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Refactor kinship to allow other code to initiate import directly (#933)
* Add action to allow external server to trigger re-import of externally computed kinship data
1 parent 64616f9 commit 134a14e

7 files changed

Lines changed: 158 additions & 2 deletions

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‎GeneticsCore/build.gradle‎

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@@ -6,6 +6,8 @@ plugins {
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dependencies {
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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")
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: 'published', depExtension: 'module')
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: 'published', depExtension: 'module')
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "apiJarFile")

‎GeneticsCore/resources/etls/KinshipDataImport.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>KinshipDataImport</name>
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<description>Import PRIMe-seq Kinship Data</description>
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<transforms>
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<transform id="kinship" type="TaskRefTransformStep">
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<taskref ref="org.labkey.GeneticsCore.etl.ImportGeneticsCalculationsStep">
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<settings>
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</settings>
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</taskref>
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</transform>
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</transforms>
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</etl>

‎GeneticsCore/resources/module.xml‎

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</editPermissions>
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<description>This is the containerPath to the folder holding the primary data for Parentage. Use of slashes is very important - it should be in the format '/myProject/folder'</description>
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</propertyDescriptor>
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<propertyDescriptor name="KinshipDataPath">
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<canSetPerContainer>true</canSetPerContainer>
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<editPermissions>
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<permission>ADMIN</permission>
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</editPermissions>
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<description>This is the filepath of a folder where externally kinship/inbreeding TSVs calculated externally will be deposited. It is used by the KinshipData ETL to initiate import.</description>
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</propertyDescriptor>
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</properties>
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<clientDependencies>
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<dependency path="clientapi/ext4.lib.xml"/>

‎GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java‎

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import org.apache.logging.log4j.Logger;
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import org.jetbrains.annotations.NotNull;
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import org.labkey.GeneticsCore.mhc.MhcTaskRef;
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import org.labkey.api.action.ApiResponse;
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import org.labkey.api.action.ApiSimpleResponse;
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import org.labkey.api.action.ConfirmAction;
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import org.labkey.api.action.MutatingApiAction;
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import org.labkey.api.action.SpringActionController;
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import org.labkey.api.di.DataIntegrationService;
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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.security.permissions.UpdatePermission;
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import org.labkey.api.util.HtmlString;
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import org.labkey.api.util.URLHelper;
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import org.labkey.api.view.HtmlView;
@@ -62,4 +67,26 @@ public URLHelper getSuccessURL(Object o)
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return getContainer().getStartURL(getUser());
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}
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}
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@RequiresPermission(UpdatePermission.class)
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public static class ImportGeneticsDataAction extends MutatingApiAction<Object>
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{
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@Override
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public ApiResponse execute(Object form, BindException errors)
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{
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try
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{
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DataIntegrationService.get().runTransformNow(getContainer(), getUser(), "{GeneticsCore}/KinshipDataImport");
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return new ApiSimpleResponse("success", true);
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}
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catch (Exception e)
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{
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_log.error("Unable to initiate genetics data import", e);
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errors.reject(ERROR_MSG, "Unable to initiate genetics data import");
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return null;
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}
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}
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}
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}

‎GeneticsCore/src/org/labkey/GeneticsCore/etl/ImportGeneticsCalculationsStep.java‎

