bimber_data/idrAnchorDateSource.sql

@@ -0,0 +1,21 @@
+SELECT
+
+Rh as subjectId,
+PID0 as date,
+'SIV Infection' as eventLabel,
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.subjects
+WHERE PID0 IS NOT NULL
+
+UNION ALL
+
+SELECT
+
+Rh as subjectId,
+D0 as date,
+'Vaccination Start' as eventLabel,
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.subjects
+WHERE D0 IS NOT NULL

IDR/resources/queries/bimber_data/idrOutcomeSource.sql

@@ -0,0 +1,14 @@
+SELECT
+
+Rh as Id,
+cohortStart as date,
+
+CASE
+    WHEN contprog = 'C' THEN 'Controller'
+    WHEN contprog = 'P' THEN 'Progressor'
+END as outcome,
+
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.subjects
+WHERE contprog IS NOT NULL AND contprog != ''

IDR/resources/queries/bimber_data/idrPvlSource.sql

@@ -0,0 +1,13 @@
+SELECT
+i_rh as Id,
+d_PVLDate as date,
+c_PVL as result,
+
+'Copies/mL' as units,
+'Plasma' as sampleType,
+'SIVmac239' as assayType,
+'SIV' as target,
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.pvl
+WHERE c_PVL != 'missing from box'

IDR/resources/queries/bimber_data/idrSampleSource.sql

@@ -0,0 +1,27 @@
+SELECT
+
+MonkeyId as Id,
+ID as sampleid,
+SampleDate as date,
+Tissue as sampleType,
+CellCnt as quantity,
+
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.ln_loc
+WHERE SampleDate IS NOT NULL
+
+UNION ALL
+
+SELECT
+
+Rh as Id,
+ID as sampleid,
+SampleDate as date,
+Tissue as sampleType,
+null as quantity,
+
+'Hansen/IDR' as dataSource
+
+FROM bimber_data.ult_loc
+WHERE SampleDate IS NOT NULL

SivStudies/resources/data/gender_codes.tsv

@@ -1,4 +1,4 @@
-v	meaning	origgender
+value	meaning	origgender
 f	Female	f
 m	Male	m
 u	Unknown

SivStudies/resources/data/labwork_types.tsv

@@ -0,0 +1,61 @@
+value	title	units	sort_order	category
+GLUC	Glucose	mg/dL	1	Chemistry
+BUN	Blood urea nitrogen	mg/dL	2	Chemistry
+CREAT	Creatinine	mg/dL	3	Chemistry
+CPK	Creatine phosphokinase	U/L	4	Chemistry
+CHOL	Cholesterol	mg/dl	5	Chemistry
+TRIG	Triglyceride	mg/dL	6	Chemistry
+SGOT	Serum glutamic oxaloacetic transaminase	IU/L	7	Chemistry
+LDL	Low-Density Lipoprotein	mg/dL	8	Chemistry
+LDH	Lactate dehydrogenase	IU/L	9	Chemistry
+TB	Total Bilirubin	mg/dL	10	Chemistry
+GGT	Gamma-glutamyltransferase	IU/L	11	Chemistry
+SGPT	Serum glutamic pyruvic transaminase	IU/L	12	Chemistry
+TP	Total Protein	g/dL	13	Chemistry
+ALB	Albumin	g/dL	14	Chemistry
+ALKP	Alkaline Phosphatase	IU/L	15	Chemistry
+CA	Calcium	mg/dL	16	Chemistry
+PHOS	Phosphorus	mg/dL	17	Chemistry
+FE	Iron	?g/dL	18	Chemistry
+K	Potassium	mmol/L	20	Chemistry
+UA	Uric Acid	mg/dL	22	Chemistry
+A/P	Albumin/Protein Ratio	ratio	999	Chemistry
+B/C	BUN/Creatinine Ratio	ratio	999	Chemistry
+CL	Chloride	mEq/L	999	Chemistry
+FIBR	Fibrinogen	mg/dL	999	Chemistry
+HDL	High-Density Lipoprotein	mg/dL	999	Chemistry
+WBC	White Blood Cells	10^3/uL	1	Hematology
+NEUT%	Neutrophils	%	2	Hematology
+BAND%	Bands		3	Hematology
+LYMPH%	Lymphocytes	%	4	Hematology
+MONO%	Monocytes	%	5	Hematology
+EOS%	Eosinophils	%	6	Hematology
+BASO%	Basophils	%	7	Hematology
+HCT	Hematocrit	%	8	Hematology
+HGB	Hemoglobin		9	Hematology
+RBC	Red Blood Cells	10^6/uL	10	Hematology
+MCV	Mean corpuscular volume	fL	11	Hematology
+MCH	Mean corpuscular hemoglobin	picograms	12	Hematology
+MCHC	Mean corpuscular hemoglobin concentration	g/dL	13	Hematology
+RETIC	Reticulocytes	%	14	Hematology
+PLT	Platelets	10^3/uL	15	Hematology
+MYELO	Myelocytes	%	999	Hematology
+MPV	Mean platelet volume	fl	999	Hematology
+Anisocytosis	Anisocytosis		999	Hematology
+GLOB	Globulin	g/dL	999	Hematology
+Hypochromic RBC	Hypochromic RBC		999	Hematology
+LUC	Large unstained cells		999	Hematology
+Macrocytic RBC	Macrocytic RBC		999	Hematology
+METAMYELO	Metamyelocytes	%	999	Hematology
+Microcytic RBC	Microcytic RBC		999	Hematology
+NRBC	Nucleated red blood cells		999	Hematology
+PCV	Packed cell volume	%	999	Hematology
+Polychromasia RBC	Polychromasia RBC		999	Hematology
+MPMN	Neutrophils		999	Hematology
+SEDRate	Sedimentation rate		999	Hematology
+RDW		%	999	Hematology
+NEUT#	Neutrophil #	10^3/uL	16	Hematology
+LYMPH#	Lymphocyte #	10^3/uL	17	Hematology
+MONO#	Monocyte #	10^3/uL	18	Hematology
+EOS#	Eosinophil #	10^3/uL	19	Hematology
+BASO#	Basophil #	10^3/uL	20	Hematology

