Refactor kinship to allow other code to initiate import directly

GeneticsCore/build.gradle

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

GeneticsCore/resources/etls/KinshipDataImport.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>KinshipDataImport</name>
+    <description>Import PRIMe-seq Kinship Data</description>
+    <transforms>
+        <transform id="kinship" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.GeneticsCore.etl.ImportGeneticsCalculationsStep">
+                <settings>
+
+                </settings>
+            </taskref>
+        </transform>
+    </transforms>
+</etl>

GeneticsCore/resources/module.xml

@@ -21,6 +21,13 @@
             </editPermissions>
             <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>
         </propertyDescriptor>
+        <propertyDescriptor name="KinshipDataPath">
+            <canSetPerContainer>true</canSetPerContainer>
+            <editPermissions>
+                <permission>ADMIN</permission>
+            </editPermissions>
+            <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>
+        </propertyDescriptor>
     </properties>
     <clientDependencies>
         <dependency path="clientapi/ext4.lib.xml"/>

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

@@ -4,10 +4,15 @@
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.GeneticsCore.mhc.MhcTaskRef;
+import org.labkey.api.action.ApiResponse;
+import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.ConfirmAction;
+import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.SpringActionController;
+import org.labkey.api.di.DataIntegrationService;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.security.permissions.UpdatePermission;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.HtmlView;
@@ -62,4 +67,26 @@ public URLHelper getSuccessURL(Object o)
             return getContainer().getStartURL(getUser());
         }
     }
+
+
+    @RequiresPermission(UpdatePermission.class)
+    public static class ImportGeneticsDataAction extends MutatingApiAction<Object>
+    {
+        @Override
+        public ApiResponse execute(Object form, BindException errors)
+        {
+            try
+            {
+                DataIntegrationService.get().runTransformNow(getContainer(), getUser(), "{GeneticsCore}/KinshipDataImport");
+
+                return new ApiSimpleResponse("success", true);
+            }
+            catch (Exception e)
+            {
+                _log.error("Unable to initiate genetics data import", e);
+                errors.reject(ERROR_MSG, "Unable to initiate genetics data import");
+                return null;
+            }
+        }
+    }
 }

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

@@ -0,0 +1,107 @@
+package org.labkey.GeneticsCore.etl;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.xmlbeans.XmlException;
+import org.jetbrains.annotations.NotNull;
+import org.labkey.GeneticsCore.GeneticsCoreModule;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.di.TaskRefTask;
+import org.labkey.api.ehr.EHRService;
+import org.labkey.api.module.Module;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.module.ModuleProperty;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.RecordedActionSet;
+import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.view.UnauthorizedException;
+import org.labkey.api.writer.ContainerUser;
+
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+public class ImportGeneticsCalculationsStep implements TaskRefTask
+{
+    protected ContainerUser _containerUser;
+
+    @Override
+    public RecordedActionSet run(@NotNull PipelineJob job) throws PipelineJobException
+    {
+        Module ehr = ModuleLoader.getInstance().getModule("ehr");
+        Module geneticsCore = ModuleLoader.getInstance().getModule(GeneticsCoreModule.class);
+
+        ModuleProperty mp = ehr.getModuleProperties().get("EHRStudyContainer");
+        String ehrContainerPath = StringUtils.trimToNull(mp.getEffectiveValue(_containerUser.getContainer()));
+        if (ehrContainerPath == null)
+        {
+            throw new PipelineJobException("EHRStudyContainer has not been set");
+        }
+
+        Container ehrContainer = ContainerManager.getForPath(ehrContainerPath);
+        if (ehrContainer == null)
+        {
+            throw new PipelineJobException("Invalid container: " + ehrContainerPath);
+        }
+
+        if (!_containerUser.getContainer().equals(ehrContainer))
+        {
+            throw new PipelineJobException("This ETL can only be run from the EHRStudyContainer");
+        }
+
+        // Downstream import events will get additional permissions checks
+        if (!ehrContainer.hasPermission(_containerUser.getUser(), UpdatePermission.class))
+        {
+            throw new UnauthorizedException();
+        }
+
+        ModuleProperty mp2 = geneticsCore.getModuleProperties().get("KinshipDataPath");
+        String pipeDirPath = StringUtils.trimToNull(mp2.getEffectiveValue(ehrContainer));
+        if (pipeDirPath == null)
+        {
+            throw new PipelineJobException("Must provide the filepath to import data using the KinshipDataPath module property");
+        }
+
+        File pipeDir = new File(pipeDirPath);
+        if (!pipeDir.exists())
+        {
+            throw new PipelineJobException("Path does not exist: " + pipeDir.getPath());
+        }
+
+        File kinship = new File(pipeDir, "kinship.txt");
+        if (!kinship.exists())
+        {
+            throw new PipelineJobException("File does not exist: " + kinship.getPath());
+        }
+
+        File inbreeding = new File(pipeDir, "inbreeding.txt");
+        if (!inbreeding.exists())
+        {
+            throw new PipelineJobException("File does not exist: " + inbreeding.getPath());
+        }
+
+        EHRService.get().standaloneProcessKinshipAndInbreeding(ehrContainer, _containerUser.getUser(), pipeDir, job.getLogger());
+
+        return new RecordedActionSet();
+    }
+
+    @Override
+    public List<String> getRequiredSettings()
+    {
+        return Collections.emptyList();
+    }
+
+    @Override
+    public void setSettings(Map<String, String> settings) throws XmlException
+    {
+
+    }
+
+    @Override
+    public void setContainerUser(ContainerUser containerUser)
+    {
+        _containerUser = containerUser;
+    }
+}

onprc_ehr/resources/queries/onprc_ehr/vet_assignment.js

@@ -1,10 +1,8 @@
 require("ehr/triggers").initScript(this);
 
 var triggerHelper = new org.labkey.onprc_ehr.query.ONPRC_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
-var console = require("console");
 
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'onprc_ehr', 'vet_assignment', function(event, helper){
-    console.log('Complete is called!');
     // NOTE: the rules behind vet assignment are complicated enough that any change to one row here could
     // impact a lot of records. Therefore, just redo everything in the cache
     triggerHelper.recalculateAllVetAssignmentRecords()

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

@@ -1261,6 +1261,7 @@ public void testGeneticsPipeline() throws Exception
         waitAndClickAndWait(Locators.bodyPanel().append(Locator.tagContainingText("a", "EHR Admin Page")));
         waitAndClickAndWait(Locator.tagContainingText("a", "Genetics Calculations"));
         _ext4Helper.checkCheckbox(Ext4Helper.Locators.checkbox(this, "Kinship validation?:"));
+        _ext4Helper.checkCheckbox(Ext4Helper.Locators.checkbox(this, "Allow Import During Business Hours?:"));
         Locator loc = Locator.inputByIdContaining("numberfield");
         waitForElement(loc);
         setFormElement(loc, "23");