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package org.labkey.GeneticsCore.etl;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.xmlbeans.XmlException;
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import org.jetbrains.annotations.NotNull;
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import org.labkey.GeneticsCore.GeneticsCoreModule;
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import org.labkey.api.data.Container;
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import org.labkey.api.data.ContainerManager;
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import org.labkey.api.di.TaskRefTask;
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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.PipelineJob;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.pipeline.RecordedActionSet;
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import org.labkey.api.security.permissions.UpdatePermission;
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import org.labkey.api.view.UnauthorizedException;
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import org.labkey.api.writer.ContainerUser;
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import java.io.File;
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import java.util.Collections;
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import java.util.List;
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import java.util.Map;
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public class ImportGeneticsCalculationsStep implements TaskRefTask
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{
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protected ContainerUser _containerUser;
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@Override
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public RecordedActionSet run(@NotNull PipelineJob job) throws PipelineJobException
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{
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Module ehr = ModuleLoader.getInstance().getModule("ehr");
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Module geneticsCore = ModuleLoader.getInstance().getModule(GeneticsCoreModule.class);
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ModuleProperty mp = ehr.getModuleProperties().get("EHRStudyContainer");
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String ehrContainerPath = StringUtils.trimToNull(mp.getEffectiveValue(_containerUser.getContainer()));
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if (ehrContainerPath == null)
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{
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throw new PipelineJobException("EHRStudyContainer has not been set");
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}
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Container ehrContainer = ContainerManager.getForPath(ehrContainerPath);
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if (ehrContainer == null)
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{
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throw new PipelineJobException("Invalid container: " + ehrContainerPath);
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}
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if (!_containerUser.getContainer().equals(ehrContainer))
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{
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throw new PipelineJobException("This ETL can only be run from the EHRStudyContainer");
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}
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// Downstream import events will get additional permissions checks
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if (!ehrContainer.hasPermission(_containerUser.getUser(), UpdatePermission.class))
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{
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throw new UnauthorizedException();
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}
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ModuleProperty mp2 = geneticsCore.getModuleProperties().get("KinshipDataPath");
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String pipeDirPath = StringUtils.trimToNull(mp2.getEffectiveValue(ehrContainer));
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if (pipeDirPath == null)
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{
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throw new PipelineJobException("Must provide the filepath to import data using the KinshipDataPath module property");
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}
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File pipeDir = new File(pipeDirPath);
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if (!pipeDir.exists())
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{
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throw new PipelineJobException("Path does not exist: " + pipeDir.getPath());
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}
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File kinship = new File(pipeDir, "kinship.txt");
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if (!kinship.exists())
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{
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throw new PipelineJobException("File does not exist: " + kinship.getPath());
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}
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File inbreeding = new File(pipeDir, "inbreeding.txt");
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if (!inbreeding.exists())
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{
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throw new PipelineJobException("File does not exist: " + inbreeding.getPath());
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}
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EHRService.get().standaloneProcessKinshipAndInbreeding(ehrContainer, _containerUser.getUser(), pipeDir, job.getLogger());
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return new RecordedActionSet();
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}
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@Override
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public List<String> getRequiredSettings()
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{
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return Collections.emptyList();
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}
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@Override
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public void setSettings(Map<String, String> settings) throws XmlException
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{
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}
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@Override
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public void setContainerUser(ContainerUser containerUser)
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{
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_containerUser = containerUser;
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}
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}

‎onprc_ehr/resources/queries/onprc_ehr/vet_assignment.js‎

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require("ehr/triggers").initScript(this);
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var triggerHelper = new org.labkey.onprc_ehr.query.ONPRC_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
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var console = require("console");
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EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'onprc_ehr', 'vet_assignment', function(event, helper){
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console.log('Complete is called!');
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// NOTE: the rules behind vet assignment are complicated enough that any change to one row here could
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// impact a lot of records. Therefore, just redo everything in the cache
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triggerHelper.recalculateAllVetAssignmentRecords()

‎onprc_ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java‎

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waitAndClickAndWait(Locators.bodyPanel().append(Locator.tagContainingText("a", "EHR Admin Page")));
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waitAndClickAndWait(Locator.tagContainingText("a", "Genetics Calculations"));
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_ext4Helper.checkCheckbox(Ext4Helper.Locators.checkbox(this, "Kinship validation?:"));
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_ext4Helper.checkCheckbox(Ext4Helper.Locators.checkbox(this, "Allow Import During Business Hours?:"));
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Locator loc = Locator.inputByIdContaining("numberfield");
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waitForElement(loc);
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setFormElement(loc, "23");

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