SivStudies/resources/data/lookup_sets.tsv

@@ -6,4 +6,6 @@ dosage_units	Dosage Units	unit
 gender_codes	Gender Codes
 geographic_origins	Geographic Origins	origin
 routes	Routes	route
-volume_units	Volume Units	unit
+volume_units	Volume Units	unit
+labwork_types	Lab Tests	test    title
+vl_sample_types	Lab Tests	test

SivStudies/resources/data/reports.tsv

@@ -1,12 +1,21 @@
-reportname	category	reporttype	reporttitle	visible	containerpath	schemaname	queryname	viewname	report	datefieldname	todayonly	queryhaslocation	sort_order	QCStateLabelFieldName	description
-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
-assignmentHistory	Assignments and Groups	query	Assignment History	true		study	Assignment			date	false	false		qcstate/publicdata	This report shows all assignments records for the animals
-activeGroups	Assignments and Groups	query	Active Groups	true		study	animal_group_members	Active Members		date	false	false		qcstate/publicdata	This report shows the active assignments for each animal
-groupHistory	Assignments and Groups	query	Group History	true		study	animal_group_members			date	false	false		qcstate/publicdata	This report shows all assignments records for the animals
-microbiology	Lab Results	query	Microbiology	true		study	Microbiology Results			date	false	false		qcstate/publicdata	
-biochemistry	Lab Results	js	Biochemistry	true		study	bloodChemistry			date	false	false			Contains results of chemistry panels.  Can be displayed either by panel, or showing reference ranges
-clinPathRuns	Lab Results	query	Lab Runs	true		study	Clinpath Runs			date	false	false		qcstate/publicdata	Contains all clinpath requests
-iStat	Lab Results	js	iStat	true		study	iStat			date	false	false		qcstate/publicdata	Contains iStat results
-hematology	Lab Results	js	Hematology	true		study	hematology			date	false	false			Contains hematology data showing cell subsets
-parasitology	Lab Results	query	Parasitology	true		study	Parasitology Results			date	false	false		qcstate/publicdata	Contains results of parasitology testing
-urinalysis	Lab Results	js	Urinalysis	true		study	urinalysisResults			date	false	false			Contains urinalysis results
+reporttype	category	schemaname	queryname	viewname	reporttitle	subjectfieldname
+query	General	study	additionalDatatypes		Additional Data	
+query	Clinical	study	weight		Weights	
+query	Clinical	study	treatments		Treatments/Medications	
+query	Clinical	study	chemistryPivot		Blood Chemistry	
+query	Clinical	study	hematologyPivot		CBC/Hematology	
+query	Study Design	study	assignment		Project/Study Assignment	
+query	Research	study	flow		Flow Cytometry	
+query	Research	study	outcomes		Study Outcomes/Phenotypes	
+query	Research	study	genetics		Genetic Data / MHC	
+query	Clinical	study	procedures		Procedures	
+query	Research	study	viralLoads		Viral Loads	
+query	General	study	samples		Samples	
+query	Research	study	immunizations		Immunizations	
+query	General	study	flags		Flags/Misc Information	
+query	General	study	demographics		Demographics	
+query	General	study	demographics	Project Summary	Project Summary	
+query	General	study	demographics	MHC Type	MHC Typing	
+query	General	study	demographics	Expanded	Expanded Information
+query	Study Design	studies	timepointToDate		Timepoints	subjectId
+query	Study Design	studies	subjectAnchorDates		Anchor Dates	subjectId

