Merge discvr-25.3 to develop

PMR/resources/etls/pmr-datasets.xml

@@ -189,8 +189,7 @@
     </transforms>
 
 <!--    <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" >-->
-<!--        &lt;!&ndash; TODO: enable once PRIMe deploys 23.7 &ndash;&gt;-->
-<!--        &lt;!&ndash;<deletedRowsSource remoteSource="EHR_ClinicalSource" schemaName="AuditSummary" queryName="DatasetUpdateAuditLog" deletedSourceKeyColumnName="primaryKey" targetKeyColumnName="objectid"/>&ndash;&gt;-->
+<!--        <deletedRowsSource remoteSource="EHR_ClinicalSource" schemaName="AuditSummary" queryName="DatasetUpdateAuditLog" deletedSourceKeyColumnName="primaryKey" targetKeyColumnName="objectid"/>-->
 <!--    </incrementalFilter>-->
     <schedule>
         <!--11PM-->

SivStudies/build.gradle

@@ -0,0 +1,20 @@
+import org.labkey.gradle.util.BuildUtils
+
+plugins {
+    id 'org.labkey.build.module'
+}
+
+dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "published", depExtension: "module")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "apiJarFile")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
+}

SivStudies/module.properties

@@ -0,0 +1,7 @@
+ModuleClass: org.labkey.sivstudies.SivStudiesModule
+Label: SIV Studies
+Description: A module designed to manage data from SIV and related studies.
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ManageVersion: false
+SupportedDatabases: mssql, pgsql

SivStudies/resources/data/amount_units.tsv

@@ -0,0 +1,11 @@
+value
+g
+IU
+U
+mEq
+mg
+no units
+ug
+units
+L/min
+%

SivStudies/resources/data/calculated_status_codes.tsv

@@ -0,0 +1,6 @@
+value
+Alive
+Dead
+No Record
+Shipped
+Unknown

SivStudies/resources/data/conc_units.tsv

@@ -0,0 +1,12 @@
+value	denominator	numerator
+g/ml	mL	g
+g/tsp	tsp	g
+IU/ml	mL	IU
+mEq/ml	mL	mEq
+mg/capsule	capsule(s)	mg
+mg/ml	mL	mg
+mg/piece	piece(s)	mg
+mg/tablet	tablet(s)	mg
+mg/tsp	tsp	mg
+ug/ml	mL	ug
+units/ml	mL	units

SivStudies/resources/data/dosage_units.tsv

@@ -0,0 +1,11 @@
+value	numerator	denominator
+g/kg	g	kg
+IU/kg	IU	kg
+mEq/kg	mEq	kg
+mg/animal	mg	
+mg/kg	mg	kg
+ml/kg	ml	kg
+no units		
+ounces/kg	ounces	kg
+ug/kg	ug	kg
+units/kg	units	kg

SivStudies/resources/data/gender_codes.tsv

@@ -0,0 +1,4 @@
+v	meaning	origgender
+f	Female	f
+m	Male	m
+u	Unknown

SivStudies/resources/data/geographic_origins.tsv

@@ -0,0 +1,4 @@
+value
+Indian
+Chinese
+Hybrid

SivStudies/resources/data/lookup_sets.tsv

@@ -0,0 +1,9 @@
+setname	label	keyfield	titleColumn
+amount_units	Amount Units	unit
+calculated_status_codes	Calculated Status Codes	code
+conc_units 	Concentraiton Units	unit
+dosage_units	Dosage Units	unit
+gender_codes	Gender Codes
+geographic_origins	Geographic Origins	origin
+routes	Routes	route
+volume_units	Volume Units	unit

SivStudies/resources/data/reports.tsv

@@ -0,0 +1,12 @@
+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

SivStudies/resources/data/routes.tsv

@@ -0,0 +1,24 @@
+value	title
+IM	
+intracardiac	
+intracarotid	
+intracorneal	Intracorneal
+intracranial	
+IP	intraperitoneal
+ID	
+INH	
+IT	
+IV	
+CRI	
+IVAG	
+oral	
+PO	
+rectal	
+Spillage	
+SQ	
+OU	
+OD	
+OS	
+topical	
+topical (eye)	
+topical (skin)	

