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Merge pull request #179 from LabKey/fb_merge_23.7_to_develop
Merge discvr-23.7 to develop
2 parents 5a27066 + 6623f74 commit 3dfea00

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‎IDR/build.gradle‎

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@@ -6,7 +6,6 @@ plugins {
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dependencies
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{
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implementation "com.sun.mail:jakarta.mail:${javaMailVersion}"
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implementation project(path: ':server:modules:LabDevKitModules:LDK')
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "apiJarFile")
@@ -16,4 +15,6 @@ dependencies
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: 'published', depExtension: 'module')
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premium", depProjectConfig: 'published', depExtension: 'module')
1817
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: 'published', depExtension: 'module')
18+
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "published", depExtension: "module")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
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}

‎IDR/src/org/labkey/idr/IDRController.java‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,24 @@
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package org.labkey.idr;
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import org.jetbrains.annotations.NotNull;
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import org.labkey.api.action.ConfirmAction;
35
import org.labkey.api.action.SpringActionController;
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import org.labkey.api.ehr.EHRService;
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import org.labkey.api.module.Module;
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import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.module.ModuleProperty;
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import org.labkey.api.pipeline.PipelineUrls;
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import org.labkey.api.security.RequiresPermission;
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import org.labkey.api.security.permissions.AdminPermission;
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import org.labkey.api.studies.StudiesService;
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import org.labkey.api.util.HtmlString;
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.api.util.Path;
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import org.labkey.api.util.URLHelper;
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import org.labkey.api.view.HtmlView;
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import org.springframework.validation.BindException;
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import org.springframework.validation.Errors;
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import org.springframework.web.servlet.ModelAndView;
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public class IDRController extends SpringActionController
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{
@@ -12,4 +30,43 @@ public IDRController()
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setActionResolver(_actionResolver);
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}
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@RequiresPermission(AdminPermission.class)
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public static class ImportStudyAction extends ConfirmAction<Object>
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{
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@Override
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public ModelAndView getConfirmView(Object o, BindException errors) throws Exception
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{
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setTitle("Import mGAP Study");
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return new HtmlView(HtmlString.unsafe("This will import the default IDR study in this folder and set the EHRStudyContainer property to point to this container. Do you want to continue?"));
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}
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@Override
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public boolean handlePost(Object o, BindException errors) throws Exception
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{
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Module ehr = ModuleLoader.getInstance().getModule("ehr");
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ModuleProperty mp = ehr.getModuleProperties().get("EHRStudyContainer");
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mp.saveValue(getUser(), getContainer(), getContainer().getPath());
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StudiesService.get().importFolderDefinition(getContainer(), getUser(), ModuleLoader.getInstance().getModule(IDRModule.NAME), new Path("referenceStudy"));
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EHRService.get().ensureStudyQCStates(getContainer(), getUser(), true);
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return true;
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}
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@Override
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public void validateCommand(Object o, Errors errors)
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{
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}
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@NotNull
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@Override
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public URLHelper getSuccessURL(Object o)
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{
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return PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
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}
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}
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}

‎PMR/build.gradle‎

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import org.labkey.gradle.util.BuildUtils
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plugins {
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id 'org.labkey.build.module'
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}
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dependencies {
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "published", depExtension: "module")
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "published", depExtension: "module")
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "published", depExtension: "module")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "apiJarFile")
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}

‎PMR/module.properties‎

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ModuleClass: org.labkey.pmr.PMRModule
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Label: PMR
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Description: This is the ONPRC Precision Medicine Resource (PMR) module
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License: Apache 2.0
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LicenseURL: http://www.apache.org/licenses/LICENSE-2.0

‎PMR/resources/etls/pmrClinicalData.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<etl xmlns="http://labkey.org/etl/xml">
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<name>PMR_ClinicalData</name>
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<description>PMR/EHR Clinical Data</description>
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<transforms>
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<transform id="dataset1" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="chemistryResults" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>testId</column>
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<column>result</column>
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<column>units</column>
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<column>runid</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="chemistryResults" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset2" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="demographics" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>gender</column>
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<column>species</column>
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<column>geographic_origin</column>
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<column>birth</column>
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<column>death</column>
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<column>status</column>
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<column>calculated_status</column>
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<column>QCState</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="demographics" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset3" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="microbiology" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>tissue</column>
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<column>organism</column>
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<column>quantity</column>
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<column>runid</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="microbiology" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset4" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="weight" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>weight</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="weight" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset5" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="clinpathRuns" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>type</column>
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<column>tissue</column>
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<column>units</column>
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<column>servicerequested</column>
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<column>collectionMethod</column>
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<column>method</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="clinpathRuns" bulkLoad="true" targetOption="merge">
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</destination>
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</transform>
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<transform id="dataset6" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="hematologyResults" remoteSource="EHR_ClinicalSource" timestampColumnName="modified">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>testid</column>
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<column>result</column>
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<column>units</column>
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<column>runid</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="hematologyResults" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset7" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="pathologyDiagnoses" remoteSource="EHR_ClinicalSource" timestampColumnName="modified" sourceTimeout="0">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>sort_order</column>
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<column>codes</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="pathologyDiagnoses" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset8" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="histology" remoteSource="EHR_ClinicalSource" timestampColumnName="modified" sourceTimeout="0">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>sort_order</column>
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<column>tissue</column>
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<column>codes</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="histology" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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<transform id="dataset9" type="RemoteQueryTransformStep">
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<source schemaName="study" queryName="parentage" remoteSource="EHR_ClinicalSource" timestampColumnName="modified" sourceTimeout="0">
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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>parent</column>
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<column>relationship</column>
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<column>method</column>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="parentage" targetOption="merge" bulkLoad="true" batchSize="2500">
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</destination>
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</transform>
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</transforms>
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<incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" pkColumnName="objectid">
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<!--TODO-->
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<deletedRowsSource remoteSource="PRIMESEQ_MHC" schemaName="pmr" queryName="study_delete_source" deletedSourceKeyColumnName="objectid" targetKeyColumnName="objectid" />
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</incrementalFilter>
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<schedule>
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<cron expression="0 30 1 * * ?"/>
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</schedule>
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</etl>