SivStudies/resources/data/species.tsv

@@ -1,4 +1,4 @@
-common	scientific_name	id_prefix	mhc_prefix	blood_per_kg	max_draw_pct	blood_draw_interval	cites_code	dateDisabled
+common_name	scientific_name	id_prefix	mhc_prefix	blood_per_kg	max_draw_pct	blood_draw_interval	cites_code	dateDisabled
 Baboon				60	0.2	30
 Cotton-top Tamarin	Saguinus oedipus	so	Saoe	60	0.2	30
 Cynomolgus	Macaca fascicularis	cy	Mafa	60	0.2	30

SivStudies/resources/data/vl_sample_types.tsv

@@ -0,0 +1,3 @@
+value
+Plasma
+Cells

SivStudies/resources/etls/idr-data.xml

@@ -0,0 +1,162 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>Hansen/IDR</name>
+    <description>SIV Studies / Hansen/IDR Data</description>
+    <transforms>
+        <transform id="assignment" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="subjects"/>
+                    <setting name="dataSourceSubjectColumn" value="Rh"/>
+                    <setting name="dataSourceColumns" value="Rh,cohortStart,cohortEnd,cohort,RhCode"/>
+                    <setting name="dataSourceColumnMapping" value="Rh=Id,cohortStart=date,cohortEnd=enddate,RhCode=cohortId,cohort=study"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+                    <setting name="dataSourceAdditionalFilters" value="cohortStart~neq=0000-00-00"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="assignment"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="samples" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="idrSampleSource"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,sampleId,sampleType,quantity"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="samples"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="pvl" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="idrPvlSource"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,target,sampleType,units,result"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="viralLoads"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="outcome" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="idrOutcomeSource"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,outcome"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="outcomes"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="immunizations" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="vacc"/>
+                    <setting name="dataSourceSubjectColumn" value="Rh"/>
+                    <setting name="dataSourceColumns" value="Rh,vacc_date,name,route,dose,ag_source"/>
+                    <setting name="dataSourceColumnMapping" value="Rh=Id,vacc_date=date,name=treatment,dose=quantity,ag_source=category"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="immunizations"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="challenge" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="subjects"/>
+                    <setting name="dataSourceSubjectColumn" value="Rh"/>
+                    <setting name="dataSourceColumns" value="Rh,PID0"/>
+                    <setting name="dataSourceColumnMapping" value="Rh=Id,PID0=date"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR;category=SIV Infection;treatment=SIV - Unknown"/>
+                    <setting name="dataSourceAdditionalFilters" value="PID0~isnonblank="/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="treatments"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR;category~eq=SIV Infection"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="anchorDates" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataSourceContainerPath" value="Labs/Bimber"/>
+                    <setting name="dataSourceSchema" value="bimber_data"/>
+                    <setting name="dataSourceQuery" value="idrAnchorDateSource"/>
+                    <setting name="dataSourceSubjectColumn" value="subjectId"/>
+                    <setting name="dataSourceColumns" value="subjectId,date,eventLabel"/>
+                    <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
+
+                    <setting name="targetSchema" value="studies"/>
+                    <setting name="targetQuery" value="subjectAnchorDates"/>
+                    <setting name="targetSubjectColumn" value="subjectId"/>
+                    <setting name="targetAdditionalFilters" value="dataSource~eq=Hansen/IDR;eventLabel~in=SIV Infection;Vaccination Start"/>
+                </settings>
+            </taskref>
+        </transform>
+    </transforms>
+    <schedule>
+        <cron expression="0 30 20 * * ?"/>
+    </schedule>
+</etl>