SivStudies/resources/data/species.tsv

@@ -0,0 +1,10 @@
+common	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
+Marmoset	Callithrix jacchus	cj	Caja	60	0.15	30
+Pigtail	Macaca Nemestrina		Mane	60	0.2	30
+Rhesus	Macaca mulatta	r|rh	Mamu	60	0.2	30
+Sooty Mangabey	Cercocebus atys		Ceat	60	0.2	30
+Stump Tailed	Macaca Arctoides		Maar	60	0.2	30
+Vervet	Chlorocebus sabaeus	ag	Chsa	60	0.2	30

SivStudies/resources/data/volume_units.tsv

@@ -0,0 +1,13 @@
+value
+capsule(s)
+cup
+drop(s)
+cube
+mL
+mL/hr
+no units
+ounce(s)
+pan
+piece(s)
+tablet(s)
+tsp

SivStudies/resources/etls/siv-studies.xml

@@ -0,0 +1,143 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>SIV_PRIMe</name>
+    <description>SIV Studies / PRIMe Data</description>
+    <transforms>
+        <transform id="demographics" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.SubjectScopedSelect">
+                <settings>
+                    <setting name="mode" value="UPDATE_ONLY"/>
+
+                    <setting name="subjectSourceSchema" value="study"/>
+                    <setting name="subjectSourceQuery" value="demographics"/>
+                    <setting name="subjectSourceColumn" value="Id"/>
+
+                    <setting name="dataRemoteSource" value="PRIMe"/>
+                    <setting name="dataSourceSchema" value="study"/>
+                    <setting name="dataSourceQuery" value="demographics"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,gender,geographic_origin,species,Id/parents/dam,Id/parents/sire,birth,death,calculated_status,objectid"/>
+                    <setting name="dataSourceColumnMapping" value="gender=sex,Id/Parents/dam=mother,Id/Parents/sire=father"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="demographics"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="weight" 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="dataRemoteSource" value="PRIMe"/>
+                    <setting name="dataSourceSchema" value="study"/>
+                    <setting name="dataSourceQuery" value="weight"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,weight,objectid"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="weight"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                </settings>
+            </taskref>
+        </transform>
+
+        <transform id="mhc" 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="Internal/MHC_Typing"/>
+                    <setting name="dataSourceSchema" value="geneticscore"/>
+                    <setting name="dataSourceQuery" value="mhc_data"/>
+                    <setting name="dataSourceSubjectColumn" value="subjectid"/>
+                    <setting name="dataSourceColumns" value="subjectid,created,assaytype,marker,result,score"/>
+                    <setting name="dataSourceColumnMapping" value="subjectId=Id,created=date"/>
+                    <setting name="dataSourceColumnDefaults" value="category=MHC Typing"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="genetics"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                </settings>
+            </taskref>
+        </transform>
+
+        <transform id="cbc" 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="dataRemoteSource" value="PRIMe"/>
+                    <setting name="dataSourceSchema" value="study"/>
+                    <setting name="dataSourceQuery" value="hematologyResults"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,testid,result,units,qualresult,objectid"/>
+                    <setting name="dataSourceColumnMapping" value="testid=test"/>
+                    <setting name="dataSourceAdditionalFilters" value="qcstate/publicdata~eq=true"/>
+                    <setting name="dataSourceColumnDefaults" value="category=CBC"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="labwork"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="category~eq=CBC"/>
+                </settings>
+            </taskref>
+        </transform>
+
+        <transform id="chem" 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="dataRemoteSource" value="PRIMe"/>
+                    <setting name="dataSourceSchema" value="study"/>
+                    <setting name="dataSourceQuery" value="chemistryResults"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,testid,result,units,qualresult,objectid"/>
+                    <setting name="dataSourceColumnMapping" value="testid=test"/>
+                    <setting name="dataSourceAdditionalFilters" value="qcstate/publicdata~eq=true"/>
+                    <setting name="dataSourceColumnDefaults" value="category=Chemistry"/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="labwork"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                    <setting name="targetAdditionalFilters" value="category~eq=Chemistry"/>
+                </settings>
+            </taskref>
+        </transform>
+
+        <transform id="procedures" 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="dataRemoteSource" value="PRIMe"/>
+                    <setting name="dataSourceSchema" value="study"/>
+                    <setting name="dataSourceQuery" value="encounters"/>
+                    <setting name="dataSourceSubjectColumn" value="Id"/>
+                    <setting name="dataSourceColumns" value="Id,date,type,procedureid/name,objectid"/>
+                    <setting name="dataSourceColumnMapping" value="procedureid/name=procedure,type=category"/>
+                    <setting name="dataSourceAdditionalFilters" value="qcstate/publicdata~eq=true;procedureid/name~isnonblank="/>
+
+                    <setting name="targetSchema" value="study"/>
+                    <setting name="targetQuery" value="procedures"/>
+                    <setting name="targetSubjectColumn" value="Id"/>
+                </settings>
+            </taskref>
+        </transform>
+    </transforms>
+    <schedule>
+        <cron expression="0 30 20 * * ?"/>
+    </schedule>
+</etl>