‎PMR/resources/folderTypes/PMR.folderType.xml‎

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<folderType xmlns="http://labkey.org/data/xml/folderType">
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<name>PMR</name>
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<description>The default folder layout for the PMR</description>
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<folderTabs>
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<folderTab>
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<name>overview</name>
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<caption>Overview</caption>
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<preferredWebParts>
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<webPart>
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<name>PMR Overview</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>animalHistory</name>
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<caption>Animal History</caption>
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<selectors>
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<selector>
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<view>animalHistory</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>PMR Animal History</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>animalSearch</name>
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<caption>Animal Search</caption>
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<selectors>
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<selector>
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<view>animalSearch</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>PMR Animal Search</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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</folderTab>
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<folderTab>
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<name>admin</name>
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<caption>Admin</caption>
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<selectors>
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<selector>
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<view>admin</view>
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</selector>
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</selectors>
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<preferredWebParts>
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<webPart>
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<name>PMR Admin</name>
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<location>body</location>
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</webPart>
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</preferredWebParts>
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<permissions>
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<permission name="org.labkey.api.security.permissions.AdminPermission"/>
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</permissions>
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</folderTab>
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</folderTabs>
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<modules>
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<moduleName>PMR</moduleName>
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<moduleName>EHR</moduleName>
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</modules>
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<defaultModule>PMR</defaultModule>
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</folderType>

‎PMR/resources/referenceStudy/folder.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<folder archiveVersion="22.0" xmlns="http://labkey.org/folder/xml">
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<study dir="study"/>
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</folder>

‎PMR/resources/referenceStudy/study/README‎

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This folder contains the reference study for IDR data. It should be generated by performing
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a folder export from the production server, then copying the datasets_manifest.xml, datasets_metadata.xml,
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PrimateElectronicHealthRecord.dataset and study.xml files. After copying, the following can be used to find/replace
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metadata in datasets_metadata.xml to remove unwanted information:
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Replace the following regex expressions with empty string:
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( )*<inputType>(.*)</inputType>\n
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( )*<isHidden>(.*)</isHidden>\n|( )*<shownIn(.*)View>(.*)</shownIn(.*)View>\n
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( )*<url>(.*)</url>\n|( )*<description>(.*)</description>\n|( )*<facetingBehavior>(.*)</facetingBehavior>\n|( )*<nullable>(.*)</nullable>\n
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( )*<formatString>(.*)</formatString>\n|( )*<columnTitle>(.*)</columnTitle>\n|( )*<fk>(.)*\n( )*<fk(.)*\n( )*<fk(.)*\n( )*<fk(.)*\n( )*</fk>(.)*\n
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( )*<dimension>(.*)</dimension>\n|( )*<measure>(.*)</measure>\n|( )*<isMvEnabled>(.*)</isMvEnabled>\n

‎PMR/resources/referenceStudy/study/datasets/PMR.dataset‎

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# default group can be used to avoid repeating definitions for each dataset
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#
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# action=[REPLACE,APPEND,DELETE] (default:REPLACE)
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# deleteAfterImport=[TRUE|FALSE] (default:FALSE)
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default.action=REPLACE
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default.deleteAfterImport=FALSE
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# map a source tsv column (right side) to a property name or full propertyURI (left)
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# predefined properties: ParticipantId, SiteId, VisitId, Created
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default.property.ParticipantId=ptid
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default.property.Created=dfcreate
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# use to map from filename->datasetid
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# NOTE: if there are NO explicit import definitions, we will try to import all files matching pattern
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# NOTE: if there are ANY explicit mapping, we will only import listed datasets
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default.filePattern=dataset(\\d*).tsv
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default.importAllMatches=TRUE

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