SivStudies/resources/folderTypes/SIV Studies.folderType.xml

@@ -0,0 +1,78 @@
+<ft:folderType xmlns:ft="http://labkey.org/data/xml/folderType">
+    <ft:name>SIV Studies Overview</ft:name>
+    <ft:description>The default folder layout for Studies</ft:description>
+    <ft:folderTabs>
+<!--        <ft:folderTab>-->
+<!--            <ft:name>overview</ft:name>-->
+<!--            <ft:caption>Overview</ft:caption>-->
+<!--            <ft:selectors>-->
+<!--            </ft:selectors>-->
+<!--            <ft:requiredWebParts>-->
+<!--            </ft:requiredWebParts>-->
+<!--            <ft:preferredWebParts>-->
+<!--                <ft:webPart>-->
+<!--                    <ft:name>Data and Analyses</ft:name>-->
+<!--                    <ft:location>body</ft:location>-->
+<!--                </ft:webPart>-->
+<!--            </ft:preferredWebParts>-->
+<!--        </ft:folderTab>-->
+        <ft:folderTab>
+            <ft:name>datasets</ft:name>
+            <ft:caption>Datasets</ft:caption>
+            <ft:selectors>
+                <ft:selector>
+                    <ft:view>datasets</ft:view>
+                </ft:selector>
+            </ft:selectors>
+            <ft:requiredWebParts>
+            </ft:requiredWebParts>
+            <ft:preferredWebParts>
+                <ft:webPart>
+                    <ft:name>Datasets</ft:name>
+                    <ft:location>body</ft:location>
+                </ft:webPart>
+            </ft:preferredWebParts>
+        </ft:folderTab>
+<!--        <ft:folderTab>-->
+<!--            <ft:name>analyses</ft:name>-->
+<!--            <ft:caption>Analyses</ft:caption>-->
+<!--            <ft:selectors>-->
+<!--                <ft:selector>-->
+<!--                    <ft:view>analyses</ft:view>-->
+<!--                </ft:selector>-->
+<!--            </ft:selectors>-->
+<!--            <ft:requiredWebParts>-->
+<!--            </ft:requiredWebParts>-->
+<!--            <ft:preferredWebParts>-->
+<!--                <ft:webPart>-->
+<!--                    <ft:name>Analyses</ft:name>-->
+<!--                    <ft:location>body</ft:location>-->
+<!--                </ft:webPart>-->
+<!--            </ft:preferredWebParts>-->
+<!--        </ft:folderTab>-->
+        <ft:folderTab>
+            <ft:name>admin</ft:name>
+            <ft:caption>Admin</ft:caption>
+            <ft:selectors>
+
+            </ft:selectors>
+            <ft:requiredWebParts>
+
+            </ft:requiredWebParts>
+            <ft:preferredWebParts>
+                <ft:webPart>
+                    <ft:name>SIV Studies Admin</ft:name>
+                    <ft:location>body</ft:location>
+                </ft:webPart>
+            </ft:preferredWebParts>
+            <ft:permissions>
+                <ft:permission name="org.labkey.api.security.permissions.AdminPermission"/>
+            </ft:permissions>
+        </ft:folderTab>
+    </ft:folderTabs>
+    <ft:modules>
+        <ft:moduleName>studies</ft:moduleName>
+    </ft:modules>
+    <ft:defaultModule>studies</ft:defaultModule>
+    <ft:forceAssayUploadIntoWorkbooks>true</ft:forceAssayUploadIntoWorkbooks>
+</ft:folderType>